Download Hi-Res ImageDownload to MS-PowerPointCite This:Chem. Rev. 2017, 117, 1, 139-155

GPCR Dynamics: Structures in Motion

Naomi R. Latorraca^†^‡^§^∥
,
A. J. Venkatakrishnan^†^§^∥
, and
Ron O. Dror^*^†^‡^§^∥

View Author Information

† ‡ § ∥ ^†Department of Computer Science, ^‡Biophysics Program, ^§Department of Molecular and Cellular Physiology, and ^∥Institute for Computational and Mathematical Engineering, Stanford University, Stanford, California 94305, United States

*E-mail: [email protected]

Cite this: Chem. Rev. 2017, 117, 1, 139–155

Publication Date (Web):September 13, 2016

https://doi.org/10.1021/acs.chemrev.6b00177

Request reuse permissions

Article Views

50546

Altmetric

Citations

461

LEARN ABOUT THESE METRICS

Article Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.

Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.

The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated.

PDF (7 MB)

Get e-Alerts

SUBJECTS:

Get e-Alerts

Abstract

The function of G protein-coupled receptors (GPCRs)—which represent the largest class of both human membrane proteins and drug targets—depends critically on their ability to change shape, transitioning among distinct conformations. Determining the structural dynamics of GPCRs is thus essential both for understanding the physiology of these receptors and for the rational design of GPCR-targeted drugs. Here we review what is currently known about the flexibility and dynamics of GPCRs, as determined through crystallography, spectroscopy, and computer simulations. We first provide an overview of the types of motion exhibited by a GPCR and then discuss GPCR dynamics in the context of ligand binding, activation, allosteric modulation, and biased signaling. Finally, we discuss the implications of GPCR conformational plasticity for drug design.

SPECIAL ISSUE

This article is part of the G-Protein Coupled Receptors special issue.

1 Introduction

ARTICLE SECTIONS

Jump To

G protein-coupled receptors (GPCRs)—which represent the largest family of human membrane proteins, with some 800 members—represent a “control panel” of the cell. These receptors are able to detect the presence of a strikingly diverse array of molecules outside the cell and to initiate a variety of intracellular signaling cascades in response. Drugs can induce, block, or modulate these effects, essentially hijacking the control panel. Indeed, GPCRs represent the largest class of drug targets, with roughly one-third of all drugs on the market acting by binding to a GPCR and modifying its intracellular signaling profile.

The ability of a GPCR to transmit a signal through the cell membrane depends on its ability to change shape. Extracellular ligands, ranging from small hormones and neurotransmitters to proteins such as chemokines, bind to the extracellular side of a GPCR and favor structural changes that allow G proteins, arrestins, and other signaling proteins to bind to a GPCR’s intracellular surface (Figure 1). This control mechanism is highly complex: for example, appropriately chosen ligands can stimulate different intracellular signaling pathways independently through a single GPCR, and many GPCRs possess multiple ligand-binding sites that influence intracellular signaling in distinct manners.

Figure 1. GPCR signaling: (A) an orthosteric ligand (orange) binds an inactive GPCR, the β₂ adrenergic receptor (β₂AR; PDB ID: 2RH1); (B) A ligand-bound GPCR undergoes a conformational change to its active state (PDB ID: 3SN6); and (C) an active GPCR binds a G protein (PDB ID: 3SN6), which subsequently promotes nucleotide release from, and activation of, the G protein α-subunit.

Understanding the structural basis for these dynamic signaling processes has represented a long-standing challenge, with critical implications for both basic science and rational drug design. The past decade has witnessed dramatic progress toward this goal. Most obvious are the recent breakthroughs in GPCR structure determination through crystallography, (1-5) part of the work recognized by the 2012 Nobel Prize in Chemistry to Brian Kobilka and Robert Lefkowitz. Atomic-resolution structures are now available for over 35 GPCRs. (6, 7)

To truly decipher the molecular basis for GPCR signaling, however, we must also understand GPCR dynamics—how a given GPCR changes its shape over time. A good deal of information is now available on this front as well, not only from crystallography but also from spectroscopic experiments and from computer simulations. Atomic-level molecular dynamics (MD) simulations, in particular, have become substantially more powerful in recent years, thanks to increased computer power, improved simulation algorithms, and refined potential energy functions that better represent the underlying physics. Starting from a static experimental structure, these simulations predict the motion of every atom in a receptor, as well as the motion of every atom in the molecules with which the receptor interacts. (8)

Here we review and synthesize what is known about GPCR dynamics. We describe the various ways in which GPCRs change conformation, both spontaneously and in response to binding or dissociation of various ligands and intracellular signaling partners. We discuss the role of receptor dynamics in functional processes such as ligand binding, activation, coupling to downstream binding partners (G proteins and arrestins), biased signaling, and allosteric modulation. We also outline a number of important, unsolved problems in this area. Finally, we discuss the implications of receptor dynamics for GPCR-targeted drug design.

2 GPCR Movement: An Overview

ARTICLE SECTIONS

Jump To

All GPCRs share a transmembrane domain with a common structural architecture (Figure 2). This domain, which is essential for the transduction of a signal across the cell membrane, is composed of a bundle of seven α-helices embedded in the cell membrane connected by three extracellular and three intracellular loops. (9) The largest phylogenetic class of GPCRs, known as class A, contains only a transmembrane domain, with amino and carboxyl termini of varying lengths and sequence content (Figure 2). Native ligands of class A GPCRs thus bind directly to the transmembrane domain. Most GPCRs in other phylogenetic classes (including classes B, C, and F) also include an extracellular domain connected to the amino terminus of the transmembrane domain. (10, 11) These extracellular domains are generally involved in binding native ligands, either in addition to or in place of the transmembrane domain.

Figure 2. Structure and topology of GPCRs. (A) GPCRs contain seven transmembrane helices (gray), three extracellular loops (ECLs) and an amino terminus (orange), and three intracellular loops (ICLs) and a carboxyl terminus (purple). The *transmembrane domain* consists of the transmembrane helices, as well as the extracellular and intracellular loops. (B) Cartoon representation of the β₂AR highlighting transmembrane helices (TMs), loops, and terminal tails.

This review focuses primarily on the dynamics of the transmembrane domain, which is common to all GPCRs and plays the critical role of mediating a GPCR’s interactions with its intracellular binding partners, such as G proteins and arrestins. We will refer to the native ligand-binding site of class A GPCRs—found in the transmembrane domain and accessible from the extracellular solvent—as the binding pocket.

Like other biomolecules, a GPCR is in constant atomic-level motion (Figure 3), even in the absence of any external stimulus. Some of these motions are highly localized and typically very fast (femtoseconds to nanoseconds): the lengths of chemical bonds and the angles between bonds fluctuate, and solvent-exposed amino acid side chains change from one rotamer to another. (12) Other motions involve a larger part of the protein and typically occur more slowly (nanoseconds to milliseconds): helices kink or change orientation relative to one another, loops change their orientation, and tightly packed side chains in the interior of a protein rearrange.

Figure 3. Atomic-level motions of a GPCR revealed through MD simulations. Representative frames from MD simulations (from ref 23) of agonist-bound β₂AR as it transitions from an active state to an inactive state, with (A) all non-hydrogen atoms represented as lines and (B) protein backbone represented as ribbons. Transmembrane helix 6 (TM6) is colored red to highlight its high degre of mobility during the transition between active and inactive states.

We use the term conformation to refer to a particular three-dimensional arrangement of atoms in a protein—that is, a snapshot at a single point in time. Over the course of time, a GPCR can take on an essentially infinite number of conformations. These conformations, however, tend to cluster into groups, and we refer to a group of similar conformations as a conformational state (Figure 4). A GPCR typically moves very quickly among conformations within a conformational state and more slowly between conformational states, but it transitions spontaneously among multiple conformational states even in the absence of any change in bound ligand or environment.

Figure 4. Protein conformations cluster into distinct conformational states. Mapping an MD simulation trajectory to a well-chosen low-dimensional space can reveal distinct clusters of conformations. (A) Plotting an MD simulation trajectory along two geometric coordinates reveals three distinct conformational states during the process of β₂AR deactivation (top). RMSD is the root-mean-square deviation. (B) Snapshots from simulation, representing each of the three conformational states (light pink, magenta and dark purple), are overlaid with the inactive-state crystal structure (blue). These are shown along with a simplified, qualitative one-dimensional energy landscape, where the depth of each energy well is inversely related to the population of the corresponding conformational state. Adapted by permission from ref 23. Copyright 2011 National Academy of Sciences.

Crystallography, spectroscopy, and simulation provide complementary sources of information on fluctuations within and across GPCR conformational states. Crystal structures usually represent only a single conformational state (typically the most common conformational state under the conditions in which the receptor was crystallized, but sometimes just the state most prone to crystallization), and the positions of atoms in the structure represent averages of conformations within that conformational state. Crystallizing a single GPCR in many conformational states has proven challenging. (13) NMR spectroscopy provides a useful way to detect subtle conformational changes within a protein, as the relative position and shape of a peak on the NMR spectrum can reflect the chemical microenvironment of a well-chosen probe atom. (14) DEER spectroscopy allows one to determine a distribution (histogram) of distances between two different probes. (15) Fluorescence spectroscopy, including fluorescence resonance energy transfer and fluorescence quenching approaches, provides a means to detect whether two probes are close to one another. (16-18) With the exception of one structure solved by NMR, (19) these spectroscopy studies have not provided a complete structural description of any one conformational state; rather, they provide localized information about the inserted chemical probes. MD simulations complement these studies, as they provide a full atomic-level picture of the structure as it changes over time, capturing atomic-level motion within conformational states as well as transitions between conformational states. These simulations are limited by the accuracy of the underlying physical models and by the fact that they are computationally intensive, but recent years have seen substantial improvements on both fronts. (20)

MD simulations reveal that GPCRs undergo substantial fluctuations even within a single conformational state. (21, 22) For example, in one simulation of the inactive-state β₂-adrenergic receptor, (23) the root-mean-square deviation (RMSD) of helical backbone atoms from the crystal structure was approximately 1 Å, while the RMSD for TM helix side-chain atoms was approximately 2 Å, and the RMSD for atoms in loop regions was approximately 3 Å. The third intracellular loop and the C terminus—which are disordered in most GPCRs and unresolved in most GPCR crystal structures—can probably move substantially more. When a GPCR transitions between major conformational states, even transmembrane helices can move 10 Å or more.

Binding of a ligand to a GPCR can affect the GPCR’s dynamics in several ways. Generally, the largest effect is simply to alter the fraction of time the GPCR spends in each of its conformational states (also known as the “population” of each state); for example, binding of certain ligands may increase the population of active conformational states (Figure 5). In some cases, binding of a ligand may allow the GPCR to adopt conformations that it did not adopt previously, at least not to a measurable extent. (24) In addition, binding of a ligand may increase or decrease the rate at which the receptor transitions among different conformational states. Binding of an intracellular partner (e.g., a G protein or arrestin), dimerization with another GPCR, post-translational modifications such as phosphorylation of certain amino acids, or a change in the pH or lipid composition of the GPCR’s immediate environment can have similar effects. (25-29) The dynamics of a GPCR over the course of its lifetime will thus reflect a combination of structural changes due to the receptor’s intrinsic dynamics and “external” perturbations, such as those due to ligand binding or dissociation.

Figure 5. Perturbations alter the populations of conformational states. Hypothetical histograms (light pink, magenta, and purple) represent the relative populations of each of three hypothetical conformational states. Hypothetical energy landscapes (gray) are inversely related to the populations of the conformational states. Compared to the distribution of conformations visited by (A) an unliganded GPCR, (B) an agonist-bound GPCR samples intermediate and fully active conformations more frequently, and (C) an agonist-bound, G protein-bound GPCR more heavily populates fully active conformations. New conformational states may arise on this energy landscape under additional conditions (not shown).

Of all the conformational changes a GPCR undergoes, several appear to be particularly important from a functional perspective. Rearrangements of the transmembrane helices—particularly TM helices 5–7—appear to play a critical role in transmitting a signal across the membrane. (5) As a GPCR transitions from an inactive state (which does not couple to intracellular signaling proteins) to an active state (which does), these helices shift, tilt, and twist relative to one another; they can also bend or kink, usually at positions in the helical sequence where a proline or glycine disrupts backbone hydrogen bonds. (30) Several lines of evidence indicate that a GPCR’s transmembrane helices can adopt multiple distinct conformational states—not just a single active state and a single inactive state—and that these states have distinct implications for receptor signaling. (22, 24, 31, 32) Phosphorylation of residues in the C terminus and certain intracellular loops can also change a receptor’s propensity to couple to various intracellular partners, likely by causing structural changes in these regions. (33, 34)

While conformational changes tend to be largest on the intracellular side of the GPCR, the extracellular half of the receptor also changes conformation. In particular, the ligand-binding pocket undergoes subtle but important changes in structure that are coupled to the conformational changes of the helices on the intracellular side. (2, 3, 35) The mobility of a receptor’s extracellular loops can affect the binding kinetics of ligands that bind in the binding pocket. (36) These loops can also form alternative binding sites for ligands known as allosteric modulators, whose presence can cause localized conformational changes that alter the properties of the binding pocket, including its affinity for native ligands. (37-39)

3 GPCR Activation

ARTICLE SECTIONS

Jump To

Structural change within a GPCR allows it to act as a molecular conduit, transmitting an extracellular signal across the cell membrane to elicit an intracellular response. Such conformational change is essential for GPCR activation, the process by which a GPCR assumes a conformation conducive to coupling with and activating an intracellular binding protein. In this section we will focus, in particular, on the process by which a GPCR goes from an inactive conformational state to a G protein-coupling conformational state, and we will refer to the crystallographically observed G protein-coupling conformational state as the canonical active state.

3.1 Mechanism of GPCR Activation

The β₂-adrenergic receptor (β₂AR) has served as a model system for studying GPCR activation. The crystal structure of the β₂AR bound to a G protein indicates that the largest conformational changes to the receptor upon activation occur on the intracellular side, at the intracellular coupling interface, where transmembrane helices 5–7 rearrange to accommodate G protein insertion (Figure 6). TM6 rotates and swings nearly 14 Å away from the center of the helical bundle, accompanied by rotations and slight inward movements of TM5 and TM7. (2, 3) The ligand-binding pocket also rearranges: polar moieties on the ligand form hydrogen bonds with Ser5.42 and Ser5.46, pulling the upper portion of TM5 toward TM6 and causing the binding pocket to contract in volume. (Residues are identified using the Ballesteros–Weinstein numbering scheme, in which the first number refers to the transmembrane helix on which the residue resides. (40)) Crystal structures suggest, and simulations confirm, that motions of several residues in a “connector” or “transmission” region the conformational changes in the binding pocket to those at the intracellular coupling interface: in response to the inward movement of TM5, Ile3.40 shifts away from its position separating Pro5.50 and Phe6.44 in the inactive state, permitting the lower half of TM6 to move outward. (23, 35) An allosteric network of residues in TM3, TM5, TM6, and TM7 thus serves as a central hub for sensing and responding to conformational change in β₂AR.

Figure 6. Structural rearrangements during GPCR activation. Inactive (light pink) and active (dark purple) conformations of the β₂AR show differences in helix position and side-chain orientation in three distinct regions of the GPCR: the binding pocket (top, left); the connector region, or conserved core triad (bottom, left); and the intracellular coupling site (top and bottom, right).

How tight is the coupling between the conformation of the ligand-binding pocket and that of the intracellular coupling interface? A GPCR’s ability to transmit a transmembrane signal depends on the fact that the binding of an agonist (an activating ligand) in the binding pocket favors intracellular G protein binding. Conversely, G protein binding will favor agonist binding; that is, an agonist will bind with higher affinity to a GPCR in its active state than in its inactive state. (41, 42) One would thus expect conformational changes in one site to be coupled to conformational changes in the other. Recent evidence suggests that while the conformations of the two regions in the β₂AR are indeed coupled, the coupling is surprisingly loose. (22-24) That is, the binding pocket conformation influences but does not dictate the intracellular coupling interface conformation, and vice versa.

The most explicit evidence for this “loose allosteric coupling” comes from simulation. (23, 43) We observed that, in simulations of the β₂AR, each of the three regions described above—the binding pocket, the connector region, and the intracellular coupling interface—transitions spontaneously between two or more discrete conformations, including conformations matching the active and inactive crystal structure (Figure 7). (23) Each region could change conformation independently of the other regions, although the probability that a region would be in a particular conformation depended on the conformation of those other regions. NMR data also supports the notion of loose coupling between different regions of the β₂AR. (22, 24)

Figure 7. Loose allosteric coupling underlies GPCR activation. (A) During simulations of β₂AR deactivation, three key regions (the binding pocket, the connector region, and the intracellular coupling interface) spontaneously transition between at least two conformations independently of the other regions. (B) Horizontal bars represent the conformations sampled by each region over the course of four 2-μs deactivation simulations of the β₂AR. Adapted by permission from ref 23. Copyright 2011 National Academy of Sciences.

MD simulations (23) suggest that activation of the β₂AR does not typically occur “sequentially”, with an agonist inducing an active conformation of the ligand-binding pocket and the change then propagating toward the intracellular coupling interface. Instead, the intracellular coupling interface is likely in equilibrium between inactive conformations and more active-like conformations, even in the absence of an agonist. The presence of a bound agonist helps to stabilize active conformations of the binding pocket and thus increases the likelihood that the connector region and intracellular coupling interface will similarly adopt active conformations.

As a corollary, binding of a full agonist appears insufficient to stabilize the active, G protein-coupling state of the β₂AR. Instead, this conformation only dominates when the receptor is also bound to a G protein (or to a G protein mimetic). (44) A crystal structure of β₂AR bound to a potent agonist in the absence of an intracellular binding partner shows a conformation that matches the inactive, antagonist-bound crystal structure almost perfectly. (45) In simulation, agonist-bound β₂AR transitions spontaneously from the crystallographic active conformation to the crystallographic inactive conformation upon removal of the bound G protein. (23) NMR and DEER studies indicate that, although agonist binding substantially increases the conformational heterogeneity of the receptor, binding of a G protein or G protein mimetic to the intracellular coupling interface is required to stabilize the β₂AR in a single conformational state corresponding to the crystallographic, or canonical, active conformational state. (22, 24)

3.2 Conservation of Activation Mechanism across GPCRs

How does activation of other GPCRs compare to that of β₂AR? Crystal structures of other GPCRs captured in both inactive and active states (in particular, the M2 muscarinic acetylcholine receptor (M2R), the μ-opioid receptor (μOR), and rhodopsin) indicate that the global conformational changes involved in receptor activation are similar, particularly on the cytoplasmic side. (35, 39, 46-48, 157) In each case, upon receptor activation, the intracellular end of TM6 moves away from the center of the helical bundle (though the extent of its motion ranges from 6 to 14 Å, at least partly due to the fact that different intracellular binding partners were used to stabilize the different active-state structures) (Figure 8). Outward movement of TM6 expands a crevice on the intracellular side, creating an opening flanked by TM3, TM5, and TM7. This crevice holds the G protein-binding interface and, along with the second and third intracellular loops, forms polar and hydrophobic interactions with the G protein. Similarly, TM5 and TM7 change conformation upon activation, and key residues on these helices (specifically, Tyr5.58 and Tyr7.53) form direct and water-mediated polar contacts that are unique to GPCR active states. (2, 35, 39, 49-51)

Figure 8. Conformational changes in class A GPCRs upon activation. Three class A GPCRs captured in their crystallographic inactive and active conformations reveal similar conformational changes upon activation. TM6 is highlighted. M2 is the M2 muscarinic acetylcholine receptor and μOR is the μ-opioid receptor.

Activation of different GPCRs varies in several ways. Most notably, the interactions of the agonist with the binding pocket differ markedly between GPCRs, likely reflecting the fact that different GPCRs have evolved to recognize vastly different ligands. (44, 52) In β₂AR, for example, polar interactions with the agonist pull TM5 inward, whereas in the M2 muscarinic receptor, polar interactions with the agonist pull TM6 inward. (39) The μ-opioid receptor (μOR) undergoes very similar conformational changes to β₂AR upon activation—including inward motion of TM5 near the binding pocket and rearrangement of the conserved core triad—but the μOR agonist does not form polar interactions with TM5. (35) MD simulations suggest that the agonist instead triggers activation by pushing aside TM3. (35) Thus, GPCRs appear to have evolved widely varying ligand recognition mechanisms, even though their intracellular surfaces undergo similar conformational changes upon activation and couple to a common set of intracellular proteins. (48)

Many GPCRs likely share the loose allosteric coupling of β₂AR. (53) Some notable examples include μOR (54) and the adenosine A_2A receptor (A_2AR), (55) which appear to explore intermediate and active-like states even in the absence of bound agonist. By contrast, the light-activated GPCR rhodopsin appears to exhibit much tighter coupling between the binding pocket and the intracellular coupling interface. (56-59) Light-induced conversion of the native ligand retinal to an agonist shifts rhodopsin abruptly away from its inactive, dark state, allowing for extremely efficient activation and G protein coupling. (60)

4 Conformational Diversity and Biased Signaling

ARTICLE SECTIONS

Jump To

In this section, we describe the global conformational states of a GPCR as observed through crystallography, spectroscopy, and simulation, and we speculate on how this conformational diversity affects the ability of the GPCR to signal downstream. We discuss global conformational states primarily in terms of features within the cytoplasmic half of the GPCR, because this region directly binds intracellular proteins. We also discuss potential links between these various conformational states and biased signaling, a phenomenon in which a ligand determines which of several possible signaling pathways a GPCR stimulates. Biased signaling, also known as functional selectivity, is of tremendous pharmaceutical interest, because it raises the possibility of creating drugs that stimulate desirable signaling pathways without stimulating harmful ones, thus dramatically reducing drug side effects and safety issues. (61) The structural basis for biased signaling remains poorly understood, but it most likely depends on the ability of the GPCR’s intracellular coupling interface to assume more than just a single inactive and a single active conformational state. (62)

4.1 Diverse Conformational States of a GPCR

Molecular dynamics simulations reveal several “intermediate” conformational states of a GPCR that differ from the crystallographically observed active and inactive conformations. For example, we performed simulations of an agonist-bound β₂AR, which transitioned spontaneously from its crystallographic active conformation to its crystallographic inactive conformation (after removal of the G protein or G protein-mimetic nanobody). (23) These simulations revealed several intermediate conformational states en route between the crystallographic active and inactive states. These intermediate states are metastable, in the sense that once a simulation reaches one of them it generally remains there for at least several hundred nanoseconds before transitioning to another state. Perhaps the most notable intermediate state in these simulations is one where TM7 adopts its crystallographically observed inactive conformation while TM6 remains in its active, outward-shifted conformation (albeit with increased mobility) (Figure 9, intermediate A). This was the only major intermediate state observed in a number of the “deactivating” simulations of β₂AR (Figure 9). Subsequent NMR studies revealed that differences in the core region of TM5 and TM7, rather than changes in the position of TM6, distinguished two states of the β₂AR favored in the presence of agonist; these conformational states may correspond to the intermediate and fully active states observed in simulation. (22, 24)

Figure 9. Diverse conformational states of the β₂AR. During MD simulations of β₂AR beginning in the active state (dark gray; PDB ID: 3P0G) (A), β₂AR transitions along (B) a dominant pathway through an intermediate (intermediate A) in which TM6 is still displaced outward relative to the inactive crystal structure but TM7 is straightened (light blue) or (C) an alternative pathway through two intermediates, B and C, which exhibit a conformation of TM7 distinct from that seen in the inactive and active crystal structures of the β₂AR. Simulations were taken from ref 23.

In some of these simulations, the transition between active and inactive conformational states took place along a different pathway. This pathway had two intermediates, both characterized by a distinctive “alternative” conformation of TM7 different from that observed in either the active or the inactive β₂AR crystal structures (Figure 9, intermediates B and C). The two intermediates differed in the position of TM6, which was in an outward, active-like conformation in the first intermediate (intermediate B) and in an inward, inactive-like conformation in the second (intermediate C). Intriguingly, simulations initiated from the crystallographic inactive structure with either an inverse agonist or no ligand bound occasionally transitioned to intermediate C, referred to as “intermediate 2” (23) and as an “alternative inactive” conformation (22) in previous publications. These simulation results were consistent with NMR data demonstrating an equilibrium between two conformations with either an inverse agonist or no ligand bound. (22)

Conformational fluctuations can also arise within the ensemble of inactive conformations. In simulations initiated from the crystallographic inactive β₂AR conformation (whether unliganded or bound to the cocrystallized ligand), TM6 and TM7 as a whole remained in their crystallographic, inactive conformations, but the intracellular end of TM6 frequently alternated between two positions. (21) In one of these conformational substates—adopted a majority of the time—the intracellular end of TM6 is bent toward TM3, so that a network of salt bridges known as the ionic lock is formed. In particular, Glu6.30 at the base of TM6 forms a salt bridge with Arg3.50 at the base of TM3, which simultaneously forms a salt bridge with Asp3.49. In the other conformational substate, the intracellular end of TM6 straightens, moving away from TM3 and breaking the ionic lock. The observation of this equilibrium in these and other simulations (63, 158) resolved prior, seemingly conflicting experimental observations: the ionic lock is consistently formed in several inactive rhodopsin crystal structures, (64-66) and biochemical studies suggested it played a role in stabilizing the inactive state of β₂AR as well, but it was broken in the initial crystal structures of inactive-state β₂AR and β₁AR. (67-70) Later crystal structures of β₁AR showed both ionic-lock-broken and ionic-lock-formed conformations with the same ligand bound (71)—as observed in simulation—and more recently, DEER spectroscopy of β₂AR has provided evidence for both ionic-lock-broken and ionic-lock-intact states. (24)

Additional evidence for the diversity of the global conformational states adopted by a GPCR comes from comparing crystal structures of different GPCRs, particularly those bound to agonists. Most GPCRs appear not to crystallize in a fully active conformation capable of binding to a G protein unless a G protein or G protein-mimetic nanobody is crystallized in complex with the receptor. Several agonist-bound GPCRs have instead adopted crystallographic conformations that appear to be partway between the canonical active and canonical inactive states. (52) These crystallized conformations are often referred to as “intermediates”, although they are not necessarily intermediates on the activation pathway. Structures of the adenosine A_2A receptor (A_2AR) bound to adenosine and other agonists reveal that structural elements on TM3, TM5, and TM7 take on conformations similar to those seen in fully active β₂AR structures, while TM6 has moved slightly away from the center of the helical bundle but remains in an occluded position that would still likely prevent G protein binding. (52, 72, 73) Notably, one A_2AR structure exhibits structural features of TM7 seen in intermediate C, described above. (73) The extent to which “active” features can be induced by the presence of agonist alone may depend on the physical properties of each type of GPCR. Many agonist-bound GPCRs resemble their inactive structures on the intracellular side (in the absence of an intracellular binding partner). (74) In contrast, the viral chemokine receptor US28 crystallized in a canonical active conformation with an agonist bound even in the absence of an intracellular binding partner, likely reflecting its high degree of constitutive activity. (75) Thus, the extent to which agonists induce “active-like” properties in GPCRs appears to reflect variable conformational plasticity within the GPCR family.

4.2 Implications for Biased Signaling

The relevance of alternative conformations on the intracellular side of the GPCR to downstream signaling has recently come into focus due to intensified interest in biased signaling. (61) For example, an active-state GPCR typically couples to both G proteins and arrestins and stimulates signaling through each, but some ligands favor G protein signaling without arrestin signaling or arrestin signaling without G protein signaling. This suggests that ligands select among not just one active and one inactive conformational state but among multiple conformational states with different abilities to couple to intracellular binding partners. (76) Biased ligands may also affect the kinetics of signaling, which might lead to apparent bias toward distinct pathways at different points in time. (77) What are the consequences of signaling through these distinct pathways? Upon binding to GPCRs, arrestins can not only sterically prevent coupling of GPCRs to G proteins (damping cAMP-mediated signaling) but also facilitate clathrin-mediated endocytosis of GPCRs and initiate G protein-independent signaling through downstream kinase cascades. (78-80) Although our focus here is on bias between arrestins and G proteins, we note that many different types of bias exist and include bias between, for example, different G protein subtypes. (81)

Recent spectroscopic efforts to characterize conformations induced by arrestin- and G protein-biased ligands have revealed some differences in conformation on the intracellular face of the GPCR. A ¹⁹F NMR study monitored how the local chemical environment on the intracellular ends of TM6 and TM7, and at a location on helix 8, changed in response to the binding of various ligands to the β₂AR. (82) The authors observed differences in chemical shifts in the presence of unbiased ligands, which stimulate G protein-mediated and arrestin-mediated signaling equally, and arrestin-biased ligands, which stimulate arrestin-mediated signaling more than G protein-mediated signaling. Specifically, while unbiased agonists shifted the chemical environment near both TM6 and TM7, arrestin-biased ligands largely appeared to affect only the environment in the vicinity of TM7. A caveat is that for biophysical studies performed in the absence of intracellular binding partners, it might be challenging to determine how the observed conformational differences directly impact the formation or stability of GPCR–G protein or GPCR–arrestin complexes.

Crystal structures of GPCRs bound to ligands with biased signaling profiles have recently provided additional evidence that bias may involve subtle changes on the intracellular face of the GPCR. Recently, high-resolution structures of serotonin receptor subtypes 5-HT_1BR and 5-HT_2BR, each bound to an agonist ergotamine, have revealed structural features that might serve as determinants for functional selectivity. (83, 84) Ergotamine primarily stimulates arrestin signaling at the 5-HT_2BR, but stimulates arrestin and G protein signaling roughly equally at the 5-HT_1BR. The crystal structure of 5-HT_1BR bound to ergotamine closely resembles the canonical active conformation in the intracellular region. In contrast, the ergotamine-bound 5-HT_2BR structure is similar in conformation to the intermediates B and C observed in simulations of the β₂AR (Figure 9), with the TM7 conformation matching almost perfectly. (22, 23, 31) Taken together, these spectroscopic, computational, and crystallographic data provide support for the notion that arrestin-biased ligands may work, in part, by favoring an alternative set of conformations for TM7.

The determination of a crystal structure of a GPCR bound to an arrestin was highly anticipated, as it held the potential to reveal arrestin-specific coupling conformations of the GPCR. This past year saw the determination of the first crystal structure of a GPCR–arrestin complex, rhodopsin bound to arrestin-1. (85) Comparison of this structure to the G protein-bound β₂AR structure (3) reveals strikingly similar conformations of the two receptors, including in both TM6 and TM7 (Figure 10). Coupling between arrestin and rhodopsin appears to be primarily mediated by hydrophobic contacts within the intracellular coupling interface of the GPCR, in agreement with a structure of rhodopsin bound to an arrestin peptide. (86) In contrast, several polar interactions appear to mediate G protein coupling with β₂AR. Despite the similarity in the receptor conformation observed in the G protein-bound and arrestin-bound crystal structures, conformational selectivity for arrestins and G proteins might still be achieved if (1) a GPCR adopts other conformational states that couple to only a G protein or only arrestin or (2) subtle fluctuations about the crystallographically observed conformational states favor G protein coupling or arrestin coupling by strengthening or weakening certain interactions between the proteins. To take advantage of functional selectivity for the development of safer and more effective therapeutics, we require a way to determine the molecular signatures of biased GPCRs and ligand-mediated bias at these receptors.

Figure 10. Structural comparison of G protein-bound and arrestin-bound GPCRs. Crystal structures of β₂AR bound to G_s (left; PDB ID: 3SN6) and of rhodopsin bound to arrestin-1 (right; PDB ID: 4ZWJ) similar conformations of the GPCRs’ intracellular coupling sites.

A third potential mechanistic explanation for biased signaling depends upon the idea that biased ligands can induce differential phosphorylation patterns of residues in certain regions of the GPCR, including the C-terminus and third intracellular loop. (87) Arrestin-biased ligands may favor GPCR coupling with particular kinases, (88) which may give rise to these distinct phosphorylation patterns. (88-90) Recently, ¹⁹F NMR experiments have revealed that differently phosphorylated C-terminal peptides can induce variable structural changes in arrestin; these structural changes occurred in regions associated with downstream functions of arrestin, including association with clathrin and Src kinase. (91) The structural mechanism by which different GPCR phosphopeptides stabilize alternative arrestin conformations is currently not well understood, nor have the arrestin conformations that arise from the binding of different phosphopeptides been fully characterized, although crystal structures of a phosphopeptide-bound arrestin-2 and of a preactivated arrestin-1 reveal common phosphopeptide binding modes and active conformations of arrestin. (92, 93) Future research in this direction may improve our understanding of how the phosphorylation state of the GPCR C-terminus, in combination with the conformation of the transmembrane bundle, correlates with the conformational state of arrestin. Indeed, recent studies performed using fluorescence and bioluminescence spectroscopy support the idea that arrestin conformation varies depending on the identity of the coupled GPCR and that these arrestin conformations may lead to different downstream effects. (94, 95)

5 Allosteric Modulation of GPCRs

ARTICLE SECTIONS

Jump To

The great majority of ligands generally bind a GPCR at the same site as the native ligand. This site (the binding pocket in class A GPCRs) is known as the orthosteric site and these ligands as orthosteric ligands. However, certain ligands—known as allosteric ligands or allosteric modulators—bind at other sites. Allosteric modulators can influence the structure, dynamics, and function of GPCRs in multiple ways. (37, 96) Pharmacologically, the classical effect of an allosteric modulator is to increase or decrease the affinity of orthosteric ligands. Allosteric modulators can also alter the efficacy of orthosteric ligands, that is, the extent to which these orthosteric ligands activate the GPCR when bound. (41) In some cases, allosteric ligands can also induce activation even in the absence of an orthosteric ligand and might thus be considered agonists in their own right.

Discovery and development of allosteric modulators for GPCRs represents an area of intense pharmaceutical interest. Allosteric modulators may achieve selectivity between receptor subtypes that possess nearly identical orthosteric sites [e.g., the M1 and M2 muscarinic acetylcholine receptors (M1R and M2R)]. (97-99) In addition, because they act largely by altering the affinity or efficacy of native ligands, allosteric modulators may provide a means to fine-tune cellular responses to the body’s natural signaling patterns. (97)

Many allosteric modulators appear to bind on the extracellular surface of the receptor. Until recently, this was inferred largely on the basis of mutagenesis data, (100-102) particularly for muscarinic acetylcholine receptors, which have served as model receptors for the study of allosteric modulation in GPCRs. In a recent simulation study, we determined the binding modes of multiple allosteric modulators at M2R by allowing each modulator to freely diffuse in surrounding water until it stably bound the receptor. (38) Each of the modulators consistently bound a site we refer to as the extracellular vestibule, located approximately 15 Å above the orthosteric binding site (Figure 11). A subsequently published crystal structure—the first of a drug-like modulator bound to a GPCR—showed a different allosteric modulator bound to the M2R at this same site and in a similar pose. (39)

Figure 11. Structural basis of allosteric modulation in GPCRs. (A) Conformational changes to the orthosteric and allosteric binding sites in the presence of different ligands. The presence of the orthosteric ligand (green) favors a widened allosteric site. The allosteric modulator in blue requires a widened allosteric site to bind, while the allosteric modulator in pink does not. Adapted by permission from ref 38. Copyright 2013 Macmillan Publishers Ltd. (B) Sites of allosteric modulation in GPCRs (gray) include the extracellular loops in the M2R (top; PDB ID: 4MQT), the centrally located sodium-binding site in the adenosine A_2A receptor (middle, with sodium in yellow; PDB ID: 4EIY) and the base of TM6 in glucagon receptor (bottom; PDB ID: 5EE7).

Our simulation study also allowed us to determine two separate mechanisms by which certain allosteric modulators affect the affinity of certain orthosteric ligands at the M2R. The first mechanism, interestingly, does not require any structural change in the receptor: electrostatic repulsion between a positively charged allosteric ligand and a positively charged orthosteric ligand destabilizes the binding of one in the presence of the other. The second mechanism involves structural change: certain allosteric modulators increase the width of both the allosteric and orthosteric binding sites, and certain orthosteric antagonists have a similar effect (Figure 11A); thus, the presence of either the allosteric or orthosteric ligand increases the affinity of the other. By contrast, the modulator-bound M2R crystal structure provides an example of an allosteric modulator and an orthosteric ligand that both appear to favor narrow conformations of the two binding sites. (39)

Although the extracellular vestibule might represent the most common binding site for drug-like allosteric modulators, it is certainly not the only one. A recent crystal structure of the glucagon receptor shows an allosteric modulator bound on the intracellular surface, at the interface between TM6, TM7 and the surrounding lipids (Figure 11B). (103) Several allosteric modulators of the glucagon-like peptide 1 (GLP1) receptor appear to bind at a similar location by binding covalently to a cysteine residue proximal to TM6 in the third intracellular loop. (104) The molecular mechanism of these modulators is not clear, but they may act by aiding or blocking the outward motion of TM6 and thus favoring or preventing receptor activation, respectively. (105) Indeed, we note that at least one of these compounds, sometimes referred to as compound 2, can act as an allosteric agonist to induce receptor activation even in the absence of an orthosteric agonist. (106-108)

A number of endogenous ligands—those that occur naturally within the body—can also act as allosteric modulators. (41) For example, sodium is known to disfavor agonist binding and activation at many GPCRs. Several high-resolution crystal structures of inactive-state class A GPCRs reveal a bound sodium ion located in a hydrated pocket located below the binding pocket (Figure 11B) and stabilized by its interaction with conserved residues, particularly Asp2.50. (109, 110) In active-state GPCR structures and simulations, on the other hand, this pocket has collapsed, such that sodium can no longer be accommodated. (111) As a result, the binding of sodium tends to stabilize the inactive state.

Other endogenous ligands appear to bind on the GPCR’s intracellular surface. Experimental studies indicate that phospholipids can act as allosteric modulators, with phosphatidylgycerol lipids favoring agonist binding and facilitating receptor activation and phosphatidylethanolamine lipids favoring antagonist binding and impeding receptor activation. (29, 112-114) Recent simulation studies have suggested that phosphatidylglycerol lipids insert between the intracellular ends of TM6 and TM7, disrupting TM3–TM6 interactions and thus favoring the active state. (29, 115) G proteins also act as allosteric modulators, affecting the conformation of the orthosteric site, even in the absence of an orthosteric ligand. (42)

6 Importance of GPCR Dynamics in Drug Discovery

ARTICLE SECTIONS

Jump To

The recent breakthroughs in GPCR crystallography have led to widespread adoption of structure-based drug design methodologies for GPCR targets. (116-120) Even single-crystal structures of a GPCR are very useful in this regard; docking to such structures has proven to be highly effective in discovery of novel ligands. (121-123) A number of drug candidates developed through structure-based methods are currently in preclinical development or clinical trials for indications ranging from Alzheimer’s disease to cancer. (124, 159) Fully exploiting the power of structure-based drug design at GPCRs, however, requires an understanding of the dynamic properties of these receptors. Here we describe several ways in which the dynamics of GPCRs are relevant to drug discovery.

GPCR binding pockets exhibit substantial flexibility. The binding pocket geometry generally differs from one conformational state to another. Even within a single conformational state, the binding pocket may be highly flexible, as illustrated by the distinct structures of agonist-bound A_2A receptors. (52) Docking to a single structure will thus lead to identification of only a subset of the compounds that bind to the GPCR. Considering multiple possible receptor structures will generally increase the diversity of binding ligands identified.

Perhaps more importantly, the goal when designing a GPCR-targeted drug is typically to find a ligand that not only binds to the target but also achieves a particular signaling profile. One might wish to find a full agonist that strongly stimulates receptor activation and signaling, a partial agonist that stimulates receptor signaling to a lesser degree, a neutral antagonist that does not signal on its own but blocks the body’s native agonists from binding, or an inverse agonist that reduces signaling below its basal (unliganded) levels. Achieving a given signaling profile requires that the drug stabilize specific conformational states of the receptor and thus specific conformational states of the binding pocket. An agonist, for example, stabilizes active states relative to inactive states. Designing such a ligand with confidence requires an understanding of how subtle changes in the binding pocket are coupled to different signaling profiles and different conformations of the intracellular coupling interface. Rational design of a biased ligand—for example, a drug that stimulates arrestin signaling but not G protein signaling—is even more of a challenge, requiring an understanding of conformations associated with G protein signaling and arrestin signaling.

Information on binding pocket dynamics, and the relationship between binding pocket conformation and receptor signaling, thus promises to guide the design of drugs with desired signaling profiles. This information may come in the form of crystal structures of multiple conformational states; docking studies have already demonstrated that an active-state structure is helpful in identifying agonists. (122) Simulations can provide more detailed information on binding pocket dynamics, both when crystal structures of multiple conformational states are available (35) and when they are not, and can be used to compare a ligand’s interactions with different conformational states of the receptor. Simulations can also be used to identify differences in the dynamics of binding pockets of closely related receptor subtypes, pointing to opportunities for designing drugs that select for one subtype over another.

Dynamics are equally important in the lead optimization process, where one modifies a ligand to improve its efficacy or to preserve its efficacy while improving other properties. Simulations may help identify the key interactions the lead ligand makes with the binding pocket or rearrangements to the binding pocket induced by the ligand. These results suggest opportunities for ligand optimization. Biophysical measurements may also be useful in this process. (125)

Receptor dynamics are particularly critical to the design of allosteric modulators, an area of great interest in GPCR drug discovery. (126) Allosteric binding sites are often not evident from crystal structures; their very formation may depend on the fact that receptors are constantly changing conformation. Simulations have proven capable of capturing “cryptic” binding pockets in various proteins (127, 128) and of identifying allosteric ligand binding sites at GPCRs. (38) Moreover, the effects of an allosteric drug generally depend on the manner in which it alters the receptor’s conformation, either modulating signaling directly or altering the affinity or efficacy of the native, orthosteric ligand. Enabling the rational design of allosteric drugs with desired effects requires deciphering the coupling of allosteric sites to the orthosteric binding pocket and the intracellular-coupling interface. In a recent proof-of-concept study, we used a simulation-based approach to design chemical modifications that substantially altered a modulator’s allosteric effects. (38) Efforts in this direction will also benefit from additional crystal structures of GPCRs bound to allosteric modulators and from spectroscopic studies of the effects of modulators on receptor dynamics.

The kinetics of drug binding and unbinding have been recognized in recent years to be critical to the effectiveness and safety of many drugs. For example, the efficacy of ligands at certain GPCRs correlates better with residence time than with binding affinity. (129) Binding kinetics depend on receptor dynamics, as conformational change is often required for ligand binding and unbinding. In some cases, these conformational changes are subtle and short-lived rearrangements of amino acid side chains, as illustrated by a study in which we captured the full process of ligands binding to the β₂AR spontaneously in simulation. (130) In other cases, large-scale motions of extracellular loops control binding kinetics, as observed in more recent simulation studies illuminating the clinically important differences in dissociation kinetics of the respiratory drug tiotropium at the M2 and M3 muscarinic acetylcholine receptors. (46, 131) Deciphering the factors that control binding kinetics, including receptor and ligand dynamics, promises to enable the rational design of drugs with desired kinetic properties.

7 Concluding Remarks

ARTICLE SECTIONS

Jump To

We have reviewed, in broad strokes, what is currently known about the atomic-level motions of GPCRs and how those motions enable GPCR function. Our current understanding is based on a combination of experimental data and computational results. Experimental methods for studying GPCR structure and dynamics have advanced dramatically in recent years, not only leading to an explosion of GPCR crystal structures but also enabling multiple spectroscopy techniques and other biophysical experiments that were previously beyond reach for GPCRs. Likewise, computational methods such as MD simulations have benefited from substantial recent advances in speed and accuracy, as well as new techniques for analyzing simulation results to pick out subtle conformational changes and allosteric networks. (132-138) Computational approaches still suffer from a number of limitations, (139, 140) but they serve as a powerful complement to experimental methods. Advances on both computational and experimental fronts have also now enabled the experimental validation of a variety of computational predictions, including the “loose coupling” between the binding pocket and the intracellular coupling interface, (22-24, 55) the binding poses and molecular mechanisms of allosteric modulators, (38, 39) the distinct conformations of the ionic lock, (21, 24, 55, 71) and the role of G protein dynamics in nucleotide exchange. (141-144)

A complete description of GPCR dynamics will require far more investigation. Our understanding of activation mechanisms remains incomplete, and we are just beginning to grasp the mechanistic basis for allosteric modulation and biased signaling, even for the best-studied GPCRs. Much additional work will be necessary to understand how these properties vary across the large GPCR family. In the remainder of this section, we discuss several other important areas that call for further research.

First, we lack a clear understanding of the dynamics of disordered segments of GPCRs, including the C terminus and, in many receptors, the large third intracellular loop. These regions are typically unresolved in crystal structures, but they play important roles in interactions with intracellular binding partners and can become ordered in the presence of such partners. (33) What conformations can these disordered regions adopt, and how does the binding of intracellular proteins influence the disordered-to-ordered transition? How do post-translational modifications of these regions, such as phosphorylation, affect their dynamics and their propensity to bind intracellular partners? How do the C-termini of nearly 800 human GPCRs, which exhibit low sequence conservation and high variability in length, enable coupling to just four highly related arrestin subtypes?

Second, while we have a reasonable sense for how GPCRs catalyze nucleotide release from G proteins—thanks to extensive mutagenesis, spectroscopy, and simulation studies (141-144)—we have a poorer mechanistic understanding of how GPCRs couple with other intracellular proteins, including arrestins and GPCR kinases (GRKs). How do GPCRs activate arrestins? To what degree does GPCR coupling determine the downstream effects of arrestin—for example, whether it facilitates endocytosis, mediates downstream kinase signaling, or both? What does the GPCR-bound state of a GRK look like? We have some knowledge of the sites on a GRK responsible for GPCR binding, (145) but we do not know how certain GPCR ligands can selectively promote GPCR coupling to one kinase over another. (88)

Third, we now appreciate that GPCRs move extensively within cells; that is, they diffuse within lipid membranes and undergo trafficking among different membrane compartments. It remains unclear, however, how the intrinsic dynamics and signaling properties of a GPCR vary as the GPCR moves about the cell. (146-149) Some recent advances in this field include the development of fluorescently tagged, conformationally selective nanobodies to enable the detection of active-state GPCRs in cells. (150, 151) Single-molecule imaging of GPCRs in cell membrane has also revealed that various ligands may influence patterns of GPCR oligomerization in cells, (26, 152-156) but the mechanistic basis for these effects is not known. Moreover, how does the spatial distribution of GPCRs in cells affect the spatial organization of downstream signaling pathway components, and what are the functional consequences of changes in spatial organization?

Answering these questions will help us to understand how GPCRs, and the ligands that bind them, can achieve fine control over all their downstream signaling pathways. Doing so will likely require a variety of cutting-edge experimental methods, including single-molecule fluorescence microscopy and spectroscopy, electron microscopy, and X-ray free electron laser crystallography. Simulations at multiple scales—not limited to atomic-level MD simulations—will likely prove necessary, as will a computational framework to integrate data from a wide variety of experiments. We envision that this framework will allow us to predict how GPCRs communicate with downstream signaling proteins in cells as a function of all of the molecules in their surrounding environments. By combining information across multiple spatial and temporal scales, we will come closer to directly linking multiple facets of GPCR structure and dynamics to cellular physiology, a critical step in the rational design of finely tuned drugs to target difficult-to-treat human ailments and diseases.

Author Information

ARTICLE SECTIONS

Jump To

Corresponding Author
- Ron O. Dror - †Department of Computer Science, ‡Biophysics Program, §Department of Molecular and Cellular Physiology, and ∥Institute for Computational and Mathematical Engineering, Stanford University, Stanford, California 94305, United States; Email: [email protected]
Authors
- Naomi R. Latorraca - †Department of Computer Science, ‡Biophysics Program, §Department of Molecular and Cellular Physiology, and ∥Institute for Computational and Mathematical Engineering, Stanford University, Stanford, California 94305, United States
- A. J. Venkatakrishnan - †Department of Computer Science, ‡Biophysics Program, §Department of Molecular and Cellular Physiology, and ∥Institute for Computational and Mathematical Engineering, Stanford University, Stanford, California 94305, United States
Notes
The authors declare no competing financial interest.

Biographies

ARTICLE SECTIONS

Jump To

Naomi R. Latorraca

Download MS PowerPoint Slide

Naomi R. Latorraca graduated from the University of Pittsburgh (Pittsburgh, PA) in 2013 with a B.A./B.S. in history and molecular biology, where she performed research under the mentorship of Prof. Michael Grabe. She is currently a Ph.D. student in the biophysics program at Stanford University (Stanford, CA). Under the advisorship of Prof. Ron Dror, she is using molecular dynamics simulations to investigate the conformational dynamics of various membrane proteins, including G protein-coupled receptors.

A. J. Venkatakrishnan

Download MS PowerPoint Slide

A. J. Venkatakrishnan completed his B.Tech in bioinformatics from VIT University (Tamil Nadu, India) in 2008 and a research assistantship at the Indian Institute of Science (Bangalore, India) with Dr. Nagasuma Chandra in 2009. He completed his Ph.D. in biological sciences (focusing on computational biology) as a St. Johns College Benefactor Scholar and an LMB-Cambridge International Scholar from the University of Cambridge and the MRC Laboratory of Molecular Biology (Cambridge, UK) in 2013. His Ph.D. was advised primarily by Dr. M. Madan Babu and coadvised by Prof. Gebhard Schertler. He then worked as an investigator scientist at the MRC Laboratory of Molecular Biology supported by an MRC Early Career Award. Presently, he is a postdoctoral researcher at Stanford University (Stanford, CA) working jointly with Profs. Ron Dror and Brian Kobilka. His research interests are focused on the structure, dynamics, and design of G protein-coupled receptors.

Ron O. Dror

Download MS PowerPoint Slide

Ron O. Dror completed a B.A./B.S. at Rice University (Houston, TX), an M.Phil. as a Churchill Scholar at the University of Cambridge (Cambridge, UK), and a Ph.D. at Massachusetts Institute of Technology (Cambridge, MA). He served for over a decade as second-in-command of D. E. Shaw Research, where he focused on biomolecular simulation and high-performance computing (part of a project highlighted by Science as one of the top 10 scientific breakthroughs of 2010). He is currently an associate professor of computer science and, by courtesy, molecular and cellular physiology at Stanford University (Stanford, CA), where he employs a broad range of computational methods to study the spatial organization and dynamics of biomolecules and cells.

Acknowledgment

ARTICLE SECTIONS

Jump To

We thank Robin Betz, Connor Brinton, Brendan Kelly, João Rodrigues, Raphael Townshend, Aashish Manglik, Matthieu Masureel, Antoine Koehl, and Brian Kobilka for helpful comments and discussions. We also thank D. E. Shaw Research for access to published MD simulation trajectories. This work was supported by a Terman Faculty Fellowship, by Pfizer, Inc., by Eli Lilly and Co. through the Lilly Research Program, and by a National Science Foundation Graduate Research Fellowship.

References

ARTICLE SECTIONS

Jump To

This article references 159 other publications.

1
Rosenbaum, D. M.; Cherezov, V.; Hanson, M. A.; Rasmussen, S. G.; Thian, F. S.; Kobilka, T. S.; Choi, H. J.; Yao, X. J.; Weis, W. I.; Stevens, R. C. GPCR Engineering Yields High-Resolution Structural Insights into Beta2-Adrenergic Receptor Function Science 2007, 318, 1266– 1273 DOI: 10.1126/science.1150609
Google Scholar
1
GPCR Engineering Yields High-Resolution Structural Insights into β2-Adrenergic Receptor Function
Rosenbaum, Daniel M.; Cherezov, Vadim; Hanson, Michael A.; Rasmussen, Soren G. F.; Thian, Foon Sun; Kobilka, Tong Sun; Choi, Hee-Jung; Yao, Xiao-Jie; Weis, William I.; Stevens, Raymond C.; Kobilka, Brian K.; Pierce, K. L.; Premont, R. T.; Lefkowitz, R. J.; Kobilka, B. K.; Deupi, X.; Cherezov, V.; Rasmussen, S. G. F.
Science (Washington, DC, United States) (2007), 318 (5854), 1266-1273CODEN: SCIEAS; ISSN:0036-8075. (American Association for the Advancement of Science)
The β2-adrenergic receptor (β2AR) is a well-studied prototype for heterotrimeric guanine nucleotide-binding protein (G protein)-coupled receptors (GPCRs) that respond to diffusible hormones and neurotransmitters. To overcome the structural flexibility of the β2AR and to facilitate its crystn., we engineered a β2AR fusion protein in which T4 lysozyme (T4L) replaces most of the third intracellular loop of the GPCR ("β2AR-T4L") and showed that this protein retains near-native pharmacol. properties. Anal. of adrenergic receptor ligand-binding mutants within the context of the reported high-resoln. structure of β2AR-T4L provides insights into inverse-agonist binding and the structural changes required to accommodate catecholamine agonists. Amino acids known to regulate receptor function are linked through packing interactions and a network of hydrogen bonds, suggesting a conformational pathway from the ligand-binding pocket to regions that interact with G proteins.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2sXhtlGmur7J&md5=d422ff1e7a28719848c0e16fede045db
2
Rasmussen, S. G.; Choi, H. J.; Fung, J. J.; Pardon, E.; Casarosa, P.; Chae, P. S.; Devree, B. T.; Rosenbaum, D. M.; Thian, F. S.; Kobilka, T. S. Structure of a Nanobody-Stabilized Active State of the Beta(2) Adrenoceptor Nature 2011, 469, 175– 180 DOI: 10.1038/nature09648
Google Scholar
2
Structure of a nanobody-stabilized active state of the β2 adrenoceptor
Rasmussen, Soren G. F.; Choi, Hee-Jung; Fung, Juan Jose; Pardon, Els; Casarosa, Paola; Chae, Pil Seok; DeVree, Brian T.; Rosenbaum, Daniel M.; Thian, Foon Sun; Kobilka, Tong Sun; Schnapp, Andreas; Konetzki, Ingo; Sunahara, Roger K.; Gellman, Samuel H.; Pautsch, Alexander; Steyaert, Jan; Weis, William I.; Kobilka, Brian K.
Nature (London, United Kingdom) (2011), 469 (7329), 175-180CODEN: NATUAS; ISSN:0028-0836. (Nature Publishing Group)
G protein coupled receptors (GPCRs) exhibit a spectrum of functional behaviors in response to natural and synthetic ligands. Recent crystal structures provide insights into inactive states of several GPCRs. Efforts to obtain an agonist-bound active-state GPCR structure have proven difficult due to the inherent instability of this state in the absence of a G protein. We generated a camelid antibody fragment (nanobody) to the human β2 adrenergic receptor (β2AR) that exhibits G protein-like behavior, and obtained an agonist-bound, active-state crystal structure of the receptor-nanobody complex. Comparison with the inactive β2AR structure reveals subtle changes in the binding pocket; however, these small changes are assocd. with an 11 Å outward movement of the cytoplasmic end of transmembrane segment 6, and rearrangements of transmembrane segments 5 and 7 that are remarkably similar to those obsd. in opsin, an active form of rhodopsin. This structure provides insights into the process of agonist binding and activation.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3MXkvFartA%253D%253D&md5=3a1d3bac6d92c9d54cf1ddd14d56ab8c
3
Rasmussen, S. G.; DeVree, B. T.; Zou, Y.; Kruse, A. C.; Chung, K. Y.; Kobilka, T. S.; Thian, F. S.; Chae, P. S.; Pardon, E.; Calinski, D. Crystal Structure of the Beta2 Adrenergic Receptor-Gs Protein Complex Nature 2011, 477, 549– 555 DOI: 10.1038/nature10361
Google Scholar
3
Crystal structure of the β2 adrenergic receptor-Gs protein complex
Rasmussen, Soren G. F.; DeVree, Brian T.; Zou, Yao-Zhong; Kruse, Andrew C.; Chung, Ka-Young; Kobilka, Tong-Sun; Thian, Foon-Sun; Chae, Pil-Seok; Pardon, Els; Calinski, Diane; Mathiesen, Jesper M.; Shah, Syed T. A.; Lyons, Joseph A.; Caffrey, Martin; Gellman, Samuel H.; Steyaert, Jan; Skiniotis, Georgios; Weis, William I.; Sunahara, Roger K.; Kobilka, Brian K.
Nature (London, United Kingdom) (2011), 477 (7366), 549-555CODEN: NATUAS; ISSN:0028-0836. (Nature Publishing Group)
G protein-coupled receptors (GPCRs) are responsible for the majority of cellular responses to hormones and neurotransmitters as well as the senses of sight, olfaction and taste. The paradigm of GPCR signalling is the activation of a heterotrimeric GTP binding protein (G protein) by an agonist-occupied receptor. The β2 adrenergic receptor (β2AR) activation of Gs, the stimulatory G protein for adenylyl cyclase, has long been a model system for GPCR signalling. Here we present the crystal structure of the active state ternary complex composed of agonist-occupied monomeric β2AR and nucleotide-free Gs heterotrimer. The principal interactions between the β2AR and Gs involve the amino- and carboxy-terminal α-helixes of Gs, with conformational changes propagating to the nucleotide-binding pocket. The largest conformational changes in the β2AR include a 14 Å outward movement at the cytoplasmic end of transmembrane segment 6 (TM6) and an α-helical extension of the cytoplasmic end of TM5. The most surprising observation is a major displacement of the α-helical domain of Gαs relative to the Ras-like GTPase domain. This crystal structure represents the first high-resoln. view of transmembrane signalling by a GPCR.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3MXht1equrrL&md5=d22a43dd677ac255d138b1aedff357d3
4
Warne, T.; Serrano-Vega, M. J.; Baker, J. G.; Moukhametzianov, R.; Edwards, P. C.; Henderson, R.; Leslie, A. G.; Tate, C. G.; Schertler, G. F. Structure of a Beta1-Adrenergic G-Protein-Coupled Receptor Nature 2008, 454, 486– 491 DOI: 10.1038/nature07101
Google Scholar
4
Structure of a β1-adrenergic G-protein-coupled receptor
Warne, Tony; Serrano-Vega, Maria J.; Baker, Jillian G.; Moukhametzianov, Rouslan; Edwards, Patricia C.; Henderson, Richard; Leslie, Andrew G. W.; Tate, Christopher G.; Schertler, Gebhard F. X.
Nature (London, United Kingdom) (2008), 454 (7203), 486-491CODEN: NATUAS; ISSN:0028-0836. (Nature Publishing Group)
G-protein-coupled receptors have a major role in transmembrane signaling in most eukaryotes and many are important drug targets. Here we report the 2.7Å resoln. crystal structure of a β1-adrenergic receptor in complex with high affinity antagonist cyanopindolol. The modified turkey (Meleagris gallopavo) receptor was selected to be in its antagonist conformation and its thermostability improved by earlier limited mutagenesis. The ligand-binding pocket comprises 15 side chains from amino acid residues in 4 transmembrane α-helixes and extracellular loop 2. This loop defines the entrance of the ligand-binding pocket and is stabilized by two disulfide bonds and a sodium ion. Binding of cyanopindolol to the β1-adrenergic receptor and binding of Carazolol to the β2-adrenergic receptor involve similar interactions. A short well-defined helix in cytoplasmic loop 2, not obsd. in either rhodopsin or the β2-adrenergic receptor, directly interacts by means of a tyrosine with the highly conserved DRY motif at the end of helix 3 that is essential for receptor activation.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD1cXovV2mtLg%253D&md5=de1d476a6ff0b995cd344c248d1bc490
5
Venkatakrishnan, A. J.; Deupi, X.; Lebon, G.; Tate, C. G.; Schertler, G. F.; Babu, M. M. Molecular Signatures of G-Protein-Coupled Receptors Nature 2013, 494, 185– 194 DOI: 10.1038/nature11896
Google Scholar
5
Molecular signatures of G-protein-coupled receptors
Venkatakrishnan, A. J.; Deupi, Xavier; Lebon, Guillaume; Tate, Christopher G.; Schertler, Gebhard F.; Babu, M. Madan
Nature (London, United Kingdom) (2013), 494 (7436), 185-194CODEN: NATUAS; ISSN:0028-0836. (Nature Publishing Group)
A review. G-protein-coupled receptors (GPCRs) are physiol. important membrane proteins that sense signaling mols. such as hormones and neurotransmitters, and are the targets of several prescribed drugs. Recent exciting developments are providing unprecedented insights into the structure and function of several medically important GPCRs. Here, through a systematic anal. of high-resoln. GPCR structures, we uncover a conserved network of non-covalent contacts that defines the GPCR fold. Furthermore, our comparative anal. reveals characteristic features of ligand binding and conformational changes during receptor activation. A holistic understanding that integrates mol. and systems biol. of GPCRs holds promise for new therapeutics and personalized medicine.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3sXis1Wrt7Y%253D&md5=5dd040bf5f3b4b81249c02d493a1fbf3
6
Isberg, V.; Mordalski, S.; Munk, C.; Rataj, K.; Harpsoe, K.; Hauser, A. S.; Vroling, B.; Bojarski, A. J.; Vriend, G.; Gloriam, D. E. GPCRdb: An Information System for G Protein-Coupled Receptors Nucleic Acids Res. 2016, 44, D356– D364 DOI: 10.1093/nar/gkv1178
Google Scholar
6
GPCRdb: an information system for G protein-coupled receptors
Isberg, Vignir; Mordalski, Stefan; Munk, Christian; Rataj, Krzysztof; Harpsoee, Kasper; Hauser, Alexander S.; Vroling, Bas; Bojarski, Andrzej J.; Vriend, Gert; Gloriam, David E.
Nucleic Acids Research (2016), 44 (D1), D356-D364CODEN: NARHAD; ISSN:0305-1048. (Oxford University Press)
A review. Recent developments in G protein-coupled receptor (GPCR) structural biol. and pharmacol. have greatly enhanced our knowledge of receptor structure-function relations, and have helped improve the scientific foundation for drug design studies. The GPCR database, GPCRdb, serves a dual role in disseminating and enabling new scientific developments by providing ref. data, anal. tools and interactive diagrams. This paper highlights new features in the fifth major GPCRdb release: (i) GPCR crystal structure browsing, superposition and display of ligand interactions; (ii) direct deposition by users of point mutations and their effects on ligand binding; (iii) refined snake and helix box residue diagram looks; and (iv) phylogenetic trees with receptor classification color schemes. Under the hood, the entire GPCRdb front- and back-ends have been recoded within one infrastructure, ensuring a smooth browsing experience and development. GPCRdb is available at http://www.gpcrdb.org/ and it's open source code at https://bitbucket.org/gpcr/protwis.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2sXhtV2gu7bJ&md5=ee7db0ef81d65cf6e5ab8750b990bb78
7
GPCRdb: An Information System for G Protein-Coupled Receptors. http://gpcrdb.org/structure/statistics, accessed July 18, 2016.
Google Scholar
There is no corresponding record for this reference.
8
Adcock, S. A.; McCammon, J. A. Molecular Dynamics: Survey of Methods for Simulating the Activity of Proteins Chem. Rev. 2006, 106, 1589– 1615 DOI: 10.1021/cr040426m
Google Scholar
8
Molecular dynamics: Survey of methods for simulating the activity of proteins
Adcock, Stewart A.; McCammon, J. Andrew
Chemical Reviews (Washington, DC, United States) (2006), 106 (5), 1589-1615CODEN: CHREAY; ISSN:0009-2665. (American Chemical Society)
A review. Mol. dynamics simulations (MDS) of proteins have provided many insights into the internal motions of these biomols. Simulation of in silico models aids in the interpretation and reconciliation of exptl. data. With ongoing advances in both methodol. and computational resources, MDS are being extended to larger systems and longer time scales. This enables the investigation of motions and conformational changes that have functional implications and yields information that is not available though any other means. Today's results suggest that (subject to the continuing utilization of synergies between expt. and simulation) the applications of MDS will command an increasingly crit. role in the understanding of biol. systems.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD28Xht1eqtro%253D&md5=56cae2eff1ab9c443756dba4fde5500e
9
Rosenbaum, D. M.; Rasmussen, S. G.; Kobilka, B. K. The Structure and Function of G-Protein-Coupled Receptors Nature 2009, 459, 356– 363 DOI: 10.1038/nature08144
Google Scholar
9
The structure and function of G-protein-coupled receptors
Rosenbaum, Daniel M.; Rasmussen, Soren G. F.; Kobilka, Brian K.
Nature (London, United Kingdom) (2009), 459 (7245), 356-363CODEN: NATUAS; ISSN:0028-0836. (Nature Publishing Group)
A review. G-protein-coupled receptors (GPCRs) mediate most of the physiol. responses to hormones, neurotransmitters and environmental stimulants, and so have great potential as therapeutic targets for a broad spectrum of diseases. They are also fascinating mols. from the perspective of membrane protein structure and biol. Great progress has been made over the past 3 decades in understanding diverse GPCRs, from pharmacol. to functional characterization in vivo. Recent high-resoln. structural studies have provided insights into the mol. mechanisms of GPCR activation and constitutive activity.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD1MXmtFKmsLg%253D&md5=4d0271a5aacc58c4d255ddb7531ca8ed
10
Fredriksson, R.; Lagerstrom, M. C.; Lundin, L.-G.; Schioth, H. B. The G-Protein-Coupled Receptors in the Human Genome Form Five Main Families. Phylogenetic Analysis, Paralogon Groups, and Fingerprints Mol. Pharmacol. 2003, 63, 1256– 1272 DOI: 10.1124/mol.63.6.1256
Google Scholar
10
The G-protein-coupled receptors in the human genome form five main families. Phylogenetic analysis, paralogon groups, and fingerprints
Fredriksson, Robert; Lagerstrom, Malin C.; Lundin, Lars-Gustav; Schioth, Helgi B.
Molecular Pharmacology (2003), 63 (6), 1256-1272CODEN: MOPMA3; ISSN:0026-895X. (American Society for Pharmacology and Experimental Therapeutics)
The superfamily of G-protein-coupled receptors (GPCRs) is very diverse in structure and function and its members are among the most pursued targets for drug development. We identified more than 800 human GPCR sequences and simultaneously analyzed 342 unique functional nonolfactory human GPCR sequences with phylogenetic analyses. Our results show, with high bootstrap support, five main families, named glutamate, rhodopsin, adhesion, frizzled/taste2, and secretin, forming the GRAFS classification system. The rhodopsin family is the largest and forms four main groups with 13 subbranches. Positions of the GPCRs in chromosomal paralogons regions indicate the importance of tetraploidizations or local gene duplication events for their creation. We also searched for "fingerprint" motifs using Hidden Markov Models delineating the putative inter-relationship of the GRAFS families. We show several common structural features indicating that the human GPCRs in the GRAFS families share a common ancestor. This study represents the first overall map of the GPCRs in a single mammalian genome. Our novel approach of analyzing such large and diverse sequence sets may be useful for studies on GPCRs in other genomes and divergent protein families.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD3sXkt1Shu7k%253D&md5=504ea873ee8469cd0b6016bc94943836
11
Lagerstrom, M. C.; Schioth, H. B. Structural Diversity of G Protein-Coupled Receptors and Significance for Drug Discovery Nat. Rev. Drug Discovery 2008, 7, 339– 357 DOI: 10.1038/nrd2518
Google Scholar
11
Structural diversity of G protein-coupled receptors and significance for drug discovery
Lagerstrom Malin C; Schioth Helgi B
Nature reviews. Drug discovery (2008), 7 (4), 339-57 ISSN:.
G protein-coupled receptors (GPCRs) are the largest family of membrane-bound receptors and also the targets of many drugs. Understanding of the functional significance of the wide structural diversity of GPCRs has been aided considerably in recent years by the sequencing of the human genome and by structural studies, and has important implications for the future therapeutic potential of targeting this receptor family. This article aims to provide a comprehensive overview of the five main human GPCR families--Rhodopsin, Secretin, Adhesion, Glutamate and Frizzled/Taste2--with a focus on gene repertoire, general ligand preference, common and unique structural features, and the potential for future drug discovery.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A280%3ADC%252BD1c3itl2juw%253D%253D&md5=3e9de54162c071b7927d975b964abea2
12
Henzler-Wildman, K.; Kern, D. Dynamic Personalities of Proteins Nature 2007, 450, 964– 972 DOI: 10.1038/nature06522
Google Scholar
12
Dynamic personalities of proteins
Henzler-Wildman, Katherine; Kern, Dorothee
Nature (London, United Kingdom) (2007), 450 (7172), 964-972CODEN: NATUAS; ISSN:0028-0836. (Nature Publishing Group)
A review. Because proteins are central to cellular function, researchers have sought to uncover the secrets of how these complex macromols. execute such a fascinating variety of functions. Although static structures are known for many proteins, the functions of proteins are governed ultimately by their dynamic character (or 'personality'). The dream is to 'watch' proteins in action in real time at at. resoln. This requires the addn. of a fourth dimension, time, to structural biol. so that the positions in space and time of all atoms in a protein can be described in detail.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2sXhsVaqtr%252FL&md5=27ca36106100f487683d714de5335dc2
13
Granier, S.; Kobilka, B. A New Era of GPCR Structural and Chemical Biology Nat. Chem. Biol. 2012, 8, 670– 673 DOI: 10.1038/nchembio.1025
Google Scholar
13
A new era of GPCR structural and chemical biology
Granier, Sebastien; Kobilka, Brian
Nature Chemical Biology (2012), 8 (8), 670-673CODEN: NCBABT; ISSN:1552-4450. (Nature Publishing Group)
A review. G protein-coupled receptors (GPCRs) are versatile mol. machines that regulate the majority of physiol. responses to chem. diverse hormones and neurotransmitters. Recent breakthroughs in structural studies have advanced the understanding of GPCR signaling, particularly the selectivity of ligand recognition and receptor activation of G proteins.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC38XhtVCltLvK&md5=43f50b2b5f0d6fae2bf77ffe369fa899
14
Wishart, D. S. Interpreting Protein Chemical Shift Data Prog. Nucl. Magn. Reson. Spectrosc. 2011, 58, 62– 87 DOI: 10.1016/j.pnmrs.2010.07.004
Google Scholar
14
Interpreting protein chemical shift data
Wishart, David S.
Progress in Nuclear Magnetic Resonance Spectroscopy (2011), 58 (1-2), 62-87CODEN: PNMRAT; ISSN:0079-6565. (Elsevier B.V.)
There is no expanded citation for this reference.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3MXmtVKqtg%253D%253D&md5=88c1ea81ee5bc5748b2e7215d946c792
15
Jeschke, G. DEER Distance Measurements on Proteins Annu. Rev. Phys. Chem. 2012, 63, 419– 446 DOI: 10.1146/annurev-physchem-032511-143716
Google Scholar
15
DEER distance measurements on proteins
Jeschke, Gunnar
Annual Review of Physical Chemistry (2012), 63 (), 419-446CODEN: ARPLAP; ISSN:0066-426X. (Annual Reviews Inc.)
A review. Distance distributions between paramagnetic centers in the range of 1.8 to 6 nm in membrane proteins and up to 10 nm in deuterated sol. proteins can be measured by the DEER technique. The no. of paramagnetic centers and their relative orientation can be characterized. DEER does not require crystn. and is not limited with respect to the size of the protein or protein complex. Diamagnetic proteins are accessible by site-directed spin labeling. To characterize structure or structural changes, exptl. protocols were optimized and techniques for artifact suppression were introduced. Data anal. programs were developed, and it was realized that interpretation of the distance distributions must take into account the conformational distribution of spin labels. First methods have appeared for deriving structural models from a small no. of distance constraints. The present scope and limitations of the technique are illustrated.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC38Xnt1Gksr0%253D&md5=d63283b52c83f9d81847d0ce070dbde3
16
Lohse, M. J.; Hein, P.; Hoffmann, C.; Nikolaev, V. O.; Vilardaga, J. P.; Bunemann, M. Kinetics of G-Protein-Coupled Receptor Signals in Intact Cells Br. J. Pharmacol. 2008, 153 (S1) S125– S132 DOI: 10.1038/sj.bjp.0707656
Google Scholar
There is no corresponding record for this reference.
17
Lohse, M. J.; Nuber, S.; Hoffmann, C. Fluorescence/Bioluminescence Resonance Energy Transfer Techniques to Study G-Protein-Coupled Receptor Activation and Signaling Pharmacol. Rev. 2012, 64, 299– 336 DOI: 10.1124/pr.110.004309
Google Scholar
17
Fluorescence/bioluminescence resonance energy transfer techniques to study G-protein-coupled receptor activation and signaling
Lohse, Martin J.; Nuber, Susanne; Hoffmann, Carsten
Pharmacological Reviews (2012), 64 (2), 299-336CODEN: PAREAQ; ISSN:1521-0081. (American Society for Pharmacology and Experimental Therapeutics)
A review. Fluorescence and bioluminescence resonance energy transfer (FRET and BRETT) techniques allow the sensitive monitoring of distances between two labels at the nanometer scale. Depending on the placement of the labels, this permits the anal. of conformational changes within a single protein (for example of a receptor) or the monitoring of protein-protein interactions (for example, between receptors and G-protein subunits). Over the past decade, numerous such techniques have been developed to monitor the activation and signaling of G-protein-coupled receptors (GPCRs) in both the purified, reconstituted state and in intact cells. These techniques span the entire spectrum from ligand binding to the receptors down to intracellular second messengers. They allow the detn. and the visualization of signaling processes with high temporal and spatial resoln. With these techniques, it has been demonstrated that GPCR signals may show spatial and temporal patterning. In particular, evidence has been provided for spatial compartmentalization of GPCRs and their signals in intact cells and for distinct physiol. consequences of such spatial patterning. We review here the FRET and BRET technologies that have been developed for G-protein-coupled receptors and their signaling proteins (G-proteins, effectors) and the concepts that result from such expts.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC38XmslKktr8%253D&md5=76146f70e0e0776aa1d10dae884462aa
18
Mansoor, S. E.; Dewitt, M. A.; Farrens, D. L. Distance Mapping in Proteins Using Fluorescence Spectroscopy: The Tryptophan-Induced Quenching (TrIQ) Method Biochemistry 2010, 49, 9722– 9731 DOI: 10.1021/bi100907m
Google Scholar
18
Distance Mapping in Proteins Using Fluorescence Spectroscopy: The Tryptophan-Induced Quenching (TrIQ) Method
Mansoor, Steven E.; DeWitt, Mark A.; Farrens, David L.
Biochemistry (2010), 49 (45), 9722-9731CODEN: BICHAW; ISSN:0006-2960. (American Chemical Society)
Studying the interplay between protein structure and function remains a daunting task. Esp. lacking are methods for measuring structural changes in real time. Here the authors report their most recent improvements to a method that can be used to address such challenges. This method, which the authors now call tryptophan-induced quenching (TrIQ), provides a straightforward, sensitive, and inexpensive way to address questions of conformational dynamics and short-range protein interactions. Importantly, TrIQ only occurs over relatively short distances (∼5-15 Å), making it complementary to traditional fluorescence resonance energy transfer (FRET) methods that occur over distances too large for precise studies of protein structure. As implied in the name, TrIQ measures the efficient quenching induced in some fluorophores by tryptophan (Trp). The authors present here an anal. of the TrIQ effect for 5 different fluorophores that span a range of sizes and spectral properties. Each probe was attached to four different cysteine residues on T4 lysozyme, and the extent of TrIQ caused by a nearby Trp was measured. The authors' results show that, at least for smaller probes, the extent of TrIQ is distance dependent. Moreover, the authors also demonstrate how TrIQ data can be analyzed to det. the fraction of fluorophores involved in a static, nonfluorescent complex with Trp. Based on this anal., the authors' study shows that each fluorophore has a different TrIQ profile, or "sphere of quenching", which correlates with its size, rotational flexibility, and the length of attachment linker. This TrIQ-based "sphere of quenching" is unique to every Trp-probe pair and reflects the distance within which one can expect to see the TrIQ effect. Thus,TrIQ provides a straightforward, readily accessible approach for mapping distances within proteins and monitoring conformational changes using fluorescence spectroscopy.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3cXhtlalu7%252FP&md5=ff88cce765239dbddedb872c7f41019a
19
Park, S. H.; Das, B. B.; Casagrande, F.; Tian, Y.; Nothnagel, H. J.; Chu, M.; Kiefer, H.; Maier, K.; De Angelis, A. A.; Marassi, F. M. Structure of the Chemokine Receptor CXCR1 in Phospholipid Bilayers Nature 2012, 491, 779– 783 DOI: 10.1038/nature11580
Google Scholar
19
Structure of the chemokine receptor CXCR1 in phospholipid bilayers
Park, Sang Ho; Das, Bibhuti B.; Casagrande, Fabio; Tian, Ye; Nothnagel, Henry J.; Chu, Mignon; Kiefer, Hans; Maier, Klaus; De Angelis, Anna A.; Marassi, Francesca M.; Opella, Stanley J.
Nature (London, United Kingdom) (2012), 491 (7426), 779-783CODEN: NATUAS; ISSN:0028-0836. (Nature Publishing Group)
CXCR1 is one of two high-affinity receptors for the CXC chemokine interleukin-8 (IL-8), a major mediator of immune and inflammatory responses implicated in many disorders, including tumor growth. IL-8, released in response to inflammatory stimuli, binds to the extracellular side of CXCR1. The ligand-activated intracellular signaling pathways result in neutrophil migration to the site of inflammation. CXCR1 is a class A, rhodopsin-like G-protein-coupled receptor (GPCR), the largest class of integral membrane proteins responsible for cellular signal transduction and targeted as drug receptors. Despite its importance, the mol. mechanism of CXCR1 signal transduction is poorly understood owing to the limited structural information available. Recent structural detn. of GPCRs has advanced by modifying the receptors with stabilizing mutations, insertion of the protein T4 lysozyme and truncations of their amino acid sequences, as well as addn. of stabilizing antibodies and small mols. that facilitate crystn. in cubic phase monoolein mixts. The intracellular loops of GPCRs are crucial for G-protein interactions, and activation of CXCR1 involves both amino-terminal residues and extracellular loops. Our previous NMR studies indicate that IL-8 binding to the N-terminal residues is mediated by the membrane, underscoring the importance of the phospholipid bilayer for physiol. activity. Here we report the three-dimensional structure of human CXCR1 detd. by NMR spectroscopy. The receptor is in liq. cryst. phospholipid bilayers, without modification of its amino acid sequence and under physiol. conditions. Features important for intracellular G-protein activation and signal transduction are revealed. The structure of human CXCR1 in a lipid bilayer should help to facilitate the discovery of new compds. that interact with GPCRs and combat diseases such as breast cancer.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC38XhsFCns73O&md5=e6333d33cd9b1ac916dbf2932cea0420
20
Dror, R. O.; Dirks, R. M.; Grossman, J. P.; Xu, H.; Shaw, D. E. Biomolecular Simulation: A Computational Microscope for Molecular Biology Annu. Rev. Biophys. 2012, 41, 429– 452 DOI: 10.1146/annurev-biophys-042910-155245
Google Scholar
20
Biomolecular simulation: a computational microscope for molecular biology
Dror, Ron O.; Dirks, Robert M.; Grossman, J. P.; Xu, Huafeng; Shaw, David E.
Annual Review of Biophysics (2012), 41 (), 429-452CODEN: ARBNCV; ISSN:1936-122X. (Annual Reviews Inc.)
A review. Mol. dynamics simulations capture the behavior of biol. macromols. in full at. detail, but their computational demands, combined with the challenge of appropriately modeling the relevant physics, have historically restricted their length and accuracy. Dramatic recent improvements in achievable simulation speed and the underlying phys. models have enabled at.-level simulations on timescales as long as milliseconds that capture key biochem. processes such as protein folding, drug binding, membrane transport, and the conformational changes crit. to protein function. Such simulation may serve as a computational microscope, revealing biomol. mechanisms at spatial and temporal scales that are difficult to observe exptl. We describe the rapidly evolving state of the art for at.-level biomol. simulation, illustrate the types of biol. discoveries that can now be made through simulation, and discuss challenges motivating continued innovation in this field.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC38Xpt1yhs7s%253D&md5=3f872bcd93c1c2141ef3f020c5c6d45d
21
Dror, R. O.; Arlow, D. H.; Borhani, D. W.; Jensen, M. O.; Piana, S.; Shaw, D. E. Identification of Two Distinct Inactive Conformations of the Beta2-Adrenergic Receptor Reconciles Structural and Biochemical Observations Proc. Natl. Acad. Sci. U. S. A. 2009, 106, 4689– 4694 DOI: 10.1073/pnas.0811065106
Google Scholar
There is no corresponding record for this reference.
22
Nygaard, R.; Zou, Y.; Dror, R. O.; Mildorf, T. J.; Arlow, D. H.; Manglik, A.; Pan, A. C.; Liu, C. W.; Fung, J. J.; Bokoch, M. P. The Dynamic Process of Beta(2)-Adrenergic Receptor Activation Cell 2013, 152, 532– 542 DOI: 10.1016/j.cell.2013.01.008
Google Scholar
22
The Dynamic Process of β2-Adrenergic Receptor Activation
Nygaard, Rie; Zou, Yaozhong; Dror, Ron O.; Mildorf, Thomas J.; Arlow, Daniel H.; Manglik, Aashish; Pan, Albert C.; Liu, Corey W.; Fung, Juan Jose; Bokoch, Michael P.; Thian, Foon Sun; Kobilka, Tong Sun; Shaw, David E.; Mueller, Luciano; Prosser, R. Scott; Kobilka, Brian K.
Cell (Cambridge, MA, United States) (2013), 152 (3), 532-542CODEN: CELLB5; ISSN:0092-8674. (Cell Press)
G-protein-coupled receptors (GPCRs) can modulate diverse signaling pathways, often in a ligand-specific manner. The full range of functionally relevant GPCR conformations is poorly understood. Here, the authors use NMR spectroscopy to characterize the conformational dynamics of the transmembrane core of the β2-adrenergic receptor (β2AR), a prototypical GPCR. The authors labeled β2AR with 13CH3ε-methionine and obtained HSQC spectra of unliganded receptor as well as receptor bound to an inverse agonist, an agonist, and a G-protein-mimetic nanobody. These studies provide evidence for conformational states not obsd. in crystal structures, as well as substantial conformational heterogeneity in agonist- and inverse-agonist-bound prepns. They also show that for β2AR, unlike rhodopsin, an agonist alone does not stabilize a fully active conformation, suggesting that the conformational link between the agonist-binding pocket and the G-protein-coupling surface is not rigid. The obsd. heterogeneity may be important for β2AR's ability to engage multiple signaling and regulatory proteins.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3sXhvFaiu7s%253D&md5=8f9aaa581027657b166b92ef617e950d
23
Dror, R. O.; Arlow, D. H.; Maragakis, P.; Mildorf, T. J.; Pan, A. C.; Xu, H.; Borhani, D. W.; Shaw, D. E. Activation Mechanism of the Beta2-Adrenergic Receptor Proc. Natl. Acad. Sci. U. S. A. 2011, 108, 18684– 18689 DOI: 10.1073/pnas.1110499108
Google Scholar
23
Activation mechanism of the β2-adrenergic receptor
Dror, Ron O.; Arlow, Daniel H.; Maragakis, Paul; Mildorf, Thomas J.; Pan, Albert C.; Xu, Huafeng; Borhani, David W.; Shaw, David E.
Proceedings of the National Academy of Sciences of the United States of America (2011), 108 (46), 18684-18689, S18684/1-S18684/12CODEN: PNASA6; ISSN:0027-8424. (National Academy of Sciences)
A third of marketed drugs act by binding to a G-protein-coupled, receptor (GPCR) and either triggering or preventing receptor activation. Although recent crystal structures have provided snapshots of both active and inactive functional states of GPCRs, these structures do not reveal the mechanism by which GPCRs transition between these states. Here we propose an activation mechanism for the β2-adrenergic receptor, a prototypical GPCR, based on at.-level simulations in which an agonist-bound receptor transitions spontaneously from the active to the inactive crystallog. obsd. conformation. A loosely coupled allosteric network, comprising three regions that can each switch individually between multiple distinct conformations, links small perturbations at the extracellular drug-binding site to large conformational changes at the intracellular G-protein-binding site. Our simulations also exhibit an intermediate that may represent a receptor conformation to which a G protein binds during activation, and suggest that the first structural changes during receptor activation often take place on the intracellular side of the receptor, far from the drug-binding site. By capturing this fundamental signaling process in at. detail, our results may provide a foundation for the design of drugs that control receptor signaling more precisely by stabilizing specific receptor conformations.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3MXhs1Wns7bK&md5=54303d4160a7372ab31cc0e415653eb8
24
Manglik, A.; Kim, T. H.; Masureel, M.; Altenbach, C.; Yang, Z.; Hilger, D.; Lerch, M. T.; Kobilka, T. S.; Thian, F. S.; Hubbell, W. L. Structural Insights into the Dynamic Process of Beta2-Adrenergic Receptor Signaling Cell 2015, 161, 1101– 1111 DOI: 10.1016/j.cell.2015.04.043
Google Scholar
24
Structural Insights into the Dynamic Process of β2-Adrenergic Receptor Signaling
Manglik, Aashish; Kim, Tae Hun; Masureel, Matthieu; Altenbach, Christian; Yang, Zhongyu; Hilger, Daniel; Lerch, Michael T.; Kobilka, Tong Sun; Thian, Foon Sun; Hubbell, Wayne L.; Prosser, R. Scott; Kobilka, Brian K.
Cell (Cambridge, MA, United States) (2015), 161 (5), 1101-1111CODEN: CELLB5; ISSN:0092-8674. (Cell Press)
G-protein-coupled receptors (GPCRs) transduce signals from the extracellular environment to intracellular proteins. To gain structural insight into the regulation of receptor cytoplasmic conformations by extracellular ligands during signaling, we examine the structural dynamics of the cytoplasmic domain of the β2-adrenergic receptor (β2AR) using 19F-fluorine NMR and double electron-electron resonance spectroscopy. These studies show that unliganded and inverse-agonist-bound β2AR exists predominantly in two inactive conformations that exchange within hundreds of microseconds. Although agonists shift the equil. toward a conformation capable of engaging cytoplasmic G proteins, they do so incompletely, resulting in increased conformational heterogeneity and the coexistence of inactive, intermediate, and active states. Complete transition to the active conformation requires subsequent interaction with a G protein or an intracellular G protein mimetic. These studies demonstrate a loose allosteric coupling of the agonist-binding site and G-protein-coupling interface that may generally be responsible for the complex signaling behavior obsd. for many GPCRs.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2MXosVaqsLw%253D&md5=aa8772ca46629b75b503d89f3ad0dd8d
25
Kobilka, B. K.; Deupi, X. Conformational Complexity of G-Protein-Coupled Receptors Trends Pharmacol. Sci. 2007, 28, 397– 406 DOI: 10.1016/j.tips.2007.06.003
Google Scholar
25
Conformational complexity of G-protein-coupled receptors
Kobilka, Brian K.; Deupi, Xavier
Trends in Pharmacological Sciences (2007), 28 (8), 397-406CODEN: TPHSDY; ISSN:0165-6147. (Elsevier B.V.)
A review. G-protein-coupled receptors (GPCRs) are remarkably versatile signaling mols. Members of this large family of membrane proteins respond to structurally diverse ligands and mediate most transmembrane signal transduction in response to hormones and neurotransmitters, and in response to the senses of sight, smell and taste. Individual GPCRs can signal through several G-protein subtypes and through G-protein-independent pathways, often in a ligand-specific manner. This functional plasticity can be attributed to structural flexibility of GPCRs and the ability of ligands to induce or to stabilize ligand-specific conformations. Here, we review what has been learned about the dynamic nature of the structure and mechanism of GPCR activation, primarily focusing on spectroscopic studies of purified human β2 adrenergic receptor.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2sXotlWltLk%253D&md5=dd89d366cec983ffa0526e59950d91ee
26
Xue, L.; Rovira, X.; Scholler, P.; Zhao, H.; Liu, J.; Pin, J. P.; Rondard, P. Major Ligand-Induced Rearrangement of the Heptahelical Domain Interface in a GPCR Dimer Nat. Chem. Biol. 2015, 11, 134– 140 DOI: 10.1038/nchembio.1711
Google Scholar
26
Major ligand-induced rearrangement of the heptahelical domain interface in a GPCR dimer
Xue, Li; Rovira, Xavier; Scholler, Pauline; Zhao, Han; Liu, Jianfeng; Pin, Jean-Philippe; Rondard, Philippe
Nature Chemical Biology (2015), 11 (2), 134-140CODEN: NCBABT; ISSN:1552-4450. (Nature Publishing Group)
G protein-coupled receptors (GPCRs) are major players in cell communication. Although they form functional monomers, increasing evidence indicates that GPCR dimerization has a crit. role in cooperative phenomena that are important for cell signal integration. However, the structural bases of these phenomena remain elusive. Here, using well-characterized receptor dimers, the metabotropic glutamate receptors (mGluRs), the authors show that structural changes at the dimer interface are linked to receptor activation. The authors demonstrate that the main dimer interface is formed by transmembrane α helix 4 (TM4) and TM5 in the inactive state and by TM6 in the active state. This major change in the dimer interface is required for receptor activity because locking the TM4-TM5 interface prevents activation by agonist, whereas locking the TM6 interface leads to a constitutively active receptor. These data provide important information on the activation mechanism of mGluRs and improve the authors' understanding of the structural basis of the neg. cooperativity obsd. in these GPCR dimers.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2cXitFKltL%252FI&md5=0b9901b138949ad704a261bc435d0c9c
27
Tobin, A. B. G-Protein-Coupled Receptor Phosphorylation: Where, When and by Whom Br. J. Pharmacol. 2008, 153 (S1) S167– S176 DOI: 10.1038/sj.bjp.0707662
Google Scholar
There is no corresponding record for this reference.
28
Ranganathan, A.; Dror, R. O.; Carlsson, J. Insights into the Role of Asp79(2.50) in Beta2 Adrenergic Receptor Activation from Molecular Dynamics Simulations Biochemistry 2014, 53, 7283– 7296 DOI: 10.1021/bi5008723
Google Scholar
28
Insights into the Role of Asp792.50 in β2 Adrenergic Receptor Activation from Molecular Dynamics Simulations
Ranganathan, Anirudh; Dror, Ron O.; Carlsson, Jens
Biochemistry (2014), 53 (46), 7283-7296CODEN: BICHAW; ISSN:0006-2960. (American Chemical Society)
Achieving a mol.-level understanding of G-protein-coupled receptor (GPCR) activation has been a long-standing goal in biol. and could be important for the development of novel drugs. Recent breakthroughs in structural biol. have led to the detn. of high-resoln. crystal structures for the β2 adrenergic receptor (β2AR) in inactive and active states, which provided an unprecedented opportunity to understand receptor signaling at the at. level. We used mol. dynamics (MD) simulations to explore the potential roles of ionizable residues in β2AR activation. One such residue is the strongly conserved Asp792.50, which is buried in a transmembrane cavity and becomes dehydrated upon β2AR activation. MD free energy calcns. based on β2AR crystal structures suggested an increase in the population of the protonated state of Asp792.50 upon activation, which may contribute to the exptl. obsd. pH-dependent activation of this receptor. Anal. of MD simulations (in total >100 μs) with two different protonation states further supported the conclusion that the protonated Asp792.50 shifts the conformation of the β2AR toward more active-like states. On the basis of our calcns. and anal. of other GPCR crystal structures, we suggest that the protonation state of Asp2.50 may act as a functionally important microswitch in the activation of the β2AR and other class A receptors.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2cXhvVSrt7jN&md5=91bd168764df3658bf7575a4de9fef3a
29
Dawaliby, R.; Trubbia, C.; Delporte, C.; Masureel, M.; Van Antwerpen, P.; Kobilka, B. K.; Govaerts, C. Allosteric Regulation of G Protein-Coupled Receptor Activity by Phospholipids Nat. Chem. Biol. 2016, 12, 35– 39 DOI: 10.1038/nchembio.1960
Google Scholar
29
Allosteric regulation of G protein-coupled receptor activity by phospholipids
Dawaliby, Rosie; Trubbia, Cataldo; Delporte, Cedric; Masureel, Matthieu; Van Antwerpen, Pierre; Kobilka, Brian K.; Govaerts, Cedric
Nature Chemical Biology (2016), 12 (1), 35-39CODEN: NCBABT; ISSN:1552-4450. (Nature Publishing Group)
Lipids are emerging as key regulators of membrane protein structure and activity. These effects can be attributed either to the modification of bilayer properties (thickness, curvature and surface tension) or to the binding of specific lipids to the protein surface. For G protein-coupled receptors (GPCRs), the effects of phospholipids on receptor structure and activity remain poorly understood. Here we reconstituted purified β2-adrenergic receptor (β2R) in high-d. lipoparticles to systematically characterize the effect of biol. relevant phospholipids on receptor activity. We obsd. that the lipid headgroup type affected ligand binding (agonist and antagonist) and receptor activation. Specifically, phosphatidylglycerol (PG) markedly favored agonist binding and facilitated receptor activation, whereas phosphatidylethanolamine (PE) favored antagonist binding and stabilized the inactive state of the receptor. We then showed that these effects could be recapitulated with detergent-solubilized lipids, demonstrating that the functional modulation occurred in the absence of a bilayer. Our data suggest that phospholipids act as direct allosteric modulators of GPCR activity.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2MXhvVOgtLnO&md5=2aca6e59104a38ceb733c2613b027ef8
30
Yohannan, S.; Faham, S.; Yang, D.; Whitelegge, J. P.; Bowie, J. U. The Evolution of Transmembrane Helix Kinks and the Structural Diversity of G Protein-Coupled Receptors Proc. Natl. Acad. Sci. U. S. A. 2004, 101, 959– 963 DOI: 10.1073/pnas.0306077101
Google Scholar
30
The evolution of transmembrane helix kinks and the structural diversity of G protein-coupled receptors
Yohannan, Sarah; Faham, Salem; Yang, Duan; Whitelegge, Julian P.; Bowie, James U.
Proceedings of the National Academy of Sciences of the United States of America (2004), 101 (4), 959-963CODEN: PNASA6; ISSN:0027-8424. (National Academy of Sciences)
One of the hallmarks of membrane protein structure is the high frequency of transmembrane helix kinks, which commonly occur at proline residues. Because the proline side chain usually precludes normal helix geometry, it is reasonable to expect that proline residues generate these kinks. We observe however that the three prolines in bacteriorhodopsin transmembrane helixes can be changed to alanine with little structural consequences. This finding leads to a conundrum: if proline is not required for helix bending, why are prolines commonly present at bends in transmembrane helixes. We propose an evolutionary hypothesis in which a mutation to proline initially induces the kink. The resulting packing defects are later repaired by further mutation, thereby locking the kink in the structure. Thus, most prolines in extant proteins can be removed without major structural consequences. We further propose that nonproline kinks are places where vestigial prolines were later removed during evolution. Consistent with this hypothesis, at 14 of 17 nonproline kinks in membrane proteins of known structure, we find prolines in homologous sequences. Our anal. allows us to predict kink positions with >90% reliability. Kink prediction indicates that different G protein-coupled receptor proteins have different kink patterns and therefore different structures.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2cXhtFSksbs%253D&md5=3761c05e2050c485a7c9a2e396202966
31
Yuan, S.; Filipek, S.; Palczewski, K.; Vogel, H. Activation of G-Protein-Coupled Receptors Correlates with the Formation of a Continuous Internal Water Pathway Nat. Commun. 2014, 5, 4733 DOI: 10.1038/ncomms5733
Google Scholar
31
Activation of G-protein-coupled receptors correlates with the formation of a continuous internal water pathway
Yuan, Shuguang; Filipek, Slawomir; Palczewski, Krzysztof; Vogel, Horst
Nature Communications (2014), 5 (), 4733CODEN: NCAOBW; ISSN:2041-1723. (Nature Publishing Group)
Recent crystal structures of G-protein-coupled receptors (GPCRs) have revealed ordered internal water mols., raising questions about the functional role of those waters for receptor activation that could not be answered by the static structures. Here, we used mol. dynamics simulations to monitor-at at. and high temporal resoln.-conformational changes of central importance for the activation of three prototypical GPCRs with known crystal structures: the adenosine A2A receptor, the β2-adrenergic receptor and rhodopsin. Our simulations reveal that a hydrophobic layer of amino acid residues next to the characteristic NPxxY motif forms a gate that opens to form a continuous water channel only upon receptor activation. The highly conserved tyrosine residue Y7.53 undergoes transitions between three distinct conformations representative of inactive, G-protein activated and GPCR metastates. Addnl. anal. of the available GPCR crystal structures reveals general principles governing the functional roles of internal waters in GPCRs.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2cXitVShs7fO&md5=2dffebeb31040c3cbc86a579da2cb7c3
32
Staus, D. P.; Strachan, R. T.; Manglik, A.; Pani, B.; Kahsai, A. W.; Kim, T. H.; Wingler, L. M.; Ahn, S.; Chatterjee, A.; Masoudi, A. Allosteric Nanobodies Reveal the Dynamic Range and Diverse Mechanisms of G-Protein-Coupled Receptor Activation Nature 2016, 535, 448 DOI: 10.1038/nature18636
Google Scholar
32
Allosteric nanobodies reveal the dynamic range and diverse mechanisms of G-protein-coupled receptor activation
Staus, Dean P.; Strachan, Ryan T.; Manglik, Aashish; Pani, Biswaranjan; Kahsai, Alem W.; Kim, Tae Hun; Wingler, Laura M.; Ahn, Seungkirl; Chatterjee, Arnab; Masoudi, Ali; Kruse, Andrew C.; Pardon, Els; Steyaert, Jan; Weis, William I.; Prosser, R. Scott; Kobilka, Brian K.; Costa, Tommaso; Lefkowitz, Robert J.
Nature (London, United Kingdom) (2016), 535 (7612), 448-452CODEN: NATUAS; ISSN:0028-0836. (Nature Publishing Group)
G-protein-coupled receptors (GPCRs) modulate many physiol. processes by transducing a variety of extracellular cues into intracellular responses. Ligand binding to an extracellular orthosteric pocket propagates conformational change to the receptor cytosolic region to promote binding and activation of downstream signaling effectors such as G proteins and β-arrestins. It is well known that different agonists can share the same binding pocket but evoke unique receptor conformations leading to a wide range of downstream responses ('efficacy'). Furthermore, increasing biophys. evidence, primarily using the β2-adrenergic receptor (β2AR) as a model system, supports the existence of multiple active and inactive conformational states. However, how agonists with varying efficacy modulate these receptor states to initiate cellular responses is not well understood. Here the authors report stabilization of two distinct β2AR conformations using single domain camelid antibodies (nanobodies)-a previously described pos. allosteric nanobody (Nb80) and a newly identified neg. allosteric nanobody (Nb60). The authors show that Nb60 stabilizes a previously unappreciated low-affinity receptor state which corresponds to one of two inactive receptor conformations as delineated by x-ray crystallog. and NMR spectroscopy. The authors find that the agonist isoprenaline has a 15,000-fold higher affinity for β2AR in the presence of Nb80 compared to the affinity of isoprenaline for β2AR in the presence of Nb60, highlighting the full allosteric range of a GPCR. Assessing the binding of 17 ligands of varying efficacy to the β2AR in the absence and presence of Nb60 or Nb80 reveals large ligand-specific effects that can only be explained using an allosteric model which assumes equil. amongst at least three receptor states. Agonists generally exert efficacy by stabilizing the active Nb80-stabilized receptor state (R80). In contrast, for a no. of partial agonists, both stabilization of R80 and destabilization of the inactive, Nb60-bound state (R60) contribute to their ability to modulate receptor activation. These data demonstrate that ligands can initiate a wide range of cellular responses by differentially stabilizing multiple receptor states.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC28Xht1yqsLnE&md5=d7506f14cab5319482accdd9199205aa
33
Venkatakrishnan, A. J.; Flock, T.; Prado, D. E.; Oates, M. E.; Gough, J.; Madan Babu, M. Structured and Disordered Facets of the GPCR Fold Curr. Opin. Struct. Biol. 2014, 27, 129– 137 DOI: 10.1016/j.sbi.2014.08.002
Google Scholar
33
Structured and disordered facets of the GPCR fold
Venkatakrishnan, AJ; Flock, Tilman; Prado, Daniel Estevez; Oates, Matt E.; Gough, Julian; Madan Babu, M.
Current Opinion in Structural Biology (2014), 27 (), 129-137CODEN: COSBEF; ISSN:0959-440X. (Elsevier Ltd.)
A review. The seven-transmembrane (7TM) helix fold of G-protein coupled receptors (GPCRs) has been adapted for a wide variety of physiol. important signaling functions. Here, the authors discuss the diversity in the structured and disordered regions of GPCRs based on the recently published crystal structures and sequence anal. of all human GPCRs. A comparison of the structures of rhodopsin-like receptors (class A), secretin-like receptors (class B), metabotropic receptors (class C) and frizzled receptors (class F) shows that the relative arrangement of the transmembrane helixes is conserved across all 4 GPCR classes although individual receptors can be activated by ligand binding at varying positions within and around the transmembrane helical bundle. A systematic anal. of GPCR sequences reveals the presence of disordered segments in the cytoplasmic side, abundant post-translational modification sites, evidence for alternative splicing, and several putative linear peptide motifs that have the potential to mediate interactions with cytosolic proteins. While the structured regions permit the receptor to bind diverse ligands, the disordered regions appear to have an underappreciated role in modulating downstream signaling in response to the cellular state. An integrated paradigm combining the knowledge of structured and disordered regions is imperative for gaining a holistic understanding of the GPCR (un)structure-function relation.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2cXhsVakurfN&md5=567801fcef9b341c901741f0f8dfae89
34
Butcher, A. J.; Kong, K. C.; Prihandoko, R.; Tobin, A. B. Physiological Role of G-Protein Coupled Receptor Phosphorylation Handb. Exp. Pharmacol. 2012, 208, 79– 94 DOI: 10.1007/978-3-642-23274-9_5
Google Scholar
34
Physiological role of G-protein coupled receptor phosphorylation
Butcher, Adrian J.; Kong, Kok Choi; Prihandoko, Rudi; Tobin, Andrew B.
Handbook of Experimental Pharmacology (2012), 208 (Muscarinic Receptors), 79-94CODEN: HEPHD2; ISSN:0171-2004. (Springer GmbH)
A review. It is now well established that G-protein coupled receptors (GPCRs) are hyper-phosphorylated following agonist occupation usually at serine and threonine residues contained on the third intracellular loop and C-terminal tail. After some 2 decades of intensive research, the nature of protein kinases involved in this process together with the signalling consequences of receptor phosphorylation has been firmly established. The major challenge that the field currently faces is placing all this information within a physiol. context and detg. to what extent does phosphoregulation of GPCRs impact on whole animal responses. In this chapter, we address this issue by describing how GPCR phosphorylation might vary depending on the cell type in which the receptor is expressed and how this might be employed to drive selective regulation of physiol. responses.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC38XhsFChsb%252FP&md5=7857f18da8fa1de7a6aa659757a8766b
35
Huang, W.; Manglik, A.; Venkatakrishnan, A. J.; Laeremans, T.; Feinberg, E. N.; Sanborn, A. L.; Kato, H. E.; Livingston, K. E.; Thorsen, T. S.; Kling, R. C. Structural Insights into Micro-Opioid Receptor Activation Nature 2015, 524, 315– 321 DOI: 10.1038/nature14886
Google Scholar
35
Structural insights into μ-opioid receptor activation
Huang, Weijiao; Manglik, Aashish; Venkatakrishnan, A. J.; Laeremans, Toon; Feinberg, Evan N.; Sanborn, Adrian L.; Kato, Hideaki E.; Livingston, Kathryn E.; Thorsen, Thor S.; Kling, Ralf C.; Granier, Sebastien; Gmeiner, Peter; Husbands, Stephen M.; Traynor, John R.; Weis, William I.; Steyaert, Jan; Dror, Ron O.; Kobilka, Brian K.
Nature (London, United Kingdom) (2015), 524 (7565), 315-321CODEN: NATUAS; ISSN:0028-0836. (Nature Publishing Group)
Activation of the μ-opioid receptor (μOR) is responsible for the efficacy of the most effective analgesics. To shed light on the structural basis for μOR activation, here we report a 2.1 Å X-ray crystal structure of the murine μOR bound to the morphinan agonist BU72 and a G protein mimetic camelid antibody fragment Nb39 (nanobody 39). The BU72-stabilized changes in the μOR binding pocket are subtle and differ from those obsd. for agonist-bound structures of the β2-adrenergic receptor (β2AR) and the M2 muscarinic receptor (M2R). Comparison with active β2AR reveals a common rearrangement in the packing of three conserved amino acids in the core of the μOR, and mol. dynamics simulations illustrate how the ligand-binding pocket is conformationally linked to this conserved triad. Addnl., an extensive polar network between the ligand-binding pocket and the cytoplasmic domains appears to play a similar role in signal propagation for all three G-protein-coupled receptors.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2MXht12jtbzM&md5=b9af3e1351b04539379532c127c02651
36
Wheatley, M.; Wootten, D.; Conner, M. T.; Simms, J.; Kendrick, R.; Logan, R. T.; Poyner, D. R.; Barwell, J. Lifting the Lid on GPCRs: The Role of Extracellular Loops Br. J. Pharmacol. 2012, 165, 1688– 1703 DOI: 10.1111/j.1476-5381.2011.01629.x
Google Scholar
36
Lifting the lid on GPCRs: the role of extracellular loops
Wheatley, M.; Wootten, D.; Conner, M. T.; Simms, J.; Kendrick, R.; Logan, R. T.; Poyner, D. R.; Barwell, J.
British Journal of Pharmacology (2012), 165 (6), 1688-1703CODEN: BJPCBM; ISSN:1476-5381. (Wiley-Blackwell)
A review. GPCRs exhibit a common architecture of seven transmembrane helixes (TMs) linked by intracellular loops and extracellular loops (ECLs). Given their peripheral location to the site of G-protein interaction, it might be assumed that ECL segments merely link the important TMs within the helical bundle of the receptor. However, compelling evidence has emerged in recent years revealing a crit. role for ECLs in many fundamental aspects of GPCR function, which supported by recent GPCR crystal structures has provided mechanistic insights. This review will present current understanding of the key roles of ECLs in ligand binding, activation and regulation of both family A and family B GPCRs.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC38XjsVKqur0%253D&md5=32433dbd28c1b128dc019772f5606a59
37
Wootten, D.; Christopoulos, A.; Sexton, P. M. Emerging Paradigms in GPCR Allostery: Implications for Drug Discovery Nat. Rev. Drug Discovery 2013, 12, 630– 644 DOI: 10.1038/nrd4052
Google Scholar
37
Emerging paradigms in GPCR allostery: implications for drug discovery
Wootten, Denise; Christopoulos, Arthur; Sexton, Patrick M.
Nature Reviews Drug Discovery (2013), 12 (8), 630-644CODEN: NRDDAG; ISSN:1474-1776. (Nature Publishing Group)
A review. Allosteric ligands bind to G protein-coupled receptors (GPCRs; also known as seven-transmembrane receptors) at sites that are distinct from the sites to which endogenous ligands bind. The existence of allosteric ligands has enriched the ways in which the functions of GPCRs can be manipulated for potential therapeutic benefit, yet the complexity of their actions provides both challenges and opportunities for drug screening and development. Converging avenues of research in areas such as biased signalling by allosteric ligands and the mechanisms by which allosteric ligands modulate the effects of diverse endogenous ligands have provided new insights into how interactions between allosteric ligands and GPCRs could be exploited for drug discovery. These new findings have the potential to alter how screening for allosteric drugs is performed and may increase the chances of success in the development of allosteric modulators as clin. lead compds.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3sXht1SjtbvO&md5=59b74e5fbd5eeb832785dd879daa7c77
38
Dror, R. O.; Green, H. F.; Valant, C.; Borhani, D. W.; Valcourt, J. R.; Pan, A. C.; Arlow, D. H.; Canals, M.; Lane, J. R.; Rahmani, R. Structural Basis for Modulation of a G-Protein-Coupled Receptor by Allosteric Drugs Nature 2013, 503, 295– 299 DOI: 10.1038/nature12595
Google Scholar
38
Structural basis for modulation of a G-protein-coupled receptor by allosteric drugs
Dror, Ron O.; Green, Hillary F.; Valant, Celine; Borhani, David W.; Valcourt, James R.; Pan, Albert C.; Arlow, Daniel H.; Canals, Meritxell; Lane, J. Robert; Rahmani, Raphael; Baell, Jonathan B.; Sexton, Patrick M.; Christopoulos, Arthur; Shaw, David E.
Nature (London, United Kingdom) (2013), 503 (7475), 295-299CODEN: NATUAS; ISSN:0028-0836. (Nature Publishing Group)
The design of G-protein-coupled receptor (GPCR) allosteric modulators, an active area of modern pharmaceutical research, has proved challenging because neither the binding modes nor the mol. mechanisms of such drugs are known. Here we det. binding sites, bound conformations and specific drug-receptor interactions for several allosteric modulators of the M2 muscarinic acetylcholine receptor (M2 receptor), a prototypical family A GPCR, using at.-level simulations in which the modulators spontaneously assoc. with the receptor. Despite substantial structural diversity, all modulators form cation-π interactions with clusters of arom. residues in the receptor extracellular vestibule, approx. 15 Å from the classical, 'orthosteric' ligand-binding site. We validate the obsd. modulator binding modes through radioligand binding expts. on receptor mutants designed, on the basis of our simulations, either to increase or to decrease modulator affinity. Simulations also revealed mechanisms that contribute to pos. and neg. allosteric modulation of classical ligand binding, including coupled conformational changes of the two binding sites and electrostatic interactions between ligands in these sites. These observations enabled the design of chem. modifications that substantially alter a modulator's allosteric effects. Our findings thus provide a structural basis for the rational design of allosteric modulators targeting muscarinic and possibly other GPCRs.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3sXhslSns7nN&md5=2fa40ecd46ce62125ce4a12c18270b1f
39
Kruse, A. C.; Ring, A. M.; Manglik, A.; Hu, J.; Hu, K.; Eitel, K.; Hubner, H.; Pardon, E.; Valant, C.; Sexton, P. M. Activation and Allosteric Modulation of a Muscarinic Acetylcholine Receptor Nature 2013, 504, 101– 106 DOI: 10.1038/nature12735
Google Scholar
39
Activation and allosteric modulation of a muscarinic acetylcholine receptor
Kruse, Andrew C.; Ring, Aaron M.; Manglik, Aashish; Hu, Jianxin; Hu, Kelly; Eitel, Katrin; Huebner, Harald; Pardon, Els; Valant, Celine; Sexton, Patrick M.; Christopoulos, Arthur; Felder, Christian C.; Gmeiner, Peter; Steyaert, Jan; Weis, William I.; Garcia, K. Christopher; Wess, Juergen; Kobilka, Brian K.
Nature (London, United Kingdom) (2013), 504 (7478), 101-106CODEN: NATUAS; ISSN:0028-0836. (Nature Publishing Group)
Despite recent advances in crystallog. and the availability of G-protein-coupled receptor (GPCR) structures, little is known about the mechanism of their activation process, as only the β2 adrenergic receptor (β2AR) and rhodopsin have been crystd. in fully active conformations. Here we report the structure of an agonist-bound, active state of the human M2 muscarinic acetylcholine receptor stabilized by a G-protein mimetic camelid antibody fragment isolated by conformational selection using yeast surface display. In addn. to the expected changes in the intracellular surface, the structure reveals larger conformational changes in the extracellular region and orthosteric binding site than obsd. in the active states of the β2AR and rhodopsin. We also report the structure of the M2 receptor simultaneously bound to the orthosteric agonist iperoxo and the pos. allosteric modulator LY2119620. This structure reveals that LY2119620 recognizes a largely pre-formed binding site in the extracellular vestibule of the iperoxo-bound receptor, inducing a slight contraction of this outer binding pocket. These structures offer important insights into the activation mechanism and allosteric modulation of muscarinic receptors.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3sXhvVyisLjP&md5=ecddab0ab467321ac243b86bb82b71f8
40
Ballesteros, J. A. W. H. Integrated Methods for the Construction of Three-Dimensional Models and Computational Probing of Structure-Function Relations in G Protein-Coupled Receptors Methods Neurosci. 1995, 25, 366– 428 DOI: 10.1016/S1043-9471(05)80049-7
Google Scholar
40
Integrated methods for the construction of three-dimensional models and computational probing of structure-function relations in G protein-coupled receptors
Ballesteros, Juan A.; Weinstein, Harel
Methods in Neurosciences (1995), 25 (), 366-428CODEN: MENEE5; ISSN:1043-9471.
A review, with 135 refs., on approaches that can be used to resolve the apparent ambiguities that burden the pharmacol. testing of G protein-coupled receptor (GPCR) models, based on the integration of structural information about the receptor, about mutants, and about the changes induced by ligand binding.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaK2MXmt1Kmtrk%253D&md5=d3f99e9d07cea245a770f3f099bc8cc7
41
van der Westhuizen, E. T.; Valant, C.; Sexton, P. M.; Christopoulos, A. Endogenous Allosteric Modulators of G Protein-Coupled Receptors J. Pharmacol. Exp. Ther. 2015, 353, 246– 260 DOI: 10.1124/jpet.114.221606
Google Scholar
41
Endogenous allosteric modulators of G protein-coupled receptors
van der Westhuizen, Emma T.; Valant, Celine; Sexton, Patrick M.; Christopoulos, Christopoulos
Journal of Pharmacology and Experimental Therapeutics (2015), 353 (2), 246-260CODEN: JPETAB; ISSN:1521-0103. (American Society for Pharmacology and Experimental Therapeutics)
A review. G protein-coupled receptors (GPCRs) are the largest superfamily of receptors encoded by the human genome, and represent the largest class of current drug targets. Over the last decade and a half, it has become widely accepted that most, if not all, GPCRs possess spatially distinct allosteric sites that can be targeted by exogenous substances to modulate the receptors' biol. state. Although many of these allosteric sites are likely to serve other (e.g., structural) roles, they nonetheless possess appropriate properties to be serendipitously targeted by synthetic mols. However, there are also examples of endogenous substances that can act as allosteric modulators of GPCRs. These include not only the obvious example, i.e., the G protein, but also a variety of ions, lipids, amino acids, peptides, and accessory proteins that display different degrees of receptor-specific modulatory effects. This also suggests that some GPCRs may possess true "orphan" allosteric sites for hitherto unappreciated endogenous modulators. Of note, the increasing identification of allosteric modulator lipids, inflammatory peptides, and GPCR-targeted autoantibodies indicates that disease context plays an important role in the generation of putative endogenous GPCR modulators. If an endogenous allosteric substance can be shown to play a role in disease, this could also serve as an impetus to pursue synthetic neutral allosteric ligands as novel therapeutic agents.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2MXlvVWntb4%253D&md5=4e9eacb10df4523109feba729fbb9409
42
DeVree, B. T.; Mahoney, J. P.; Velez-Ruiz, G. A.; Rasmussen, S. G.; Kuszak, A. J.; Edwald, E.; Fung, J. J.; Manglik, A.; Masureel, M.; Du, Y. Allosteric Coupling from G Protein to the Agonist-Binding Pocket in GPCRs Nature 2016, 535, 182– 186 DOI: 10.1038/nature18324
Google Scholar
42
Allosteric coupling from G protein to the agonist-binding pocket in GPCRs
DeVree, Brian T.; Mahoney, Jacob P.; Velez-Ruiz, Gisselle A.; Rasmussen, Soren G. F.; Kuszak, Adam J.; Edwald, Elin; Fung, Juan-Jose; Manglik, Aashish; Masureel, Matthieu; Du, Yang; Matt, Rachel A.; Pardon, Els; Steyaert, Jan; Kobilka, Brian K.; Sunahara, Roger K.
Nature (London, United Kingdom) (2016), 535 (7610), 182-186CODEN: NATUAS; ISSN:0028-0836. (Nature Publishing Group)
G protein-coupled receptors (GPCRs) remain the primary conduit by which cells detect environmental stimuli and communicate with each other. Upon activation by extracellular agonists, these seven-transmembrane-domain-contg. receptors interact with heterotrimeric G proteins to regulate downstream second messenger and/or protein kinase cascades. Crystallog. evidence from a prototypic GPCR, the β2-adrenergic receptor (β2AR), in complex with its cognate G protein, Gs, has provided a model for how agonist binding promotes conformational changes that propagate through the GPCR and into the nucleotide-binding pocket of the G protein α-subunit to catalyze GDP release, the key step required for GTP binding and activation of G proteins. The structure also offers hints about how G protein binding may, in turn, allosterically influence ligand binding. Here we provide functional evidence that G protein coupling to the β2AR stabilizes a 'closed' receptor conformation characterized by restricted access to and egress from the hormone-binding site. Surprisingly, the effects of G protein on the hormone-binding site can be obsd. in the absence of a bound agonist, where G protein coupling driven by basal receptor activity impedes the assocn. of agonists, partial agonists, antagonists and inverse agonists. The ability of bound ligands to dissoc. from the receptor is also hindered, providing a structural explanation for the G protein-mediated enhancement of agonist affinity, which has been obsd. for many GPCR-G protein pairs. Our data also indicate that in contrast to agonist binding alone, coupling of a G protein in the absence of an agonist stabilizes large structural changes in a GPCR. The effects of nucleotide-free G protein on ligand-binding kinetics are shared by other members of the superfamily of GPCRs, suggesting that a common mechanism may underlie G protein-mediated enhancement of agonist affinity.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC28XhtVOns7fP&md5=1ed997230a3d1eb6d7960958e9e9669c
43
Kohlhoff, K. J.; Shukla, D.; Lawrenz, M.; Bowman, G. R.; Konerding, D. E.; Belov, D.; Altman, R. B.; Pande, V. S. Cloud-Based Simulations on Google Exacycle Reveal Ligand Modulation of GPCR Activation Pathways Nat. Chem. 2014, 6, 15– 21 DOI: 10.1038/nchem.1821
Google Scholar
43
Cloud-based simulations on Google Exacycle reveal ligand modulation of GPCR activation pathways
Kohlhoff, Kai J.; Shukla, Diwakar; Lawrenz, Morgan; Bowman, Gregory R.; Konerding, David E.; Belov, Dan; Altman, Russ B.; Pande, Vijay S.
Nature Chemistry (2014), 6 (1), 15-21CODEN: NCAHBB; ISSN:1755-4330. (Nature Publishing Group)
Simulations can provide tremendous insight into the atomistic details of biol. mechanisms, but micro- to millisecond timescales are historically only accessible on dedicated supercomputers. We demonstrate that cloud computing is a viable alternative that brings long-timescale processes within reach of a broader community. We used Google's Exacycle cloud-computing platform to simulate two milliseconds of dynamics of a major drug target, the G-protein-coupled receptor β2AR. Markov state models aggregate independent simulations into a single statistical model that is validated by previous computational and exptl. results. Moreover, our models provide an atomistic description of the activation of a G-protein-coupled receptor and reveal multiple activation pathways. Agonists and inverse agonists interact differentially with these pathways, with profound implications for drug design.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3sXhvFensbjJ&md5=57d0a54611a59b0275091ab8231e8d64
44
Katritch, V.; Cherezov, V.; Stevens, R. C. Structure-Function of the G Protein-Coupled Receptor Superfamily Annu. Rev. Pharmacol. Toxicol. 2013, 53, 531– 556 DOI: 10.1146/annurev-pharmtox-032112-135923
Google Scholar
44
Structure-function of the G protein-coupled receptor superfamily
Katritch, Vsevolod; Cherezov, Vadim; Stevens, Raymond C.
Annual Review of Pharmacology and Toxicology (2013), 53 (), 531-556CODEN: ARPTDI; ISSN:0362-1642. (Annual Reviews Inc.)
A review. During the past few years, crystallog. of G protein-coupled receptors (GPCRs) has experienced exponential growth, resulting in the detn. of the structures of 16 distinct receptors-9 of them in 2012 alone. Including closely related subtype homol. models, this coverage amts. to approx. 12% of the human GPCR superfamily. The adrenergic, rhodopsin, and adenosine receptor systems are also described by agonist-bound active-state structures, including a structure of the receptor-G protein complex for the β2-adrenergic receptor. Biochem. and biophys. techniques, such as NMR and hydrogen-deuterium exchange coupled with mass spectrometry, are providing complementary insights into ligand-dependent dynamic equil. between different functional states. Addnl. details revealed by high-resoln. structures illustrate the receptors as allosteric machines that are controlled not only by ligands but also by ions, lipids, cholesterol, and water. This wealth of data is helping redefine the authors' knowledge of how GPCRs recognize such a diverse array of ligands and how they transmit signals 30 angstroms across the cell membrane; it also is shedding light on a structural basis of GPCR allosteric modulation and biased signaling.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3sXjt1Wgurc%253D&md5=5e8c26100a9eb33a32755af09199138d
45
Rosenbaum, D. M.; Zhang, C.; Lyons, J. A.; Holl, R.; Aragao, D.; Arlow, D. H.; Rasmussen, S. G.; Choi, H. J.; Devree, B. T.; Sunahara, R. K. Structure and Function of an Irreversible Agonist-Beta(2) Adrenoceptor Complex Nature 2011, 469, 236– 240 DOI: 10.1038/nature09665
Google Scholar
45
Structure and function of an irreversible agonist-β2 adrenoceptor complex
Rosenbaum, Daniel M.; Zhang, Cheng; Lyons, Joseph A.; Holl, Ralph; Aragao, David; Arlow, Daniel H.; Rasmussen, Soren G. F.; Choi, Hee-Jung; DeVree, Brian T.; Sunahara, Roger K.; Chae, Pil Seok; Gellman, Samuel H.; Dror, Ron O.; Shaw, David E.; Weis, William I.; Caffrey, Martin; Gmeiner, Peter; Kobilka, Brian K.
Nature (London, United Kingdom) (2011), 469 (7329), 236-240CODEN: NATUAS; ISSN:0028-0836. (Nature Publishing Group)
G-protein-coupled receptors (GPCRs) are eukaryotic integral membrane proteins that modulate biol. function by initiating cellular signaling in response to chem. diverse agonists. Despite recent progress in the structural biol. of GPCRs, the mol. basis for agonist binding and allosteric modulation of these proteins is poorly understood. Structural knowledge of agonist-bound states is essential for deciphering the mechanism of receptor activation, and for structure-guided design and optimization of ligands. However, the crystn. of agonist-bound GPCRs has been hampered by modest affinities and rapid off-rates of available agonists. Using the inactive structure of the human β2 adrenergic receptor (β2AR) as a guide, we designed a β2AR agonist that can be covalently tethered to a specific site on the receptor through a disulfide bond. The covalent β2AR-agonist complex forms efficiently, and is capable of activating a heterotrimeric G protein. We crystd. a covalent agonist-bound β2AR-T4L fusion protein in lipid bilayers through the use of the lipidic mesophase method, and detd. its structure at 3.5 Å resoln. A comparison to the inactive structure and an antibody-stabilized active structure (companion paper) shows how binding events at both the extracellular and intracellular surfaces are required to stabilize an active conformation of the receptor. The structures are in agreement with long-timescale (up to 30 μs) mol. dynamics simulations showing that an agonist-bound active conformation spontaneously relaxes to an inactive-like conformation in the absence of a G protein or stabilizing antibody.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3MXkvFehsQ%253D%253D&md5=8629b93e43fb692395e2aa6f8bb011a9
46
Kruse, A. C.; Hu, J.; Pan, A. C.; Arlow, D. H.; Rosenbaum, D. M.; Rosemond, E.; Green, H. F.; Liu, T.; Chae, P. S.; Dror, R. O. Structure and Dynamics of the M3Muscarinic Acetylcholine Receptor Nature 2012, 482, 552– 556 DOI: 10.1038/nature10867
Google Scholar
46
Structure and dynamics of the M3 muscarinic acetylcholine receptor
Kruse, Andrew C.; Hu, Jianxin; Pan, Albert C.; Arlow, Daniel H.; Rosenbaum, Daniel M.; Rosemond, Erica; Green, Hillary F.; Liu, Tong; Chae, Pil Seok; Dror, Ron O.; Shaw, David E.; Weis, William I.; Wess, Jurgen; Kobilka, Brian K.
Nature (London, United Kingdom) (2012), 482 (7386), 552-556CODEN: NATUAS; ISSN:0028-0836. (Nature Publishing Group)
Acetylcholine, the first neurotransmitter to be identified, exerts many of its physiol. actions via activation of a family of G-protein-coupled receptors (GPCRs) known as muscarinic acetylcholine receptors (mAChRs). Although the five mAChR subtypes (M1-M5) share a high degree of sequence homol., they show pronounced differences in G-protein coupling preference and the physiol. responses they mediate. Unfortunately, despite decades of effort, no therapeutic agents endowed with clear mAChR subtype selectivity have been developed to exploit these differences. We describe here the structure of the Gq/11-coupled M3 mAChR ('M3 receptor', from rat) bound to the bronchodilator drug tiotropium and identify the binding mode for this clin. important drug. This structure, together with that of the Gi/o-coupled M2 receptor, offers possibilities for the design of mAChR subtype-selective ligands. Importantly, the M3 receptor structure allows a structural comparison between two members of a mammalian GPCR subfamily displaying different G-protein coupling selectivities. Furthermore, mol. dynamics simulations suggest that tiotropium binds transiently to an allosteric site en route to the binding pocket of both receptors. These simulations offer a structural view of an allosteric binding mode for an orthosteric GPCR ligand and provide addnl. opportunities for the design of ligands with different affinities or binding kinetics for different mAChR subtypes. Our findings not only offer insights into the structure and function of one of the most important GPCR families, but may also facilitate the design of improved therapeutics targeting these crit. receptors.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC38Xis1eqs7k%253D&md5=31bb89b1d14cf122353fced8f905e996
47
Manglik, A.; Kruse, A. C.; Kobilka, T. S.; Thian, F. S.; Mathiesen, J. M.; Sunahara, R. K.; Pardo, L.; Weis, W. I.; Kobilka, B. K.; Granier, S. Crystal Structure of the Micro-Opioid Receptor Bound to a Morphinan Antagonist Nature 2012, 485, 321– 326 DOI: 10.1038/nature10954
Google Scholar
47
Crystal structure of the μ-opioid receptor bound to a morphinan antagonist
Manglik, Aashish; Kruse, Andrew C.; Kobilka, Tong Sun; Thian, Foon Sun; Mathiesen, Jesper M.; Sunahara, Roger K.; Pardo, Leonardo; Weis, William I.; Kobilka, Brian K.; Granier, Sebastien
Nature (London, United Kingdom) (2012), 485 (7398), 321-326CODEN: NATUAS; ISSN:0028-0836. (Nature Publishing Group)
Opium is one of the world's oldest drugs, and its derivs. morphine and codeine are among the most used clin. drugs to relieve severe pain. These prototypical opioids produce analgesia as well as many undesirable side effects (sedation, apnea and dependence) by binding to and activating the G-protein-coupled μ-opioid receptor (μ-OR) in the central nervous system. Here the authors describe the 2.8 Å crystal structure of the mouse μ-OR in complex with an irreversible morphinan antagonist. Compared to the buried binding pocket obsd. in most G-protein-coupled receptors published so far, the morphinan ligand binds deeply within a large solvent-exposed pocket. Of particular interest, the μ-OR crystallizes as a two-fold sym. dimer through a four-helix bundle motif formed by transmembrane segments 5 and 6. These high-resoln. insights into opioid receptor structure will enable the application of structure-based approaches to develop better drugs for the management of pain and addiction.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC38XksVehs7Y%253D&md5=563d5ebda53f9a408be21d60a7e5a97d
48
Venkatakrishnan, A. J.; Deupi, X.; Lebon, G.; Heydenreich, F. M.; Flock, T.; Miljus, T.; Balaji, S.; Bouvier, M.; Veprintsev, D. B.; Tate, C. G.; Schertler, G. F. X.; Babu, M. M. Diverse Activation Pathways in Class a GPCRs Converge near the G Protein-Coupling Region Nature 2016, 536, 484– 487 DOI: 10.1038/nature19107
Google Scholar
There is no corresponding record for this reference.
49
Park, J. H.; Scheerer, P.; Hofmann, K. P.; Choe, H. W.; Ernst, O. P. Crystal Structure of the Ligand-Free G-Protein-Coupled Receptor Opsin Nature 2008, 454, 183– 187 DOI: 10.1038/nature07063
Google Scholar
49
Crystal structure of the ligand-free G-protein-coupled receptor opsin
Park, Jung Hee; Scheerer, Patrick; Hofmann, Klaus Peter; Choe, Hui-Woog; Ernst, Oliver Peter
Nature (London, United Kingdom) (2008), 454 (7201), 183-187CODEN: NATUAS; ISSN:0028-0836. (Nature Publishing Group)
In the G-protein-coupled receptor (GPCR), rhodopsin, the inactivating ligand, 11-cis-retinal, is bound in the seven-transmembrane helix (TM) bundle and is cis/trans isomerized by light to form active metarhodopsin II. With metarhodopsin II decay, all-trans-retinal is released, and opsin is reloaded with new 11-cis-retinal. Here, the authors present the crystal structure of ligand-free native opsin from bovine retinal rod cells at 2.9-Å resoln. Compared to rhodopsin, opsin showed prominent structural changes in the conserved E(D)RY and NPxxY(x)5,6F regions and in TM5-TM7. At the cytoplasmic side, TM6 was tilted outward by 6-7 Å, whereas the helix structure of TM5 was more elongated and close to TM6. These structural changes, some of which were attributed to an active GPCR state, reorganized the empty retinal-binding pocket to disclose 2 openings that may serve the entry and exit of retinal. The opsin structure shed new light on ligand binding to GPCRs and on GPCR activation.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD1cXot1ygtr4%253D&md5=d3319bba0a49a4fee2ea9ecb54d2e0d4
50
Blankenship, E.; Vahedi-Faridi, A.; Lodowski, D. T. The High-Resolution Structure of Activated Opsin Reveals a Conserved Solvent Network in the Transmembrane Region Essential for Activation Structure 2015, 23, 2358– 2364 DOI: 10.1016/j.str.2015.09.015
Google Scholar
There is no corresponding record for this reference.
51
Granier, S.; Manglik, A.; Kruse, A. C.; Kobilka, T. S.; Thian, F. S.; Weis, W. I.; Kobilka, B. K. Structure of the Delta-Opioid Receptor Bound to Naltrindole Nature 2012, 485, 400– 404 DOI: 10.1038/nature11111
Google Scholar
51
Structure of the δ-opioid receptor bound to naltrindole
Granier, Sebastien; Manglik, Aashish; Kruse, Andrew C.; Kobilka, Tong Sun; Thian, Foon Sun; Weis, William I.; Kobilka, Brian K.
Nature (London, United Kingdom) (2012), 485 (7398), 400-404CODEN: NATUAS; ISSN:0028-0836. (Nature Publishing Group)
The opioid receptor family comprises three members, the μ-, δ- and κ-opioid receptors, which respond to classical opioid alkaloids such as morphine and heroin as well as to endogenous peptide ligands like endorphins. They belong to the G-protein-coupled receptor (GPCR) superfamily, and are excellent therapeutic targets for pain control. The δ-opioid receptor (δ-OR) has a role in analgesia, as well as in other neurol. functions that remain poorly understood. The structures of the μ-OR and κ-OR have recently been solved. Here we report the crystal structure of the mouse δ-OR, bound to the subtype-selective antagonist naltrindole. Together with the structures of the μ-OR and κ-OR, the δ-OR structure provides insights into conserved elements of opioid ligand recognition while also revealing structural features assocd. with ligand-subtype selectivity. The binding pocket of opioid receptors can be divided into two distinct regions. Whereas the lower part of this pocket is highly conserved among opioid receptors, the upper part contains divergent residues that confer subtype selectivity. This provides a structural explanation and validation for the 'message-address' model of opioid receptor pharmacol., in which distinct 'message' (efficacy) and 'address' (selectivity) determinants are contained within a single ligand. Comparison of the address region of the δ-OR with other GPCRs reveals that this structural organization may be a more general phenomenon, extending to other GPCR families as well.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC38XntF2gtrc%253D&md5=892a5da1140fbfea502ee5d598455e73
52
Lebon, G.; Warne, T.; Tate, C. G. Agonist-Bound Structures of G Protein-Coupled Receptors Curr. Opin. Struct. Biol. 2012, 22, 482– 490 DOI: 10.1016/j.sbi.2012.03.007
Google Scholar
52
Agonist-bound structures of G protein-coupled receptors
Lebon, Guillaume; Warne, Tony; Tate, Christopher G.
Current Opinion in Structural Biology (2012), 22 (4), 482-490CODEN: COSBEF; ISSN:0959-440X. (Elsevier Ltd.)
A review. G protein-coupled receptors (GPCRs) play a major role in intercellular communication by binding small diffusible ligands (agonists) at the extracellular surface. Agonist-binding induces a conformational change in the receptor, which results in the binding and activation of heterotrimeric G proteins within the cell. Ten agonist-bound structures of non-rhodopsin GPCRs published last year defined for the 1st time the mol. details of receptor activated states and how inverse agonists, partial agonists, and full agonists bind to produce different effects on the receptor. In addn., the structure of the β2-adrenoceptor coupled to a heterotrimeric G protein showed how the opening of a cleft in the cytoplasmic face of the receptor as a consequence of agonist binding results in G protein coupling and activation of the G protein.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC38XltVeit7g%253D&md5=9d9a390eca0636d08918938c7a7e2eea
53
Isogai, S.; Deupi, X.; Opitz, C.; Heydenreich, F. M.; Tsai, C. J.; Brueckner, F.; Schertler, G. F.; Veprintsev, D. B.; Grzesiek, S. Backbone NMR Reveals Allosteric Signal Transduction Networks in the Beta1-Adrenergic Receptor Nature 2016, 530, 237– 241 DOI: 10.1038/nature16577
Google Scholar
There is no corresponding record for this reference.
54
Sounier, R.; Mas, C.; Steyaert, J.; Laeremans, T.; Manglik, A.; Huang, W.; Kobilka, B. K.; Demene, H.; Granier, S. Propagation of Conformational Changes During Mu-Opioid Receptor Activation Nature 2015, 524, 375– 378 DOI: 10.1038/nature14680
Google Scholar
54
Propagation of conformational changes during μ-opioid receptor activation
Sounier, Remy; Mas, Camille; Steyaert, Jan; Laeremans, Toon; Manglik, Aashish; Huang, Weijiao; Kobilka, Brian K.; Demene, Helene; Granier, Sebastien
Nature (London, United Kingdom) (2015), 524 (7565), 375-378CODEN: NATUAS; ISSN:0028-0836. (Nature Publishing Group)
μ-Opioid receptors (μORs) are G-protein-coupled receptors that are activated by a structurally diverse spectrum of natural and synthetic agonists including endogenous endorphin peptides, morphine and methadone. The recent structures of the μOR in inactive and agonist-induced active states (W. Huang et al., 2015) provide snapshots of the receptor at the beginning and end of a signalling event, but little is known about the dynamic sequence of events that span these two states. Here we use soln.-state NMR to examine the process of μOR activation using a purified receptor (mouse sequence) prepn. in an amphiphile membrane-like environment. We obtain spectra of the μOR in the absence of ligand, and in the presence of the high-affinity agonist BU 72 alone, or with BU 72 and a G protein mimetic nanobody. Our results show that conformational changes in transmembrane segments 5 and 6 (TM5 and TM6), which are required for the full engagement of a G protein, are almost completely dependent on the presence of both the agonist and the G protein mimetic nanobody, revealing a weak allosteric coupling between the agonist-binding pocket and the G-protein-coupling interface (TM5 and TM6), similar to that obsd. for the β2-adrenergic receptor. Unexpectedly, in the presence of agonist alone, we find larger spectral changes involving intracellular loop 1 and helix 8 compared to changes in TM5 and TM6. These results suggest that one or both of these domains may play a role in the initial interaction with the G protein, and that TM5 and TM6 are only engaged later in the process of complex formation. The initial interactions between the G protein and intracellular loop 1 and/or helix 8 may be involved in G-protein coupling specificity, as has been suggested for other family A G-protein-coupled receptors.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2MXht12jtb%252FN&md5=0dd0dedcce583a52b4adc3084726a862
55
Ye, L.; Van Eps, N.; Zimmer, M.; Ernst, O. P.; Prosser, R. S. Activation of the A2a Adenosine G-Protein-Coupled Receptor by Conformational Selection Nature 2016, 533, 265– 268 DOI: 10.1038/nature17668
Google Scholar
55
Activation of the A2A adenosine G-protein-coupled receptor by conformational selection
Ye, Libin; Van Eps, Ned; Zimmer, Marco; Ernst, Oliver P.; Scott Prosser, R.
Nature (London, United Kingdom) (2016), 533 (7602), 265-268CODEN: NATUAS; ISSN:0028-0836. (Nature Publishing Group)
Conformational selection and induced fit are two prevailing mechanisms to explain the mol. basis for ligand-based activation of receptors. G protein-coupled receptors (GPCRs) are the largest class of cell surface receptors and are important drug targets. A mol. understanding of their activation mechanism is crit. for drug discovery and design. However, direct evidence that addresses how agonist binding leads to the formation of an active receptor state is scarce. Here we use 19F NMR to quantify the conformational landscape occupied by the adenosine A2A receptor (A2AR), a prototypical class A G protein-coupled receptor. We find an ensemble of four states in equil.: (1) two inactive states in millisecond exchange, consistent with a formed (state S1) and a broken (state S2) salt bridge (known as 'ionic lock') between transmembrane helixes 3 and 6; and (2) two active states, S3 and S3', as identified by binding of a G protein-derived peptide. In contrast to a recent study of the β2-adrenergic receptor, the present approach allowed identification of a second active state for A2AR. Addn. of inverse agonist (ZM241385) increases the population of the inactive states, while full agonists (UK432097 or NECA) stabilize the active state, S3', in a manner consistent with conformational selection. In contrast, partial agonist (LUF5834) and an allosteric modulator (HMA) exclusively increase the population of the S3 state. Thus, partial agonism is achieved here by conformational selection of a distinct active state which we predict will have compromised coupling to the G protein. Direct observation of the conformational equil. of ligand-dependent G protein-coupled receptor and deduction of the underlying mechanisms of receptor activation will have wide-reaching implications for our understanding of the function of G protein-coupled receptor in health and disease.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC28Xnt1Ogsrc%253D&md5=d346565e2dcb9c96858554fb9f6d5085
56
Manglik, A.; Kobilka, B. The Role of Protein Dynamics in GPCR Function: Insights from the Beta2ar and Rhodopsin Curr. Opin. Cell Biol. 2014, 27, 136– 143 DOI: 10.1016/j.ceb.2014.01.008
Google Scholar
56
The role of protein dynamics in GPCR function: insights from the β2AR and rhodopsin
Manglik, Aashish; Kobilka, Brian
Current Opinion in Cell Biology (2014), 27 (), 136-143CODEN: COCBE3; ISSN:0955-0674. (Elsevier Ltd.)
A review. G protein-coupled receptors (GPCRs) are versatile signaling proteins that mediate complex cellular responses to hormones and neurotransmitters. Recent advances in GPCR crystallog. have provided inactive and active state structures for rhodopsin and the β2 adrenergic receptor (β2AR). Although these structures suggest a 2-state 'on-off' mechanism of receptor activation, other biophys. studies and obsd. signaling versatility suggest that GPCRs are highly dynamic and exist in a multitude of functionally distinct conformations. To fully understand how GPCRs work, one must characterize these conformations and det. how ligands affect their energetics and rates of interconversion. This brief review compares and contrasts the dynamic properties of rhodopsin and β2AR that shed light on the role of structural dynamics in their distinct signaling behaviors.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2cXmtVCqsLY%253D&md5=89c7146a8485fb0048f7e811d22f0036
57
Leioatts, N.; Romo, T. D.; Danial, S. A.; Grossfield, A. Retinal Conformation Changes Rhodopsin’s Dynamic Ensemble Biophys. J. 2015, 109, 608– 617 DOI: 10.1016/j.bpj.2015.06.046
Google Scholar
There is no corresponding record for this reference.
58
Ye, S.; Zaitseva, E.; Caltabiano, G.; Schertler, G. F.; Sakmar, T. P.; Deupi, X.; Vogel, R. Tracking G-Protein-Coupled Receptor Activation Using Genetically Encoded Infrared Probes Nature 2010, 464, 1386– 1389 DOI: 10.1038/nature08948
Google Scholar
58
Tracking G-protein-coupled receptor activation using genetically encoded infrared probes
Ye, Shixin; Zaitseva, Ekaterina; Caltabiano, Gianluigi; Schertler, Gebhard F. X.; Sakmar, Thomas P.; Deupi, Xavier; Vogel, Reiner
Nature (London, United Kingdom) (2010), 464 (7293), 1386-1389CODEN: NATUAS; ISSN:0028-0836. (Nature Publishing Group)
Rhodopsin is a prototypical heptahelical family A G-protein-coupled receptor (GPCR) responsible for dim-light vision. Light isomerizes rhodopsin's retinal chromophore and triggers concerted movements of transmembrane helixes, including an outward tilting of helix 6 (H6) and a smaller movement of H5, to create a site for G-protein binding and activation. However, the precise temporal sequence and mechanism underlying these helix rearrangements is unclear. We used site-directed non-natural amino acid mutagenesis to engineer rhodopsin with p-azido-l-phenylalanine residues incorporated at selected sites, and monitored the azido vibrational signatures using IR spectroscopy as rhodopsin proceeded along its activation pathway. Here we report significant changes in electrostatic environments of the azido probes even in the inactive photoproduct Meta I, well before the active receptor state was formed. These early changes suggest a significant rotation of H6 and movement of the cytoplasmic part of H5 away from H3. Subsequently, a large outward tilt of H6 leads to opening of the cytoplasmic surface to form the active receptor photoproduct Meta II. Thus, our results reveal early conformational changes that precede larger rigid-body helix movements, and provide a basis to interpret recent GPCR crystal structures and to understand conformational sub-states obsd. during the activation of other GPCRs.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3cXksFalsL8%253D&md5=9a1f060d59cd6e9efe94008a1382a1b9
59
Altenbach, C.; Kusnetzow, A. K.; Ernst, O. P.; Hofmann, K. P.; Hubbell, W. L. High-Resolution Distance Mapping in Rhodopsin Reveals the Pattern of Helix Movement Due to Activation Proc. Natl. Acad. Sci. U. S. A. 2008, 105, 7439– 7444 DOI: 10.1073/pnas.0802515105
Google Scholar
59
High-resolution distance mapping in rhodopsin reveals the pattern of helix movement due to activation
Altenbach, Christian; Kusnetzow, Ana Karin; Ernst, Oliver P.; Hofmann, Klaus Peter; Hubbell, Wayne L.
Proceedings of the National Academy of Sciences of the United States of America (2008), 105 (21), 7439-7444CODEN: PNASA6; ISSN:0027-8424. (National Academy of Sciences)
Site-directed spin labeling has qual. shown that a key event during activation of rhodopsin is a rigid-body movement of transmembrane helix 6 (TM6) at the cytoplasmic surface of the mol. To place this result on a quant. footing, and to identify movements of other helixes upon photoactivation, double electron-electron resonance (DEER) spectroscopy was used to det. distances and distance changes between pairs of nitroxide side chains introduced in helixes at the cytoplasmic surface of rhodopsin. Sixteen pairs were selected from a set of nine individual sites, each located on the solvent exposed surface of the protein where structural perturbation due to the presence of the label is minimized. Importantly, the EPR spectra of the labeled proteins change little or not at all upon photoactivation, suggesting that rigid-body motions of helixes rather than rearrangement of the nitroxide side chains are responsible for obsd. distance changes. For inactive rhodopsin, it was possible to find a globally minimized arrangement of nitroxide locations that simultaneously satisfied the crystal structure of rhodopsin (Protein Data Bank entry 1GZM), the exptl. measured distance data, and the known rotamers of the nitroxide side chain. A similar anal. of the data for activated rhodopsin yielded a new geometry consistent with a 5-Å outward movement of TM6 and smaller movements involving TM1, TM7, and the C-terminal sequence following helix H8. The positions of nitroxides in other helixes at the cytoplasmic surface remained largely unchanged.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD1cXmvFOltLg%253D&md5=1ef918a505c12b68f3064d7622c0975c
60
Hofmann, K. P.; Scheerer, P.; Hildebrand, P. W.; Choe, H. W.; Park, J. H.; Heck, M.; Ernst, O. P. A G Protein-Coupled Receptor at Work: The Rhodopsin Model Trends Biochem. Sci. 2009, 34, 540– 552 DOI: 10.1016/j.tibs.2009.07.005
Google Scholar
60
A G protein-coupled receptor at work: The rhodopsin model
Hofmann, Klaus Peter; Scheerer, Patrick; Hildebrand, Peter W.; Choe, Hui-Woog; Park, Jung Hee; Heck, Martin; Ernst, Oliver P.
Trends in Biochemical Sciences (2009), 34 (11), 540-552CODEN: TBSCDB; ISSN:0968-0004. (Elsevier B.V.)
A review. G protein-coupled receptors (GPCRs) are ubiquitous signal transducers in cell membranes as well as important drug targets. Interaction with extracellular agonists turns the seven transmembrane helix (7TM) scaffold of a GPCR into a catalyst for GDP and GTP exchange in heterotrimeric Gαβγ proteins. Activation of the model GPCR, rhodopsin, is triggered by photoisomerization of its retinal ligand. From the augmentation of biochem. and biophys. studies by recent high-resoln. 3D structures, its activation intermediates can now be interpreted as the stepwise engagement of protein domains. Rearrangement of TM5-TM6 opens a crevice at the cytoplasmic side of the receptor into which the C-terminus of the Gα subunit can bind. The Gα C-terminal helix is used as a transmission rod to the nucleotide binding site. The mechanism relies on dynamic interactions between conserved residues and could therefore be common to other GPCRs.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD1MXhtlCku77K&md5=56052451af3455524ef11c4a28c9fe9f
61
Violin, J. D.; Crombie, A. L.; Soergel, D. G.; Lark, M. W. Biased Ligands at G-Protein-Coupled Receptors: Promise and Progress Trends Pharmacol. Sci. 2014, 35, 308– 316 DOI: 10.1016/j.tips.2014.04.007
Google Scholar
61
Biased ligands at G-protein-coupled receptors: promise and progress
Violin, Jonathan D.; Crombie, Aimee L.; Soergel, David G.; Lark, Michael W.
Trends in Pharmacological Sciences (2014), 35 (7), 308-316CODEN: TPHSDY; ISSN:0165-6147. (Elsevier Ltd.)
A review. Drug discovery targeting G protein-coupled receptors (GPCRs) is no longer limited to seeking agonists or antagonists to stimulate or block cellular responses assocd. with a particular receptor. GPCRs are now known to support a diversity of pharmacol. profiles, a concept broadly referred to as functional selectivity. In particular, the concept of ligand bias, whereby a ligand stabilizes subsets of receptor conformations to engender novel pharmacol. profiles, has recently gained increasing prominence. This review discusses how biased ligands may deliver safer, better tolerated, and more efficacious drugs, and highlights several biased ligands that are in clin. development. Biased ligands targeting the angiotensin II type 1 receptor and the μ opioid receptor illustrate the translation of the biased ligand concept from basic biol. to clin. drug development.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2cXosl2htr4%253D&md5=768953e7aa5726d1a47ecbdb068469d8
62
Rajagopal, S.; Rajagopal, K.; Lefkowitz, R. J. Teaching Old Receptors New Tricks: Biasing Seven-Transmembrane Receptors Nat. Rev. Drug Discovery 2010, 9, 373– 386 DOI: 10.1038/nrd3024
Google Scholar
62
Teaching old receptors new tricks: biasing seven-transmembrane receptors
Rajagopal, Sudarshan; Rajagopal, Keshava; Lefkowitz, Robert J.
Nature Reviews Drug Discovery (2010), 9 (5), 373-386CODEN: NRDDAG; ISSN:1474-1776. (Nature Publishing Group)
A review. Seven-transmembrane receptors (7TMRs; also known as G protein-coupled receptors) are the largest class of receptors in the human genome and are common targets for therapeutics. Originally identified as mediators of 7TMR desensitization, β-arrestins (arrestin 2 and arrestin 3) are now recognized as true adaptor proteins that transduce signals to multiple effector pathways. Signaling that is mediated by β-arrestins has distinct biochem. and functional consequences from those mediated by G proteins, and several biased ligands and receptors have been identified that preferentially signal through either G protein- or β-arrestin-mediated pathways. These ligands are not only useful tools for investigating the biochem. of 7TMR signaling, but they also have the potential to be developed into new classes of therapeutics.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3cXlsVWjs7k%253D&md5=ff525016c0ba5aa0ebc4ed86f87594d0
63
Romo, T. D.; Grossfield, A.; Pitman, M. C. Concerted Interconversion between Ionic Lock Substates of the Beta(2) Adrenergic Receptor Revealed by Microsecond Timescale Molecular Dynamics Biophys. J. 2010, 98, 76– 84 DOI: 10.1016/j.bpj.2009.09.046
Google Scholar
There is no corresponding record for this reference.
64
Okada, T.; Fujiyoshi, Y.; Silow, M.; Navarro, J.; Landau, E. M.; Shichida, Y. Functional Role of Internal Water Molecules in Rhodopsin Revealed by X-Ray Crystallography Proc. Natl. Acad. Sci. U. S. A. 2002, 99, 5982– 5987 DOI: 10.1073/pnas.082666399
Google Scholar
64
Functional role of internal water molecules in rhodopsin revealed by x-ray crystallography
Okada, Tetsuji; Fujiyoshi, Yoshinori; Silow, Maria; Navarro, Javier; Landau, Ehud M.; Shichida, Yoshinori
Proceedings of the National Academy of Sciences of the United States of America (2002), 99 (9), 5982-5987CODEN: PNASA6; ISSN:0027-8424. (National Academy of Sciences)
Activation of G protein-coupled receptors (GPCRs) is triggered and regulated by structural rearrangement of the transmembrane heptahelical bundle contg. a no. of highly conserved residues. In rhodopsin, a prototypical GPCR, the helical bundle accommodates an intrinsic inverse-agonist 11-cis-retinal, which undergoes photo-isomerization to the all-trans form upon light absorption. Such a trigger by the chromophore corresponds to binding of a diffusible ligand to other GPCRs. Here we have explored the functional role of water mols. in the transmembrane region of bovine rhodopsin by using x-ray diffraction to 2.6 Å. The structural model suggests that water mols., which were obsd. in the vicinity of highly conserved residues and in the retinal pocket, regulate the activity of rhodopsin-like GPCRs and spectral tuning in visual pigments, resp. To confirm the physiol. relevance of the structural findings, we conducted single-crystal microspectrophotometry on rhodopsin packed in our three-dimensional crystals and show that its spectroscopic properties are similar to those previously found by using bovine rhodopsin in suspension or membrane environment.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD38XjslWguro%253D&md5=4e831e36d192c6a3eff3a70d9a3fd1e3
65
Okada, T.; Sugihara, M.; Bondar, A. N.; Elstner, M.; Entel, P.; Buss, V. The Retinal Conformation and Its Environment in Rhodopsin in Light of a New 2.2 a Crystal Structure J. Mol. Biol. 2004, 342, 571– 583 DOI: 10.1016/j.jmb.2004.07.044
Google Scholar
65
The Retinal Conformation and its Environment in Rhodopsin in Light of a New 2.2 Å Crystal Structure
Okada, Tetsuji; Sugihara, Minoru; Bondar, Ana-Nicoleta; Elstner, Marcus; Entel, Peter; Buss, Volker
Journal of Molecular Biology (2004), 342 (2), 571-583CODEN: JMOBAK; ISSN:0022-2836. (Elsevier B.V.)
A new high-resoln. structure is reported for bovine rhodopsin, the visual pigment in rod photoreceptor cells. Substantial improvement of the resoln. limit to 2.2 Å has been achieved by new crystn. conditions, which also reduce significantly the probability of merohedral twinning in the crystals. The new structure completely resolves the polypeptide chain and provides further details of the chromophore binding site including the configuration about the C6-C7 single bond of the 11-cis-retinal Schiff base. Based on both an earlier structure and the new improved model of the protein, a theor. study of the chromophore geometry has been carried out using combined quantum mechanics/force field mol. dynamics. The consistency between the exptl. and calcd. chromophore structures is found to be significantly improved for the 2.2 Å model, including the angle of the neg. twisted 6-s-cis-bond. Importantly, the new crystal structure refinement reveals significant neg. pre-twist of the C11-C12 double bond and this is also supported by the theor. calcn. although the latter converges to a smaller value. Bond alternation along the unsatd. chain is significant, but weaker in the calcd. structure than the one obtained from the X-ray data. Other differences between the exptl. and theor. structures in the chromophore binding site are discussed with respect to the unique spectral properties and excited state reactivity of the chromophore.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2cXmvFWlsbk%253D&md5=0db53d638b4db47ce86297b8d67a253b
66
Li, J.; Edwards, P. C.; Burghammer, M.; Villa, C.; Schertler, G. F. Structure of Bovine Rhodopsin in a Trigonal Crystal Form J. Mol. Biol. 2004, 343, 1409– 1438 DOI: 10.1016/j.jmb.2004.08.090
Google Scholar
66
Structure of Bovine Rhodopsin in a Trigonal Crystal Form
Li, Jade; Edwards, Patricia C.; Burghammer, Manfred; Villa, Claudio; Schertler, Gebhard F. X.
Journal of Molecular Biology (2004), 343 (5), 1409-1438CODEN: JMOBAK; ISSN:0022-2836. (Elsevier B.V.)
We have detd. the structure of bovine rhodopsin at 2.65 Å resoln. using untwinned native crystals in the space group P31, by mol. replacement from the 2.8 Å model (1F88) solved in space group P41. The new structure reveals mechanistically important details unresolved previously, which are considered in the membrane context by docking the structure into a cryo-electron microscopy map of 2D crystals. Kinks in the transmembrane helixes facilitate inter-helical polar interactions. Ordered water mols. extend the hydrogen bonding networks, linking Trp265 in the retinal binding pocket to the NPxxY motif near the cytoplasmic boundary, and the Glu113 counterion for the protonated Schiff base to the extracellular surface. Glu113 forms a complex with a water mol. hydrogen bonded between its main chain and side-chain oxygen atoms. This can be expected to stabilize the salt-bridge with the protonated Schiff base linking the 11-cis-retinal to Lys296. The cytoplasmic ends of helixes H5 and H6 have been extended by one turn. The G-protein interaction sites mapped to the cytoplasmic ends of H5 and H6 and a spiral extension of H5 are elevated above the bilayer. There is a surface cavity next to the conserved Glu134-Arg135 ion pair. The cytoplasmic loops have the highest temp. factors in the structure, indicative of their flexibility when not interacting with G protein or regulatory proteins. An ordered detergent mol. is seen wrapped around the kink in H6, stabilizing the structure around the potential hinge in H6. These findings provide further explanation for the stability of the dark state structure. They support a mechanism for the activation, initiated by photo-isomerisation of the chromophore to its all-trans form, that involves pivoting movements of kinked helixes, which, while maintaining hydrophobic contacts in the membrane interior, can be coupled to amplified translation of the helix ends near the membrane surfaces.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2cXos1Kksrw%253D&md5=f1905d044d125714900ae140ab29372d
67
Shapiro, D. A.; Kristiansen, K.; Weiner, D. M.; Kroeze, W. K.; Roth, B. L. Evidence for a Model of Agonist-Induced Activation of 5-Hydroxytryptamine 2a Serotonin Receptors That Involves the Disruption of a Strong Ionic Interaction between Helices 3 and 6 J. Biol. Chem. 2002, 277, 11441– 11449 DOI: 10.1074/jbc.M111675200
Google Scholar
There is no corresponding record for this reference.
68
Ballesteros, J. A.; Jensen, A. D.; Liapakis, G.; Rasmussen, S. G.; Shi, L.; Gether, U.; Javitch, J. A. Activation of the Beta 2-Adrenergic Receptor Involves Disruption of an Ionic Lock between the Cytoplasmic Ends of Transmembrane Segments 3 and 6 J. Biol. Chem. 2001, 276, 29171– 29177 DOI: 10.1074/jbc.M103747200
Google Scholar
68
Activation of the β2-adrenergic receptor involves disruption of an ionic lock between the cytoplasmic ends of transmembrane segments 3 and 6
Ballesteros, Juan A.; Jensen, Anne D.; Liapakis, George; Rasmussen, Soren G. F.; Shi, Lei; Gether, Ulrik; Javitch, Jonathan A.
Journal of Biological Chemistry (2001), 276 (31), 29171-29177CODEN: JBCHA3; ISSN:0021-9258. (American Society for Biochemistry and Molecular Biology)
The movements of transmembrane segments (TMs) 3 and 6 at the cytoplasmic side of the membrane play an important role in the activation of G-protein-coupled receptors. Here we provide evidence for the existence of an ionic lock that constrains the relative mobility of the cytoplasmic ends of TM3 and TM6 in the inactive state of the β2-adrenergic receptor. We propose that the highly conserved Arg-1313.50 at the cytoplasmic end of TM3 interacts both with the adjacent Asp-1303.49 and with Glu-2686.30 at the cytoplasmic end of TM6. Such a network of ionic interactions has now been directly supported by the high-resoln. structure of the inactive state of rhodopsin. We hypothesized that the network of interactions would serve to constrain the receptor in the inactive state, and the release of this ionic lock could be a key step in receptor activation. To test this hypothesis, we made charge-neutralizing mutations of Glu-2686.30 and of Asp-1303.49 in the β2-adrenergic receptor. Alone and in combination, we obsd. a significant increase in basal and pindolol-stimulated cAMP accumulation in COS-7 cells transiently transfected with the mutant receptors. Moreover, based on the increased accessibility of Cys-2856.47 in TM6, we provide evidence for a conformational rearrangement of TM6 that is highly correlated with the extent of constitutive activity of the different mutants. The present exptl. data together with the recent high-resoln. structure of rhodopsin suggest that ionic interactions between Asp/Glu3.49, Arg3.50, and Glu6.30 may constitute a common switch governing the activation of many rhodopsin-like G-protein-coupled receptors.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD3MXlvFSqsbc%253D&md5=44ce9914d365b0e96e831a3dcd574f3a
69
Greasley, P. J.; Fanelli, F.; Rossier, O.; Abuin, L.; Cotecchia, S. Mutagenesis and Modelling of the Alpha(1b)-Adrenergic Receptor Highlight the Role of the Helix 3/Helix 6 Interface in Receptor Activation Mol. Pharmacol. 2002, 61, 1025– 1032 DOI: 10.1124/mol.61.5.1025
Google Scholar
There is no corresponding record for this reference.
70
Yao, X.; Parnot, C.; Deupi, X.; Ratnala, V. R.; Swaminath, G.; Farrens, D.; Kobilka, B. Coupling Ligand Structure to Specific Conformational Switches in the Beta2-Adrenoceptor Nat. Chem. Biol. 2006, 2, 417– 422 DOI: 10.1038/nchembio801
Google Scholar
70
Coupling ligand structure to specific conformational switches in the β2-adrenoceptor
Yao, Xiaojie; Parnot, Charles; Deupi, Xavier; Ratnala, Venkata R. P.; Swaminath, Gayathri; Farrens, David; Kobilka, Brian
Nature Chemical Biology (2006), 2 (8), 417-422CODEN: NCBABT; ISSN:1552-4450. (Nature Publishing Group)
G protein-coupled receptors (GPCRs) regulate a wide variety of physiol. functions in response to structurally diverse ligands ranging from cations and small org. mols. to peptides and glycoproteins. For many GPCRs, structurally related ligands can have diverse efficacy profiles. To investigate the process of ligand binding and activation, we used fluorescence spectroscopy to study the ability of ligands having different efficacies to induce a specific conformational change in the human β2-adrenoceptor (β2-AR). The 'ionic lock' is a mol. switch found in rhodopsin-family GPCRs that has been proposed to link the cytoplasmic ends of transmembrane domains 3 and 6 in the inactive state. We found that most partial agonists were as effective as full agonists in disrupting the ionic lock. Our results show that disruption of this important mol. switch is necessary, but not sufficient, for full activation of the β2-AR.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD28XmvFyqsr4%253D&md5=991e6c5559c6c2afb8b5bc21fafc601f
71
Moukhametzianov, R.; Warne, T.; Edwards, P. C.; Serrano-Vega, M. J.; Leslie, A. G.; Tate, C. G.; Schertler, G. F. Two Distinct Conformations of Helix 6 Observed in Antagonist-Bound Structures of a Beta1-Adrenergic Receptor Proc. Natl. Acad. Sci. U. S. A. 2011, 108, 8228– 8232 DOI: 10.1073/pnas.1100185108
Google Scholar
71
Two distinct conformations of helix 6 observed in antagonist-bound structures of a β1-adrenergic receptor
Moukhametzianov, Rouslan; Warne, Tony; Edwards, Patricia C.; Serrano-Vega, Maria J.; Leslie, Andrew G. W.; Tate, Christopher G.; Schertler, Gebhard F. X.
Proceedings of the National Academy of Sciences of the United States of America (2011), 108 (20), 8228-8232, S8228/1-S8228/5CODEN: PNASA6; ISSN:0027-8424. (National Academy of Sciences)
The β1-adrenergic receptor (β1AR) is a G-protein-coupled receptor whose inactive state structure was detd. using a thermostabilized mutant (β1AR-M23). However, it was not thought to be in a fully inactivated state because there was no salt bridge between Arg139 and Glu285 linking the cytoplasmic ends of transmembrane helixes 3 and 6 (the R3.50-D/E6.30 "ionic lock"). Here we compare eight new structures of β1AR-M23, detd. from crystallog. independent mols. in four different crystals with three different antagonists bound. These structures are all in the inactive R state and show clear electron d. for cytoplasmic loop 3 linking transmembrane helixes 5 and 6 that had not been seen previously. Despite significantly different crystal packing interactions, there are only two distinct conformations of the cytoplasmic end of helix 6, bent and straight. In the bent conformation, the Arg139-Glu285 salt bridge is present, as in the crystal structure of dark-state rhodopsin. The straight conformation, obsd. in previously solved structures of β-receptors, results in the ends of helixes 3 and 6 being too far apart for the ionic lock to form. In the bent conformation, the R3.50-E6.30 distance is significantly longer than in rhodopsin, suggesting that the interaction is also weaker, which could explain the high basal activity in β1AR compared to rhodopsin. Many mutations that increase the constitutive activity of G-protein-coupled receptors are found in the bent region at the cytoplasmic end of helix 6, supporting the idea that this region plays an important role in receptor activation.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3MXmsF2jsb8%253D&md5=7888634ffd4ff20895c6c02c4ed10496
72
Lebon, G.; Warne, T.; Edwards, P. C.; Bennett, K.; Langmead, C. J.; Leslie, A. G.; Tate, C. G. Agonist-Bound Adenosine A2a Receptor Structures Reveal Common Features of GPCR Activation Nature 2011, 474, 521– 525 DOI: 10.1038/nature10136
Google Scholar
72
Agonist-bound adenosine A2A receptor structures reveal common features of GPCR activation
Lebon, Guillaume; Warne, Tony; Edwards, Patricia C.; Bennett, Kirstie; Langmead, Christopher J.; Leslie, Andrew G. W.; Tate, Christopher G.
Nature (London, United Kingdom) (2011), 474 (7352), 521-525CODEN: NATUAS; ISSN:0028-0836. (Nature Publishing Group)
Adenosine receptors and β-adrenoceptors are G-protein-coupled receptors (GPCRs) that activate intracellular G proteins on binding the agonists adenosine or noradrenaline, resp. GPCRs have similar structures consisting of seven transmembrane helixes that contain well-conserved sequence motifs, indicating that they are probably activated by a common mechanism. Recent structures of β-adrenoceptors highlight residues in transmembrane region 5 that initially bind specifically to agonists rather than to antagonists, indicating that these residues have an important role in agonist-induced activation of receptors. Here we present two crystal structures of the thermostabilized human adenosine A2A receptor (A2AR-GL31) bound to its endogenous agonist adenosine and the synthetic agonist NECA. The structures represent an intermediate conformation between the inactive and active states, because they share all the features of GPCRs that are thought to be in a fully activated state, except that the cytoplasmic end of transmembrane helix 6 partially occludes the G-protein-binding site. The adenine substituent of the agonists binds in a similar fashion to the chem. related region of the inverse agonist ZM241385 (ref. 8). Both agonists contain a ribose group, not found in ZM241385, which extends deep into the ligand-binding pocket where it makes polar interactions with conserved residues in H7 (Ser 2777.42 and His 2787.43; superscripts refer to Ballesteros-Weinstein numbering) and non-polar interactions with residues in H3. In contrast, the inverse agonist ZM241385 does not interact with any of these residues and comparison with the agonist-bound structures indicates that ZM241385 sterically prevents the conformational change in H5 and therefore it acts as an inverse agonist. Comparison of the agonist-bound structures of A2AR with the agonist-bound structures of β-adrenoceptors indicates that the contraction of the ligand-binding pocket caused by the inward motion of helixes 3, 5 and 7 may be a common feature in the activation of all GPCRs.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3MXmsFyqsrg%253D&md5=1b8161216b878db48ad33d7e8e007dc7
73
Xu, F.; Wu, H.; Katritch, V.; Han, G. W.; Jacobson, K. A.; Gao, Z. G.; Cherezov, V.; Stevens, R. C. Structure of an Agonist-Bound Human A2a Adenosine Receptor Science 2011, 332, 322– 327 DOI: 10.1126/science.1202793
Google Scholar
73
Structure of an Agonist-Bound Human A2A Adenosine Receptor
Xu, Fei; Wu, Huixian; Katritch, Vsevolod; Han, Gye Won; Jacobson, Kenneth A.; Gao, Zhan-Guo; Cherezov, Vadim; Stevens, Raymond C.
Science (Washington, DC, United States) (2011), 332 (6027), 322-327CODEN: SCIEAS; ISSN:0036-8075. (American Association for the Advancement of Science)
Activation of G protein-coupled receptors upon agonist binding is a crit. step in the signaling cascade for this family of cell surface proteins. We report the crystal structure of the A2A adenosine receptor (A2AAR) bound to an agonist UK-432097 at 2.7 angstrom resoln. Relative to inactive, antagonist-bound A2AAR, the agonist-bound structure displays an outward tilt and rotation of the cytoplasmic half of helix VI, a movement of helix V, and an axial shift of helix III, resembling the changes assocd. with the active-state opsin structure. Addnl., a seesaw movement of helix VII and a shift of extracellular loop 3 are likely specific to A2AAR and its ligand. The results define the mol. UK-432097 as a "conformationally selective agonist" capable of receptor stabilization in a specific active-state configuration.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3MXksFWjt7s%253D&md5=b1e074f38f45c95d4cc3b40378b24923
74
Egloff, P.; Hillenbrand, M.; Klenk, C.; Batyuk, A.; Heine, P.; Balada, S.; Schlinkmann, K. M.; Scott, D. J.; Schutz, M.; Pluckthun, A. Structure of Signaling-Competent Neurotensin Receptor 1 Obtained by Directed Evolution in Escherichia Coli Proc. Natl. Acad. Sci. U. S. A. 2014, 111, E655– 662 DOI: 10.1073/pnas.1317903111
Google Scholar
74
Structure of signaling-competent neurotensin receptor 1 obtained by directed evolution in Escherichia coli
Egloff, Pascal; Hillenbrand, Matthias; Klenk, Christoph; Batyuk, Alexander; Heine, Philipp; Balada, Stefanie; Schlinkmann, Karola M.; Scott, Daniel J.; Schutz, Marco; Pluckthun, Andreas
Proceedings of the National Academy of Sciences of the United States of America (2014), 111 (6), E655-E662CODEN: PNASA6; ISSN:0027-8424. (National Academy of Sciences)
Crystallog. has advanced our understanding of G protein-coupled receptors, but low expression levels and instability in soln. have limited structural insights to very few selected members of this large protein family. Using neurotensin receptor 1 (NTR1) as a proof of principle, we show that two directed evolution technologies that we recently developed have the potential to overcome these problems. We purified three neurotensin-bound NTR1 variants from Escherichia coli and detd. their x-ray structures at up to 2.75 Å resoln. using vapor diffusion crystn. expts. A crystd. construct was pharmacol. characterized and exhibited ligand-dependent signaling, internalization, and wild-type-like agonist and antagonist affinities. Our structures are fully consistent with all biochem. defined ligand-contacting residues, and they represent an inactive NTR1 state at the cytosolic side. They exhibit significant differences to a previously detd. NTR1 structure (Protein Data Bank ID code 4GRV) in the ligand-binding pocket and by the presence of the amphipathic helix 8. A comparison of helix 8 stability determinants between NTR1 and other crystd. G protein-coupled receptors suggests that the occupancy of the canonical position of the amphipathic helix is reduced to various extents in many receptors, and we have elucidated the sequence determinants for a stable helix 8. Our anal. also provides a structural rationale for the long-known effects of C-terminal palmitoylation reactions on G protein-coupled receptor signaling, receptor maturation, and desensitization.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2cXisFOntrc%253D&md5=036230389cacc05a6462cf7b6a55278b
75
Burg, J. S.; Ingram, J. R.; Venkatakrishnan, A. J.; Jude, K. M.; Dukkipati, A.; Feinberg, E. N.; Angelini, A.; Waghray, D.; Dror, R. O.; Ploegh, H. L. Structural Biology. Structural Basis for Chemokine Recognition and Activation of a Viral G Protein-Coupled Receptor Science 2015, 347, 1113– 1117 DOI: 10.1126/science.aaa5026
Google Scholar
75
Structural basis for chemokine recognition and activation of a viral G protein-coupled receptor
Burg, John S.; Ingram, Jessica R.; Venkatakrishnan, A. J.; Jude, Kevin M.; Dukkipati, Abhiram; Feinberg, Evan N.; Angelini, Alessandro; Waghray, Deepa; Dror, Ron O.; Ploegh, Hidde L.; Garcia, K. Christopher
Science (Washington, DC, United States) (2015), 347 (6226), 1113-1117CODEN: SCIEAS; ISSN:0036-8075. (American Association for the Advancement of Science)
Chemokines are small proteins that function as immune modulators through activation of chemokine G protein-coupled receptors (GPCRs). Several viruses also encode chemokines and chemokine receptors to subvert the host immune response. How protein ligands activate GPCRs remains unknown. We report the crystal structure at 2.9 angstrom resoln. of the human cytomegalovirus GPCR US28 in complex with the chemokine domain of human CX3CL1 (fractalkine). The globular body of CX3CL1 is perched on top of the US28 extracellular vestibule, whereas its amino terminus projects into the central core of US28. The transmembrane helixes of US28 adopt an active-state-like conformation. Atomic-level simulations suggest that the agonist-independent activity of US28 may be due to an amino acid network evolved in the viral GPCR to destabilize the receptor's inactive state.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2MXjsF2hs74%253D&md5=6a6bf9a8f24760249f8cc8eb988c3d8a
76
Strachan, R. T.; Sun, J. P.; Rominger, D. H.; Violin, J. D.; Ahn, S.; Rojas Bie Thomsen, A.; Zhu, X.; Kleist, A.; Costa, T.; Lefkowitz, R. J. Divergent Transducer-Specific Molecular Efficacies Generate Biased Agonism at a G Protein-Coupled Receptor (GPCR) J. Biol. Chem. 2014, 289, 14211– 14224 DOI: 10.1074/jbc.M114.548131
Google Scholar
There is no corresponding record for this reference.
77
Klein Herenbrink, C.; Sykes, D. A.; Donthamsetti, P.; Canals, M.; Coudrat, T.; Shonberg, J.; Scammells, P. J.; Capuano, B.; Sexton, P. M.; Charlton, S. J. The Role of Kinetic Context in Apparent Biased Agonism at GPCRs Nat. Commun. 2016, 7, 10842 DOI: 10.1038/ncomms10842
Google Scholar
77
The role of kinetic context in apparent biased agonism at GPCRs
Klein Herenbrink, Carmen; Sykes, David A.; Donthamsetti, Prashant; Canals, Meritxell; Coudrat, Thomas; Shonberg, Jeremy; Scammells, Peter J.; Capuano, Ben; Sexton, Patrick M.; Charlton, Steven J.; Javitch, Jonathan A.; Christopoulos, Arthur; Lane, J. Robert
Nature Communications (2016), 7 (), 10842CODEN: NCAOBW; ISSN:2041-1723. (Nature Publishing Group)
Biased agonism describes the ability of ligands to stabilize different conformations of a GPCR linked to distinct functional outcomes and offers the prospect of designing pathway-specific drugs that avoid on-target side effects. This mechanism is usually inferred from pharmacol. data with the assumption that the confounding influences of observational (i.e., assay dependent) and system (i.e., cell background dependent) bias are excluded by exptl. design and anal. Here we reveal that 'kinetic context', as detd. by ligand-binding kinetics and the temporal pattern of receptor-signalling processes, can have a profound influence on the apparent bias of a series of agonists for the dopamine D2 receptor and can even lead to reversals in the direction of bias. We propose that kinetic context must be acknowledged in the design and interpretation of studies of biased agonism.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC28Xjt1emtbk%253D&md5=3afdebd5ad1c8a8b1db93478e9b2c7d4
78
Shukla, A. K.; Xiao, K.; Lefkowitz, R. J. Emerging Paradigms of Beta-Arrestin-Dependent Seven Transmembrane Receptor Signaling Trends Biochem. Sci. 2011, 36, 457– 469 DOI: 10.1016/j.tibs.2011.06.003
Google Scholar
There is no corresponding record for this reference.
79
Gurevich, V. V.; Gurevich, E. V. Unit 2.10. Overview of Different Mechanisms of Arrestin-Mediated Signaling Curr. Protoc. Pharmacol. 2014, 67, 2.10.1– 2.10.9 DOI: 10.1002/0471141755.ph0210s67
Google Scholar
There is no corresponding record for this reference.
80
Kang, D. S.; Tian, X.; Benovic, J. L. Beta-Arrestins and G Protein-Coupled Receptor Trafficking Methods Enzymol. 2013, 521, 91– 108 DOI: 10.1016/B978-0-12-391862-8.00005-3
Google Scholar
There is no corresponding record for this reference.
81
Sivertsen, B.; Holliday, N.; Madsen, A. N.; Holst, B. Functionally Biased Signalling Properties of 7TM Receptors - Opportunities for Drug Development for the Ghrelin Receptor Br. J. Pharmacol. 2013, 170, 1349– 1362 DOI: 10.1111/bph.12361
Google Scholar
81
Functionally biased signalling properties of 7TM receptors - opportunities for drug development for the ghrelin receptor
Sivertsen, B.; Holliday, N.; Madsen, A. N.; Holst, B.
British Journal of Pharmacology (2013), 170 (7), 1349-1362CODEN: BJPCBM; ISSN:1476-5381. (Wiley-Blackwell)
A review. The ghrelin receptor is a 7 transmembrane (7TM) receptor involved in a variety of physiol. functions including growth hormone secretion, increased food intake, and fat accumulation as well as modulation of reward and cognitive functions. Because of its important role in metab. and energy expenditure, the ghrelin receptor has become an important therapeutic target for drug design and the development of anti-obesity compds. However, none of the compds. developed so far were approved for com. use. Interestingly, the ghrelin receptor is able to signal through several different signaling pathways including Gαq, Gαi/o, Gα12/13, and arrestin recruitment. These multiple signaling pathways allow for functionally biased signaling, where one signaling pathway may be favored over another either by selective ligands or through mutations in the receptor. In the present review, we have described how ligands and mutations in the 7TM receptor may bias the receptors to favor either one G-protein over another or to promote G-protein independent signaling pathways rather than G-protein-dependent pathways. For the ghrelin receptor, both agonist and inverse agonists were demonstrated to signal more strongly through the Gαq-coupled pathway than the Gα12/13-coupled pathway. Similarly a ligand that promotes Gαq coupling over Gαi coupling was described and it was suggested that several different active conformations of the receptor may exist dependent on the properties of the agonist. Importantly, ligands with such biased s signaling properties may allow the development of drugs that selectively modulate only the therapeutically relevant physiol. functions, thereby decreasing the risk of side effects.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3sXhslOmsbfJ&md5=30f715b33abcce514e71ed64d536be9e
82
Liu, J. J.; Horst, R.; Katritch, V.; Stevens, R. C.; Wuthrich, K. Biased Signaling Pathways in Beta2-Adrenergic Receptor Characterized by 19f-NMR Science 2012, 335, 1106– 1110 DOI: 10.1126/science.1215802
Google Scholar
82
Biased signaling pathways in β2-adrenergic receptor characterized by 19F-NMR
Liu, Jeffrey J.; Horst, Reto; Katritch, Vsevolod; Stevens, Raymond C.; Wuethrich, Kurt
Science (Washington, DC, United States) (2012), 335 (6072), 1106-1110CODEN: SCIEAS; ISSN:0036-8075. (American Association for the Advancement of Science)
Extracellular ligand binding to G protein-coupled receptors (GPCRs) modulates G protein and β-arrestin signaling by changing the conformational states of the cytoplasmic region of the receptor. Using site-specific 19F-NMR (fluorine-19 NMR) labels in the β2-adrenergic receptor (β2AR) in complexes with various ligands, we obsd. that the cytoplasmic ends of helixes VI and VII adopt two major conformational states. Changes in the NMR signals reveal that agonist binding primarily shifts the equil. toward the G protein-specific active state of helix VI. In contrast, β-arrestin-biased ligands predominantly impact the conformational states of helix VII. The selective effects of different ligands on the conformational equil. involving helixes VI and VII provide insights into the long-range structural plasticity of β2AR in partial and biased agonist signaling.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC38XivVGhtrs%253D&md5=abae5755ddcacf42a029e7fd0dd4fdc9
83
Wacker, D.; Wang, C.; Katritch, V.; Han, G. W.; Huang, X. P.; Vardy, E.; McCorvy, J. D.; Jiang, Y.; Chu, M.; Siu, F. Y. Structural Features for Functional Selectivity at Serotonin Receptors Science 2013, 340, 615– 619 DOI: 10.1126/science.1232808
Google Scholar
83
Structural Features for Functional Selectivity at Serotonin Receptors
Wacker, Daniel; Wang, Chong; Katritch, Vsevolod; Han, Gye Won; Huang, Xi-Ping; Vardy, Eyal; McCorvy, John D.; Jiang, Yi; Chu, Meihua; Siu, Fai Yiu; Liu, Wei; Xu, H. Eric; Cherezov, Vadim; Roth, Bryan L.; Stevens, Raymond C.
Science (Washington, DC, United States) (2013), 340 (6132), 615-619CODEN: SCIEAS; ISSN:0036-8075. (American Association for the Advancement of Science)
Drugs active at G protein-coupled receptors (GPCRs) can differentially modulate either canonical or noncanonical signaling pathways via a phenomenon known as functional selectivity or biased signaling. The authors report biochem. studies showing that the hallucinogen lysergic acid diethylamide, its precursor ergotamine (ERG), and related ergolines display strong functional selectivity for β-arrestin signaling at the 5-HT2B 5-hydroxytryptamine (5-HT) receptor, whereas they are relatively unbiased at the 5-HT1B receptor. To investigate the structural basis for biased signaling, the authors detd. the crystal structure of the human 5-HT2B receptor bound to ERG and compared it with the 5-HT1B/ERG structure. Given the relatively poor understanding of GPCR structure and function to date, insight into different GPCR signaling pathways is important to better understand both adverse and favorable therapeutic activities.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3sXmslWksb0%253D&md5=16e96d0255be3ac367aeda7187aa4c15
84
Wang, C.; Jiang, Y.; Ma, J.; Wu, H.; Wacker, D.; Katritch, V.; Han, G. W.; Liu, W.; Huang, X. P.; Vardy, E. Structural Basis for Molecular Recognition at Serotonin Receptors Science 2013, 340, 610– 614 DOI: 10.1126/science.1232807
Google Scholar
84
Structural Basis for Molecular Recognition at Serotonin Receptors
Wang, Chong; Jiang, Yi; Ma, Jinming; Wu, Huixian; Wacker, Daniel; Katritch, Vsevolod; Han, Gye Won; Liu, Wei; Huang, Xi-Ping; Vardy, Eyal; McCorvy, John D.; Gao, Xiang; Zhou, X. Edward; Melcher, Karsten; Zhang, Chenghai; Bai, Fang; Yang, Huaiyu; Yang, Linlin; Jiang, Hualiang; Roth, Bryan L.; Cherezov, Vadim; Stevens, Raymond C.; Xu, H. Eric
Science (Washington, DC, United States) (2013), 340 (6132), 610-614CODEN: SCIEAS; ISSN:0036-8075. (American Association for the Advancement of Science)
Serotonin or 5-hydroxytryptamine (5-HT) regulates a wide spectrum of human physiol. through the 5-HT receptor family. The authors report the crystal structures of the human 5-HT1B G protein-coupled receptor bound to the agonist antimigraine medications ergotamine and dihydroergotamine. The structures reveal similar binding modes for these ligands, which occupy the orthosteric pocket and an extended binding pocket close to the extracellular loops. The orthosteric pocket is formed by residues conserved in the 5-HT receptor family, clarifying the family-wide agonist activity of 5-HT. Compared with the structure of the 5-HT2B receptor, the 5-HT1B receptor displays a 3 angstrom outward shift at the extracellular end of helix V, resulting in a more open extended pocket that explains subtype selectivity. Together with docking and mutagenesis studies, these structures provide a comprehensive structural basis for understanding receptor-ligand interactions and designing subtype-selective serotonergic drugs.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3sXmslWksbw%253D&md5=ce0773088a86f6a2c83b6cb77a63e708
85
Kang, Y.; Zhou, X. E.; Gao, X.; He, Y.; Liu, W.; Ishchenko, A.; Barty, A.; White, T. A.; Yefanov, O.; Han, G. W. Crystal Structure of Rhodopsin Bound to Arrestin by Femtosecond X-Ray Laser Nature 2015, 523, 561– 567 DOI: 10.1038/nature14656
Google Scholar
85
Crystal structure of rhodopsin bound to arrestin by femtosecond X-ray laser
Kang, Yanyong; Zhou, X. Edward; Gao, Xiang; He, Yuanzheng; Liu, Wei; Ishchenko, Andrii; Barty, Anton; White, Thomas A.; Yefanov, Oleksandr; Han, Gye Won; Xu, Qingping; de Waal, Parker W.; Ke, Jiyuan; Tan, M. H. Eileen; Zhang, Chenghai; Moeller, Arne; West, Graham M.; Pascal, Bruce D.; Van Eps, Ned; Caro, Lydia N.; Vishnivetskiy, Sergey A.; Lee, Regina J.; Suino-Powell, Kelly M.; Gu, Xin; Pal, Kuntal; Ma, Jinming; Zhi, Xiaoyong; Boutet, Sebastien; Williams, Garth J.; Messerschmidt, Marc; Gati, Cornelius; Zatsepin, Nadia A.; Wang, Dingjie; James, Daniel; Basu, Shibom; Roy-Chowdhury, Shatabdi; Conrad, Chelsie E.; Coe, Jesse; Liu, Haiguang; Lisova, Stella; Kupitz, Christopher; Grotjohann, Ingo; Fromme, Raimund; Jiang, Yi; Tan, Minjia; Yang, Huaiyu; Li, Jun; Wang, Meitian; Zheng, Zhong; Li, Dianfan; Howe, Nicole; Zhao, Yingming; Standfuss, Jorg; Diederichs, Kay; Dong, Yuhui; Potter, Clinton S.; Carragher, Bridget; Caffrey, Martin; Jiang, Hualiang; Chapman, Henry N.; Spence, John C. H.; Fromme, Petra; Weierstall, Uwe; Ernst, Oliver P.; Katritch, Vsevolod; Gurevich, Vsevolod V.; Griffin, Patrick R.; Hubbell, Wayne L.; Stevens, Raymond C.; Cherezov, Vadim; Melcher, Karsten; Xu, H. Eric
Nature (London, United Kingdom) (2015), 523 (7562), 561-567CODEN: NATUAS; ISSN:0028-0836. (Nature Publishing Group)
G-protein-coupled receptors (GPCRs) signal primarily through G proteins or arrestins. Arrestin binding to GPCRs blocks G protein interaction and redirects signalling to numerous G-protein-independent pathways. Here we report the crystal structure of a constitutively active form of human rhodopsin bound to a pre-activated form of the mouse visual arrestin, detd. by serial femtosecond X-ray laser crystallog. Together with extensive biochem. and mutagenesis data, the structure reveals an overall architecture of the rhodopsin-arrestin assembly in which rhodopsin uses distinct structural elements, including transmembrane helix 7 and helix 8, to recruit arrestin. Correspondingly, arrestin adopts the pre-activated conformation, with a ∼20° rotation between the amino and carboxy domains, which opens up a cleft in arrestin to accommodate a short helix formed by the second intracellular loop of rhodopsin. This structure provides a basis for understanding GPCR-mediated arrestin-biased signalling and demonstrates the power of X-ray lasers for advancing the frontiers of structural biol.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2MXht1WksrvK&md5=574baa8ffa403be6aec8e9e1ffd81a7a
86
Szczepek, M.; Beyriere, F.; Hofmann, K. P.; Elgeti, M.; Kazmin, R.; Rose, A.; Bartl, F. J.; von Stetten, D.; Heck, M.; Sommer, M. E. Crystal Structure of a Common GPCR-Binding Interface for G Protein and Arrestin Nat. Commun. 2014, 5, 4801 DOI: 10.1038/ncomms5801
Google Scholar
86
Crystal structure of a common GPCR-binding interface for G protein and arrestin
Szczepek, Michal; Beyriere, Florent; Hofmann, Klaus Peter; Elgeti, Matthias; Kazmin, Roman; Rose, Alexander; Bartl, Franz J.; von Stetten, David; Heck, Martin; Sommer, Martha E.; Hildebrand, Peter W.; Scheerer, Patrick
Nature Communications (2014), 5 (), 4801CODEN: NCAOBW; ISSN:2041-1723. (Nature Publishing Group)
G-protein-coupled receptors (GPCRs) transmit extracellular signals to activate intracellular heterotrimeric G proteins (Gαβγ) and arrestins. For G protein signalling, the Gα C-terminus (GαCT) binds to a cytoplasmic crevice of the receptor that opens upon activation. A consensus motif is shared among GαCT from the Gi/Gt family and the 'finger loop' region (ArrFL1-4) of all four arrestins. Here we present a 2.75 Å crystal structure of ArrFL-1, a peptide analog of the finger loop of rod photoreceptor arrestin, in complex with the prototypical GPCR rhodopsin. Functional binding of ArrFL to the receptor was confirmed by UV-visible absorption spectroscopy, competitive binding assays and Fourier transform IR spectroscopy. For both GαCT and ArrFL, binding to the receptor crevice induces a similar reverse turn structure, although significant structural differences are seen at the rim of the binding crevice. Our results reflect both the common receptor-binding interface and the divergent biol. functions of G proteins and arrestins.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2MXksVertbg%253D&md5=48334457eb71e862db61543c0d66567f
87
Butcher, A. J.; Prihandoko, R.; Kong, K. C.; McWilliams, P.; Edwards, J. M.; Bottrill, A.; Mistry, S.; Tobin, A. B. Differential G-Protein-Coupled Receptor Phosphorylation Provides Evidence for a Signaling Bar Code J. Biol. Chem. 2011, 286, 11506– 11518 DOI: 10.1074/jbc.M110.154526
Google Scholar
87
Differential G-protein-coupled receptor phosphorylation provides evidence for a signaling bar code
Butcher, Adrian J.; Prihandoko, Rudi; Kong, Kok Choi; McWilliams, Phillip; Edwards, Jennifer M.; Bottrill, Andrew; Mistry, Sharad; Tobin, Andrew B.
Journal of Biological Chemistry (2011), 286 (13), 11506-11518CODEN: JBCHA3; ISSN:0021-9258. (American Society for Biochemistry and Molecular Biology)
G-protein-coupled receptors are hyper-phosphorylated in a process that controls receptor coupling to downstream signaling pathways. The pattern of receptor phosphorylation has been proposed to generate a "bar code" that can be varied in a tissue-specific manner to direct physiol. relevant receptor signaling. If such a mechanism existed, receptors would be expected to be phosphorylated in a cell/tissue-specific manner. Using tryptic phosphopeptide maps, mass spectrometry, and phospho-specific antibodies, it was detd. here that the prototypical Gq/11-coupled M3-muscarinic receptor was indeed differentially phosphorylated in various cell and tissue types supporting a role for differential receptor phosphorylation in directing tissue-specific signaling. Furthermore, the phosphorylation profile of the M3-muscarinic receptor was also dependent on the stimulus. Full and partial agonists to the M3-muscarinic receptor were obsd. to direct phosphorylation preferentially to specific sites. This hitherto unappreciated property of ligands raises the possibility that one mechanism underlying ligand bias/functional selectivity, a process where ligands direct receptors to preferred signaling pathways, may be centered on the capacity of ligands to promote receptor phosphorylation at specific sites.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3MXjslKgtr8%253D&md5=fe93fd43ccdd5ff9b51494214174680f
88
Nobles, K. N.; Xiao, K.; Ahn, S.; Shukla, A. K.; Lam, C. M.; Rajagopal, S.; Strachan, R. T.; Huang, T. Y.; Bressler, E. A.; Hara, M. R. Distinct Phosphorylation Sites on the Beta(2)-Adrenergic Receptor Establish a Barcode That Encodes Differential Functions of Beta-Arrestin Sci. Signaling 2011, 4, ra51 DOI: 10.1126/scisignal.2001707
Google Scholar
There is no corresponding record for this reference.
89
Butcher, A. J.; Hudson, B. D.; Shimpukade, B.; Alvarez-Curto, E.; Prihandoko, R.; Ulven, T.; Milligan, G.; Tobin, A. B. Concomitant Action of Structural Elements and Receptor Phosphorylation Determines Arrestin-3 Interaction with the Free Fatty Acid Receptor FFA4 J. Biol. Chem. 2014, 289, 18451– 18465 DOI: 10.1074/jbc.M114.568816
Google Scholar
There is no corresponding record for this reference.
90
Inagaki, S.; Ghirlando, R.; Vishnivetskiy, S. A.; Homan, K. T.; White, J. F.; Tesmer, J. J.; Gurevich, V. V.; Grisshammer, R. G Protein-Coupled Receptor Kinase 2 (GRK2) and 5 (GRK5) Exhibit Selective Phosphorylation of the Neurotensin Receptor in Vitro Biochemistry 2015, 54, 4320– 4329 DOI: 10.1021/acs.biochem.5b00285
Google Scholar
90
G Protein-coupled receptor kinase 2 (GRK2) and 5 (GRK5) exhibit selective phosphorylation of the neurotensin receptor in Vitro
Inagaki, Sayaka; Ghirlando, Rodolfo; Vishnivetskiy, Sergey A.; Homan, Kristoff T.; White, Jim F.; Tesmer, John J. G.; Gurevich, Vsevolod V.; Grisshammer, Reinhard
Biochemistry (2015), 54 (28), 4320-4329CODEN: BICHAW; ISSN:0006-2960. (American Chemical Society)
G protein-coupled receptor kinases (GRKs) play an important role in the desensitization of G protein-mediated signaling of G protein-coupled receptors (GPCRs). The level of interest in mapping their phosphorylation sites has increased because recent studies suggest that the differential pattern of receptor phosphorylation has distinct biol. consequences. In vitro phosphorylation expts. using well-controlled systems are useful for deciphering the complexity of these physiol. reactions and understanding the targeted event. Here, we report on the phosphorylation of the class A GPCR neurotensin receptor 1 (NTSR1) by GRKs under defined exptl. conditions afforded by nanodisc technol. Phosphorylation of NTSR1 by GRK2 was agonist-dependent, whereas phosphorylation by GRK5 occurred in an activation-independent manner. In addn., the neg. charged lipids in the immediate vicinity of NTSR1 directly affect phosphorylation by GRKs. Identification of phosphorylation sites in agonist-activated NTSR1 revealed that GRK2 and GRK5 target different residues located on the intracellular receptor elements. GRK2 phosphorylates only the C-terminal Ser residues, whereas GRK5 phosphorylates Ser and Thr residues located in intracellular loop 3 and the C-terminus. Interestingly, phosphorylation assays using a series of NTSR1 mutants show that GRK2 does not require acidic residues upstream of the phospho-acceptors for site-specific phosphorylation, in contrast to the β2-adrenergic and μ-opioid receptors. Differential phosphorylation of GPCRs by GRKs is thought to encode a particular signaling outcome, and our in vitro study revealed NTSR1 differential phosphorylation by GRK2 and GRK5.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2MXhtVyitL3J&md5=b44be356ca0b9416a5b813574a141923
91
Yang, F.; Yu, X.; Liu, C.; Qu, C. X.; Gong, Z.; Liu, H. D.; Li, F. H.; Wang, H. M.; He, D. F.; Yi, F. Phospho-Selective Mechanisms of Arrestin Conformations and Functions Revealed by Unnatural Amino Acid Incorporation and (19)F-NMR Nat. Commun. 2015, 6, 8202 DOI: 10.1038/ncomms9202
Google Scholar
91
Phospho-selective mechanisms of arrestin conformations and functions revealed by unnatural amino acid incorporation and (19)F-NMR
Yang Fan; Li Fa-Hui; Wang Jiang-Yun; Yang Fan; Yu Xiao; Liu Chuan; Qu Chang-Xiu; Gong Zheng; Liu Hong-Da; He Dong-Fang; Sun Jin-Peng; Yang Fan; Yu Xiao; Wang Hong-Mei; He Dong-Fang; Sun Jin-Peng; Yi Fan; Song Chen; Tian Chang-Lin; Xiao Kun-Hong; Xiao Kun-Hong
Nature communications (2015), 6 (), 8202 ISSN:.
Specific arrestin conformations are coupled to distinct downstream effectors, which underlie the functions of many G-protein-coupled receptors (GPCRs). Here, using unnatural amino acid incorporation and fluorine-19 nuclear magnetic resonance ((19)F-NMR) spectroscopy, we demonstrate that distinct receptor phospho-barcodes are translated to specific β-arrestin-1 conformations and direct selective signalling. With its phosphate-binding concave surface, β-arrestin-1 'reads' the message in the receptor phospho-C-tails and distinct phospho-interaction patterns are revealed by (19)F-NMR. Whereas all functional phosphopeptides interact with a common phosphate binding site and induce the movements of finger and middle loops, different phospho-interaction patterns induce distinct structural states of β-arrestin-1 that are coupled to distinct arrestin functions. Only clathrin recognizes and stabilizes GRK2-specific β-arrestin-1 conformations. The identified receptor-phospho-selective mechanism for arrestin conformation and the spacing of the multiple phosphate-binding sites in the arrestin enable arrestin to recognize plethora phosphorylation states of numerous GPCRs, contributing to the functional diversity of receptors.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A280%3ADC%252BC283gsFaqsA%253D%253D&md5=a202ed5f08842a9da7cf3295abb66689
92
Kim, Y. J.; Hofmann, K. P.; Ernst, O. P.; Scheerer, P.; Choe, H. W.; Sommer, M. E. Crystal Structure of Pre-Activated Arrestin P44 Nature 2013, 497, 142– 146 DOI: 10.1038/nature12133
Google Scholar
92
Crystal structure of pre-activated arrestin p44
Kim, Yong Ju; Hofmann, Klaus Peter; Ernst, Oliver P.; Scheerer, Patrick; Choe, Hui-Woog; Sommer, Martha E.
Nature (London, United Kingdom) (2013), 497 (7447), 142-146CODEN: NATUAS; ISSN:0028-0836. (Nature Publishing Group)
Arrestins interact with G-protein-coupled receptors (GPCRs) to block interaction with G proteins and initiate G-protein-independent signalling. Arrestins have a bi-lobed structure that is stabilized by a long carboxy-terminal tail (C-tail), and displacement of the C-tail by receptor-attached phosphates activates arrestins for binding active GPCRs. Structures of the inactive state of arrestin are available, but it is not known how C-tail displacement activates arrestin for receptor coupling. Here we present a 3.0 Å crystal structure of the bovine arrestin-1 splice variant p44, in which the activation step is mimicked by C-tail truncation. The structure of this pre-activated arrestin is profoundly different from the basal state and gives insight into the activation mechanism. P44 displays breakage of the central polar core and other interlobe hydrogen-bond networks, leading to a ∼21° rotation of the two lobes as compared to basal arrestin-1. Rearrangements in key receptor-binding loops in the central crest region include the finger loop, loop 139 (refs. 8, 10, 11) and the sequence Asp 296-Asn 305 (or gate loop), here identified as controlling the polar core. We verified the role of these conformational alterations in arrestin activation and receptor binding by site-directed fluorescence spectroscopy. The data indicate a mechanism for arrestin activation in which C-tail displacement releases crit. central-crest loops from restricted to extended receptor-interacting conformations. In parallel, increased flexibility between the two lobes facilitates a proper fitting of arrestin to the active receptor surface. Our results provide a snapshot of an arrestin ready to bind the active receptor, and give an insight into the role of naturally occurring truncated arrestins in the visual system.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3sXmt1SmtL8%253D&md5=afdfdfbfef3ba99584d01cc39357ad74
93
Shukla, A. K.; Manglik, A.; Kruse, A. C.; Xiao, K.; Reis, R. I.; Tseng, W. C.; Staus, D. P.; Hilger, D.; Uysal, S.; Huang, L. Y. Structure of Active Beta-Arrestin-1 Bound to a G-Protein-Coupled Receptor Phosphopeptide Nature 2013, 497, 137– 141 DOI: 10.1038/nature12120
Google Scholar
93
Structure of active β-arrestin-1 bound to a G-protein-coupled receptor phosphopeptide
Shukla, Arun K.; Manglik, Aashish; Kruse, Andrew C.; Xiao, Kunhong; Reis, Rosana I.; Tseng, Wei-Chou; Staus, Dean P.; Hilger, Daniel; Uysal, Serdar; Huang, Li-Yin; Paduch, Marcin; Tripathi-Shukla, Prachi; Koide, Akiko; Koide, Shohei; Weis, William I.; Kossiakoff, Anthony A.; Kobilka, Brian K.; Lefkowitz, Robert J.
Nature (London, United Kingdom) (2013), 497 (7447), 137-141CODEN: NATUAS; ISSN:0028-0836. (Nature Publishing Group)
The functions of G-protein-coupled receptors (GPCRs) are primarily mediated and modulated by three families of proteins: the heterotrimeric G proteins, the G-protein-coupled receptor kinases (GRKs) and the arrestins. G proteins mediate activation of second-messenger-generating enzymes and other effectors, GRKs phosphorylate activated receptors, and arrestins subsequently bind phosphorylated receptors and cause receptor desensitization. Arrestins activated by interaction with phosphorylated receptors can also mediate G-protein-independent signalling by serving as adaptors to link receptors to numerous signalling pathways. Despite their central role in regulation and signalling of GPCRs, a structural understanding of β-arrestin activation and interaction with GPCRs is still lacking. Here we report the crystal structure of β-arrestin-1 (also called arrestin-2) in complex with a fully phosphorylated 29-amino-acid carboxy-terminal peptide derived from the human V2 vasopressin receptor (V2Rpp). This peptide has previously been shown to functionally and conformationally activate β-arrestin-1 (ref. 5). To capture this active conformation, we used a conformationally selective synthetic antibody fragment (Fab30) that recognizes the phosphopeptide-activated state of β-arrestin-1. The structure of the β-arrestin-1-V2Rpp-Fab30 complex shows marked conformational differences in β-arrestin-1 compared to its inactive conformation. These include rotation of the amino- and carboxy-terminal domains relative to each other, and a major reorientation of the 'lariat loop' implicated in maintaining the inactive state of β-arrestin-1. These results reveal, at high resoln., a receptor-interacting interface on β-arrestin, and they indicate a potentially general mol. mechanism for activation of these multifunctional signalling and regulatory proteins.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3sXmt1WjtLg%253D&md5=2d2f2d657625eae90e1cd485af42cbd3
94
Nuber, S.; Zabel, U.; Lorenz, K.; Nuber, A.; Milligan, G.; Tobin, A. B.; Lohse, M. J.; Hoffmann, C. Beta-Arrestin Biosensors Reveal a Rapid, Receptor-Dependent Activation/Deactivation Cycle Nature 2016, 531, 661– 664 DOI: 10.1038/nature17198
Google Scholar
94
β-Arrestin biosensors reveal a rapid, receptor-dependent activation/deactivation cycle
Nuber, Susanne; Zabel, Ulrike; Lorenz, Kristina; Nuber, Andreas; Milligan, Graeme; Tobin, Andrew B.; Lohse, Martin J.; Hoffmann, Carsten
Nature (London, United Kingdom) (2016), 531 (7596), 661-664CODEN: NATUAS; ISSN:0028-0836. (Nature Publishing Group)
β-Arrestins are important regulators of G-protein-coupled receptors (GPCRs). They bind to active, phosphorylated GPCRs and thereby shut off 'classical' signaling to G proteins, trigger internalization of GPCRs via interaction with the clathrin machinery, and mediate signaling via 'non-classical' pathways. In addn. to 2 visual arrestins that bind to rod and cone photoreceptors (termed arrestin1 and arrestin4), there are only 2 (non-visual) β-arrestin proteins (β-arrestin1 and β-arrestin2, also termed arrestin2 and arrestin3), which regulate hundreds of different (non-visual) GPCRs. The binding of these proteins to GPCRs usually requires the active form of the receptors plus their phosphorylation by G-protein-coupled receptor kinases (GRKs). The binding of receptors or their C-terminus as well as certain truncations induce active conformations of β-arrestins that have recently been solved by x-ray crystallog. Here, the authors investigated both the interaction of β-arrestin with GPCRs, and the β-arrestin conformational changes in real time and in living human cells, using a series of FRET-based β-arrestin2 biosensors. The authors obsd. receptor-specific patterns of conformational changes in β-arrestin2 that occurred rapidly after the receptor-β-arrestin2 interaction. After agonist removal, these changes persisted for longer than the direct receptor interaction. The data indicated a rapid, receptor-type-specific, 2-step binding and activation process between GPCRs and β-arrestins. They further indicated that β-arrestins remained active after dissocn. from receptors, allowing them to remain at the cell surface and presumably signal independently. Thus, GPCRs trigger a rapid, receptor-specific activation/deactivation cycle of β-arrestins, which permits their active signaling.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC28XksFCqs7w%253D&md5=d14022d577cae8d2ccc63b2ae234ce1f
95
Lee, M. H.; Appleton, K. M.; Strungs, E. G.; Kwon, J. Y.; Morinelli, T. A.; Peterson, Y. K.; Laporte, S. A.; Luttrell, L. M. The Conformational Signature of Beta-Arrestin2 Predicts Its Trafficking and Signalling Functions Nature 2016, 531, 665– 668 DOI: 10.1038/nature17154
Google Scholar
There is no corresponding record for this reference.
96
Gentry, P. R.; Sexton, P. M.; Christopoulos, A. Novel Allosteric Modulators of G Protein-Coupled Receptors J. Biol. Chem. 2015, 290, 19478– 19488 DOI: 10.1074/jbc.R115.662759
Google Scholar
96
Novel Allosteric Modulators of G Protein-coupled Receptors
Gentry, Patrick R.; Sexton, Patrick M.; Christopoulos, Arthur
Journal of Biological Chemistry (2015), 290 (32), 19478-19488CODEN: JBCHA3; ISSN:0021-9258. (American Society for Biochemistry and Molecular Biology)
A review. G protein-coupled receptors (GPCRs) are allosteric proteins, because their signal transduction relies on interactions between topog. distinct, yet conformationally linked, domains. Much of the focus on GPCR allostery in the new millennium, however, has been on modes of targeting GPCR allosteric sites with chem. probes due to the potential for novel therapeutics. It is now apparent that some GPCRs possess more than one targetable allosteric site, in addn. to a growing list of putative endogenous modulators. Advances in structural biol. are also shedding new insights into mechanisms of allostery, although the complexities of candidate allosteric drugs necessitate rigorous biol. characterization.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2MXht12mt7rI&md5=7c3b5c0ddd375e0c05a18b91f2c68e56
97
Jakubik, J.; Bacakova, L.; El-Fakahany, E. E.; Tucek, S. Positive Cooperativity of Acetylcholine and Other Agonists with Allosteric Ligands on Muscarinic Acetylcholine Receptors Mol. Pharmacol. 1997, 52, 172– 179
Google Scholar
There is no corresponding record for this reference.
98
Conn, P. J.; Christopoulos, A.; Lindsley, C. W. Allosteric Modulators of GPCRs: A Novel Approach for the Treatment of CNS Disorders Nat. Rev. Drug Discovery 2009, 8, 41– 54 DOI: 10.1038/nrd2760
Google Scholar
98
Allosteric modulators of GPCRs: a novel approach for the treatment of CNS disorders
Conn, P. Jeffrey; Christopoulos, Arthur; Lindsley, Craig W.
Nature Reviews Drug Discovery (2009), 8 (1), 41-54CODEN: NRDDAG; ISSN:1474-1776. (Nature Publishing Group)
A review. Despite G-protein-coupled receptors (GPCRs) being among the most fruitful targets for marketed drugs, intense discovery efforts for several GPCR subtypes have failed to deliver selective drug candidates. Historically, drug discovery programs for GPCR ligands have been dominated by efforts to develop agonists and antagonists that act at orthosteric sites for endogenous ligands. However, in recent years, there have been tremendous advances in the discovery of novel ligands for GPCRs that act at allosteric sites to regulate receptor function. These compds. provide high selectivity, novel modes of efficacy and may lead to novel therapeutic agents for the treatment of multiple psychiatric and neurol. human disorders.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD1cXhsFCkurfF&md5=e109e94fe3e2c1fcfd480dc84c6609f7
99
Thal, D. M.; Sun, B.; Feng, D.; Nawaratne, V.; Leach, K.; Felder, C. C.; Bures, M. G.; Evans, D. A.; Weis, W. I.; Bachhawat, P. Crystal Structures of the M1 and M4Muscarinic Acetylcholine Receptors Nature 2016, 531, 335– 340 DOI: 10.1038/nature17188
Google Scholar
99
Crystal structures of the M1 and M4 muscarinic acetylcholine receptors
Thal, David M.; Sun, Bingfa; Feng, Dan; Nawaratne, Vindhya; Leach, Katie; Felder, Christian C.; Bures, Mark G.; Evans, David A.; Weis, William I.; Bachhawat, Priti; Kobilka, Tong Sun; Sexton, Patrick M.; Kobilka, Brian K.; Christopoulos, Arthur
Nature (London, United Kingdom) (2016), 531 (7594), 335-340CODEN: NATUAS; ISSN:0028-0836. (Nature Publishing Group)
Muscarinic M1-M5 acetylcholine receptors are G protein-coupled receptors (GPCRs) that regulate many vital functions of the central and peripheral nervous systems. In particular, the M1 and M4 receptor subtypes have emerged as attractive drug targets for treatments of neurol. disorders, such as Alzheimer's disease and schizophrenia, but the high conservation of the acetylcholine-binding pocket has spurred current research into targeting allosteric sites on these receptors. Here we report the crystal structures of the M1 and M4 muscarinic receptors bound to the inverse agonist, tiotropium. Comparison of these structures with each other, as well as with the previously reported M2 and M3 receptor structures, reveals differences in the orthosteric and allosteric binding sites that contribute to a role in drug selectivity at this important receptor family. We also report identification of a cluster of residues that form a network linking the orthosteric and allosteric sites of the M4 receptor, which provides new insight into how allosteric modulation may be transmitted between the two spatially distinct domains.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC28XktlGjurg%253D&md5=8ed3f453737ad0291cf5b2c088f528da
100
Hulme, E. C.; Lu, Z. L.; Bee, M. S. Scanning Mutagenesis Studies of the M1Muscarinic Acetylcholine Receptor Recept. Channels 2003, 9, 215– 228 DOI: 10.1080/10606820308261
Google Scholar
100
Scanning mutagenesis studies of the M1 muscarinic acetylcholine receptor
Hulme, E. C.; Lu, Z. L.; Bee, M. S.
Receptors and Channels (2003), 9 (4), 215-228CODEN: RCHAE4; ISSN:1060-6823. (Taylor & Francis, Inc.)
A review. Following the soln. of the structure of bovine rhodopsin by x-ray crystallog., it has been possible to build an improved homol. model of the M1 muscarinic acetylcholine receptor. This has been used to interpret the outcome of an extensive series of scanning and point mutagenesis studies on the transmembrane domain of the receptor. Potential intramol. interactions enhancing the stability of the protein fold have been identified. The residues contributing to the binding site for the antagonist, N-methylscopolamine, and the agonist, acetylcholine have been mapped. The pos. charged headgroups of these ligands appear to bind in a charge-stabilized arom. cage formed by amino acid side chains in transmembrane (TM) helixes 3, 6, and 7, while residues in TM 4 may participate in a peripheral docking site. Closure of the cage around the headgroup of acetylcholine may help to transduce binding energy into receptor activation, possibly disrupting a set of Van der Waals interactions between a set of residues underlying the binding site which help to constrain the receptor to the inactive state, in the absence of agonist. This may trigger the reorganization of a hydrogen bonding network between highly conserved residues in the core of the receptor, whose integrity is crucial for activation.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD3sXmtVelsb0%253D&md5=f355557a297bd661e718bc5516341059
101
Matsui, H.; Lazareno, S.; Birdsall, N. J. Probing of the Location of the Allosteric Site on M1 Muscarinic Receptors by Site-Directed Mutagenesis Mol. Pharmacol. 1995, 47, 88– 98
Google Scholar
101
Probing of the location of the allosteric site on m1 muscarinic receptors by site-directed mutagenesis
Matsui, Hideki; Lazareno, Sebastian; Birdsall, Nigel J. M.
Molecular Pharmacology (1995), 47 (1), 88-98CODEN: MOPMA3; ISSN:0026-895X. (Williams & Wilkins)
To locate the allosteric site on muscarinic receptors to which gallamine binds, 21 residues in the putative external loops and loop/transmembrane helix interfaces have been mutated to alanine. These residues are conserved in mammalian m1-m5 receptors. All mutant receptors can be expressed in COS-7 cells at high levels and appear to be functional, in that acetylcholine binding is sensitive to GTP. The gallamine binding site does not appear to involve the first, second, and most of the third extracellular loops. Tryptophan-400 and -101 inhibit gallamine binding when mutated to alanine or to phenylalanine and may form part of the allosteric site. Several mutations also effect antagonist binding. Surprisingly, tryptophan-91, a residue conserved in monoamine and peptide receptors, is important for antagonist binding. This residue, present in the middle of the first extracellular loop, may have a structural role in many G protein-coupled receptors. Antagonist binding is also affected by mutations of tryptophan-101 and tyrosine-404 to alanine or phenylalanine. In a helical wheel model, tryptophan-101 and tyrosine-404, in conjunction with serine-78, aspartate-105, and tyrosine-408, form a cluster of residues that have been reported to affect antagonist binding when mutated, and they may therefore be part of the antagonist binding site. It is suggested that the allosteric site may be located close to and just extracellular to the antagonist binding site. The binding of methoctramine, an antagonist with allosteric properties, is not substantially affected by mutations at tryptophan-91, -101, and -400 and tyrosine-404, and thus these amino acids are not important for its binding. The binding of himbacine, another antagonist with allosteric properties, is affected by these mutations but in a manner different from that of gallamine or competitive antagonists. It has not been possible to det. whether methoctramine and himbacine bind exclusively to the allosteric site or to both the competitive site and the allosteric site.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaK2MXjsVSntbY%253D&md5=5897f2468e20698235b50b4de9039f69
102
Mohr, K.; Trankle, C.; Holzgrabe, U. Structure/Activity Relationships of M2Muscarinic Allosteric Modulators Recept. Channels 2003, 9, 229– 240 DOI: 10.3109/10606820308264
Google Scholar
102
Structure/activity relationships of M2 muscarinic allosteric modulators
Mohr, K.; Traenkle, C.; Holzgrabe, U.
Receptors and Channels (2003), 9 (4), 229-240CODEN: RCHAE4; ISSN:1060-6823. (Taylor & Francis, Inc.)
A review. Allosteric modulation of G protein-coupled receptors has been intensively studied at muscarinic acetylcholine receptors. Findings made with archetypal allosteric agents such as gallamine, alcuronium, and bis(ammonio)alkane-type agents revealed that binding of orthosteric ligands that attach to the acetylcholine site can be allosterically decreased or increased or left unaltered in a subtype-selective fashion. Analyses of structure/activity relationships (SARs) help to elucidate the mol. events underlying the allosteric action and they may pilot the development of new allosteric agents with improved properties and therapeutic perspectives. With a focus on SARs, this review illustrates the principles of muscarinic allosteric interactions, gives an overview of SARs in congeners of archetypal allosteric agents, and considers the topol. of M2 muscarinic allosteric interactions that are characterized by divergent binding modes.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD3sXmtVelsbg%253D&md5=5f8cae3b1cc11511271c4923978f3776
103
Jazayeri, A.; Dore, A. S.; Lamb, D.; Krishnamurthy, H.; Southall, S. M.; Baig, A. H.; Bortolato, A.; Koglin, M.; Robertson, N. J.; Errey, J. C. Extra-Helical Binding Site of a Glucagon Receptor Antagonist Nature 2016, 533, 274– 277 DOI: 10.1038/nature17414
Google Scholar
103
Extra-helical binding site of a glucagon receptor antagonist
Jazayeri, Ali; Dore, Andrew S.; Lamb, Daniel; Krishnamurthy, Harini; Southall, Stacey M.; Baig, Asma H.; Bortolato, Andrea; Koglin, Markus; Robertson, Nathan J.; Errey, James C.; Andrews, Stephen P.; Teobald, Iryna; Brown, Alastair J. H.; Cooke, Robert M.; Weir, Malcolm; Marshall, Fiona H.
Nature (London, United Kingdom) (2016), 533 (7602), 274-277CODEN: NATUAS; ISSN:0028-0836. (Nature Publishing Group)
Glucagon is a 29-amino-acid peptide released from the α-cells of the islet of Langerhans, which has a key role in glucose homeostasis. Glucagon action is transduced by the class B G-protein-coupled glucagon receptor (GCGR), which is located on liver, kidney, intestinal smooth muscle, brain, adipose tissue, heart and pancreas cells, and this receptor has been considered an important drug target in the treatment of diabetes. Administration of recently identified small-mol. GCGR antagonists in patients with type 2 diabetes results in a substantial redn. of fasting and postprandial glucose concns. Although an x-ray structure of the transmembrane domain of the GCGR has previously been solved, the ligand (NNC0640) was not resolved. Here the authors report the 2.5 Å structure of human GCGR in complex with the antagonist MK-0893 (ref. 4), which is found to bind to an allosteric site outside the seven transmembrane (7TM) helical bundle in a position between TM6 and TM7 extending into the lipid bilayer. Mutagenesis of key residues identified in the x-ray structure confirms their role in the binding of MK-0893 to the receptor. The unexpected position of the binding site for MK-0893, which is structurally similar to other GCGR antagonists, suggests that glucagon activation of the receptor is prevented by restriction of the outward helical movement of TM6 required for G-protein coupling. Structural knowledge of class B receptors is limited, with only one other ligand-binding site defined-for the corticotropin-releasing hormone receptor 1 (CRF1R)-which was located deep within the 7TM bundle. The authors describe a completely novel allosteric binding site for class B receptors, providing an opportunity for structure-based drug design for this receptor class and furthering the authors' understanding of the mechanisms of activation of these receptors.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC28XmvVGnt7w%253D&md5=5b45af53e0870f497967c113095da9b4
104
Nolte, W. M.; Fortin, J. P.; Stevens, B. D.; Aspnes, G. E.; Griffith, D. A.; Hoth, L. R.; Ruggeri, R. B.; Mathiowetz, A. M.; Limberakis, C.; Hepworth, D. A Potentiator of Orthosteric Ligand Activity at GLP-1R Acts Via Covalent Modification Nat. Chem. Biol. 2014, 10, 629– 631 DOI: 10.1038/nchembio.1581
Google Scholar
104
A potentiator of orthosteric ligand activity at GLP-1R acts via covalent modification
Nolte, Whitney M.; Fortin, Jean-Philippe; Stevens, Benjamin D.; Aspnes, Gary E.; Griffith, David A.; Hoth, Lise R.; Ruggeri, Roger B.; Mathiowetz, Alan M.; Limberakis, Chris; Hepworth, David; Carpino, Philip A.
Nature Chemical Biology (2014), 10 (8), 629-631CODEN: NCBABT; ISSN:1552-4450. (Nature Publishing Group)
We report that 4-(3-(benzyloxy)phenyl)-2-ethylsulfinyl-6-(trifluoromethyl)pyrimidine (BETP), which behaves as a pos. allosteric modulator at the glucagon-like peptide-1 receptor (GLP-1R), covalently modifies cysteines 347 and 438 in GLP-1R. C347, located in intracellular loop 3 of GLP-1R, is crit. to the activity of BETP and a structurally distinct GLP-1R ago-allosteric modulator, N-(tert-butyl)-6,7-dichloro-3-(methylsulfonyl)quinoxalin-2-amine. We further show that substitution of cysteine for phenylalanine 345 in the glucagon receptor is sufficient to confer sensitivity to BETP.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2cXhtFSlsLrO&md5=9b0d431ea2c96e8889f774c50fdf9452
105
Bueno, A. B.; Showalter, A. D.; Wainscott, D. B.; Stutsman, C.; Marin, A.; Ficorilli, J.; Cabrera, O.; Willard, F. S.; Sloop, K. W. Positive Allosteric Modulation of the Glucagon-Like Peptide-1 Receptor by Diverse Electrophiles J. Biol. Chem. 2016, 291, 10700– 10715 DOI: 10.1074/jbc.M115.696039
Google Scholar
105
Positive Allosteric Modulation of the Glucagon-like Peptide-1 Receptor by Diverse Electrophiles
Bueno, Ana B.; Showalter, Aaron D.; Wainscott, David B.; Stutsman, Cynthia; Marin, Aranzazu; Ficorilli, James; Cabrera, Over; Willard, Francis S.; Sloop, Kyle W.
Journal of Biological Chemistry (2016), 291 (20), 10700-10715CODEN: JBCHA3; ISSN:0021-9258. (American Society for Biochemistry and Molecular Biology)
Therapeutic intervention to activate the glucagon-like peptide-1 receptor (GLP-1R) enhances glucose-dependent insulin secretion and improves energy balance in patients with type 2 diabetes mellitus. Studies investigating mechanisms whereby peptide ligands activate GLP-1R have utilized mutagenesis, receptor chimeras, photo-affinity labeling, hydrogen-deuterium exchange, and crystallog. of the ligand-binding ectodomain to establish receptor homol. models. However, this has not enabled the design or discovery of drug-like non-peptide GLP-1R activators. Recently, studies investigating 4-(3-benzyloxyphenyl)-2-ethylsulfinyl-6-(trifluoromethyl)pyrimidine (BETP), a GLP-1R-pos. allosteric modulator, detd. that Cys 347 in the GLP-1R is required for pos. allosteric modulator activity via covalent modification. To advance small mol. activation of the GLP-1R, the authors characterized the insulinotropic mechanism of BETP. In guanosine 5'-3-O-(thio)triphosphate binding and INS1 832-3 insulinoma cell cAMP assays, BETP enhanced GLP-1(9-36)-NH2-stimulated cAMP signaling. Using isolated pancreatic islets, BETP potentiated insulin secretion in a glucose-dependent manner that requires both the peptide ligand and GLP-1R. In studies of the covalent mechanism, PAGE fluorog. showed labeling of GLP-1R in immunopptn. expts. from GLP-1R-expressing cells incubated with [3H]BETP. Furthermore, the authors investigated whether other reported GLP-1R activators and compds. identified from screening campaigns modulate GLP-1R by covalent modification. Similar to BETP, several mols. were found to enhance GLP-1R signaling in a Cys 347-dependent manner. These chemotypes are electrophiles that react with GSH, and LC/MS detd. the cysteine adducts formed upon conjugation. Together, the authors' results suggest covalent modification may be used to stabilize the GLP-1R in an active conformation. Moreover, the findings provide pharmacol. guidance for the discovery and characterization of small mol. GLP-1R ligands as possible therapeutics.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC28XnvVamt7w%253D&md5=5b003ca0630b264ebd333a374dc3fabf
106
Langmead, C. J.; Christopoulos, A. Allosteric Agonists of 7TM Receptors: Expanding the Pharmacological Toolbox Trends Pharmacol. Sci. 2006, 27, 475– 481 DOI: 10.1016/j.tips.2006.07.009
Google Scholar
There is no corresponding record for this reference.
107
Knudsen, L. B.; Kiel, D.; Teng, M.; Behrens, C.; Bhumralkar, D.; Kodra, J. T.; Holst, J. J.; Jeppesen, C. B.; Johnson, M. D.; de Jong, J. C. Small-Molecule Agonists for the Glucagon-Like Peptide 1 Receptor Proc. Natl. Acad. Sci. U. S. A. 2007, 104, 937– 942 DOI: 10.1073/pnas.0605701104
Google Scholar
107
Small-molecule agonists for the glucagon-like peptide 1 receptor
Knudsen, Lotte Bjerre; Kiel, Dan; Teng, Min; Behrens, Carsten; Bhumralkar, Dilip; Kodra, Janos T.; Holst, Jens J.; Jeppesen, Claus B.; Johnson, Michael D.; de Jong, Johannes Cornelis; Jorgensen, Anker Steen; Kercher, Tim; Kostrowicki, Jarek; Madsen, Peter; Olesen, Preben H.; Petersen, Jacob S.; Poulsen, Fritz; Sidelmann, Ulla G.; Sturis, Jeppe; Truesdale, Larry; May, John; Lau, Jesper
Proceedings of the National Academy of Sciences of the United States of America (2007), 104 (3), 937-942CODEN: PNASA6; ISSN:0027-8424. (National Academy of Sciences)
The peptide hormone glucagon-like peptide (GLP)-1 has important actions resulting in glucose lowering along with wt. loss in patients with type 2 diabetes. As a peptide hormone, GLP-1 has to be administered by injection. Only a few small-mol. agonists to peptide hormone receptors have been described and none in the B family of the G protein coupled receptors to which the GLP-1 receptor belongs. We have discovered a series of small mols. known as ago-allosteric modulators selective for the human GLP-1 receptor. These compds. act as both allosteric activators of the receptor and independent agonists. Potency of GLP-1 was not changed by the allosteric agonists, but affinity of GLP-1 for the receptor was increased. The most potent compd. identified (I) stimulates glucose-dependent insulin release from normal mouse islets but, importantly, not from GLP-1 receptor knockout mice. Also, the compd. stimulates insulin release from perfused rat pancreas in a manner additive with GLP-1 itself. These compds. may lead to the identification or design of orally active GLP-1 agonists.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2sXhtVegtL8%253D&md5=b4d15353341ee3cd2ff27e950df5681f
108
Coopman, K.; Huang, Y.; Johnston, N.; Bradley, S. J.; Wilkinson, G. F.; Willars, G. B. Comparative Effects of the Endogenous Agonist Glucagon-Like Peptide-1 (Glp-1)-(7–36) Amide and the Small-Molecule Ago-Allosteric Agent ″Compound 2″ at the Glp-1 Receptor J. Pharmacol. Exp. Ther. 2010, 334, 795– 808 DOI: 10.1124/jpet.110.166009
Google Scholar
108
Comparative effects of the endogenous agonist glucagon-like peptide-1 (GLP-1)-(7-36) amide and the small-molecule agoallosteric agent compound 2 at the GLP-1 receptor
Coopman, Karen; Huang, Yan; Johnston, Neil; Bradley, Sophie J.; Wilkinson, Graeme F.; Willars, Gary B.
Journal of Pharmacology and Experimental Therapeutics (2010), 334 (3), 795-808CODEN: JPETAB; ISSN:0022-3565. (American Society for Pharmacology and Experimental Therapeutics)
Glucagon-like peptide-1 (GLP-1) mediates antidiabetogenic effects through the GLP-1 receptor (GLP-1R), which is targeted for the treatment of type 2 diabetes. Small-mol. GLP-1R agonists have been sought due to difficulties with peptide therapeutics. Recently, 6,7-dichloro-2-methylsulfonyl-3-N-tert-butylaminoquinoxaline (compd. 2) has been described as a GLP-1R allosteric modulator and agonist. Using human embryonic kidney-293 cells expressing human GLP-1Rs, we extended this work to consider the impact of compd. 2 on G protein activation, Ca2+ signaling and receptor internalization and particularly to compare compd. 2 and GLP-1 across a range of functional assays in intact cells. GLP-1 and compd. 2 activated Gαs in cell membranes and increased cellular cAMP in intact cells, with compd. 2 being a partial and almost full agonist, resp. GLP-1 increased intracellular [Ca2+] by release from intracellular stores, which was mimicked by compd. 2, with slower kinetics. In either intact cells or membranes, the orthosteric antagonist exendin-(9-39), inhibited GLP-1 cAMP generation but increased the efficacy of compd. 2. GLP-1 internalized enhanced green fluorescent protein-tagged GLP-1Rs, but the speed and magnitude evoked by compd. 2 were less. Exendin-(9-39) inhibited internalization by GLP-1 and also surprisingly that by compd. 2. Compd. 2 displays GLP-1R agonism consistent with action at an allosteric site, although an orthosteric antagonist increased its efficacy on cAMP and blocked compd. 2-mediated receptor internalization. Full assessment of the properties of compd. 2 was potentially hampered by damaging effects that were particularly manifest in either longer term assays with intact cells or in acute assays with membranes.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3cXhtFyksL%252FJ&md5=0134b03ec49f7c33c30e809b438417af
109
Katritch, V.; Fenalti, G.; Abola, E. E.; Roth, B. L.; Cherezov, V.; Stevens, R. C. Allosteric Sodium in Class a GPCR Signaling Trends Biochem. Sci. 2014, 39, 233– 244 DOI: 10.1016/j.tibs.2014.03.002
Google Scholar
109
Allosteric sodium in class A GPCR signaling
Katritch, Vsevolod; Fenalti, Gustavo; Abola, Enrique E.; Roth, Bryan L.; Cherezov, Vadim; Stevens, Raymond C.
Trends in Biochemical Sciences (2014), 39 (5), 233-244CODEN: TBSCDB; ISSN:0968-0004. (Elsevier Ltd.)
A review. Despite their functional and structural diversity, G-protein-coupled receptors (GPCRs) share a common mechanism of signal transduction via conformational changes in the seven-transmembrane (7TM) helical domain. New major insights into this mechanism come from the recent crystallog. discoveries of a partially hydrated sodium ion that is specifically bound in the middle of the 7TM bundle of multiple class A GPCRs. This review discusses the remarkable structural conservation and distinct features of the Na+ pocket in this most populous GPCR class, as well as the conformational collapse of the pocket upon receptor activation. New insights help to explain allosteric effects of sodium on GPCR agonist binding and activation, and sodium's role as a potential co-factor in class A GPCR function.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2cXmsFCqs7k%253D&md5=c217e7eb69c93b1c76559cc587b318b5
110
Liu, W.; Chun, E.; Thompson, A. A.; Chubukov, P.; Xu, F.; Katritch, V.; Han, G. W.; Roth, C. B.; Heitman, L. H.; AP, I. J. Structural Basis for Allosteric Regulation of GPCRs by Sodium Ions Science 2012, 337, 232– 236 DOI: 10.1126/science.1219218
Google Scholar
110
Structural Basis for Allosteric Regulation of GPCRs by Sodium Ions
Liu, Wei; Chun, Eugene; Thompson, Aaron A.; Chubukov, Pavel; Xu, Fei; Katritch, Vsevolod; Han, Gye Won; Roth, Christopher B.; Heitman, Laura H.; IJzerman, Adriaan P.; Cherezov, Vadim; Stevens, Raymond C.
Science (Washington, DC, United States) (2012), 337 (6091), 232-236CODEN: SCIEAS; ISSN:0036-8075. (American Association for the Advancement of Science)
Pharmacol. responses of G protein-coupled receptors (GPCRs) can be fine-tuned by allosteric modulators. Structural studies of such effects have been limited due to the medium resoln. of GPCR structures. We reengineered the human A2A adenosine receptor by replacing its third intracellular loop with apocytochrome b562RIL and solved the structure at 1.8 angstrom resoln. The high-resoln. structure allowed us to identify 57 ordered water mols. inside the receptor comprising three major clusters. The central cluster harbors a putative sodium ion bound to the highly conserved aspartate residue Asp2.50. Addnl., two cholesterols stabilize the conformation of helix VI, and one of 23 ordered lipids intercalates inside the ligand-binding pocket. These high-resoln. details shed light on the potential role of structured water mols., sodium ions, and lipids/cholesterol in GPCR stabilization and function.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC38XpvVKqtbs%253D&md5=782b2235b76ef77b11b6456f8e4485e1
111
Gutierrez-de-Teran, H.; Massink, A.; Rodriguez, D.; Liu, W.; Han, G. W.; Joseph, J. S.; Katritch, I.; Heitman, L. H.; Xia, L.; Ijzerman, A. P. The Role of a Sodium Ion Binding Site in the Allosteric Modulation of the a(2a) Adenosine G Protein-Coupled Receptor Structure 2013, 21, 2175– 2185 DOI: 10.1016/j.str.2013.09.020
Google Scholar
There is no corresponding record for this reference.
112
Inagaki, S.; Ghirlando, R.; White, J. F.; Gvozdenovic-Jeremic, J.; Northup, J. K.; Grisshammer, R. Modulation of the Interaction between Neurotensin Receptor NTS1 and Gq Protein by Lipid J. Mol. Biol. 2012, 417, 95– 111 DOI: 10.1016/j.jmb.2012.01.023
Google Scholar
112
Modulation of the Interaction between Neurotensin Receptor NTS1 and Gq Protein by Lipid
Inagaki, Sayaka; Ghirlando, Rodolfo; White, Jim F.; Gvozdenovic-Jeremic, Jelena; Northup, John K.; Grisshammer, Reinhard
Journal of Molecular Biology (2012), 417 (1-2), 95-111CODEN: JMOBAK; ISSN:0022-2836. (Elsevier Ltd.)
Membrane lipids have been implicated to influence the activity of G-protein-coupled receptors (GPCRs). Almost all of our knowledge on the role of lipids on GPCR and G protein function comes from work on the visual pigment rhodopsin and its G protein transducin, which reside in a highly specialized membrane environment. Thus, insight gained from rhodopsin signaling may not be simply translated to other nonvisual GPCRs. Here, we investigated the effect of lipid head group charges on the signal transduction properties of the class A GPCR neurotensin (NT) receptor 1 (NTS1) under defined exptl. conditions, using self-assembled phospholipid nanodiscs prepd. with the zwitter-ionic lipid 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC), the neg. charged 1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-(1'-rac-glycerol) (POPG), or a POPC/POPG mixt. A combination of dynamic light scattering and sedimentation velocity showed that NTS1 was monomeric in POPC-, POPC/POPG-, and POPG-nanodiscs. Binding of the agonist NT to NTS1 occurred with similar affinities and was essentially unaffected by the phospholipid compn. In contrast, Gq protein coupling to NTS1 in various lipid nanodiscs was significantly different, and the apparent affinity of Gαq and Gβ1γ1 to activated NTS1 increased with increasing POPG content. NTS1-catalyzed GDP/GTPγS nucleotide exchange at Gαq in the presence of Gβ1γ1 and NT was crucially affected by the lipid type, with exchange rates higher by 1 or 2 orders of magnitude in POPC/POPG- and POPG-nanodiscs, resp., compared to POPC-nanodiscs. Our data demonstrate that neg. charged lipids in the immediate vicinity of a nonvisual GPCR modulate the G-protein-coupling step.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC38XisFKhtbk%253D&md5=e7ff73804f671945083eb0e56fc12fde
113
Botelho, A. V.; Gibson, N. J.; Thurmond, R. L.; Wang, Y.; Brown, M. F. Conformational Energetics of Rhodopsin Modulated by Nonlamellar-Forming Lipids Biochemistry 2002, 41, 6354– 6368 DOI: 10.1021/bi011995g
Google Scholar
113
Conformational Energetics of Rhodopsin Modulated by Nonlamellar-Forming Lipids
Botelho, Ana Vitoria; Gibson, Nicholas J.; Thurmond, Robin L.; Wang, Yin; Brown, Michael F.
Biochemistry (2002), 41 (20), 6354-6368CODEN: BICHAW; ISSN:0006-2960. (American Chemical Society)
Rhodopsin is an important example of a G protein-coupled receptor (GPCR) in which 11-cis-retinal is the ligand and acts as an inverse agonist. Photolysis of rhodopsin leads to formation of the activated meta II state from its precursor meta I. Various mechanisms have been proposed to explain how the membrane compn. affects the meta I-meta II conformational equil. in the visual process. For rod disk membranes and recombinant membranes contg. rhodopsin, the lipid properties have been discussed in terms of elastic deformation of the bilayer. Here we have investigated the relation of nonlamellar-forming lipids, such as dioleoylphosphatidylethanolamine (DOPE), together with dioleoylphosphatidylcholine (DOPC), to the photochem. of membrane-bound rhodopsin. We conducted flash photolysis expts. for bovine rhodopsin recombined with DOPE/DOPC mixts. (0:100 to 75:25) as a function of pH to explore the dependence of the photochem. activity on the monolayer curvature free energy of the membrane. It is well-known that DOPC forms bilayers, whereas DOPE has a propensity to adopt the nonlamellar, reverse hexagonal (HII) phase. In the case of neutral DOPE/DOPC recombinants, calcns. of the membrane surface pH confirmed that an increase in DOPE favored the meta II state. Moreover, doubling the PE headgroup content vs. the native rod membranes substituted for the polyunsatd., docosahexaenoic acyl chains (22:6ω3), suggesting rhodopsin function is assocd. with a balance of forces within the bilayer. The data are interpreted by applying a flexible surface model, in which the meta II state is stabilized by lipids tending to form the HII phase, with a neg. spontaneous curvature. A simple theory, based on principles of surface chem., for coupling the energetics of membrane proteins to material properties of the bilayer lipids is described. For rhodopsin, the free energy balance of the receptor and the lipids is altered by photoisomerization of retinal and involves curvature stress/strain of the membrane (frustration). A new biophys. principle is introduced: matching of the spontaneous curvature of the lipid bilayer to the mean curvature of the lipid/water interface adjacent to the protein, which balances the lipid/protein solvation energy. In this manner, the thermodn. driving force for the meta I-meta II conformational change of rhodopsin is tightly controlled by mixts. of nonlamellar-forming lipids having distinctive material properties.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD38XjtFGmsLo%253D&md5=2098f6baf15a7ac88a25616ab93812e7
114
Soubias, O.; Teague, W. E.; Gawrisch, K. Evidence for Specificity in Lipid-Rhodopsin Interactions J. Biol. Chem. 2006, 281, 33233– 33241 DOI: 10.1074/jbc.M603059200
Google Scholar
114
Evidence for Specificity in Lipid-Rhodopsin Interactions
Soubias, Olivier; Teague, Walter E.; Gawrisch, Klaus
Journal of Biological Chemistry (2006), 281 (44), 33233-33241CODEN: JBCHA3; ISSN:0021-9258. (American Society for Biochemistry and Molecular Biology)
The interaction of bovine rhodopsin with poly- and monounsatd. lipids was studied by 1H MAS NMR with magnetization transfer from rhodopsin to lipid. Expts. were conducted on bovine rod outer segment (ROS) disks and on recombinant membranes contg. lipids with polyunsatd. docosahexaenoyl (DHA) chains. Poly- and monounsatd. lipids interact specifically with different sites on the rhodopsin surface. Rates of magnetization transfer from protein to DHA are lipid headgroup-dependent and increased in the sequence PC < PS < PE. Boundary lipids are in fast exchange with the lipid matrix on a time scale of milliseconds or shorter. All rhodopsin photointermediates transferred magnetization preferentially to DHA-contg. lipids, but highest rates were obsd. for Meta-III rhodopsin. The expts. show clearly that the surface of rhodopsin has sites for specific interaction with lipids. Current theories of lipid-protein interaction do not account for such surface heterogeneity.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD28XhtFegsb7N&md5=0e3a5e7ba01e0109a1dec4599c5a4923
115
Neale, C.; Herce, H. D.; Pomes, R.; Garcia, A. E. Can Specific Protein-Lipid Interactions Stabilize an Active State of the Beta 2 Adrenergic Receptor? Biophys. J. 2015, 109, 1652– 1662 DOI: 10.1016/j.bpj.2015.08.028
Google Scholar
115
Can Specific Protein-Lipid Interactions Stabilize an Active State of the Beta 2 Adrenergic Receptor?
Neale, Chris; Herce, Henry D.; Pomes, Regis; Garcia, Angel E.
Biophysical Journal (2015), 109 (8), 1652-1662CODEN: BIOJAU; ISSN:0006-3495. (Cell Press)
G protein-coupled receptors (GPCRs) are eukaryotic membrane proteins with broad biol. and pharmacol. relevance. Like all membrane-embedded proteins, their location and orientation are influenced by lipids, which can also impact protein function via specific interactions. Extensive simulations totaling 0.25 ms reveal a process in which phospholipids from the membrane's cytosolic leaflet enter the empty G protein-binding site of an activated β2 adrenergic receptor and form salt-bridge interactions that inhibit ionic lock formation and prolong active-state residency. Simulations of the receptor embedded in an anionic membrane show increased lipid binding, providing a mol. mechanism for the exptl. observation that anionic lipids can enhance receptor activity. Conservation of the arginine component of the ionic lock among Rhodopsin-like G protein-coupled receptors suggests that intracellular lipid ingression between receptor helixes H6 and H7 may be a general mechanism for active-state stabilization.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2MXhsFWls7zL&md5=646918f205c38e492153e82640d6d87a
116
Shoichet, B. K.; Kobilka, B. K. Structure-Based Drug Screening for G-Protein-Coupled Receptors Trends Pharmacol. Sci. 2012, 33, 268– 272 DOI: 10.1016/j.tips.2012.03.007
Google Scholar
116
Structure-based drug screening for G-protein-coupled receptors
Shoichet, Brian K.; Kobilka, Brian K.
Trends in Pharmacological Sciences (2012), 33 (5), 268-272CODEN: TPHSDY; ISSN:0165-6147. (Elsevier Ltd.)
A review. G-protein-coupled receptors (GPCRs) represent a large family of signaling proteins that includes many therapeutic targets; however, progress in identifying new small mol. drugs has been disappointing. The past 4 years have seen remarkable progress in the structural biol. of GPCRs, raising the possibility of applying structure-based approaches to GPCR drug discovery efforts. Of the various structure-based approaches that have been applied to sol. protein targets, such as proteases and kinases, in silico docking is among the most ready applicable to GPCRs. Early studies suggest that GPCR binding pockets are well suited to docking, and docking screens have identified potent and novel compds. for these targets. This review will focus on the current state of in silico docking for GPCRs.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC38XlsFGit7Y%253D&md5=30f26646db71f5c0c8448e9d85908060
117
Jazayeri, A.; Dias, J. M.; Marshall, F. H. From G Protein-Coupled Receptor Structure Resolution to Rational Drug Design J. Biol. Chem. 2015, 290, 19489– 19495 DOI: 10.1074/jbc.R115.668251
Google Scholar
117
From G Protein-coupled Receptor Structure Resolution to Rational Drug Design
Jazayeri, Ali; Dias, Joao M.; Marshall, Fiona H.
Journal of Biological Chemistry (2015), 290 (32), 19489-19495CODEN: JBCHA3; ISSN:0021-9258. (American Society for Biochemistry and Molecular Biology)
A review. A no. of recent tech. solns. have led to significant advances in G protein-coupled receptor (GPCR) structural biol. Apart from a detailed mechanistic view of receptor activation, the new structures have revealed novel ligand binding sites. Together, these insights provide avenues for rational drug design to modulate the activities of these important drug targets. The application of structural data to GPCR drug discovery ushers in an exciting era with the potential to improve existing drugs and discover new ones. In this review, we focus on tech. solns. that have accelerated GPCR crystallog. as well as some of the salient findings from structures that are relevant to drug discovery. Finally, we outline some of the approaches used in GPCR structure based drug design.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2MXht12mt7jJ&md5=304fa0d074df15e0f2c4025a95fd8096
118
Kumari, P.; Ghosh, E.; Shukla, A. K. Emerging Approaches to GPCR Ligand Screening for Drug Discovery Trends Mol. Med. 2015, 21, 687– 701 DOI: 10.1016/j.molmed.2015.09.002
Google Scholar
118
Emerging Approaches to GPCR Ligand Screening for Drug Discovery
Kumari, Punita; Ghosh, Eshan; Shukla, Arun K.
Trends in Molecular Medicine (2015), 21 (11), 687-701CODEN: TMMRCY; ISSN:1471-4914. (Elsevier Ltd.)
The superfamily of G-protein-coupled receptors (GPCRs) represents the largest class of cell surface receptors and, thus, a prominent family of drug targets. Recently, there has been significant progress in detn. of GPCR crystal structures. The structure-based ligand discovery of GPCRs is emerging as a powerful path to drug development. Sensor surface-immobilized GPCRs can identify direct receptor-ligand interactions of a range of chem. libraries. This type of screening shows great promise as an alternative strategy for ligand discovery. Here, we summarize the most recent developments of structure- and sensor-based GPCR ligand discovery. We also highlight certain areas where GPCRs harbor great potential for the development of novel therapeutics, emphasizing the strategic approaches that may yield significant breakthroughs.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2MXhs1Squ7jJ&md5=eff5c205968fcd18802883063a1d1ca3
119
Rodriguez, D.; Ranganathan, A.; Carlsson, J. Discovery of GPCR Ligands by Molecular Docking Screening: Novel Opportunities Provided by Crystal Structures Curr. Top. Med. Chem. 2015, 15, 2484– 2503 DOI: 10.2174/1568026615666150701112853
Google Scholar
119
Discovery of GPCR Ligands by Molecular Docking Screening: Novel Opportunities Provided by Crystal Structures
Rodriguez, David; Ranganathan, Anirudh; Carlsson, Jens
Current Topics in Medicinal Chemistry (Sharjah, United Arab Emirates) (2015), 15 (24), 2484-2503CODEN: CTMCCL; ISSN:1568-0266. (Bentham Science Publishers Ltd.)
G protein-coupled receptors (GPCRs) constitute the largest group of human membrane proteins and have received significant attention in drug discovery for their important roles in physiol. processes. Drug development for GPCRs has been remarkably successful and several of the most profitable pharmaceuticals on the market target members of this superfamily. Breakthroughs in structural biol. for GPCRs have revealed how their binding sites recognize extracellular mols. at the at. level. High-resoln. crystal structures of GPCR-drug complexes capturing different receptor conformations are now available, which have provided insights into how ligands stabilize different functional states. Recently, the basis for subtype selectivity and novel allosteric binding sites has also been revealed by crystal structures. These accomplishments provide exciting opportunities to identify novel GPCR ligands using <i>in silico</i> structure-based methods such as mol. docking. Increased computational power now enables docking screens of large chem. libraries to identify mols. that complement GPCR binding sites, which may provide possibilities to identify ligands with tailored pharmacol. properties. This review focuses on prospective docking screens against GPCRs and how this technique can be used to identify lead candidates with specific signaling or selectivity profiles. The current state of this field suggests that mol. docking, in combination with further understanding of GPCR signaling, will play an important role in future drug discovery.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2MXhsFansrjN&md5=31a75abcc24bf453ad155903a7454d3e
120
Kooistra, A. J.; Leurs, R.; de Esch, I. J.; de Graaf, C. From Three-Dimensional GPCR Structure to Rational Ligand Discovery Adv. Exp. Med. Biol. 2014, 796, 129– 157 DOI: 10.1007/978-94-007-7423-0_7
Google Scholar
120
From Three-Dimensional GPCR Structure to Rational Ligand Discovery
Kooistra, Albert J.; Leurs, Rob; de Esch, Iwan J. P.; de Graaf, Chris
Advances in Experimental Medicine and Biology (2014), 796 (G Protein-Coupled Receptors--Modeling and Simulation), 129-157CODEN: AEMBAP; ISSN:2214-8019. (Springer)
This chapter will focus on G protein-coupled receptor structure-based virtual screening and ligand design. A generic virtual screening workflow and its individual elements will be introduced, covering amongst others the use of exptl. data to steer the virtual screening process, ligand binding mode prediction, virtual screening for novel ligands, and rational structure-based virtual screening hit optimization. An overview of recent successful structure-based ligand discovery and design studies shows that receptor models, despite structural inaccuracies, can be efficiently used to find novel ligands for GPCRs. Moreover, the recently solved GPCR crystal structures have further increased the opportunities in structure-based ligand discovery for this pharmaceutically important protein family. The current chapter will discuss several challenges in rational ligand discovery based on GPCR structures including: (i) structure-based identification of ligands with specific effects on GPCR mediated signaling pathways, and (ii) virtual screening and structure-based optimization of fragment -like mols.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2MXlvFGlsbo%253D&md5=eb958e2924df274157d0297d7a65d7ac
121
Negri, A.; Rives, M. L.; Caspers, M. J.; Prisinzano, T. E.; Javitch, J. A.; Filizola, M. Discovery of a Novel Selective Kappa-Opioid Receptor Agonist Using Crystal Structure-Based Virtual Screening J. Chem. Inf. Model. 2013, 53, 521– 526 DOI: 10.1021/ci400019t
Google Scholar
121
Discovery of a Novel Selective Kappa-Opioid Receptor Agonist Using Crystal Structure-Based Virtual Screening
Negri, Ana; Rives, Marie-Laure; Caspers, Michael J.; Prisinzano, Thomas E.; Javitch, Jonathan A.; Filizola, Marta
Journal of Chemical Information and Modeling (2013), 53 (3), 521-526CODEN: JCISD8; ISSN:1549-9596. (American Chemical Society)
Kappa-opioid (KOP) receptor agonists exhibit analgesic effects without activating reward pathways. In the search for nonaddictive opioid therapeutics and novel chem. tools to study physiol. functions regulated by the KOP receptor, we screened in silico its recently released inactive crystal structure. A selective novel KOP receptor agonist emerged as a notable result and is proposed as a new chemotype for the study of the KOP receptor in the etiol. of drug addiction, depression, and/or pain.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3sXjsVymurk%253D&md5=4ace2403c664ba58106b40a61773bf4b
122
Weiss, D. R.; Ahn, S.; Sassano, M. F.; Kleist, A.; Zhu, X.; Strachan, R.; Roth, B. L.; Lefkowitz, R. J.; Shoichet, B. K. Conformation Guides Molecular Efficacy in Docking Screens of Activated Beta-2 Adrenergic G Protein Coupled Receptor ACS Chem. Biol. 2013, 8, 1018– 1026 DOI: 10.1021/cb400103f
Google Scholar
122
Conformation Guides Molecular Efficacy in Docking Screens of Activated β-2 Adrenergic G Protein Coupled Receptor
Weiss, Dahlia R.; Ahn, SeungKirl; Sassano, Maria F.; Kleist, Andrew; Zhu, Xiao; Strachan, Ryan; Roth, Bryan L.; Lefkowitz, Robert J.; Shoichet, Brian K.
ACS Chemical Biology (2013), 8 (5), 1018-1026CODEN: ACBCCT; ISSN:1554-8929. (American Chemical Society)
A prospective, large library virtual screen against an activated β2-adrenergic receptor (β2AR) structure returned potent agonists to the exclusion of inverse-agonists, providing the first complement to the previous virtual screening campaigns against inverse-agonist-bound G protein coupled receptor (GPCR) structures, which predicted only inverse-agonists. In addn., two hits recapitulated the signaling profile of the co-crystal ligand with respect to the G protein and arrestin mediated signaling. This functional fidelity has important implications in drug design, as the ability to predict ligands with predefined signaling properties is highly desirable. However, the agonist-bound state provides an uncertain template for modeling the activated conformation of other GPCRs, as a dopamine D2 receptor (DRD2) activated model templated on the activated β2AR structure returned few hits of only marginal potency.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3sXjvVahtbg%253D&md5=6394521533373197c59e49b242bf0c93
123
Rodriguez, D.; Gao, Z. G.; Moss, S. M.; Jacobson, K. A.; Carlsson, J. Molecular Docking Screening Using Agonist-Bound GPCR Structures: Probing the A2a Adenosine Receptor J. Chem. Inf. Model. 2015, 55, 550– 563 DOI: 10.1021/ci500639g
Google Scholar
123
Molecular Docking Screening Using Agonist-Bound GPCR Structures: Probing the A2A Adenosine Receptor
Rodriguez, David; Gao, Zhang-Guo; Moss, Steven M.; Jacobson, Kenneth A.; Carlsson, Jens
Journal of Chemical Information and Modeling (2015), 55 (3), 550-563CODEN: JCISD8; ISSN:1549-9596. (American Chemical Society)
Crystal structures of G protein-coupled receptors (GPCRs) have recently revealed the mol. basis of ligand binding and activation, which has provided exciting opportunities for structure-based drug design. The A2A adenosine receptor (A2AAR) is a promising therapeutic target for cardiovascular diseases, but progress in this area is limited by the lack of novel agonist scaffolds. The authors carried out docking screens of 6.7 million com. available mols. against active-like conformations of the A2AAR to investigate whether these structures could guide the discovery of agonists. Nine out of the 20 predicted agonists were confirmed to be A2AAR ligands, but none of these activated the ARs. The difficulties in discovering AR agonists using structure-based methods originated from limited at.-level understanding of the activation mechanism and a chem. bias toward antagonists in the screened library. In particular, the compn. of the screened library was found to strongly reduce the likelihood of identifying AR agonists, which reflected the high ligand complexity required for receptor activation. Extension of this anal. to other pharmaceutically relevant GPCRs suggested that library screening may not be suitable for targets requiring a complex receptor-ligand interaction network. The authors' results provide specific directions for the future development of novel A2AAR agonists and general strategies for structure-based drug discovery.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2MXhsVWgtbs%253D&md5=0faec5c3d810a9ef32e5f374b6f9b447
124
Heptares Therapeutics. http://www.heptares.com/pipeline/, accessed July 20, 2016.
Google Scholar
There is no corresponding record for this reference.
125
Zhukov, A.; Andrews, S. P.; Errey, J. C.; Robertson, N.; Tehan, B.; Mason, J. S.; Marshall, F. H.; Weir, M.; Congreve, M. Biophysical Mapping of the Adenosine A2a Receptor J. Med. Chem. 2011, 54, 4312– 4323 DOI: 10.1021/jm2003798
Google Scholar
125
Biophysical Mapping of the Adenosine A2A Receptor
Zhukov, Andrei; Andrews, Stephen P.; Errey, James C.; Robertson, Nathan; Tehan, Benjamin; Mason, Jonathan S.; Marshall, Fiona H.; Weir, Malcolm; Congreve, Miles
Journal of Medicinal Chemistry (2011), 54 (13), 4312-4323CODEN: JMCMAR; ISSN:0022-2623. (American Chemical Society)
A new approach to generating information on ligand receptor interactions within the binding pocket of G protein-coupled receptors has been developed, called Biophys. Mapping (BPM). Starting from a stabilized receptor (StaR), minimally engineered for thermostability, addnl. single mutations are then added at positions that could be involved in small mol. interactions. The StaR and a panel of binding site mutants are captured onto Biacore chips to enable characterization of the binding of small mol. ligands using surface plasmon resonance (SPR) measurement. A matrix of binding data for a set of ligands vs. each active site mutation is then generated, providing specific affinity and kinetic information (KD, kon, and koff) of receptor-ligand interactions. This data set, in combination with mol. modeling and docking, is used to map the small mol. binding site for each class of compds. Taken together, the many constraints provided by these data identify key protein-ligand interactions and allow the shape of the site to be refined to produce a high quality three-dimensional picture of ligand binding, thereby facilitating structure based drug design. Results of biophys. mapping of the adenosine A2A receptor are presented.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3MXnt12nsb0%253D&md5=d7f5c6bf24f9093d823bb41db9867c09
126
Huang, X. P.; Karpiak, J.; Kroeze, W. K.; Zhu, H.; Chen, X.; Moy, S. S.; Saddoris, K. A.; Nikolova, V. D.; Farrell, M. S.; Wang, S. Allosteric Ligands for the Pharmacologically Dark Receptors GPR68 and GPR65 Nature 2015, 527, 477– 483 DOI: 10.1038/nature15699
Google Scholar
126
Allosteric ligands for the pharmacologically dark receptors GPR68 and GPR65
Huang, Xi-Ping; Karpiak, Joel; Kroeze, Wesley K.; Zhu, Hu; Chen, Xin; Moy, Sheryl S.; Saddoris, Kara A.; Nikolova, Viktoriya D.; Farrell, Martilias S.; Wang, Sheng; Mangano, Thomas J.; Deshpande, Deepak A.; Jiang, Alice; Penn, Raymond B.; Jin, Jian; Koller, Beverly H.; Kenakin, Terry; Shoichet, Brian K.; Roth, Bryan L.
Nature (London, United Kingdom) (2015), 527 (7579), 477-483CODEN: NATUAS; ISSN:0028-0836. (Nature Publishing Group)
At least 120 non-olfactory G-protein-coupled receptors in the human genome are 'orphans' for which endogenous ligands are unknown, and many have no selective ligands, hindering the detn. of their biol. functions and clin. relevance. Among these is GPR68, a proton receptor that lacks small mol. modulators for probing its biol. Using yeast-based screens against GPR68, here the authors identify the benzodiazepine drug lorazepam as a non-selective GPR68 pos. allosteric modulator. More than 3000 GPR68 homol. models were refined to recognize lorazepam in a putative allosteric site. Docking 3.1 million mols. predicted new GPR68 modulators, many of which were confirmed in functional assays. One potent GPR68 modulator, ogerin, suppressed recall in fear conditioning in wild-type but not in GPR68-knockout mice. The same approach led to the discovery of allosteric agonists and neg. allosteric modulators for GPR65. Combining phys. and structure-based screening may be broadly useful for ligand discovery for understudied and orphan GPCRs.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2MXhvVWmsrjJ&md5=a23d2d68c06b96cfbe7b53f2b17f3895
127
Tan, Y. S.; Sledz, P.; Lang, S.; Stubbs, C. J.; Spring, D. R.; Abell, C.; Best, R. B. Using Ligand-Mapping Simulations to Design a Ligand Selectively Targeting a Cryptic Surface Pocket of Polo-Like Kinase 1 Angew. Chem., Int. Ed. 2012, 51, 10078– 10081 DOI: 10.1002/anie.201205676
Google Scholar
127
Using Ligand-Mapping Simulations to Design a Ligand Selectively Targeting a Cryptic Surface Pocket of Polo-Like Kinase 1
Tan, Yaw Sing; Sledz, Pawel; Lang, Steffen; Stubbs, Christopher J.; Spring, David R.; Abell, Chris; Best, Robert B.
Angewandte Chemie, International Edition (2012), 51 (40), 10078-10081, S10078/1-S10078/15CODEN: ACIEF5; ISSN:1433-7851. (Wiley-VCH Verlag GmbH & Co. KGaA)
The treatment of protein flexibility is a major challenge in structure-based drug design (SBDD), since proteins are dynamic and commonly undergo conformational changes during ligand binding. Consequently, binding sites may not be apparent in exptl. structures of the unliganded form of a protein. The present work focuses on the polo-box domain (PBD) of polo-like kinase 1 (Plk1), a serine/threonine kinase that is overexpressed in a wide range of cancers, and represents a known anticancer target due to its crit. role in mitotic progression. The PBD helps det. subcellular localization of Plk1 by binding to serine- or threonine-phosphorylated sequences at a polar phosphopeptide binding site. Recently, a secondary hydrophobic binding site proximal to the primary phosphopeptide binding site in Plk1 has been identified. Structural studies have shown that this secondary pocket can accommodate hydrophobic side-chains of several ligands; however, when ligands are not present, this pocket exhibits a closed conformation. This cryptic pocket therefore presents a classic problem in SBDD targeting of a flexible protein surface. The present study shows that although opening the Plk1 cryptic pocket is highly unfavorable in the absence of ligand, it is possible to identify all of its known ligand-binding modes - as well as a novel mode - by using a modified ligand-mapping technique. The previously unknown binding mode was used to design a new Plk1-binding ligand, and the prediction was validated by solving the crystal structure of the Plk1-ligand complex.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC38Xhtlamtb%252FJ&md5=78c6d0d7c62a491c16c49b0437b33c95
128
Wassman, C. D.; Baronio, R.; Demir, O.; Wallentine, B. D.; Chen, C. K.; Hall, L. V.; Salehi, F.; Lin, D. W.; Chung, B. P.; Hatfield, G. W. Computational Identification of a Transiently Open L1/S3 Pocket for Reactivation of Mutant P53 Nat. Commun. 2013, 4, 1407 DOI: 10.1038/ncomms2361
Google Scholar
128
Computational identification of a transiently open L1/S3 pocket for reactivation of mutant p53
Wassman Christopher D; Baronio Roberta; Demir Ozlem; Wallentine Brad D; Chen Chiung-Kuang; Hall Linda V; Salehi Faezeh; Lin Da-Wei; Chung Benjamin P; Hatfield G Wesley; Richard Chamberlin A; Luecke Hartmut; Lathrop Richard H; Kaiser Peter; Amaro Rommie E
Nature communications (2013), 4 (), 1407 ISSN:.
The tumour suppressor p53 is the most frequently mutated gene in human cancer. Reactivation of mutant p53 by small molecules is an exciting potential cancer therapy. Although several compounds restore wild-type function to mutant p53, their binding sites and mechanisms of action are elusive. Here computational methods identify a transiently open binding pocket between loop L1 and sheet S3 of the p53 core domain. Mutation of residue Cys124, located at the centre of the pocket, abolishes p53 reactivation of mutant R175H by PRIMA-1, a known reactivation compound. Ensemble-based virtual screening against this newly revealed pocket selects stictic acid as a potential p53 reactivation compound. In human osteosarcoma cells, stictic acid exhibits dose-dependent reactivation of p21 expression for mutant R175H more strongly than does PRIMA-1. These results indicate the L1/S3 pocket as a target for pharmaceutical reactivation of p53 mutants.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A280%3ADC%252BC3szjsFGhtg%253D%253D&md5=a47e3dbbe25e7aae97dd071d4db25883
129
Guo, D.; Mulder-Krieger, T.; IJzerman, A. P.; Heitman, L. H. Functional Efficacy of Adenosine a(2)a Receptor Agonists Is Positively Correlated to Their Receptor Residence Time Br. J. Pharmacol. 2012, 166, 1846– 1859 DOI: 10.1111/j.1476-5381.2012.01897.x
Google Scholar
129
Functional efficacy of adenosine A2A receptor agonists is positively correlated to their receptor residence time
Guo, Dong; Mulder-Krieger, Thea; IJzerman, Adriaan P.; Heitman, Laura H.
British Journal of Pharmacology (2012), 166 (6), 1846-1859CODEN: BJPCBM; ISSN:1476-5381. (Wiley-Blackwell)
The adenosine A2A receptor belongs to the superfamily of GPCRs and is a promising therapeutic target. Traditionally, the discovery of novel agents for the A2A receptor has been guided by their affinity for the receptor. This parameter is detd. under equil. conditions, largely ignoring the kinetic aspects of the ligand-receptor interaction. The aim of this study was to assess the binding kinetics of A2A receptor agonists and explore a possible relationship with their functional efficacy. We set up, validated and optimized a kinetic radioligand binding assay (a so-called competition assocn. assay) at the A2A receptor from which the binding kinetics of unlabeled ligands were detd. Subsequently, functional efficacies of A2A receptor agonists were detd. in two different assays: a novel label-free impedance-based assay and a more traditional cAMP detn. A simplified competition assocn. assay yielded an accurate detn. of the assocn. and dissocn. rates of unlabeled A2A receptor ligands at their receptor. A correlation was obsd. between the receptor residence time of A2A receptor agonists and their intrinsic efficacies in both functional assays. The affinity of A2A receptor agonists was not correlated to their functional efficacy. This study indicates that the mol. basis of different agonist efficacies at the A2A receptor lies within their different residence times at this receptor.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC38XhtVOku7bL&md5=318c22c4a852bc14cb0fac5915ae7e90
130
Dror, R. O.; Pan, A. C.; Arlow, D. H.; Borhani, D. W.; Maragakis, P.; Shan, Y.; Xu, H.; Shaw, D. E. Pathway and Mechanism of Drug Binding to G-Protein-Coupled Receptors Proc. Natl. Acad. Sci. U. S. A. 2011, 108, 13118– 13123 DOI: 10.1073/pnas.1104614108
Google Scholar
130
Pathway and mechanism of drug binding to G-protein-coupled receptors
Dror, Ron O.; Pan, Albert C.; Arlow, Daniel H.; Borhani, David W.; Maragakis, Paul; Shan, Yibing; Xu, Huafeng; Shaw, David E.
Proceedings of the National Academy of Sciences of the United States of America (2011), 108 (32), 13118-13123, S13118/1-S13118/8CODEN: PNASA6; ISSN:0027-8424. (National Academy of Sciences)
How drugs bind to their receptors-from initial assocn., through drug entry into the binding pocket, to adoption of the final bound conformation, or "pose"-has remained unknown, even for G-protein-coupled receptor modulators, which constitute 1/3 of all marketed drugs. Here, the authors captured this pharmaceutically crit. process in at. detail using the 1st unbiased mol. dynamics simulations in which drug mols. spontaneously assoc. with G-protein-coupled receptors to achieve final poses matching those detd. crystallog. The authors found that several beta blockers and a beta agonist all traversed the same well-defined, dominant pathway as they bound to the β1- and β2-adrenergic receptors, initially making contact with a vestibule on each receptor's extracellular surface. Surprisingly, assocn. with this vestibule, at a distance of 15 Å from the binding pocket, often presented the largest energetic barrier to binding, despite the fact that subsequent entry into the binding pocket required the receptor to deform and the drug to squeeze through a narrow passage. The early barrier appeared to reflect the substantial dehydration that takes place as the drug assocs. with the vestibule. The at.-level description of the binding process suggests opportunities for allosteric modulation and provides a structural foundation for future optimization of drug-receptor binding and unbinding rates.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3MXhtVKit7bE&md5=9cfa8673217931cacd586321309fa72e
131
Tautermann, C. S.; Kiechle, T.; Seeliger, D.; Diehl, S.; Wex, E.; Banholzer, R.; Gantner, F.; Pieper, M. P.; Casarosa, P. Molecular Basis for the Long Duration of Action and Kinetic Selectivity of Tiotropium for the Muscarinic M3 Receptor J. Med. Chem. 2013, 56, 8746– 8756 DOI: 10.1021/jm401219y
Google Scholar
131
Molecular Basis for the Long Duration of Action and Kinetic Selectivity of Tiotropium for the Muscarinic M3 Receptor
Tautermann, Christofer S.; Kiechle, Tobias; Seeliger, Daniel; Diehl, Sonja; Wex, Eva; Banholzer, Rolf; Gantner, Florian; Pieper, Michael P.; Casarosa, Paola
Journal of Medicinal Chemistry (2013), 56 (21), 8746-8756CODEN: JMCMAR; ISSN:0022-2623. (American Chemical Society)
Antagonizing the human M3 muscarinic receptor (hM3R) over a long time is a key feature of modern bronchodilating COPD drugs aiming at symptom relief. The long duration of action of the antimuscarinic drug tiotropium and its kinetic subtype selectivity over hM2R are investigated by kinetic mapping of the binding site and the exit channel of hM3R. Hence, dissocn. expts. have been performed with a set of mol. matched pairs of tiotropium on a large variety of mutated variants of hM3R. The exceedingly long half-life of tiotropium (of more than 24 h) is attributed to interactions in the binding site; particularly a highly directed interaction of the ligands' hydroxy group with an asparagine (N5086.52) prevents rapid dissocn. via a snap-lock mechanism. The kinetic selectivity over hM2R, however, is caused by differences in the electrostatics and in the flexibility of the extracellular vestibule. Extensive mol. dynamics simulations (several microseconds) support exptl. results.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3sXhsFKksrvF&md5=2dd0ce91408c70ba97cf99cdab16b8b2
132
Bhattacharya, S.; Vaidehi, N. Computational Mapping of the Conformational Transitions in Agonist Selective Pathways of a G-Protein Coupled Receptor J. Am. Chem. Soc. 2010, 132, 5205– 5214 DOI: 10.1021/ja910700y
Google Scholar
132
Computational Mapping of the Conformational Transitions in Agonist Selective Pathways of a G-Protein Coupled Receptor
Bhattacharya, Supriyo; Vaidehi, Nagarajan
Journal of the American Chemical Society (2010), 132 (14), 5205-5214CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)
The active state conformation of a G-protein coupled receptor (GPCR) is influenced by the chem. structure and the efficacy of the bound ligand. Insight into the active state conformation as well as the activation pathway for ligands with different efficacies is crit. in designing functionally specific drugs for GPCRs. Starting from the crystal structure of the β2-adrenergic receptor, we have used coarse grain computational methods to understand the modulation of the potential energy landscape of the receptor by two full agonists, two partial agonists, and an inverse agonist. Our coarse grain method involves a systematic conformational spanning of the receptor transmembrane helixes followed by an energy minimization and ligand redocking in each sampled conformation. We have derived the activation pathways for several agonists and partial agonists, using a Monte Carlo algorithm, and these are in agreement with fluorescence spectroscopy measurements. The calcd. pathways for the full agonists start with an energy downhill step leading to a stable intermediate followed by a barrier crossing leading to the active state. We find that the barrier crossing involves breaking of an interhelical hydrogen bond between helix5 and helix6, and polarization of the binding site residues by water facilitates the barrier crossing. The uphill step in the partial agonist salbutamol induced activation is distinct from full agonist norepinephrine, and originates from steric hindrance with the arom. residues on helix6. Virtual ligand screening with the salbutamol-stabilized conformation shows enrichment of noncatechol agonists over the norepinephrine-stabilized conformation. Our computational method provides an unprecedented opportunity to derive hypotheses for expts. and also understand activation mechanisms in GPCRs.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3cXjtlahsr8%253D&md5=f52bcdf1a8f3ac6bbc6ed40fa0e6218c
133
Bahar, I.; Lezon, T. R.; Bakan, A.; Shrivastava, I. H. Normal Mode Analysis of Biomolecular Structures: Functional Mechanisms of Membrane Proteins Chem. Rev. 2010, 110, 1463– 1497 DOI: 10.1021/cr900095e
Google Scholar
133
Normal Mode Analysis of Biomolecular Structures: Functional Mechanisms of Membrane Proteins
Bahar, Ivet; Lezon, Timothy R.; Bakan, Ahmet; Shrivastava, Indira H.
Chemical Reviews (Washington, DC, United States) (2010), 110 (3), 1463-1497CODEN: CHREAY; ISSN:0009-2665. (American Chemical Society)
A review. Structural dynamics and function of membrane proteins are discussed in relation to principal component anal. of exptl. resolved conformations, normal mode anal. and elastic network models.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD1MXhtF2lurjI&md5=affd85778c800cb4582a142a268d2ec4
134
Yang, L.; Yang, D.; de Graaf, C.; Moeller, A.; West, G. M.; Dharmarajan, V.; Wang, C.; Siu, F. Y.; Song, G.; Reedtz-Runge, S. Conformational States of the Full-Length Glucagon Receptor Nat. Commun. 2015, 6, 7859 DOI: 10.1038/ncomms8859
Google Scholar
134
Conformational states of the full-length glucagon receptor
Yang, Linlin; Yang, Dehua; de Graaf, Chris; Moeller, Arne; West, Graham M.; Dharmarajan, Venkatasubramanian; Wang, Chong; Siu, Fai Y.; Song, Gaojie; Reedtz-Runge, Steffen; Pascal, Bruce D.; Wu, Beili; Potter, Clinton S.; Zhou, Hu; Griffin, Patrick R.; Carragher, Bridget; Yang, Huaiyu; Wang, Ming-Wei; Stevens, Raymond C.; Jiang, Hualiang
Nature Communications (2015), 6 (), 7859CODEN: NCAOBW; ISSN:2041-1723. (Nature Publishing Group)
Class B G protein-coupled receptors are composed of an extracellular domain (ECD) and a seven-transmembrane (7TM) domain, and their signalling is regulated by peptide hormones. Using a hybrid structural biol. approach together with the ECD and 7TM domain crystal structures of the glucagon receptor (GCGR), we examine the relationship between full-length receptor conformation and peptide ligand binding. Mol. dynamics (MD) and disulfide crosslinking studies suggest that apo-GCGR can adopt both an open and closed conformation assocd. with extensive contacts between the ECD and 7TM domain. The electron microscopy (EM) map of the full-length GCGR shows how a monoclonal antibody stabilizes the ECD and 7TM domain in an elongated conformation. Hydrogen/deuterium exchange (HDX) studies and MD simulations indicate that an open conformation is also stabilized by peptide ligand binding. The combined studies reveal the open/closed states of GCGR and suggest that glucagon binds to GCGR by a conformational selection mechanism.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2MXhtlWgsr3K&md5=6041fe71292ec47d535d7e1ed42de965
135
Floquet, N.; M’Kadmi, C.; Perahia, D.; Gagne, D.; Berge, G.; Marie, J.; Baneres, J. L.; Galleyrand, J. C.; Fehrentz, J. A.; Martinez, J. Activation of the Ghrelin Receptor Is Described by a Privileged Collective Motion: A Model for Constitutive and Agonist-Induced Activation of a Sub-Class a G-Protein Coupled Receptor (GPCR) J. Mol. Biol. 2010, 395, 769– 784 DOI: 10.1016/j.jmb.2009.09.051
Google Scholar
There is no corresponding record for this reference.
136
LeVine, M. V.; Weinstein, H. NbIT--a New Information Theory-Based Analysis of Allosteric Mechanisms Reveals Residues That Underlie Function in the Leucine Transporter LeuT PLoS Comput. Biol. 2014, 10, e1003603 DOI: 10.1371/journal.pcbi.1003603
Google Scholar
There is no corresponding record for this reference.
137
Kong, Y.; Karplus, M. The Signaling Pathway of Rhodopsin Structure 2007, 15, 611– 623 DOI: 10.1016/j.str.2007.04.002
Google Scholar
137
The Signaling Pathway of Rhodopsin
Kong, Yifei; Karplus, Martin
Structure (Cambridge, MA, United States) (2007), 15 (5), 611-623CODEN: STRUE6; ISSN:0969-2126. (Cell Press)
The signal-transduction mechanism of rhodopsin was studied by mol. dynamics (MD) simulations of the high-resoln., inactive structure in an explicit membrane environment. The simulations were employed to calc. equal-time correlations of the fluctuating interaction energy of residue pairs. The resulting interaction-correlation matrix was used to det. a network that couples retinal to the cytoplasmic interface, where transducin binds. Two highly conserved motifs, D(E)RY and NPxxY, were found to have strong interaction correlation with retinal. MD simulations with restraints on each transmembrane helix indicated that the major signal-transduction pathway involves the interdigitating side chains of helixes VI and VII. The functional roles of specific residues were elucidated by the calcd. effect of retinal isomerization from 11-cis to all-trans on the residue-residue interaction pattern. It is suggested that Glu134 may act as a "signal amplifier" and that Asp83 may introduce a threshold to prevent background noise from activating rhodopsin.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2sXlt1aitbY%253D&md5=a9ca5265e9f08145f9b4583e94b41a56
138
McClendon, C. L.; Friedland, G.; Mobley, D. L.; Amirkhani, H.; Jacobson, M. P. Quantifying Correlations between Allosteric Sites in Thermodynamic Ensembles J. Chem. Theory Comput. 2009, 5, 2486– 2502 DOI: 10.1021/ct9001812
Google Scholar
138
Quantifying Correlations Between Allosteric Sites in Thermodynamic Ensembles
McClendon, Christopher L.; Friedland, Gregory; Mobley, David L.; Amirkhani, Homeira; Jacobson, Matthew P.
Journal of Chemical Theory and Computation (2009), 5 (9), 2486-2502CODEN: JCTCCE; ISSN:1549-9618. (American Chemical Society)
Allostery describes altered protein function at one site due to a perturbation at another site. One mechanism of allostery involves correlated motions, which can occur even in the absence of substantial conformational change. We present a novel method, "MutInf", to identify statistically significant correlated motions from equil. mol. dynamics simulations. Our approach analyzes both backbone and side chain motions using internal coordinates to account for the gear-like twists that can take place even in the absence of the large conformational changes typical of traditional allosteric proteins. We quantify correlated motions using a mutual information metric, which we extend to incorporate data from multiple short simulations and to filter out correlations that are not statistically significant. Applying our approach to uncover mechanisms of cooperative small mol. binding in human interleukin-2, we identify clusters of correlated residues from 50 ns of mol. dynamics simulations. Interestingly, two of the clusters with the strongest correlations highlight known cooperative small-mol. binding sites and show substantial correlations between these sites. These cooperative binding sites on interleukin-2 are correlated not only through the hydrophobic core of the protein but also through a dynamic polar network of hydrogen bonding and electrostatic interactions. Since this approach identifies correlated conformations in an unbiased, statistically robust manner, it should be a useful tool for finding novel or "orphan" allosteric sites in proteins of biol. and therapeutic importance.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD1MXpslahsrc%253D&md5=158a76d26856825d4f19c8515f40ffc4
139
Dror, R. O.; Jensen, M. O.; Borhani, D. W.; Shaw, D. E. Exploring Atomic Resolution Physiology on a Femtosecond to Millisecond Timescale Using Molecular Dynamics Simulations J. Gen. Physiol. 2010, 135, 555– 562 DOI: 10.1085/jgp.200910373
Google Scholar
139
Exploring atomic resolution physiology on a femtosecond to millisecond timescale using molecular dynamics simulations
Dror, Ron O.; Jensen, Morten Oe.; Borhani, David W.; Shaw, David E.
Journal of General Physiology (2010), 135 (6), 555-562CODEN: JGPLAD; ISSN:0022-1295. (Rockefeller University Press)
A review. This study deals with the mechanistic insights that physiologists might garner by complementing expts. with atomistic mol. dynamics (MD) simulations. It discusses the strengths and limitations of MD as a tool for physiologists. MD simulations are important among physiologists because these allow access to a spatiotemporal domain that is difficult to probe exptl. Simulations can be particularly valuable for membrane proteins, for which exptl. characterization of structural dynamics tends to be challenging.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3cXosFensr8%253D&md5=75e55def06d3831daab98511452be286
140
Hertig, S.; Latorraca, N. R.; Dror, R. O. Revealing Atomic-Level Mechanisms of Protein Allostery with Molecular Dynamics Simulations PLoS Comput. Biol. 2016, 12, e1004746 DOI: 10.1371/journal.pcbi.1004746
Google Scholar
140
Revealing atomic-level mechanisms of protein allostery with molecular dynamics simulations
Hertig, Samuel; Latorraca, Naomi R.; Dror, Ron O.
PLoS Computational Biology (2016), 12 (6), e1004746/1-e1004746/16CODEN: PCBLBG; ISSN:1553-7358. (Public Library of Science)
Mol. dynamics (MD) simulations have become a powerful and popular method for the study of protein allostery, the widespread phenomenon in which a stimulus at one site on a protein influences the properties of another site on the protein. By capturing the motions of a protein's constituent atoms, simulations can enable the discovery of allosteric binding sites and the detn. of the mechanistic basis for allostery. These results can provide a foundation for applications including rational drug design and protein engineering. Here, we provide an introduction to the investigation of protein allostery using mol. dynamics simulation. We emphasize the importance of designing simulations that include appropriate perturbations to the mol. system, such as the addn. or removal of ligands or the application of mech. force. We also demonstrate how the bidirectional nature of allostery- the fact that the two sites involved influence one another in a sym. manner- can facilitate such investigations. Through a series of case studies, we illustrate how these concepts have been used to reveal the structural basis for allostery in several proteins and protein complexes of biol. and pharmaceutical interest.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC28Xhslyit7nI&md5=40178de113d54ac2c453d372e2dd5bfb
141
Van Eps, N.; Preininger, A. M.; Alexander, N.; Kaya, A. I.; Meier, S.; Meiler, J.; Hamm, H. E.; Hubbell, W. L. Interaction of a G Protein with an Activated Receptor Opens the Interdomain Interface in the Alpha Subunit Proc. Natl. Acad. Sci. U. S. A. 2011, 108, 9420– 9424 DOI: 10.1073/pnas.1105810108
Google Scholar
There is no corresponding record for this reference.
142
Preininger, A. M.; Meiler, J.; Hamm, H. E. Conformational Flexibility and Structural Dynamics in GPCR-Mediated G Protein Activation: A Perspective J. Mol. Biol. 2013, 425, 2288– 2298 DOI: 10.1016/j.jmb.2013.04.011
Google Scholar
142
Conformational flexibility and structural dynamics in GPCR-mediated G protein activation: A perspective
Preininger, Anita M.; Meiler, Jens; Hamm, Heidi E.
Journal of Molecular Biology (2013), 425 (13), 2288-2298CODEN: JMOBAK; ISSN:0022-2836. (Elsevier Ltd.)
A review. The structure and dynamics of G proteins and their cognate receptors, both alone and in complex, are becoming increasingly accessible to exptl. techniques. Understanding the conformational changes and timelines that govern these changes can lead to new insights into the processes of ligand binding and assocd. G protein activation. Exptl. systems may involve the use of, or otherwise stabilize, non-native environments. This can complicate the understanding of structural and dynamic features of processes such as the ionic lock, tryptophan toggle, and G protein flexibility. While elements in the receptor's transmembrane helixes and the C-terminal α5 helix of Gα undergo well-defined structural changes, regions subject to conformational flexibility may be important in fine-tuning the interactions between activated receptors and G proteins. The pairing of computational and exptl. approaches will continue to provide powerful tools to probe the conformation and dynamics of receptor-mediated G protein activation.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3sXnt1aht7g%253D&md5=7af4574924a9a9d6e7b01311ba21d6be
143
Dror, R. O.; Mildorf, T. J.; Hilger, D.; Manglik, A.; Borhani, D. W.; Arlow, D. H.; Philippsen, A.; Villanueva, N.; Yang, Z.; Lerch, M. T. Signal Transduction. Structural Basis for Nucleotide Exchange in Heterotrimeric G Proteins Science 2015, 348, 1361– 1365 DOI: 10.1126/science.aaa5264
Google Scholar
143
Structural basis for nucleotide exchange in heterotrimeric G proteins
Dror, Ron O.; Mildorf, Thomas J.; Hilger, Daniel; Manglik, Aashish; Borhani, David W.; Arlow, Daniel H.; Philippsen, Ansgar; Villanueva, Nicolas; Yang, Zhongyu; Lerch, Michael T.; Hubbell, Wayne L.; Kobilka, Brian K.; Sunahara, Roger K.; Shaw, David E.
Science (Washington, DC, United States) (2015), 348 (6241), 1361-1365CODEN: SCIEAS; ISSN:0036-8075. (American Association for the Advancement of Science)
G protein-coupled receptors (GPCRs) relay diverse extracellular signals into cells by catalyzing nucleotide release from heterotrimeric G proteins, but the mechanism underlying this quintessential mol. signaling event has remained unclear. Here, the authors used at.-level mol. dynamics simulations to elucidate the nucleotide-release mechanism. The authors found that G protein α subunit Ras and helical domains, previously obsd. to sep. widely upon receptor binding to expose the nucleotide-binding site, sepd. spontaneously and frequently even in the absence of a receptor. Domain sepn. was necessary but not sufficient for rapid nucleotide release. Rather, receptors catalyzed nucleotide release by favoring an internal structural rearrangement of the Ras domain that weakened its nucleotide affinity. The authors used double electron-electron resonance (DEER) spectroscopy and protein engineering to confirm predictions of their computationally detd. mechanism.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2MXpvFansL0%253D&md5=8cf328e9faff566ca5fe0087ea9a6289
144
Alexander, N. S.; Preininger, A. M.; Kaya, A. I.; Stein, R. A.; Hamm, H. E.; Meiler, J. Energetic Analysis of the Rhodopsin-G-Protein Complex Links the Alpha5 Helix to Gdp Release Nat. Struct. Mol. Biol. 2014, 21, 56– 63 DOI: 10.1038/nsmb.2705
Google Scholar
144
Energetic analysis of the rhodopsin-G-protein complex links the α5 helix to GDP release
Alexander, Nathan S.; Preininger, Anita M.; Kaya, Ali I.; Stein, Richard A.; Hamm, Heidi E.; Meiler, Jens
Nature Structural & Molecular Biology (2014), 21 (1), 56-63CODEN: NSMBCU; ISSN:1545-9993. (Nature Publishing Group)
We present a model of interaction of Gi protein with the activated receptor (R*) rhodopsin, which pinpoints energetic contributions to activation and reconciles the β2 adrenergic receptor-Gs crystal structure with new and previously published exptl. data. In silico anal. demonstrated energetic changes when the Gα C-terminal helix (α5) interacts with the R* cytoplasmic pocket, thus leading to displacement of the helical domain and GDP release. The model features a less dramatic domain opening compared with the crystal structure. The α5 helix undergoes a 63° rotation, accompanied by a 5.7-Å translation, that reorganizes interfaces between α5 and α1 helixes and between α5 and β6-α5. Changes in the β6-α5 loop displace αG. All of these movements lead to opening of the GDP-binding pocket. The model creates a roadmap for exptl. studies of receptor-mediated G-protein activation.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3sXhvVGqsrnI&md5=20965168b29a0807460e6f6f8e3ed4b6
145
Boguth, C. A.; Singh, P.; Huang, C. C.; Tesmer, J. J. Molecular Basis for Activation of G Protein-Coupled Receptor Kinases EMBO J. 2010, 29, 3249– 3259 DOI: 10.1038/emboj.2010.206
Google Scholar
145
Molecular basis for activation of G protein-coupled receptor kinases
Boguth, Cassandra A.; Singh, Puja; Huang, Chih-chin; Tesmer, John J. G.
EMBO Journal (2010), 29 (19), 3249-3259CODEN: EMJODG; ISSN:0261-4189. (Nature Publishing Group)
G protein-coupled receptor (GPCR) kinases (GRKs) selectively recognize and are allosterically regulated by activated GPCRs, but the mol. basis for this interaction is not understood. Herein, we report crystal structures of GRK6 in which regions known to be crit. for receptor phosphorylation have coalesced to stabilize the kinase domain in a closed state and to form a likely receptor docking site. The crux of this docking site is an extended N-terminal helix that bridges the large and small lobes of the kinase domain and lies adjacent to a basic surface of the protein proposed to bind anionic phospholipids. Mutation of exposed, hydrophobic residues in the N-terminal helix selectively inhibits receptor, but not peptide phosphorylation, suggesting that these residues interact directly with GPCRs. Our structural and biochem. results thus provide an explanation for how receptor recognition, phospholipid binding, and kinase activation are intimately coupled in GRKs.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3cXhtVGgtb%252FE&md5=15d6df48fad121f18286e4ac1db6edef
146
Scott, J. D.; Pawson, T. Cell Signaling in Space and Time: Where Proteins Come Together and When They’re Apart Science 2009, 326, 1220– 1224 DOI: 10.1126/science.1175668
Google Scholar
146
Cell signaling in space and time: Where proteins come together and when they're apart
Scott, John D.; Pawson, Tony
Science (Washington, DC, United States) (2009), 326 (5957), 1220-1224CODEN: SCIEAS; ISSN:0036-8075. (American Association for the Advancement of Science)
A review. Signal transduction can be defined as the coordinated relay of messages derived from extracellular cues to intracellular effectors. More simply put, information received on the cell surface is processed across the plasma membrane and transmitted to intracellular targets. This requires that the activators, effectors, enzymes, and substrates that respond to cellular signals come together when they need to.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD1MXhsVKhur%252FO&md5=e795882587a7cfd077fa5df18e233784
147
Neves, S. R.; Tsokas, P.; Sarkar, A.; Grace, E. A.; Rangamani, P.; Taubenfeld, S. M.; Alberini, C. M.; Schaff, J. C.; Blitzer, R. D.; Moraru, I. I. Cell Shape and Negative Links in Regulatory Motifs Together Control Spatial Information Flow in Signaling Networks Cell 2008, 133, 666– 680 DOI: 10.1016/j.cell.2008.04.025
Google Scholar
There is no corresponding record for this reference.
148
Inda, C.; Dos Santos Claro, P. A.; Bonfiglio, J. J.; Senin, S. A.; Maccarrone, G.; Turck, C. W.; Silberstein, S. Different cAMP Sources Are Critically Involved in G Protein-Coupled Receptor CRHR1 Signaling J. Cell Biol. 2016, 214, 181 DOI: 10.1083/jcb.201512075
Google Scholar
There is no corresponding record for this reference.
149
Vilardaga, J. P.; Jean-Alphonse, F. G.; Gardella, T. J. Endosomal Generation of cAMP in GPCR Signaling Nat. Chem. Biol. 2014, 10, 700– 706 DOI: 10.1038/nchembio.1611
Google Scholar
149
Endosomal generation of cAMP in GPCR signaling
Vilardaga, Jean-Pierre; Jean-Alphonse, Frederic G.; Gardella, Thomas J.
Nature Chemical Biology (2014), 10 (9), 700-706CODEN: NCBABT; ISSN:1552-4450. (Nature Publishing Group)
A review. It has been widely assumed that the prodn. of the ubiquitous second messenger cAMP, which is mediated by cell surface G protein-coupled receptors (GPCRs), and its termination take place exclusively at the plasma membrane. Recent studies reveal that diverse GPCRs do not always follow this conventional paradigm. In the new model, GPCRs mediate G-protein signaling not only from the plasma membrane but also from endosomal membranes. This model proposes that following ligand binding and activation, cell surface GPCRs internalize and redistribute into early endosomes, where trimeric G protein signaling can be maintained for an extended period of time. This Perspective discusses the mol. and cellular mechanistic subtleties as well as the physiol. consequences of this unexpected process, which is considerably changing how we think about GPCR signaling and regulation and how we study drugs that target this receptor family.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2cXhtlOlur%252FE&md5=437e81bee0c5fc175c4b57b75fe82a99
150
Irannejad, R.; Tomshine, J. C.; Tomshine, J. R.; Chevalier, M.; Mahoney, J. P.; Steyaert, J.; Rasmussen, S. G.; Sunahara, R. K.; El-Samad, H.; Huang, B. Conformational Biosensors Reveal GPCR Signalling from Endosomes Nature 2013, 495, 534– 538 DOI: 10.1038/nature12000
Google Scholar
150
Conformational biosensors reveal GPCR signalling from endosomes
Irannejad, Roshanak; Tomshine, Jin C.; Tomshine, Jon R.; Chevalier, Michael; Mahoney, Jacob P.; Steyaert, Jan; Rasmussen, Soren G. F.; Sunahara, Roger K.; El-Samad, Hana; Huang, Bo; von Zastrow, Mark
Nature (London, United Kingdom) (2013), 495 (7442), 534-538CODEN: NATUAS; ISSN:0028-0836. (Nature Publishing Group)
A long-held tenet of mol. pharmacol. is that canonical signal transduction mediated by G-protein-coupled receptor (GPCR) coupling to heterotrimeric G proteins is confined to the plasma membrane. Evidence supporting this traditional view is based on anal. methods that provide limited or no subcellular resoln. It has been subsequently proposed that signaling by internalized GPCRs is restricted to G-protein-independent mechanisms such as scaffolding by arrestins, or GPCR activation elicits a discrete form of persistent G protein signaling, or that internalized GPCRs can indeed contribute to the acute G-protein-mediated response. Evidence supporting these various latter hypotheses is indirect or subject to alternative interpretation, and it remains unknown if endosome-localized GPCRs are even present in an active form. Here we describe the application of conformation-specific single-domain antibodies (nanobodies) to directly probe activation of the β2-adrenoceptor, a prototypical GPCR, and its cognate G protein, Gs, in living mammalian cells. We show that the adrenergic agonist isoprenaline promotes receptor and G protein activation in the plasma membrane as expected, but also in the early endosome membrane, and that internalized receptors contribute to the overall cellular cAMP response within several minutes after agonist application. These findings provide direct support for the hypothesis that canonical GPCR signaling occurs from endosomes as well as the plasma membrane, and suggest a versatile strategy for probing dynamic conformational change in vivo.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3sXkslWqsb0%253D&md5=49b3088bac0be0d9eff00290875e61f2
151
Tsvetanova, N. G.; von Zastrow, M. Spatial Encoding of cyclic AMP Signaling Specificity by GPCR Endocytosis Nat. Chem. Biol. 2014, 10, 1061– 1065 DOI: 10.1038/nchembio.1665
Google Scholar
151
Spatial encoding of cyclic AMP signaling specificity by GPCR endocytosis
Tsvetanova, Nikoleta G.; von Zastrow, Mark
Nature Chemical Biology (2014), 10 (12), 1061-1065CODEN: NCBABT; ISSN:1552-4450. (Nature Publishing Group)
G protein-coupled receptors (GPCRs) are well known to signal via cAMP prodn. at the plasma membrane, but it is now clear that various GPCRs also signal after internalization. Apart from its temporal impact through prolonging the cellular response, we wondered whether the endosome-initiated signal encodes any discrete spatial information. Using the β2-adrenoceptor (β2-AR) as a model, we show that endocytosis is required for the full repertoire of downstream cAMP-dependent transcriptional control. Next, we describe an orthogonal optogenetic approach to definitively establish that the location of cAMP prodn. is indeed the crit. variable detg. the transcriptional response. Finally, our results suggest that this spatial encoding scheme helps cells functionally discriminate chem. distinct β2-AR ligands according to differences in their ability to promote receptor endocytosis. These findings reveal a discrete principle for achieving cellular signaling specificity based on endosome-mediated spatial encoding of intracellular second messenger prodn. and 'location-aware' downstream transcriptional control.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2cXhvVGiurbE&md5=3e4fd1a40b17b396b294f97594c2402b
152
Calebiro, D.; Rieken, F.; Wagner, J.; Sungkaworn, T.; Zabel, U.; Borzi, A.; Cocucci, E.; Zurn, A.; Lohse, M. J. Single-Molecule Analysis of Fluorescently Labeled G-Protein-Coupled Receptors Reveals Complexes with Distinct Dynamics and Organization Proc. Natl. Acad. Sci. U. S. A. 2013, 110, 743– 748 DOI: 10.1073/pnas.1205798110
Google Scholar
152
Single-molecule analysis of fluorescently labeled G-protein-coupled receptors reveals complexes with distinct dynamics and organization
Calebiro, Davide; Rieken, Finn; Wagner, Julia; Sungkaworn, Titiwat; Zabel, Ulrike; Borzi, Alfio; Cocucci, Emanuele; Zuern, Alexander; Lohse, Martin J.
Proceedings of the National Academy of Sciences of the United States of America (2013), 110 (2), 743-748, S743/1-S743/13CODEN: PNASA6; ISSN:0027-8424. (National Academy of Sciences)
G protein-coupled receptors (GPCRs) constitute the largest family of receptors and major pharmacol. targets. Whereas many GPCRs have been shown to form di-/oligomers, the size and stability of such complexes under physiol. conditions are largely unknown. Here, we used direct receptor labeling with SNAP-tags and total internal reflection fluorescence microscopy (TIRF-M) to dynamically monitor single receptors on intact cells and thus compare the spatial arrangement, mobility, and supramol. organization of three prototypical GPCRs: the β1-adrenergic receptor (β1AR), the β2-adrenergic receptor (β2AR), and the γ-aminobutyric acid (GABAB) receptor. These GPCRs showed very different degrees of di-/oligomerization, lowest for β1ARs (monomers/dimers) and highest for GABAB receptors (prevalently dimers/tetramers of heterodimers). The size of receptor complexes increased with receptor d. as a result of transient receptor-receptor interactions. Whereas β1-/β2ARs were apparently freely diffusing on the cell surface, GABAB receptors were prevalently organized into ordered arrays, via interaction with the actin cytoskeleton. Agonist stimulation did not alter receptor di-/oligomerization, but increased the mobility of GABAB receptor complexes. These data provide a spatiotemporal characterization of β1-/β2ARs and GABAB receptors at single-mol. resoln. The results suggest that GPCRs are present on the cell surface in a dynamic equil., with const. formation and dissocn. of new receptor complexes that can be targeted, in a ligand-regulated manner, to different cell-surface microdomains.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3sXhtFOgsrY%253D&md5=2cdbfaa492ff309c15bb0cc6ce0668d1
153
Pediani, J. D.; Ward, R. J.; Godin, A. G.; Marsango, S.; Milligan, G. Dynamic Regulation of Quaternary Organization of the M1Muscarinic Receptor by Subtype-Selective Antagonist Drugs J. Biol. Chem. 2016, 291, 13132– 13146 DOI: 10.1074/jbc.M115.712562
Google Scholar
There is no corresponding record for this reference.
154
Shan, J.; Khelashvili, G.; Mondal, S.; Mehler, E. L.; Weinstein, H. Ligand-Dependent Conformations and Dynamics of the Serotonin 5-Ht(2a) Receptor Determine Its Activation and Membrane-Driven Oligomerization Properties PLoS Comput. Biol. 2012, 8, e1002473 DOI: 10.1371/journal.pcbi.1002473
Google Scholar
There is no corresponding record for this reference.
155
Lane, J. R.; Donthamsetti, P.; Shonberg, J.; Draper-Joyce, C. J.; Dentry, S.; Michino, M.; Shi, L.; Lopez, L.; Scammells, P. J.; Capuano, B. A New Mechanism of Allostery in a G Protein-Coupled Receptor Dimer Nat. Chem. Biol. 2014, 10, 745– 752 DOI: 10.1038/nchembio.1593
Google Scholar
155
A new mechanism of allostery in a G protein-coupled receptor dimer
Lane, J. Robert; Donthamsetti, Prashant; Shonberg, Jeremy; Draper-Joyce, Christopher J.; Dentry, Samuel; Michino, Mayako; Shi, Lei; Lopez, Laura; Scammells, Peter J.; Capuano, Ben; Sexton, Patrick M.; Javitch, Jonathan A.; Christopoulos, Arthur
Nature Chemical Biology (2014), 10 (9), 745-752CODEN: NCBABT; ISSN:1552-4450. (Nature Publishing Group)
SB269652 is to our knowledge the first drug-like allosteric modulator of the dopamine D2 receptor (D2R), but it contains structural features assocd. with orthosteric D2R antagonists. Using a functional complementation system to control the identity of individual protomers within a dimeric D2R complex, we converted the pharmacol. of the interaction between SB269652 and dopamine from allosteric to competitive by impairing ligand binding to one of the protomers, indicating that the allostery requires D2R dimers. Addnl. expts. identified a 'bitopic' pose for SB269652 extending from the orthosteric site into a secondary pocket at the extracellular end of the transmembrane (TM) domain, involving TM2 and TM7. Engagement of this secondary pocket was a requirement for the allosteric pharmacol. of SB269652. This suggests a new mechanism whereby a bitopic ligand binds in an extended pose on one G protein-coupled receptor protomer to allosterically modulate the binding of a ligand to the orthosteric site of a second protomer.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2cXhtlahurrL&md5=ececb5fc0e3e9b803807f700dc2c2cad
156
Guo, W.; Shi, L.; Filizola, M.; Weinstein, H.; Javitch, J. A. Crosstalk in G Protein-Coupled Receptors: Changes at the Transmembrane Homodimer Interface Determine Activation Proc. Natl. Acad. Sci. U. S. A. 2005, 102, 17495– 17500 DOI: 10.1073/pnas.0508950102
Google Scholar
156
Crosstalk in G protein-coupled receptors: Changes at the transmembrane homodimer interface determine activation
Guo, Wen; Shi, Lei; Filizola, Marta; Weinstein, Harel; Javitch, Jonathan A.
Proceedings of the National Academy of Sciences of the United States of America (2005), 102 (48), 17495-17500CODEN: PNASA6; ISSN:0027-8424. (National Academy of Sciences)
Functional crosstalk between G protein-coupled receptors in a homo- or heterodimeric assembly likely involves conformational changes at the dimer interface, but the nature of this interface is not yet established, and the dynamic changes have not yet been identified. The authors have mapped the homodimer interface in the dopamine D2 receptor over the entire length of the fourth transmembrane segment (TM4) by crosslinking of substituted cysteines. Their susceptibilities to crosslinking are differentially altered by the presence of agonists and inverse agonists. The TM4 dimer interface in the inverse agonist-bound conformation is consistent with the dimer of the inactive form of rhodopsin modeled with constraints from at. force microscopy. Crosslinking of a different set of cysteines in TM4 was slowed by inverse agonists and accelerated in the presence of agonists; crosslinking of the latter set locks the receptor in an active state. Thus, a conformational change at the TM4 dimer interface is part of the receptor activation mechanism.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2MXhtlSqtb3N&md5=b8a4c0f082244711c12f1d4634c4c888
157
Haga, K.; Kruse, A. C.; Asada, H.; Yurugi-Kobayashi, T.; Shiroishi, M.; Zhang, C.; Weis, W. I.; Okada, T.; Kobilka, B. K.; Haga, T. Structure of the Human M2 Muscarinic Acetylcholine Receptor Bound to an Antagonist Nature 2012, 482, 547– 551 DOI: 10.1038/nature10753
Google Scholar
157
Structure of the human M2 muscarinic acetylcholine receptor bound to an antagonist
Haga, Kazuko; Kruse, Andrew C.; Asada, Hidetsugu; Yurugi-Kobayashi, Takami; Shiroishi, Mitsunori; Zhang, Cheng; Weis, William I.; Okada, Tetsuji; Kobilka, Brian K.; Haga, Tatsuya; Kobayashi, Takuya
Nature (London, United Kingdom) (2012), 482 (7386), 547-551CODEN: NATUAS; ISSN:0028-0836. (Nature Publishing Group)
The X-ray crystal structure of the M2 muscarinic acetylcholine receptor, which is essential for the physiol. control of cardiovascular function, is reported.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC38Xht1ejsro%253D&md5=c33b8d9303d58db7dfdd4c18ec4f597b
158
Vanni, S.; Neri, M.; Tavernelli, I.; Rothlisberger, U. Observation of “Ionic Lock“Formation in Molecular Dynamics Simulations of Wild-Type Beta 1 and Beta 2 Adrenergic Receptors Biochemistry 2009, 48, 4789– 4797 DOI: 10.1021/bi900299f
Google Scholar
There is no corresponding record for this reference.
159
Manglik, A.; Lin, H.; Aryal, D. K.; McCorvy, J. D.; Dengler, D.; Corder, G.; Levit, A.; Kling, R. C.; Bernat, V.; Hubner, H. Structure-Based Discovery of Opioid Analgesics with Reduced Side Effects Nature 2016, 537, 185– 190 DOI: 10.1038/nature19112
Google Scholar
159
Structure-based discovery of opioid analgesics with reduced side effects
Manglik, Aashish; Lin, Henry; Aryal, Dipendra K.; McCorvy, John D.; Dengler, Daniela; Corder, Gregory; Levit, Anat; Kling, Ralf C.; Bernat, Viachaslau; Hubner, Harald; Huang, Xi-Ping; Sassano, Maria F.; Giguere, Patrick M.; Lober, Stefan; Da Duan; Scherrer, Gregory; Kobilka, Brian K.; Gmeiner, Peter; Roth, Bryan L.; Shoichet, Brian K.
Nature (London, United Kingdom) (2016), 537 (7619), 185-190CODEN: NATUAS; ISSN:0028-0836. (Nature Publishing Group)
Morphine is an alkaloid from the opium poppy used to treat pain. The potentially lethal side effects of morphine and related opioids-which include fatal respiratory depression-are thought to be mediated by μ-opioid-receptor (μOR) signalling through the β-arrestin pathway or by actions at other receptors. Conversely, G-protein μOR signalling is thought to confer analgesia. Here we computationally dock over 3 million mols. against the μOR structure and identify new scaffolds unrelated to known opioids. Structure-based optimization yields PZM21-a potent Gi activator with exceptional selectivity for μOR and minimal β-arrestin-2 recruitment. Unlike morphine, PZM21 is more efficacious for the affective component of analgesia vs. the reflexive component and is devoid of both respiratory depression and morphine-like reinforcing activity in mice at equi-analgesic doses. PZM21 thus serves as both a probe to disentangle μOR signalling and a therapeutic lead that is devoid of many of the side effects of current opioids.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC28XhtlKmsbvI&md5=b8bb2d8575dadf4a6dc74d94c26d2c1a

Cited By

ARTICLE SECTIONS

Jump To

This article is cited by 461 publications.

Hung N. Do, Jinan Wang, Yinglong Miao. Deep Learning Dynamic Allostery of G-Protein-Coupled Receptors. JACS Au 2023, 3 (11) , 3165-3180. https://doi.org/10.1021/jacsau.3c00503
Parijat Sarkar, Amitabha Chattopadhyay. Interplay of Cholesterol and Actin in Neurotransmitter GPCR Signaling: Insights from Chronic Cholesterol Depletion Using Statin. ACS Chemical Neuroscience 2023, 14 (20) , 3855-3868. https://doi.org/10.1021/acschemneuro.3c00472
Bo Li, Krystyna Maruszko, Soo-Kyung Kim, Moon Young Yang, Amy-Doan P. Vo, William A. Goddard III. Structure and Molecular Mechanism of Signaling for the Glucagon-like Peptide-1 Receptor Bound to Gs Protein and Exendin-P5 Biased Agonist. Journal of the American Chemical Society 2023, 145 (37) , 20422-20431. https://doi.org/10.1021/jacs.3c05996
So-ong Kim, Sung Gun Kim, Hyenjin Ahn, Jin Yoo, Jyongsik Jang, Tai Hyun Park. Ni-rGO Sensor Combined with Human Olfactory Receptor-Embedded Nanodiscs for Detecting Gas-Phase DMMP as a Simulant of Nerve Agents. ACS Sensors 2023, 8 (8) , 3095-3103. https://doi.org/10.1021/acssensors.3c00744
Shubham Vishnoi, Shayon Bhattacharya, Erica M. Walsh, Grace Ilevbare Okoh, Damien Thompson. Computational Peptide Design Cotargeting Glucagon and Glucagon-like Peptide-1 Receptors. Journal of Chemical Information and Modeling 2023, 63 (15) , 4934-4947. https://doi.org/10.1021/acs.jcim.3c00752
Pedro A. Valiente, Satra Nim, Jisun Kim, Philip M. Kim. Computational Design of Potent and Selective d-Peptide Agonists of the Glucagon-like Peptide-2 Receptor. Journal of Medicinal Chemistry 2023, 66 (15) , 10342-10353. https://doi.org/10.1021/acs.jmedchem.3c00464
Shayma El-Atawneh, Amiram Goldblum. Activity Models of Key GPCR Families in the Central Nervous System: A Tool for Many Purposes. Journal of Chemical Information and Modeling 2023, 63 (11) , 3248-3262. https://doi.org/10.1021/acs.jcim.2c01531
Ruslan Gibadullin, Brian P. Cary, Samuel H. Gellman. Differential Responses of the GLP-1 and GLP-2 Receptors to N-Terminal Modification of a Dual Agonist. Journal of the American Chemical Society 2023, 145 (22) , 12105-12114. https://doi.org/10.1021/jacs.3c01628
Nicholas R. Fragola, Brittany M. Brems, Munmun Mukherjee, Meng Cui, Raymond G. Booth. Conformationally Selective 2-Aminotetralin Ligands Targeting the alpha2A- and alpha2C-Adrenergic Receptors. ACS Chemical Neuroscience 2023, 14 (10) , 1884-1895. https://doi.org/10.1021/acschemneuro.3c00148
Parisa Mollaei, Amir Barati Farimani. Activity Map and Transition Pathways of G Protein-Coupled Receptor Revealed by Machine Learning. Journal of Chemical Information and Modeling 2023, 63 (8) , 2296-2304. https://doi.org/10.1021/acs.jcim.3c00032
Yulong Jin, Pradeep K. Mandal, Juntian Wu, Niklas Böcher, Ivan Huc, Sijbren Otto. (Re-)Directing Oligomerization of a Single Building Block into Two Specific Dynamic Covalent Foldamers through pH. Journal of the American Chemical Society 2023, 145 (5) , 2822-2829. https://doi.org/10.1021/jacs.2c09325
Feng-Jie Wu, Pascal S. Rieder, Layara Akemi Abiko, Philip Rößler, Alvar D. Gossert, Daniel Häussinger, Stephan Grzesiek. Nanobody GPS by PCS: An Efficient New NMR Analysis Method for G Protein Coupled Receptors and Other Large Proteins. Journal of the American Chemical Society 2022, 144 (47) , 21728-21740. https://doi.org/10.1021/jacs.2c09692
Fuhui Zhang, Xin Chen, Jianfang Chen, Yanjiani Xu, Shiqi Li, Yanzhi Guo, Xuemei Pu. Probing Allosteric Regulation Mechanism of W7.35 on Agonist-Induced Activity for μOR by Mutation Simulation. Journal of Chemical Information and Modeling 2022, 62 (21) , 5120-5135. https://doi.org/10.1021/acs.jcim.1c00650
Jianfang Chen, Jiangting Liu, Yuan Yuan, Xin Chen, Fuhui Zhang, Xuemei Pu. Molecular Mechanisms of Diverse Activation Stimulated by Different Biased Agonists for the β2-Adrenergic Receptor. Journal of Chemical Information and Modeling 2022, 62 (21) , 5175-5192. https://doi.org/10.1021/acs.jcim.1c01016
Humanath Poudel, David M. Leitner. Energy Transport in Class B GPCRs: Role of Protein–Water Dynamics and Activation. The Journal of Physical Chemistry B 2022, 126 (42) , 8362-8373. https://doi.org/10.1021/acs.jpcb.2c03960
Mengrong Li, Yiqiong Bao, Ran Xu, Honggui La, Jingjing Guo. Critical Extracellular Ca2+ Dependence of the Binding between PTH1R and a G-Protein Peptide Revealed by MD Simulations. ACS Chemical Neuroscience 2022, 13 (11) , 1666-1674. https://doi.org/10.1021/acschemneuro.2c00176
Wenhua Li, Zhao Ma, Jiwei Chen, Gaopan Dong, Lupei Du, Minyong Li. Discovery of Environment-Sensitive Fluorescent Ligands of β-Adrenergic Receptors for Cell Imaging and NanoBRET Assay. Analytical Chemistry 2022, 94 (19) , 7021-7028. https://doi.org/10.1021/acs.analchem.1c05646
Li Liu, Xander E. Wilcox, Andrew J. Fisher, Stefanie D. Boyd, Jiahe Zhi, Duane D. Winkler, Lee A. Bulla, Jr.. Functional and Structural Analysis of the Toxin-Binding Site of the Cadherin G-Protein-Coupled Receptor, BT-R1, for Cry1A Toxins of Bacillus thuringiensis. Biochemistry 2022, 61 (9) , 752-766. https://doi.org/10.1021/acs.biochem.2c00089
Lucy Kate Ladefoged, Rebekka Koch, Philip C. Biggin, Birgit Schiøtt. Binding and Activation of Serotonergic G-Protein Coupled Receptors by the Multimodal Antidepressant Vortioxetine. ACS Chemical Neuroscience 2022, 13 (8) , 1129-1142. https://doi.org/10.1021/acschemneuro.1c00029
Prakarsh Yadav, Amir Barati Farimani. Activation Pathways of Neurotensin Receptor 1 Elucidated Using Statistical Machine Learning. ACS Chemical Neuroscience 2022, 13 (8) , 1333-1341. https://doi.org/10.1021/acschemneuro.2c00154
Corentin Bedart, Nicolas Renault, Philippe Chavatte, Adeline Porcherie, Abderrahim Lachgar, Monique Capron, Amaury Farce. SINAPs: A Software Tool for Analysis and Visualization of Interaction Networks of Molecular Dynamics Simulations. Journal of Chemical Information and Modeling 2022, 62 (6) , 1425-1436. https://doi.org/10.1021/acs.jcim.1c00854
Alessandro Nicoli, Andreas Dunkel, Toni Giorgino, Chris de Graaf, Antonella Di Pizio. Classification Model for the Second Extracellular Loop of Class A GPCRs. Journal of Chemical Information and Modeling 2022, 62 (3) , 511-522. https://doi.org/10.1021/acs.jcim.1c01056
Soumajit Dutta, Balaji Selvam, Diwakar Shukla. Distinct Binding Mechanisms for Allosteric Sodium Ion in Cannabinoid Receptors. ACS Chemical Neuroscience 2022, 13 (3) , 379-389. https://doi.org/10.1021/acschemneuro.1c00760
Yulei Li, Jie Heng, Demeng Sun, Baochang Zhang, Xin Zhang, Yupeng Zheng, Wei-Wei Shi, Tong-Yue Wang, Jiu-Yi Li, Xiaoou Sun, Xiangyu Liu, Ji-Shen Zheng, Brian K. Kobilka, Lei Liu. Chemical Synthesis of a Full-Length G-Protein-Coupled Receptor β2-Adrenergic Receptor with Defined Modification Patterns at the C-Terminus. Journal of the American Chemical Society 2021, 143 (42) , 17566-17576. https://doi.org/10.1021/jacs.1c07369
Daria B. Kokh, Rebecca C. Wade. G Protein-Coupled Receptor–Ligand Dissociation Rates and Mechanisms from τRAMD Simulations. Journal of Chemical Theory and Computation 2021, 17 (10) , 6610-6623. https://doi.org/10.1021/acs.jctc.1c00641
Humanath Poudel, David M. Leitner. Activation-Induced Reorganization of Energy Transport Networks in the β2 Adrenergic Receptor. The Journal of Physical Chemistry B 2021, 125 (24) , 6522-6531. https://doi.org/10.1021/acs.jpcb.1c03412
Shun Yokoi, Ayori Mitsutake. Molecular Dynamics Simulations for the Determination of the Characteristic Structural Differences between Inactive and Active States of Wild Type and Mutants of the Orexin2 Receptor. The Journal of Physical Chemistry B 2021, 125 (17) , 4286-4298. https://doi.org/10.1021/acs.jpcb.0c10985
Joel Paprocki, Gabriel Biener, Michael Stoneman, Valerică Raicu. In-Cell Detection of Conformational Substates of a G Protein-Coupled Receptor Quaternary Structure: Modulation of Substate Probability by Cognate Ligand Binding. The Journal of Physical Chemistry B 2020, 124 (45) , 10062-10076. https://doi.org/10.1021/acs.jpcb.0c06081
Vinicius Schmitz Nunes, Alexandre P. Rogério, Odonírio Abrahão, Jr.. Insights into the Activation Mechanism of the ALX/FPR2 Receptor. The Journal of Physical Chemistry Letters 2020, 11 (21) , 8952-8957. https://doi.org/10.1021/acs.jpclett.0c02052
Ferenc Baska, Gábor Szántó, Éva Bozó, Zoltán Szakács, Miklós Dékány, Krisztina Szondiné Kordás, Katalin Domány-Kovács, Dalma Kurkó, Barbara Hodoscsek, Ildikó Magdó, Balázs Krámos, Zoltán Béni, Mónika Vastag, Imre Bata. Discovery of New Heterocyclic Ring Systems as Novel and Potent V1A Receptor Antagonists. ACS Chemical Neuroscience 2020, 11 (21) , 3532-3540. https://doi.org/10.1021/acschemneuro.0c00486
Minsup Kim, Jun-Dong Wei, Dipesh S. Harmalkar, Ja-il Goo, Kyeong Lee, Yongseok Choi, Jae-Hong Kim, Art E. Cho. Elucidation of Mechanism for Ligand Efficacy at Leukotriene B4 Receptor 2 (BLT2). ACS Medicinal Chemistry Letters 2020, 11 (8) , 1529-1534. https://doi.org/10.1021/acsmedchemlett.0c00065
Cristina Lo Giudice, Haonan Zhang, Beili Wu, David Alsteens. Mechanochemical Activation of Class-B G-Protein-Coupled Receptor upon Peptide–Ligand Binding. Nano Letters 2020, 20 (7) , 5575-5582. https://doi.org/10.1021/acs.nanolett.0c02333
Alexander Heifetz, Inaki Morao, M. Madan Babu, Tim James, Michelle W. Y. Southey, Dmitri G. Fedorov, Matteo Aldeghi, Michael J. Bodkin, Andrea Townsend-Nicholson. Characterizing Interhelical Interactions of G-Protein Coupled Receptors with the Fragment Molecular Orbital Method. Journal of Chemical Theory and Computation 2020, 16 (4) , 2814-2824. https://doi.org/10.1021/acs.jctc.9b01136
Wijnand J. C. van der Velden, Laura H. Heitman, Mette M. Rosenkilde. Perspective: Implications of Ligand–Receptor Binding Kinetics for Therapeutic Targeting of G Protein-Coupled Receptors. ACS Pharmacology & Translational Science 2020, 3 (2) , 179-189. https://doi.org/10.1021/acsptsci.0c00012
Oliver Fleetwood, Pierre Matricon, Jens Carlsson, Lucie Delemotte. Energy Landscapes Reveal Agonist Control of G Protein-Coupled Receptor Activation via Microswitches. Biochemistry 2020, 59 (7) , 880-891. https://doi.org/10.1021/acs.biochem.9b00842
José X. Lima Neto, Katyanna S. Bezerra, Emmanuel D. Barbosa, Jonas I. N. Oliveira, Vinícius Manzoni, Vanessa P. Soares-Rachetti, Eudenilson L. Albuquerque, Umberto L. Fulco. Exploring the Binding Mechanism of GABAB Receptor Agonists and Antagonists through in Silico Simulations. Journal of Chemical Information and Modeling 2020, 60 (2) , 1005-1018. https://doi.org/10.1021/acs.jcim.9b01025
Xiaoli An, Qifeng Bai, Zhitong Bing, Hongli Liu, Qianqian Zhang, Huanxiang Liu, Xiaojun Yao. Revealing the Positive Binding Cooperativity Mechanism between the Orthosteric and the Allosteric Antagonists of CCR2 by Metadynamics and Gaussian Accelerated Molecular Dynamics Simulations. ACS Chemical Neuroscience 2020, 11 (4) , 628-637. https://doi.org/10.1021/acschemneuro.9b00630
Ting Lei, Zhenxin Hu, Ruolin Ding, Jianfang Chen, Shiqi Li, Fuhui Zhang, Xuemei Pu, Nanrong Zhao. Exploring the Activation Mechanism of a Metabotropic Glutamate Receptor Homodimer via Molecular Dynamics Simulation. ACS Chemical Neuroscience 2020, 11 (2) , 133-145. https://doi.org/10.1021/acschemneuro.9b00425
Ismail Erol, Bunyemin Cosut, Serdar Durdagi. Toward Understanding the Impact of Dimerization Interfaces in Angiotensin II Type 1 Receptor. Journal of Chemical Information and Modeling 2019, 59 (10) , 4314-4327. https://doi.org/10.1021/acs.jcim.9b00294
Xiangying Zhang, Hongbin Sun, Xiaoan Wen, Haoliang Yuan. A Selectivity Study of FFAR4/FFAR1 Agonists by Molecular Modeling. Journal of Chemical Information and Modeling 2019, 59 (10) , 4467-4474. https://doi.org/10.1021/acs.jcim.9b00735
Layara Akemi Abiko, Anne Grahl, Stephan Grzesiek. High Pressure Shifts the β1-Adrenergic Receptor to the Active Conformation in the Absence of G Protein. Journal of the American Chemical Society 2019, 141 (42) , 16663-16670. https://doi.org/10.1021/jacs.9b06042
Suvamay Jana, Soumadwip Ghosh, Sanychen Muk, Benjamin Levy, Nagarajan Vaidehi. Prediction of Conformation Specific Thermostabilizing Mutations for Class A G Protein-Coupled Receptors. Journal of Chemical Information and Modeling 2019, 59 (9) , 3744-3754. https://doi.org/10.1021/acs.jcim.9b00175
Carmen Klein Herenbrink, Ravi Verma, Herman D. Lim, Anitha Kopinathan, Alastair Keen, Jeremy Shonberg, Christopher J. Draper-Joyce, Peter J. Scammells, Arthur Christopoulos, Jonathan A. Javitch, Ben Capuano, Lei Shi, J. Robert Lane. Molecular Determinants of the Intrinsic Efficacy of the Antipsychotic Aripiprazole. ACS Chemical Biology 2019, 14 (8) , 1780-1792. https://doi.org/10.1021/acschembio.9b00342
Curtis Balusek, Hyea Hwang, Chun Hon Lau, Karl Lundquist, Anthony Hazel, Anna Pavlova, Diane L. Lynch, Patricia H. Reggio, Yi Wang, James C. Gumbart. Accelerating Membrane Simulations with Hydrogen Mass Repartitioning. Journal of Chemical Theory and Computation 2019, 15 (8) , 4673-4686. https://doi.org/10.1021/acs.jctc.9b00160
Valentina Corradi, Besian I. Sejdiu, Haydee Mesa-Galloso, Haleh Abdizadeh, Sergei Yu. Noskov, Siewert J. Marrink, D. Peter Tieleman. Emerging Diversity in Lipid–Protein Interactions. Chemical Reviews 2019, 119 (9) , 5775-5848. https://doi.org/10.1021/acs.chemrev.8b00451
Giray Enkavi, Matti Javanainen, Waldemar Kulig, Tomasz Róg, Ilpo Vattulainen. Multiscale Simulations of Biological Membranes: The Challenge To Understand Biological Phenomena in a Living Substance. Chemical Reviews 2019, 119 (9) , 5607-5774. https://doi.org/10.1021/acs.chemrev.8b00538
Lasse Karhu, Aniket Magarkar, Alex Bunker, Henri Xhaard. Determinants of Orexin Receptor Binding and Activation—A Molecular Dynamics Study. The Journal of Physical Chemistry B 2019, 123 (12) , 2609-2622. https://doi.org/10.1021/acs.jpcb.8b10220
Xiaoli An, Qifeng Bai, Zhitong Bing, Shuangyan Zhou, Danfeng Shi, Huanxiang Liu, Xiaojun Yao. How Does Agonist and Antagonist Binding Lead to Different Conformational Ensemble Equilibria of the κ-Opioid Receptor: Insight from Long-Time Gaussian Accelerated Molecular Dynamics Simulation. ACS Chemical Neuroscience 2019, 10 (3) , 1575-1584. https://doi.org/10.1021/acschemneuro.8b00535
Shu Li, Bohua Wu, Wei Han. Parametrization of MARTINI for Modeling Hinging Motions in Membrane Proteins. The Journal of Physical Chemistry B 2019, 123 (10) , 2254-2269. https://doi.org/10.1021/acs.jpcb.8b11244
Kouhei Yoshida, Satoru Nagatoishi, Daisuke Kuroda, Nanao Suzuki, Takeshi Murata, Kouhei Tsumoto. Phospholipid Membrane Fluidity Alters Ligand Binding Activity of a G Protein-Coupled Receptor by Shifting the Conformational Equilibrium. Biochemistry 2019, 58 (6) , 504-508. https://doi.org/10.1021/acs.biochem.8b01194
Shaoyong Lu, Jian Zhang. Small Molecule Allosteric Modulators of G-Protein-Coupled Receptors: Drug–Target Interactions. Journal of Medicinal Chemistry 2019, 62 (1) , 24-45. https://doi.org/10.1021/acs.jmedchem.7b01844
Ramya Rangan, Massimiliano Bonomi, Gabriella T. Heller, Andrea Cesari, Giovanni Bussi, Michele Vendruscolo. Determination of Structural Ensembles of Proteins: Restraining vs Reweighting. Journal of Chemical Theory and Computation 2018, 14 (12) , 6632-6641. https://doi.org/10.1021/acs.jctc.8b00738
L. Maggi, P. Carloni, G. Rossetti. Vibrational Energy in Proteins Correlates with Topology. The Journal of Physical Chemistry Letters 2018, 9 (22) , 6393-6398. https://doi.org/10.1021/acs.jpclett.8b02380
Qiansen Zhang, Mang Zhou, Lifen Zhao, Hualiang Jiang, Huaiyu Yang. Dynamic States of the Ligand-Free Class A G Protein-Coupled Receptor Extracellular Side. Biochemistry 2018, 57 (32) , 4767-4775. https://doi.org/10.1021/acs.biochem.8b00146
Benjamin Schreiber, Michael Kauk, Hannah S. Heil, Monika Emmerling, Ingrid Tessmer, Martin Kamp, Sven Höfling, Ulrike Holzgrabe, Carsten Hoffmann, Katrin G. Heinze. Enhanced Fluorescence Resonance Energy Transfer in G-Protein-Coupled Receptor Probes on Nanocoated Microscopy Coverslips. ACS Photonics 2018, 5 (6) , 2225-2233. https://doi.org/10.1021/acsphotonics.8b00072
Durba Sengupta, Xavier Prasanna, Madhura Mohole, Amitabha Chattopadhyay. Exploring GPCR–Lipid Interactions by Molecular Dynamics Simulations: Excitements, Challenges, and the Way Forward. The Journal of Physical Chemistry B 2018, 122 (22) , 5727-5737. https://doi.org/10.1021/acs.jpcb.8b01657
Marina Casiraghi, Marjorie Damian, Ewen Lescop, Jean-Louis Banères, Laurent J. Catoire. Illuminating the Energy Landscape of GPCRs: The Key Contribution of Solution-State NMR Associated with Escherichia coli as an Expression Host. Biochemistry 2018, 57 (16) , 2297-2307. https://doi.org/10.1021/acs.biochem.8b00035
Vishnu Shankar, William A. Goddard III, Soo-Kyung Kim, Ravinder Abrol, Fan Liu. The 3D Structure of Human DP Prostaglandin G-Protein-Coupled Receptor Bound to Cyclopentanoindole Antagonist, Predicted Using the DuplexBiHelix Modification of the GEnSeMBLE Method. Journal of Chemical Theory and Computation 2018, 14 (3) , 1624-1642. https://doi.org/10.1021/acs.jctc.7b00842
Phuoc Jake Vu, Xin-Qiu Yao, Mohamed Momin, and Donald Hamelberg . Unraveling Allosteric Mechanisms of Enzymatic Catalysis with an Evolutionary Analysis of Residue–Residue Contact Dynamical Changes. ACS Catalysis 2018, 8 (3) , 2375-2384. https://doi.org/10.1021/acscatal.7b04263
Tao Liang, Yuan Yuan, Ran Wang, Yanzhi Guo, Menglong Li, Xuemei Pu, and Chuan Li . Structural Features and Ligand Selectivity for 10 Intermediates in the Activation Process of β2-Adrenergic Receptor. ACS Omega 2017, 2 (12) , 8557-8567. https://doi.org/10.1021/acsomega.7b01031
Aashish Manglik and Andrew C. Kruse . Structural Basis for G Protein-Coupled Receptor Activation. Biochemistry 2017, 56 (42) , 5628-5634. https://doi.org/10.1021/acs.biochem.7b00747
Laura M. Bohn and Jeffrey Aubé . Seeking (and Finding) Biased Ligands of the Kappa Opioid Receptor. ACS Medicinal Chemistry Letters 2017, 8 (7) , 694-700. https://doi.org/10.1021/acsmedchemlett.7b00224
Woldeamanuel A. Birru, Dallas B. Warren, Stephen J. Headey, Hassan Benameur, Christopher J. H. Porter, Colin W. Pouton, and David K. Chalmers . Computational Models of the Gastrointestinal Environment. 1. The Effect of Digestion on the Phase Behavior of Intestinal Fluids. Molecular Pharmaceutics 2017, 14 (3) , 566-579. https://doi.org/10.1021/acs.molpharmaceut.6b00888
Yueyi Chen, Amol Sonawane, Rajesh Manda, Ranjith Kumar Gadi, John J.G. Tesmer, Arun K. Ghosh. Development of a new class of potent and highly selective G protein-coupled receptor kinase 5 inhibitors and structural insight from crystal structures of inhibitor complexes. European Journal of Medicinal Chemistry 2024, 264 , 115931. https://doi.org/10.1016/j.ejmech.2023.115931
Andrey V. Struts, Alexander V. Barmasov, Steven D.E. Fried, Kushani S.K. Hewage, Suchithranga M.D.C. Perera, Michael F. Brown. Osmotic stress studies of G-protein-coupled receptor rhodopsin activation. Biophysical Chemistry 2024, 304 , 107112. https://doi.org/10.1016/j.bpc.2023.107112
Mingyang Zhang, Xiaobing Lan, Xiaolong Li, Shaoyong Lu. Pharmacologically targeting intracellular allosteric sites of GPCRs for drug discovery. Drug Discovery Today 2023, 28 (12) , 103803. https://doi.org/10.1016/j.drudis.2023.103803
Thian-Sze Wong, Guangzhi Li, Shiliang Li, Wei Gao, Geng Chen, Shiyi Gan, Manzhan Zhang, Honglin Li, Song Wu, Yang Du. G protein-coupled receptors in neurodegenerative diseases and psychiatric disorders. Signal Transduction and Targeted Therapy 2023, 8 (1) https://doi.org/10.1038/s41392-023-01427-2
Sathvik Anantakrishnan, Athi N. Naganathan. Thermodynamic architecture and conformational plasticity of GPCRs. Nature Communications 2023, 14 (1) https://doi.org/10.1038/s41467-023-35790-z
David P. Tilly, Jean-Paul Heeb, Simon J. Webb, Jonathan Clayden. Switching imidazole reactivity by dynamic control of tautomer state in an allosteric foldamer. Nature Communications 2023, 14 (1) https://doi.org/10.1038/s41467-023-38339-2
Lukas Grätz, Maria Kowalski-Jahn, Magdalena M. Scharf, Pawel Kozielewicz, Michael Jahn, Julien Bous, Nevin A. Lambert, David E. Gloriam, Gunnar Schulte. Pathway selectivity in Frizzleds is achieved by conserved micro-switches defining pathway-determining, active conformations. Nature Communications 2023, 14 (1) https://doi.org/10.1038/s41467-023-40213-0
Arne Thies, Vikram Sunkara, Sourav Ray, Hanna Wulkow, M. Özgür Celik, Fatih Yergöz, Christof Schütte, Christoph Stein, Marcus Weber, Stefanie Winkelmann. Modelling altered signalling of G-protein coupled receptors in inflamed environment to advance drug design. Scientific Reports 2023, 13 (1) https://doi.org/10.1038/s41598-023-27699-w
Silvia Gervasoni, Camilla Guccione, Viviana Fanti, Andrea Bosin, Giancarlo Cappellini, Bruno Golosio, Paolo Ruggerone, Giuliano Malloci. Molecular simulations of SSTR2 dynamics and interaction with ligands. Scientific Reports 2023, 13 (1) https://doi.org/10.1038/s41598-023-31823-1
Soumajit Dutta, Diwakar Shukla. Distinct activation mechanisms regulate subtype selectivity of Cannabinoid receptors. Communications Biology 2023, 6 (1) https://doi.org/10.1038/s42003-023-04868-1
Mengrong Li, Yiqiong Bao, Miaomiao Li, Jingjing Guo. GPCR Allostery: A View from Computational Biology. Current Medicinal Chemistry 2023, 30 (40) , 4533-4553. https://doi.org/10.2174/0929867330666230113125246
Marina Gorostiola González, Remco L. van den Broek, Thomas G. M. Braun, Magdalini Chatzopoulou, Willem Jespers, Adriaan P. IJzerman, Laura H. Heitman, Gerard J. P. van Westen. 3DDPDs: describing protein dynamics for proteochemometric bioactivity prediction. A case for (mutant) G protein-coupled receptors. Journal of Cheminformatics 2023, 15 (1) https://doi.org/10.1186/s13321-023-00745-5
Juan Manuel López-Correa, Caroline König, Alfredo Vellido. GPCR molecular dynamics forecasting using recurrent neural networks. Scientific Reports 2023, 13 (1) https://doi.org/10.1038/s41598-023-48346-4
Pauline Raynaud, Vinesh Jugnarain, Océane Vaugrente, Amandine Vallet, Thomas Boulo, Camille Gauthier, Asuka Inoue, Nathalie Sibille, Christophe Gauthier, Frédéric Jean‐Alphonse, Eric Reiter, Pascale Crépieux, Gilles Bruneau. A single‐domain intrabody targeting the follicle‐stimulating hormone receptor impacts FSH ‐induced G protein‐dependent signalling. FEBS Letters 2023, 117 https://doi.org/10.1002/1873-3468.14765
Aolei Tan, Xiaoxiao Ma. Exploring the functional roles of small-molecule metabolites in disease research: Recent advancements in metabolomics. Chinese Chemical Letters 2023, 86 , 109276. https://doi.org/10.1016/j.cclet.2023.109276
Sarbani Mishra, Madhusmita Rout, Mahender Kumar Singh, Budheswar Dehury, Sanghamitra Pati. Illuminating the structural basis of human neurokinin 1 receptor (NK1R) antagonism through classical all‐atoms molecular dynamics simulations. Journal of Cellular Biochemistry 2023, 124 (11) , 1848-1869. https://doi.org/10.1002/jcb.30493
Tao Che, Bryan L. Roth. Molecular basis of opioid receptor signaling. Cell 2023, 186 (24) , 5203-5219. https://doi.org/10.1016/j.cell.2023.10.029
Liyi Fu, Yang Zhang, Ryan A. Farokhzad, Bárbara B. Mendes, João Conde, Jinjun Shi. ‘Passive’ nanoparticles for organ-selective systemic delivery: design, mechanism and perspective. Chemical Society Reviews 2023, 52 (21) , 7579-7601. https://doi.org/10.1039/D2CS00998F
Siddhanta V. Nikte, Manali Joshi, Durba Sengupta. State‐dependent dynamics of extramembrane domains in the β 2 ‐adrenergic receptor. Proteins: Structure, Function, and Bioinformatics 2023, https://doi.org/10.1002/prot.26613
Subhadip Senapati, Paul S.‐H. Park. Understanding the Rhodopsin Worldview Through Atomic Force Microscopy (AFM): Structure, Stability, and Activity Studies. The Chemical Record 2023, 23 (10) https://doi.org/10.1002/tcr.202300113
Beining Jin, Naveen Thakur, Anuradha V. Wijesekara, Matthew T. Eddy. Illuminating GPCR signaling mechanisms by NMR spectroscopy with stable-isotope labeled receptors. Current Opinion in Pharmacology 2023, 72 , 102364. https://doi.org/10.1016/j.coph.2023.102364
Jia-Le Wang, Xiao-Dong Dou, Jie Cheng, Ming-Xin Gao, Guo-Feng Xu, Wei Ding, Jin-Hui Ding, Yu Li, Si-Han Wang, Zhao-Wei Ji, Xin-Yi Zhao, Tong-Yu Huo, Cai-Fang Zhang, Ya-Meng Liu, Xue-Ying Sha, Jia-Rui Gao, Wen-Hui Zhang, Yong Hao, Cheng Zhang, Jin-Peng Sun, Ning Jiao, Xiao Yu. Functional screening and rational design of compounds targeting GPR132 to treat diabetes. Nature Metabolism 2023, 5 (10) , 1726-1746. https://doi.org/10.1038/s42255-023-00899-4
Monica Chinellato, Matteo Gasparotto, Santina Quarta, Mariagrazia Ruvoletto, Alessandra Biasiolo, Francesco Filippini, Luca Spiezia, Laura Cendron, Patrizia Pontisso. 1-Piperidine Propionic Acid as an Allosteric Inhibitor of Protease Activated Receptor-2. Pharmaceuticals 2023, 16 (10) , 1486. https://doi.org/10.3390/ph16101486
Luis Martínez‐Crespo, Iñigo J. Vitórica‐Yrezábal, George F. S. Whitehead, Simon J. Webb. Chemically Fueled Communication Along a Scaffolded Nanoscale Array of Squaramides. Angewandte Chemie 2023, 135 (38) https://doi.org/10.1002/ange.202307841
Luis Martínez‐Crespo, Iñigo J. Vitórica‐Yrezábal, George F. S. Whitehead, Simon J. Webb. Chemically Fueled Communication Along a Scaffolded Nanoscale Array of Squaramides. Angewandte Chemie International Edition 2023, 62 (38) https://doi.org/10.1002/anie.202307841
Naoto Kajitani, Mami Okada-Tsuchioka, Asuka Inoue, Kanako Miyano, Takeshi Masuda, Shuken Boku, Kazuya Iwamoto, Sumio Ohtsuki, Yasuhito Uezono, Junken Aoki, Minoru Takebayashi. G protein-biased LPAR1 agonism of prototypic antidepressants: Implication in the identification of novel therapeutic target for depression. Neuropsychopharmacology 2023, 391 https://doi.org/10.1038/s41386-023-01727-9
Yu Guo, Qingtong Zhou, Bin Wei, Ming-Wei Wang, Suwen Zhao. GPCRana: A web server for quantitative analysis of GPCR structures. Structure 2023, 31 (9) , 1132-1142.e2. https://doi.org/10.1016/j.str.2023.06.008
Kihang Choi. The Structure-property Relationships of GPCR-targeted Drugs Approved between 2011 and 2021. Current Medicinal Chemistry 2023, 30 (31) , 3527-3549. https://doi.org/10.2174/1573399819666221102113217
Albert A. Smith, Emelyne M. Pacull, Sabrina Stecher, Peter W. Hildebrand, Alexander Vogel, Daniel Huster. Dynamikuntersuchungen des Wachstumshormon‐Sekreteagogum‐Rezeptors geben Einblicke in seine Energielandschaft. Angewandte Chemie 2023, 135 (35) https://doi.org/10.1002/ange.202302003
Albert A. Smith, Emelyne M. Pacull, Sabrina Stecher, Peter W. Hildebrand, Alexander Vogel, Daniel Huster. Analysis of the Dynamics of the Human Growth Hormone Secretagogue Receptor Reveals Insights into the Energy Landscape of the Molecule. Angewandte Chemie International Edition 2023, 62 (35) https://doi.org/10.1002/anie.202302003
Phil Addis, Utsav Bali, Frank Baron, Adrian Campbell, Steven Harborne, Liz Jagger, Gavin Milne, Martin Pearce, Elizabeth M Rosethorne, Rupert Satchell, Denise Swift, Barbara Young, John F Unitt. Key aspects of modern GPCR drug discovery. SLAS Discovery 2023, 93 https://doi.org/10.1016/j.slasd.2023.08.007
Florian Seufert, Yin Kwan Chung, Peter W. Hildebrand, Tobias Langenhan. 7TM domain structures of adhesion GPCRs: what's new and what's missing?. Trends in Biochemical Sciences 2023, 48 (8) , 726-739. https://doi.org/10.1016/j.tibs.2023.05.007
Jürgen Wess. The third intracellular loop of GPCRs: size matters. Trends in Pharmacological Sciences 2023, 44 (8) , 492-494. https://doi.org/10.1016/j.tips.2023.05.001
Teresa Gianferrara, Matteo Pavan, Davide Bassani, Fabrizio Vincenzi, Silvia Pasquini, Giovanni Bolcato, Katia Varani, Giampiero Spalluto, Stephanie Federico, Stefano Moro. Are Two Riboses Better Than One? The Case of the Recognition and Activation of Adenosine Receptors. ChemMedChem 2023, 18 (14) https://doi.org/10.1002/cmdc.202300109
Gabriele Kockelkoren, Line Lauritsen, Christopher G. Shuttle, Eleftheria Kazepidou, Ivana Vonkova, Yunxiao Zhang, Artù Breuer, Celeste Kennard, Rachel M. Brunetti, Elisa D’Este, Orion D. Weiner, Mark Uline, Dimitrios Stamou. Molecular mechanism of GPCR spatial organization at the plasma membrane. Nature Chemical Biology 2023, 3 https://doi.org/10.1038/s41589-023-01385-4
Simone Scrima, Matteo Tiberti, Ulf Ryde, Matteo Lambrughi, Elena Papaleo. Comparison of force fields to study the zinc-finger containing protein NPL4, a target for disulfiram in cancer therapy. Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics 2023, 1871 (4) , 140921. https://doi.org/10.1016/j.bbapap.2023.140921
Eugenio Frixione, Lourdes Ruiz-Zamarripa. Proteins turn “Proteans” – The over 40-year delayed paradigm shift in structural biology: From “native proteins in uniquely defined configurations” to “intrinsically disordered proteins”. Biomolecular Concepts 2023, 14 (1) https://doi.org/10.1515/bmc-2022-0030

Load more citations

Download PDF

Abstract
High Resolution Image
Download MS PowerPoint Slide
Figure 1
Figure 1. GPCR signaling: (A) an orthosteric ligand (orange) binds an inactive GPCR, the β₂ adrenergic receptor (β₂AR; PDB ID: 2RH1); (B) A ligand-bound GPCR undergoes a conformational change to its active state (PDB ID: 3SN6); and (C) an active GPCR binds a G protein (PDB ID: 3SN6), which subsequently promotes nucleotide release from, and activation of, the G protein α-subunit.
High Resolution Image
Download MS PowerPoint Slide
Figure 2
Figure 2. Structure and topology of GPCRs. (A) GPCRs contain seven transmembrane helices (gray), three extracellular loops (ECLs) and an amino terminus (orange), and three intracellular loops (ICLs) and a carboxyl terminus (purple). The transmembrane domain consists of the transmembrane helices, as well as the extracellular and intracellular loops. (B) Cartoon representation of the β₂AR highlighting transmembrane helices (TMs), loops, and terminal tails.
High Resolution Image
Download MS PowerPoint Slide
Figure 3
Figure 3. Atomic-level motions of a GPCR revealed through MD simulations. Representative frames from MD simulations (from ref 23) of agonist-bound β₂AR as it transitions from an active state to an inactive state, with (A) all non-hydrogen atoms represented as lines and (B) protein backbone represented as ribbons. Transmembrane helix 6 (TM6) is colored red to highlight its high degre of mobility during the transition between active and inactive states.
High Resolution Image
Download MS PowerPoint Slide
Figure 4
Figure 4. Protein conformations cluster into distinct conformational states. Mapping an MD simulation trajectory to a well-chosen low-dimensional space can reveal distinct clusters of conformations. (A) Plotting an MD simulation trajectory along two geometric coordinates reveals three distinct conformational states during the process of β₂AR deactivation (top). RMSD is the root-mean-square deviation. (B) Snapshots from simulation, representing each of the three conformational states (light pink, magenta and dark purple), are overlaid with the inactive-state crystal structure (blue). These are shown along with a simplified, qualitative one-dimensional energy landscape, where the depth of each energy well is inversely related to the population of the corresponding conformational state. Adapted by permission from ref 23. Copyright 2011 National Academy of Sciences.
High Resolution Image
Download MS PowerPoint Slide
Figure 5
Figure 5. Perturbations alter the populations of conformational states. Hypothetical histograms (light pink, magenta, and purple) represent the relative populations of each of three hypothetical conformational states. Hypothetical energy landscapes (gray) are inversely related to the populations of the conformational states. Compared to the distribution of conformations visited by (A) an unliganded GPCR, (B) an agonist-bound GPCR samples intermediate and fully active conformations more frequently, and (C) an agonist-bound, G protein-bound GPCR more heavily populates fully active conformations. New conformational states may arise on this energy landscape under additional conditions (not shown).
High Resolution Image
Download MS PowerPoint Slide
Figure 6
Figure 6. Structural rearrangements during GPCR activation. Inactive (light pink) and active (dark purple) conformations of the β₂AR show differences in helix position and side-chain orientation in three distinct regions of the GPCR: the binding pocket (top, left); the connector region, or conserved core triad (bottom, left); and the intracellular coupling site (top and bottom, right).
High Resolution Image
Download MS PowerPoint Slide
Figure 7
Figure 7. Loose allosteric coupling underlies GPCR activation. (A) During simulations of β₂AR deactivation, three key regions (the binding pocket, the connector region, and the intracellular coupling interface) spontaneously transition between at least two conformations independently of the other regions. (B) Horizontal bars represent the conformations sampled by each region over the course of four 2-μs deactivation simulations of the β₂AR. Adapted by permission from ref 23. Copyright 2011 National Academy of Sciences.
High Resolution Image
Download MS PowerPoint Slide
Figure 8
Figure 8. Conformational changes in class A GPCRs upon activation. Three class A GPCRs captured in their crystallographic inactive and active conformations reveal similar conformational changes upon activation. TM6 is highlighted. M2 is the M2 muscarinic acetylcholine receptor and μOR is the μ-opioid receptor.
High Resolution Image
Download MS PowerPoint Slide
Figure 9
Figure 9. Diverse conformational states of the β₂AR. During MD simulations of β₂AR beginning in the active state (dark gray; PDB ID: 3P0G) (A), β₂AR transitions along (B) a dominant pathway through an intermediate (intermediate A) in which TM6 is still displaced outward relative to the inactive crystal structure but TM7 is straightened (light blue) or (C) an alternative pathway through two intermediates, B and C, which exhibit a conformation of TM7 distinct from that seen in the inactive and active crystal structures of the β₂AR. Simulations were taken from ref 23.
High Resolution Image
Download MS PowerPoint Slide
Figure 10
Figure 10. Structural comparison of G protein-bound and arrestin-bound GPCRs. Crystal structures of β₂AR bound to G_s (left; PDB ID: 3SN6) and of rhodopsin bound to arrestin-1 (right; PDB ID: 4ZWJ) similar conformations of the GPCRs’ intracellular coupling sites.
High Resolution Image
Download MS PowerPoint Slide
Figure 11
Figure 11. Structural basis of allosteric modulation in GPCRs. (A) Conformational changes to the orthosteric and allosteric binding sites in the presence of different ligands. The presence of the orthosteric ligand (green) favors a widened allosteric site. The allosteric modulator in blue requires a widened allosteric site to bind, while the allosteric modulator in pink does not. Adapted by permission from ref 38. Copyright 2013 Macmillan Publishers Ltd. (B) Sites of allosteric modulation in GPCRs (gray) include the extracellular loops in the M2R (top; PDB ID: 4MQT), the centrally located sodium-binding site in the adenosine A_2A receptor (middle, with sodium in yellow; PDB ID: 4EIY) and the base of TM6 in glucagon receptor (bottom; PDB ID: 5EE7).
High Resolution Image
Download MS PowerPoint Slide
References
ARTICLE SECTIONS
Jump To
This article references 159 other publications.
1. 1
  Rosenbaum, D. M.; Cherezov, V.; Hanson, M. A.; Rasmussen, S. G.; Thian, F. S.; Kobilka, T. S.; Choi, H. J.; Yao, X. J.; Weis, W. I.; Stevens, R. C. GPCR Engineering Yields High-Resolution Structural Insights into Beta2-Adrenergic Receptor Function Science 2007, 318, 1266– 1273 DOI: 10.1126/science.1150609
  Google Scholar
  1
  GPCR Engineering Yields High-Resolution Structural Insights into β2-Adrenergic Receptor Function
  Rosenbaum, Daniel M.; Cherezov, Vadim; Hanson, Michael A.; Rasmussen, Soren G. F.; Thian, Foon Sun; Kobilka, Tong Sun; Choi, Hee-Jung; Yao, Xiao-Jie; Weis, William I.; Stevens, Raymond C.; Kobilka, Brian K.; Pierce, K. L.; Premont, R. T.; Lefkowitz, R. J.; Kobilka, B. K.; Deupi, X.; Cherezov, V.; Rasmussen, S. G. F.
  Science (Washington, DC, United States) (2007), 318 (5854), 1266-1273CODEN: SCIEAS; ISSN:0036-8075. (American Association for the Advancement of Science)
  The β2-adrenergic receptor (β2AR) is a well-studied prototype for heterotrimeric guanine nucleotide-binding protein (G protein)-coupled receptors (GPCRs) that respond to diffusible hormones and neurotransmitters. To overcome the structural flexibility of the β2AR and to facilitate its crystn., we engineered a β2AR fusion protein in which T4 lysozyme (T4L) replaces most of the third intracellular loop of the GPCR ("β2AR-T4L") and showed that this protein retains near-native pharmacol. properties. Anal. of adrenergic receptor ligand-binding mutants within the context of the reported high-resoln. structure of β2AR-T4L provides insights into inverse-agonist binding and the structural changes required to accommodate catecholamine agonists. Amino acids known to regulate receptor function are linked through packing interactions and a network of hydrogen bonds, suggesting a conformational pathway from the ligand-binding pocket to regions that interact with G proteins.
  >> More from SciFinder ^®
  https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2sXhtlGmur7J&md5=d422ff1e7a28719848c0e16fede045db
2. 2
  Rasmussen, S. G.; Choi, H. J.; Fung, J. J.; Pardon, E.; Casarosa, P.; Chae, P. S.; Devree, B. T.; Rosenbaum, D. M.; Thian, F. S.; Kobilka, T. S. Structure of a Nanobody-Stabilized Active State of the Beta(2) Adrenoceptor Nature 2011, 469, 175– 180 DOI: 10.1038/nature09648
  Google Scholar
  2
  Structure of a nanobody-stabilized active state of the β2 adrenoceptor
  Rasmussen, Soren G. F.; Choi, Hee-Jung; Fung, Juan Jose; Pardon, Els; Casarosa, Paola; Chae, Pil Seok; DeVree, Brian T.; Rosenbaum, Daniel M.; Thian, Foon Sun; Kobilka, Tong Sun; Schnapp, Andreas; Konetzki, Ingo; Sunahara, Roger K.; Gellman, Samuel H.; Pautsch, Alexander; Steyaert, Jan; Weis, William I.; Kobilka, Brian K.
  Nature (London, United Kingdom) (2011), 469 (7329), 175-180CODEN: NATUAS; ISSN:0028-0836. (Nature Publishing Group)
  G protein coupled receptors (GPCRs) exhibit a spectrum of functional behaviors in response to natural and synthetic ligands. Recent crystal structures provide insights into inactive states of several GPCRs. Efforts to obtain an agonist-bound active-state GPCR structure have proven difficult due to the inherent instability of this state in the absence of a G protein. We generated a camelid antibody fragment (nanobody) to the human β2 adrenergic receptor (β2AR) that exhibits G protein-like behavior, and obtained an agonist-bound, active-state crystal structure of the receptor-nanobody complex. Comparison with the inactive β2AR structure reveals subtle changes in the binding pocket; however, these small changes are assocd. with an 11 Å outward movement of the cytoplasmic end of transmembrane segment 6, and rearrangements of transmembrane segments 5 and 7 that are remarkably similar to those obsd. in opsin, an active form of rhodopsin. This structure provides insights into the process of agonist binding and activation.
  >> More from SciFinder ^®
  https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3MXkvFartA%253D%253D&md5=3a1d3bac6d92c9d54cf1ddd14d56ab8c
3. 3
  Rasmussen, S. G.; DeVree, B. T.; Zou, Y.; Kruse, A. C.; Chung, K. Y.; Kobilka, T. S.; Thian, F. S.; Chae, P. S.; Pardon, E.; Calinski, D. Crystal Structure of the Beta2 Adrenergic Receptor-Gs Protein Complex Nature 2011, 477, 549– 555 DOI: 10.1038/nature10361
  Google Scholar
  3
  Crystal structure of the β2 adrenergic receptor-Gs protein complex
  Rasmussen, Soren G. F.; DeVree, Brian T.; Zou, Yao-Zhong; Kruse, Andrew C.; Chung, Ka-Young; Kobilka, Tong-Sun; Thian, Foon-Sun; Chae, Pil-Seok; Pardon, Els; Calinski, Diane; Mathiesen, Jesper M.; Shah, Syed T. A.; Lyons, Joseph A.; Caffrey, Martin; Gellman, Samuel H.; Steyaert, Jan; Skiniotis, Georgios; Weis, William I.; Sunahara, Roger K.; Kobilka, Brian K.
  Nature (London, United Kingdom) (2011), 477 (7366), 549-555CODEN: NATUAS; ISSN:0028-0836. (Nature Publishing Group)
  G protein-coupled receptors (GPCRs) are responsible for the majority of cellular responses to hormones and neurotransmitters as well as the senses of sight, olfaction and taste. The paradigm of GPCR signalling is the activation of a heterotrimeric GTP binding protein (G protein) by an agonist-occupied receptor. The β2 adrenergic receptor (β2AR) activation of Gs, the stimulatory G protein for adenylyl cyclase, has long been a model system for GPCR signalling. Here we present the crystal structure of the active state ternary complex composed of agonist-occupied monomeric β2AR and nucleotide-free Gs heterotrimer. The principal interactions between the β2AR and Gs involve the amino- and carboxy-terminal α-helixes of Gs, with conformational changes propagating to the nucleotide-binding pocket. The largest conformational changes in the β2AR include a 14 Å outward movement at the cytoplasmic end of transmembrane segment 6 (TM6) and an α-helical extension of the cytoplasmic end of TM5. The most surprising observation is a major displacement of the α-helical domain of Gαs relative to the Ras-like GTPase domain. This crystal structure represents the first high-resoln. view of transmembrane signalling by a GPCR.
  >> More from SciFinder ^®
  https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3MXht1equrrL&md5=d22a43dd677ac255d138b1aedff357d3
4. 4
  Warne, T.; Serrano-Vega, M. J.; Baker, J. G.; Moukhametzianov, R.; Edwards, P. C.; Henderson, R.; Leslie, A. G.; Tate, C. G.; Schertler, G. F. Structure of a Beta1-Adrenergic G-Protein-Coupled Receptor Nature 2008, 454, 486– 491 DOI: 10.1038/nature07101
  Google Scholar
  4
  Structure of a β1-adrenergic G-protein-coupled receptor
  Warne, Tony; Serrano-Vega, Maria J.; Baker, Jillian G.; Moukhametzianov, Rouslan; Edwards, Patricia C.; Henderson, Richard; Leslie, Andrew G. W.; Tate, Christopher G.; Schertler, Gebhard F. X.
  Nature (London, United Kingdom) (2008), 454 (7203), 486-491CODEN: NATUAS; ISSN:0028-0836. (Nature Publishing Group)
  G-protein-coupled receptors have a major role in transmembrane signaling in most eukaryotes and many are important drug targets. Here we report the 2.7Å resoln. crystal structure of a β1-adrenergic receptor in complex with high affinity antagonist cyanopindolol. The modified turkey (Meleagris gallopavo) receptor was selected to be in its antagonist conformation and its thermostability improved by earlier limited mutagenesis. The ligand-binding pocket comprises 15 side chains from amino acid residues in 4 transmembrane α-helixes and extracellular loop 2. This loop defines the entrance of the ligand-binding pocket and is stabilized by two disulfide bonds and a sodium ion. Binding of cyanopindolol to the β1-adrenergic receptor and binding of Carazolol to the β2-adrenergic receptor involve similar interactions. A short well-defined helix in cytoplasmic loop 2, not obsd. in either rhodopsin or the β2-adrenergic receptor, directly interacts by means of a tyrosine with the highly conserved DRY motif at the end of helix 3 that is essential for receptor activation.
  >> More from SciFinder ^®
  https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD1cXovV2mtLg%253D&md5=de1d476a6ff0b995cd344c248d1bc490
5. 5
  Venkatakrishnan, A. J.; Deupi, X.; Lebon, G.; Tate, C. G.; Schertler, G. F.; Babu, M. M. Molecular Signatures of G-Protein-Coupled Receptors Nature 2013, 494, 185– 194 DOI: 10.1038/nature11896
  Google Scholar
  5
  Molecular signatures of G-protein-coupled receptors
  Venkatakrishnan, A. J.; Deupi, Xavier; Lebon, Guillaume; Tate, Christopher G.; Schertler, Gebhard F.; Babu, M. Madan
  Nature (London, United Kingdom) (2013), 494 (7436), 185-194CODEN: NATUAS; ISSN:0028-0836. (Nature Publishing Group)
  A review. G-protein-coupled receptors (GPCRs) are physiol. important membrane proteins that sense signaling mols. such as hormones and neurotransmitters, and are the targets of several prescribed drugs. Recent exciting developments are providing unprecedented insights into the structure and function of several medically important GPCRs. Here, through a systematic anal. of high-resoln. GPCR structures, we uncover a conserved network of non-covalent contacts that defines the GPCR fold. Furthermore, our comparative anal. reveals characteristic features of ligand binding and conformational changes during receptor activation. A holistic understanding that integrates mol. and systems biol. of GPCRs holds promise for new therapeutics and personalized medicine.
  >> More from SciFinder ^®
  https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3sXis1Wrt7Y%253D&md5=5dd040bf5f3b4b81249c02d493a1fbf3
6. 6
  Isberg, V.; Mordalski, S.; Munk, C.; Rataj, K.; Harpsoe, K.; Hauser, A. S.; Vroling, B.; Bojarski, A. J.; Vriend, G.; Gloriam, D. E. GPCRdb: An Information System for G Protein-Coupled Receptors Nucleic Acids Res. 2016, 44, D356– D364 DOI: 10.1093/nar/gkv1178
  Google Scholar
  6
  GPCRdb: an information system for G protein-coupled receptors
  Isberg, Vignir; Mordalski, Stefan; Munk, Christian; Rataj, Krzysztof; Harpsoee, Kasper; Hauser, Alexander S.; Vroling, Bas; Bojarski, Andrzej J.; Vriend, Gert; Gloriam, David E.
  Nucleic Acids Research (2016), 44 (D1), D356-D364CODEN: NARHAD; ISSN:0305-1048. (Oxford University Press)
  A review. Recent developments in G protein-coupled receptor (GPCR) structural biol. and pharmacol. have greatly enhanced our knowledge of receptor structure-function relations, and have helped improve the scientific foundation for drug design studies. The GPCR database, GPCRdb, serves a dual role in disseminating and enabling new scientific developments by providing ref. data, anal. tools and interactive diagrams. This paper highlights new features in the fifth major GPCRdb release: (i) GPCR crystal structure browsing, superposition and display of ligand interactions; (ii) direct deposition by users of point mutations and their effects on ligand binding; (iii) refined snake and helix box residue diagram looks; and (iv) phylogenetic trees with receptor classification color schemes. Under the hood, the entire GPCRdb front- and back-ends have been recoded within one infrastructure, ensuring a smooth browsing experience and development. GPCRdb is available at http://www.gpcrdb.org/ and it's open source code at https://bitbucket.org/gpcr/protwis.
  >> More from SciFinder ^®
  https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2sXhtV2gu7bJ&md5=ee7db0ef81d65cf6e5ab8750b990bb78
7. 7
  GPCRdb: An Information System for G Protein-Coupled Receptors. http://gpcrdb.org/structure/statistics, accessed July 18, 2016.
  Google Scholar
  There is no corresponding record for this reference.
8. 8
  Adcock, S. A.; McCammon, J. A. Molecular Dynamics: Survey of Methods for Simulating the Activity of Proteins Chem. Rev. 2006, 106, 1589– 1615 DOI: 10.1021/cr040426m
  Google Scholar
  8
  Molecular dynamics: Survey of methods for simulating the activity of proteins
  Adcock, Stewart A.; McCammon, J. Andrew
  Chemical Reviews (Washington, DC, United States) (2006), 106 (5), 1589-1615CODEN: CHREAY; ISSN:0009-2665. (American Chemical Society)
  A review. Mol. dynamics simulations (MDS) of proteins have provided many insights into the internal motions of these biomols. Simulation of in silico models aids in the interpretation and reconciliation of exptl. data. With ongoing advances in both methodol. and computational resources, MDS are being extended to larger systems and longer time scales. This enables the investigation of motions and conformational changes that have functional implications and yields information that is not available though any other means. Today's results suggest that (subject to the continuing utilization of synergies between expt. and simulation) the applications of MDS will command an increasingly crit. role in the understanding of biol. systems.
  >> More from SciFinder ^®
  https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD28Xht1eqtro%253D&md5=56cae2eff1ab9c443756dba4fde5500e
9. 9
  Rosenbaum, D. M.; Rasmussen, S. G.; Kobilka, B. K. The Structure and Function of G-Protein-Coupled Receptors Nature 2009, 459, 356– 363 DOI: 10.1038/nature08144
  Google Scholar
  9
  The structure and function of G-protein-coupled receptors
  Rosenbaum, Daniel M.; Rasmussen, Soren G. F.; Kobilka, Brian K.
  Nature (London, United Kingdom) (2009), 459 (7245), 356-363CODEN: NATUAS; ISSN:0028-0836. (Nature Publishing Group)
  A review. G-protein-coupled receptors (GPCRs) mediate most of the physiol. responses to hormones, neurotransmitters and environmental stimulants, and so have great potential as therapeutic targets for a broad spectrum of diseases. They are also fascinating mols. from the perspective of membrane protein structure and biol. Great progress has been made over the past 3 decades in understanding diverse GPCRs, from pharmacol. to functional characterization in vivo. Recent high-resoln. structural studies have provided insights into the mol. mechanisms of GPCR activation and constitutive activity.
  >> More from SciFinder ^®
  https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD1MXmtFKmsLg%253D&md5=4d0271a5aacc58c4d255ddb7531ca8ed
10. 10
  Fredriksson, R.; Lagerstrom, M. C.; Lundin, L.-G.; Schioth, H. B. The G-Protein-Coupled Receptors in the Human Genome Form Five Main Families. Phylogenetic Analysis, Paralogon Groups, and Fingerprints Mol. Pharmacol. 2003, 63, 1256– 1272 DOI: 10.1124/mol.63.6.1256
  Google Scholar
  10
  The G-protein-coupled receptors in the human genome form five main families. Phylogenetic analysis, paralogon groups, and fingerprints
  Fredriksson, Robert; Lagerstrom, Malin C.; Lundin, Lars-Gustav; Schioth, Helgi B.
  Molecular Pharmacology (2003), 63 (6), 1256-1272CODEN: MOPMA3; ISSN:0026-895X. (American Society for Pharmacology and Experimental Therapeutics)
  The superfamily of G-protein-coupled receptors (GPCRs) is very diverse in structure and function and its members are among the most pursued targets for drug development. We identified more than 800 human GPCR sequences and simultaneously analyzed 342 unique functional nonolfactory human GPCR sequences with phylogenetic analyses. Our results show, with high bootstrap support, five main families, named glutamate, rhodopsin, adhesion, frizzled/taste2, and secretin, forming the GRAFS classification system. The rhodopsin family is the largest and forms four main groups with 13 subbranches. Positions of the GPCRs in chromosomal paralogons regions indicate the importance of tetraploidizations or local gene duplication events for their creation. We also searched for "fingerprint" motifs using Hidden Markov Models delineating the putative inter-relationship of the GRAFS families. We show several common structural features indicating that the human GPCRs in the GRAFS families share a common ancestor. This study represents the first overall map of the GPCRs in a single mammalian genome. Our novel approach of analyzing such large and diverse sequence sets may be useful for studies on GPCRs in other genomes and divergent protein families.
  >> More from SciFinder ^®
  https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD3sXkt1Shu7k%253D&md5=504ea873ee8469cd0b6016bc94943836
11. 11
  Lagerstrom, M. C.; Schioth, H. B. Structural Diversity of G Protein-Coupled Receptors and Significance for Drug Discovery Nat. Rev. Drug Discovery 2008, 7, 339– 357 DOI: 10.1038/nrd2518
  Google Scholar
  11
  Structural diversity of G protein-coupled receptors and significance for drug discovery
  Lagerstrom Malin C; Schioth Helgi B
  Nature reviews. Drug discovery (2008), 7 (4), 339-57 ISSN:.
  G protein-coupled receptors (GPCRs) are the largest family of membrane-bound receptors and also the targets of many drugs. Understanding of the functional significance of the wide structural diversity of GPCRs has been aided considerably in recent years by the sequencing of the human genome and by structural studies, and has important implications for the future therapeutic potential of targeting this receptor family. This article aims to provide a comprehensive overview of the five main human GPCR families--Rhodopsin, Secretin, Adhesion, Glutamate and Frizzled/Taste2--with a focus on gene repertoire, general ligand preference, common and unique structural features, and the potential for future drug discovery.
  >> More from SciFinder ^®
  https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A280%3ADC%252BD1c3itl2juw%253D%253D&md5=3e9de54162c071b7927d975b964abea2
12. 12
  Henzler-Wildman, K.; Kern, D. Dynamic Personalities of Proteins Nature 2007, 450, 964– 972 DOI: 10.1038/nature06522
  Google Scholar
  12
  Dynamic personalities of proteins
  Henzler-Wildman, Katherine; Kern, Dorothee
  Nature (London, United Kingdom) (2007), 450 (7172), 964-972CODEN: NATUAS; ISSN:0028-0836. (Nature Publishing Group)
  A review. Because proteins are central to cellular function, researchers have sought to uncover the secrets of how these complex macromols. execute such a fascinating variety of functions. Although static structures are known for many proteins, the functions of proteins are governed ultimately by their dynamic character (or 'personality'). The dream is to 'watch' proteins in action in real time at at. resoln. This requires the addn. of a fourth dimension, time, to structural biol. so that the positions in space and time of all atoms in a protein can be described in detail.
  >> More from SciFinder ^®
  https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2sXhsVaqtr%252FL&md5=27ca36106100f487683d714de5335dc2
13. 13
  Granier, S.; Kobilka, B. A New Era of GPCR Structural and Chemical Biology Nat. Chem. Biol. 2012, 8, 670– 673 DOI: 10.1038/nchembio.1025
  Google Scholar
  13
  A new era of GPCR structural and chemical biology
  Granier, Sebastien; Kobilka, Brian
  Nature Chemical Biology (2012), 8 (8), 670-673CODEN: NCBABT; ISSN:1552-4450. (Nature Publishing Group)
  A review. G protein-coupled receptors (GPCRs) are versatile mol. machines that regulate the majority of physiol. responses to chem. diverse hormones and neurotransmitters. Recent breakthroughs in structural studies have advanced the understanding of GPCR signaling, particularly the selectivity of ligand recognition and receptor activation of G proteins.
  >> More from SciFinder ^®
  https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC38XhtVCltLvK&md5=43f50b2b5f0d6fae2bf77ffe369fa899
14. 14
  Wishart, D. S. Interpreting Protein Chemical Shift Data Prog. Nucl. Magn. Reson. Spectrosc. 2011, 58, 62– 87 DOI: 10.1016/j.pnmrs.2010.07.004
  Google Scholar
  14
  Interpreting protein chemical shift data
  Wishart, David S.
  Progress in Nuclear Magnetic Resonance Spectroscopy (2011), 58 (1-2), 62-87CODEN: PNMRAT; ISSN:0079-6565. (Elsevier B.V.)
  There is no expanded citation for this reference.
  >> More from SciFinder ^®
  https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3MXmtVKqtg%253D%253D&md5=88c1ea81ee5bc5748b2e7215d946c792
15. 15
  Jeschke, G. DEER Distance Measurements on Proteins Annu. Rev. Phys. Chem. 2012, 63, 419– 446 DOI: 10.1146/annurev-physchem-032511-143716
  Google Scholar
  15
  DEER distance measurements on proteins
  Jeschke, Gunnar
  Annual Review of Physical Chemistry (2012), 63 (), 419-446CODEN: ARPLAP; ISSN:0066-426X. (Annual Reviews Inc.)
  A review. Distance distributions between paramagnetic centers in the range of 1.8 to 6 nm in membrane proteins and up to 10 nm in deuterated sol. proteins can be measured by the DEER technique. The no. of paramagnetic centers and their relative orientation can be characterized. DEER does not require crystn. and is not limited with respect to the size of the protein or protein complex. Diamagnetic proteins are accessible by site-directed spin labeling. To characterize structure or structural changes, exptl. protocols were optimized and techniques for artifact suppression were introduced. Data anal. programs were developed, and it was realized that interpretation of the distance distributions must take into account the conformational distribution of spin labels. First methods have appeared for deriving structural models from a small no. of distance constraints. The present scope and limitations of the technique are illustrated.
  >> More from SciFinder ^®
  https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC38Xnt1Gksr0%253D&md5=d63283b52c83f9d81847d0ce070dbde3
16. 16
  Lohse, M. J.; Hein, P.; Hoffmann, C.; Nikolaev, V. O.; Vilardaga, J. P.; Bunemann, M. Kinetics of G-Protein-Coupled Receptor Signals in Intact Cells Br. J. Pharmacol. 2008, 153 (S1) S125– S132 DOI: 10.1038/sj.bjp.0707656
  Google Scholar
  There is no corresponding record for this reference.
17. 17
  Lohse, M. J.; Nuber, S.; Hoffmann, C. Fluorescence/Bioluminescence Resonance Energy Transfer Techniques to Study G-Protein-Coupled Receptor Activation and Signaling Pharmacol. Rev. 2012, 64, 299– 336 DOI: 10.1124/pr.110.004309
  Google Scholar
  17
  Fluorescence/bioluminescence resonance energy transfer techniques to study G-protein-coupled receptor activation and signaling
  Lohse, Martin J.; Nuber, Susanne; Hoffmann, Carsten
  Pharmacological Reviews (2012), 64 (2), 299-336CODEN: PAREAQ; ISSN:1521-0081. (American Society for Pharmacology and Experimental Therapeutics)
  A review. Fluorescence and bioluminescence resonance energy transfer (FRET and BRETT) techniques allow the sensitive monitoring of distances between two labels at the nanometer scale. Depending on the placement of the labels, this permits the anal. of conformational changes within a single protein (for example of a receptor) or the monitoring of protein-protein interactions (for example, between receptors and G-protein subunits). Over the past decade, numerous such techniques have been developed to monitor the activation and signaling of G-protein-coupled receptors (GPCRs) in both the purified, reconstituted state and in intact cells. These techniques span the entire spectrum from ligand binding to the receptors down to intracellular second messengers. They allow the detn. and the visualization of signaling processes with high temporal and spatial resoln. With these techniques, it has been demonstrated that GPCR signals may show spatial and temporal patterning. In particular, evidence has been provided for spatial compartmentalization of GPCRs and their signals in intact cells and for distinct physiol. consequences of such spatial patterning. We review here the FRET and BRET technologies that have been developed for G-protein-coupled receptors and their signaling proteins (G-proteins, effectors) and the concepts that result from such expts.
  >> More from SciFinder ^®
  https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC38XmslKktr8%253D&md5=76146f70e0e0776aa1d10dae884462aa
18. 18
  Mansoor, S. E.; Dewitt, M. A.; Farrens, D. L. Distance Mapping in Proteins Using Fluorescence Spectroscopy: The Tryptophan-Induced Quenching (TrIQ) Method Biochemistry 2010, 49, 9722– 9731 DOI: 10.1021/bi100907m
  Google Scholar
  18
  Distance Mapping in Proteins Using Fluorescence Spectroscopy: The Tryptophan-Induced Quenching (TrIQ) Method
  Mansoor, Steven E.; DeWitt, Mark A.; Farrens, David L.
  Biochemistry (2010), 49 (45), 9722-9731CODEN: BICHAW; ISSN:0006-2960. (American Chemical Society)
  Studying the interplay between protein structure and function remains a daunting task. Esp. lacking are methods for measuring structural changes in real time. Here the authors report their most recent improvements to a method that can be used to address such challenges. This method, which the authors now call tryptophan-induced quenching (TrIQ), provides a straightforward, sensitive, and inexpensive way to address questions of conformational dynamics and short-range protein interactions. Importantly, TrIQ only occurs over relatively short distances (∼5-15 Å), making it complementary to traditional fluorescence resonance energy transfer (FRET) methods that occur over distances too large for precise studies of protein structure. As implied in the name, TrIQ measures the efficient quenching induced in some fluorophores by tryptophan (Trp). The authors present here an anal. of the TrIQ effect for 5 different fluorophores that span a range of sizes and spectral properties. Each probe was attached to four different cysteine residues on T4 lysozyme, and the extent of TrIQ caused by a nearby Trp was measured. The authors' results show that, at least for smaller probes, the extent of TrIQ is distance dependent. Moreover, the authors also demonstrate how TrIQ data can be analyzed to det. the fraction of fluorophores involved in a static, nonfluorescent complex with Trp. Based on this anal., the authors' study shows that each fluorophore has a different TrIQ profile, or "sphere of quenching", which correlates with its size, rotational flexibility, and the length of attachment linker. This TrIQ-based "sphere of quenching" is unique to every Trp-probe pair and reflects the distance within which one can expect to see the TrIQ effect. Thus,TrIQ provides a straightforward, readily accessible approach for mapping distances within proteins and monitoring conformational changes using fluorescence spectroscopy.
  >> More from SciFinder ^®
  https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3cXhtlalu7%252FP&md5=ff88cce765239dbddedb872c7f41019a
19. 19
  Park, S. H.; Das, B. B.; Casagrande, F.; Tian, Y.; Nothnagel, H. J.; Chu, M.; Kiefer, H.; Maier, K.; De Angelis, A. A.; Marassi, F. M. Structure of the Chemokine Receptor CXCR1 in Phospholipid Bilayers Nature 2012, 491, 779– 783 DOI: 10.1038/nature11580
  Google Scholar
  19
  Structure of the chemokine receptor CXCR1 in phospholipid bilayers
  Park, Sang Ho; Das, Bibhuti B.; Casagrande, Fabio; Tian, Ye; Nothnagel, Henry J.; Chu, Mignon; Kiefer, Hans; Maier, Klaus; De Angelis, Anna A.; Marassi, Francesca M.; Opella, Stanley J.
  Nature (London, United Kingdom) (2012), 491 (7426), 779-783CODEN: NATUAS; ISSN:0028-0836. (Nature Publishing Group)
  CXCR1 is one of two high-affinity receptors for the CXC chemokine interleukin-8 (IL-8), a major mediator of immune and inflammatory responses implicated in many disorders, including tumor growth. IL-8, released in response to inflammatory stimuli, binds to the extracellular side of CXCR1. The ligand-activated intracellular signaling pathways result in neutrophil migration to the site of inflammation. CXCR1 is a class A, rhodopsin-like G-protein-coupled receptor (GPCR), the largest class of integral membrane proteins responsible for cellular signal transduction and targeted as drug receptors. Despite its importance, the mol. mechanism of CXCR1 signal transduction is poorly understood owing to the limited structural information available. Recent structural detn. of GPCRs has advanced by modifying the receptors with stabilizing mutations, insertion of the protein T4 lysozyme and truncations of their amino acid sequences, as well as addn. of stabilizing antibodies and small mols. that facilitate crystn. in cubic phase monoolein mixts. The intracellular loops of GPCRs are crucial for G-protein interactions, and activation of CXCR1 involves both amino-terminal residues and extracellular loops. Our previous NMR studies indicate that IL-8 binding to the N-terminal residues is mediated by the membrane, underscoring the importance of the phospholipid bilayer for physiol. activity. Here we report the three-dimensional structure of human CXCR1 detd. by NMR spectroscopy. The receptor is in liq. cryst. phospholipid bilayers, without modification of its amino acid sequence and under physiol. conditions. Features important for intracellular G-protein activation and signal transduction are revealed. The structure of human CXCR1 in a lipid bilayer should help to facilitate the discovery of new compds. that interact with GPCRs and combat diseases such as breast cancer.
  >> More from SciFinder ^®
  https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC38XhsFCns73O&md5=e6333d33cd9b1ac916dbf2932cea0420
20. 20
  Dror, R. O.; Dirks, R. M.; Grossman, J. P.; Xu, H.; Shaw, D. E. Biomolecular Simulation: A Computational Microscope for Molecular Biology Annu. Rev. Biophys. 2012, 41, 429– 452 DOI: 10.1146/annurev-biophys-042910-155245
  Google Scholar
  20
  Biomolecular simulation: a computational microscope for molecular biology
  Dror, Ron O.; Dirks, Robert M.; Grossman, J. P.; Xu, Huafeng; Shaw, David E.
  Annual Review of Biophysics (2012), 41 (), 429-452CODEN: ARBNCV; ISSN:1936-122X. (Annual Reviews Inc.)
  A review. Mol. dynamics simulations capture the behavior of biol. macromols. in full at. detail, but their computational demands, combined with the challenge of appropriately modeling the relevant physics, have historically restricted their length and accuracy. Dramatic recent improvements in achievable simulation speed and the underlying phys. models have enabled at.-level simulations on timescales as long as milliseconds that capture key biochem. processes such as protein folding, drug binding, membrane transport, and the conformational changes crit. to protein function. Such simulation may serve as a computational microscope, revealing biomol. mechanisms at spatial and temporal scales that are difficult to observe exptl. We describe the rapidly evolving state of the art for at.-level biomol. simulation, illustrate the types of biol. discoveries that can now be made through simulation, and discuss challenges motivating continued innovation in this field.
  >> More from SciFinder ^®
  https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC38Xpt1yhs7s%253D&md5=3f872bcd93c1c2141ef3f020c5c6d45d
21. 21
  Dror, R. O.; Arlow, D. H.; Borhani, D. W.; Jensen, M. O.; Piana, S.; Shaw, D. E. Identification of Two Distinct Inactive Conformations of the Beta2-Adrenergic Receptor Reconciles Structural and Biochemical Observations Proc. Natl. Acad. Sci. U. S. A. 2009, 106, 4689– 4694 DOI: 10.1073/pnas.0811065106
  Google Scholar
  There is no corresponding record for this reference.
22. 22
  Nygaard, R.; Zou, Y.; Dror, R. O.; Mildorf, T. J.; Arlow, D. H.; Manglik, A.; Pan, A. C.; Liu, C. W.; Fung, J. J.; Bokoch, M. P. The Dynamic Process of Beta(2)-Adrenergic Receptor Activation Cell 2013, 152, 532– 542 DOI: 10.1016/j.cell.2013.01.008
  Google Scholar
  22
  The Dynamic Process of β2-Adrenergic Receptor Activation
  Nygaard, Rie; Zou, Yaozhong; Dror, Ron O.; Mildorf, Thomas J.; Arlow, Daniel H.; Manglik, Aashish; Pan, Albert C.; Liu, Corey W.; Fung, Juan Jose; Bokoch, Michael P.; Thian, Foon Sun; Kobilka, Tong Sun; Shaw, David E.; Mueller, Luciano; Prosser, R. Scott; Kobilka, Brian K.
  Cell (Cambridge, MA, United States) (2013), 152 (3), 532-542CODEN: CELLB5; ISSN:0092-8674. (Cell Press)
  G-protein-coupled receptors (GPCRs) can modulate diverse signaling pathways, often in a ligand-specific manner. The full range of functionally relevant GPCR conformations is poorly understood. Here, the authors use NMR spectroscopy to characterize the conformational dynamics of the transmembrane core of the β2-adrenergic receptor (β2AR), a prototypical GPCR. The authors labeled β2AR with 13CH3ε-methionine and obtained HSQC spectra of unliganded receptor as well as receptor bound to an inverse agonist, an agonist, and a G-protein-mimetic nanobody. These studies provide evidence for conformational states not obsd. in crystal structures, as well as substantial conformational heterogeneity in agonist- and inverse-agonist-bound prepns. They also show that for β2AR, unlike rhodopsin, an agonist alone does not stabilize a fully active conformation, suggesting that the conformational link between the agonist-binding pocket and the G-protein-coupling surface is not rigid. The obsd. heterogeneity may be important for β2AR's ability to engage multiple signaling and regulatory proteins.
  >> More from SciFinder ^®
  https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3sXhvFaiu7s%253D&md5=8f9aaa581027657b166b92ef617e950d
23. 23
  Dror, R. O.; Arlow, D. H.; Maragakis, P.; Mildorf, T. J.; Pan, A. C.; Xu, H.; Borhani, D. W.; Shaw, D. E. Activation Mechanism of the Beta2-Adrenergic Receptor Proc. Natl. Acad. Sci. U. S. A. 2011, 108, 18684– 18689 DOI: 10.1073/pnas.1110499108
  Google Scholar
  23
  Activation mechanism of the β2-adrenergic receptor
  Dror, Ron O.; Arlow, Daniel H.; Maragakis, Paul; Mildorf, Thomas J.; Pan, Albert C.; Xu, Huafeng; Borhani, David W.; Shaw, David E.
  Proceedings of the National Academy of Sciences of the United States of America (2011), 108 (46), 18684-18689, S18684/1-S18684/12CODEN: PNASA6; ISSN:0027-8424. (National Academy of Sciences)
  A third of marketed drugs act by binding to a G-protein-coupled, receptor (GPCR) and either triggering or preventing receptor activation. Although recent crystal structures have provided snapshots of both active and inactive functional states of GPCRs, these structures do not reveal the mechanism by which GPCRs transition between these states. Here we propose an activation mechanism for the β2-adrenergic receptor, a prototypical GPCR, based on at.-level simulations in which an agonist-bound receptor transitions spontaneously from the active to the inactive crystallog. obsd. conformation. A loosely coupled allosteric network, comprising three regions that can each switch individually between multiple distinct conformations, links small perturbations at the extracellular drug-binding site to large conformational changes at the intracellular G-protein-binding site. Our simulations also exhibit an intermediate that may represent a receptor conformation to which a G protein binds during activation, and suggest that the first structural changes during receptor activation often take place on the intracellular side of the receptor, far from the drug-binding site. By capturing this fundamental signaling process in at. detail, our results may provide a foundation for the design of drugs that control receptor signaling more precisely by stabilizing specific receptor conformations.
  >> More from SciFinder ^®
  https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3MXhs1Wns7bK&md5=54303d4160a7372ab31cc0e415653eb8
24. 24
  Manglik, A.; Kim, T. H.; Masureel, M.; Altenbach, C.; Yang, Z.; Hilger, D.; Lerch, M. T.; Kobilka, T. S.; Thian, F. S.; Hubbell, W. L. Structural Insights into the Dynamic Process of Beta2-Adrenergic Receptor Signaling Cell 2015, 161, 1101– 1111 DOI: 10.1016/j.cell.2015.04.043
  Google Scholar
  24
  Structural Insights into the Dynamic Process of β2-Adrenergic Receptor Signaling
  Manglik, Aashish; Kim, Tae Hun; Masureel, Matthieu; Altenbach, Christian; Yang, Zhongyu; Hilger, Daniel; Lerch, Michael T.; Kobilka, Tong Sun; Thian, Foon Sun; Hubbell, Wayne L.; Prosser, R. Scott; Kobilka, Brian K.
  Cell (Cambridge, MA, United States) (2015), 161 (5), 1101-1111CODEN: CELLB5; ISSN:0092-8674. (Cell Press)
  G-protein-coupled receptors (GPCRs) transduce signals from the extracellular environment to intracellular proteins. To gain structural insight into the regulation of receptor cytoplasmic conformations by extracellular ligands during signaling, we examine the structural dynamics of the cytoplasmic domain of the β2-adrenergic receptor (β2AR) using 19F-fluorine NMR and double electron-electron resonance spectroscopy. These studies show that unliganded and inverse-agonist-bound β2AR exists predominantly in two inactive conformations that exchange within hundreds of microseconds. Although agonists shift the equil. toward a conformation capable of engaging cytoplasmic G proteins, they do so incompletely, resulting in increased conformational heterogeneity and the coexistence of inactive, intermediate, and active states. Complete transition to the active conformation requires subsequent interaction with a G protein or an intracellular G protein mimetic. These studies demonstrate a loose allosteric coupling of the agonist-binding site and G-protein-coupling interface that may generally be responsible for the complex signaling behavior obsd. for many GPCRs.
  >> More from SciFinder ^®
  https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2MXosVaqsLw%253D&md5=aa8772ca46629b75b503d89f3ad0dd8d
25. 25
  Kobilka, B. K.; Deupi, X. Conformational Complexity of G-Protein-Coupled Receptors Trends Pharmacol. Sci. 2007, 28, 397– 406 DOI: 10.1016/j.tips.2007.06.003
  Google Scholar
  25
  Conformational complexity of G-protein-coupled receptors
  Kobilka, Brian K.; Deupi, Xavier
  Trends in Pharmacological Sciences (2007), 28 (8), 397-406CODEN: TPHSDY; ISSN:0165-6147. (Elsevier B.V.)
  A review. G-protein-coupled receptors (GPCRs) are remarkably versatile signaling mols. Members of this large family of membrane proteins respond to structurally diverse ligands and mediate most transmembrane signal transduction in response to hormones and neurotransmitters, and in response to the senses of sight, smell and taste. Individual GPCRs can signal through several G-protein subtypes and through G-protein-independent pathways, often in a ligand-specific manner. This functional plasticity can be attributed to structural flexibility of GPCRs and the ability of ligands to induce or to stabilize ligand-specific conformations. Here, we review what has been learned about the dynamic nature of the structure and mechanism of GPCR activation, primarily focusing on spectroscopic studies of purified human β2 adrenergic receptor.
  >> More from SciFinder ^®
  https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2sXotlWltLk%253D&md5=dd89d366cec983ffa0526e59950d91ee
26. 26
  Xue, L.; Rovira, X.; Scholler, P.; Zhao, H.; Liu, J.; Pin, J. P.; Rondard, P. Major Ligand-Induced Rearrangement of the Heptahelical Domain Interface in a GPCR Dimer Nat. Chem. Biol. 2015, 11, 134– 140 DOI: 10.1038/nchembio.1711
  Google Scholar
  26
  Major ligand-induced rearrangement of the heptahelical domain interface in a GPCR dimer
  Xue, Li; Rovira, Xavier; Scholler, Pauline; Zhao, Han; Liu, Jianfeng; Pin, Jean-Philippe; Rondard, Philippe
  Nature Chemical Biology (2015), 11 (2), 134-140CODEN: NCBABT; ISSN:1552-4450. (Nature Publishing Group)
  G protein-coupled receptors (GPCRs) are major players in cell communication. Although they form functional monomers, increasing evidence indicates that GPCR dimerization has a crit. role in cooperative phenomena that are important for cell signal integration. However, the structural bases of these phenomena remain elusive. Here, using well-characterized receptor dimers, the metabotropic glutamate receptors (mGluRs), the authors show that structural changes at the dimer interface are linked to receptor activation. The authors demonstrate that the main dimer interface is formed by transmembrane α helix 4 (TM4) and TM5 in the inactive state and by TM6 in the active state. This major change in the dimer interface is required for receptor activity because locking the TM4-TM5 interface prevents activation b

All Types

GPCR Dynamics: Structures in Motion

Article Views

Altmetric

Citations

Abstract

SPECIAL ISSUE

1 Introduction

Figure 1

2 GPCR Movement: An Overview

Figure 2

Figure 3

Figure 4

Figure 5

3 GPCR Activation

3.1 Mechanism of GPCR Activation

Figure 6

Figure 7

3.2 Conservation of Activation Mechanism across GPCRs

Figure 8

4 Conformational Diversity and Biased Signaling

4.1 Diverse Conformational States of a GPCR

Figure 9

4.2 Implications for Biased Signaling

Figure 10

5 Allosteric Modulation of GPCRs

Figure 11

6 Importance of GPCR Dynamics in Drug Discovery

7 Concluding Remarks

Author Information

Biographies

Naomi R. Latorraca

A. J. Venkatakrishnan

Ron O. Dror

Acknowledgment

References

Cited By

Abstract

Figure 1

Figure 2

Figure 3

Figure 4

Figure 5

Figure 6

Figure 7

Figure 8

Figure 9

Figure 10

Figure 11

References