ACS Publications. Most Trusted. Most Cited. Most Read
My Activity

Figure 1Loading Img

A General Method for Mapping Tertiary Contacts between Amino Acid Residues in Membrane-Embedded Proteins

Cite this: Biochemistry 1995, 34, 46, 14963–14969
Publication Date (Print):November 1, 1995
    ACS Legacy Archive

    Article Views





    Other access options

    Note: In lieu of an abstract, this is the article's first page.

    Free first page

    Read this article

    To access this article, please review the available access options below.

    Get instant access

    Purchase Access

    Read this article for 48 hours. Check out below using your ACS ID or as a guest.


    Access through Your Institution

    You may have access to this article through your institution.

    Your institution does not have access to this content. You can change your affiliated institution below.

    Cited By

    This article is cited by 93 publications.

    1. Masahiro Kono and Rosalie K. Crouch . Probing Human Red Cone Opsin Activity with Retinal Analogues. Journal of Natural Products 2011, 74 (3) , 391-394.
    2. Heejung Kim, Byung-Kwon Lee, Fred Naider and Jeffrey M. Becker . Identification of Specific Transmembrane Residues and Ligand-Induced Interface Changes Involved In Homo-Dimer Formation of a Yeast G Protein-Coupled Receptor. Biochemistry 2009, 48 (46) , 10976-10987.
    3. Arianna Rath, David V. Tulumello and Charles M. Deber . Peptide Models of Membrane Protein Folding. Biochemistry 2009, 48 (14) , 3036-3045.
    4. Masahiro Kono, Patrice W. Goletz and Rosalie K. Crouch. 11-cis- and All-trans-Retinols Can Activate Rod Opsin: Rational Design of the Visual Cycle. Biochemistry 2008, 47 (28) , 7567-7571.
    5. Hania Wehbi,, Arianna Rath,, Mira Glibowicka, and, Charles M. Deber. Role of the Extracellular Loop in the Folding of a CFTR Transmembrane Helical Hairpin. Biochemistry 2007, 46 (24) , 7099-7106.
    6. Kevin R. MacKenzie. Folding and Stability of α-Helical Integral Membrane Proteins. Chemical Reviews 2006, 106 (5) , 1931-1977.
    7. Judith S. Landin,, Madan Katragadda, and, Arlene D. Albert. Thermal Destabilization of Rhodopsin and Opsin by Proteolytic Cleavage in Bovine Rod Outer Segment Disk Membranes. Biochemistry 2001, 40 (37) , 11176-11183.
    8. Shiv Kumar Sharma,, Robert M. Jones,, Thomas G. Metzger,, David M. Ferguson, and, Philip S. Portoghese. Transformation of a κ-Opioid Receptor Antagonist to a κ-Agonist by Transfer of a Guanidinium Group from the 5‘- to 6‘-Position of Naltrindole. Journal of Medicinal Chemistry 2001, 44 (13) , 2073-2079.
    9. Negin P. Martin,, LuAnn M. Leavitt,, Christine M. Sommers, and, Mark E. Dumont. Assembly of G Protein-Coupled Receptors from Fragments:  Identification of Functional Receptors with Discontinuities in Each of the Loops Connecting Transmembrane Segments. Biochemistry 1999, 38 (2) , 682-695.
    10. Jack Andrew Bikker,, Susanne Trumpp-Kallmeyer, and, Christine Humblet. G-Protein Coupled Receptors:  Models, Mutagenesis, and Drug Design. Journal of Medicinal Chemistry 1998, 41 (16) , 2911-2927.
    11. M. Seraj Uddin, Fred Naider, Jeffrey M. Becker. Dynamic roles for the N-terminus of the yeast G protein-coupled receptor Ste2p. Biochimica et Biophysica Acta (BBA) - Biomembranes 2017, 1859 (10) , 2058-2067.
    12. Christopher Mulligan, Joseph A. Mindell. Pinning Down the Mechanism of Transport: Probing the Structure and Function of Transporters Using Cysteine Cross-Linking and Site-Specific Labeling. 2017, 165-202.
    13. Kristine A. Mackin, Richard A. Roy, Douglas L. Theobald. An Empirical Test of Convergent Evolution in Rhodopsins. Molecular Biology and Evolution 2014, 31 (1) , 85-95.
    14. Martin J. Lohse, Susanne Nuber, Carsten Hoffmann, . Fluorescence/Bioluminescence Resonance Energy Transfer Techniques to Study G-Protein-Coupled Receptor Activation and Signaling. Pharmacological Reviews 2012, 64 (2) , 299-336.
    15. M. Seraj Uddin, Heejung Kim, Amanda Deyo, Fred Naider, Jeffrey M. Becker. Identification of residues involved in homodimer formation located within a β-strand region of the N-terminus of a Yeast G protein-coupled receptor. Journal of Receptors and Signal Transduction 2012, 32 (2) , 65-75.
    16. Kazumi Sakai, Yasushi Imamoto, Takahiro Yamashita, Yoshinori Shichida. Functional analysis of the second extracellular loop of rhodopsin by characterizing split variants. Photochemical & Photobiological Sciences 2010, 9 (11) , 1490-1497.
    17. Masahiro Kono, Rosalie K. Crouch. In Vitro Assays of Rod and Cone Opsin Activity: Retinoid Analogs as Agonists and Inverse Agonists. 2010, 85-94.
    18. Masahiro Kono. Assays for Inverse Agonists in the Visual System. 2010, 213-224.
    19. Petri Ala-Laurila, M. Carter Cornwall, Rosalie K. Crouch, Masahiro Kono. The Action of 11-cis-Retinol on Cone Opsins and Intact Cone Photoreceptors. Journal of Biological Chemistry 2009, 284 (24) , 16492-16500.
    20. Moez Bali, Michaela Jansen, Myles H. Akabas. GABA-Induced Intersubunit Conformational Movement in the GABA A Receptor α1M1-β2M3 Transmembrane Subunit Interface: Experimental Basis for Homology Modeling of an Intravenous Anesthetic Binding Site. The Journal of Neuroscience 2009, 29 (10) , 3083-3092.
    21. Debarshi Mustafi, Krzysztof Palczewski. Topology of Class A G Protein-Coupled Receptors: Insights Gained from Crystal Structures of Rhodopsins, Adrenergic and Adenosine Receptors. Molecular Pharmacology 2009, 75 (1) , 1-12.
    22. Takahiro Yamashita, Akihisa Terakita, Toshihiro Kai, Yoshinori Shichida. Conformational change of the transmembrane helices II and IV of metabotropic glutamate receptor involved in G protein activation. Journal of Neurochemistry 2008, 106 (2) , 850-859.
    23. Larry H. Matherly, Zhanjun Hou. Chapter 5 Structure and Function of the Reduced Folate Carrier. 2008, 145-184.
    24. Philip L. Yeagle, Arlene D. Albert. G-protein coupled receptor structure. Biochimica et Biophysica Acta (BBA) - Biomembranes 2007, 1768 (4) , 808-824.
    25. Arianna Rath, Rachel M. Johnson, Charles M. Deber. Peptides as transmembrane segments: Decrypting the determinants for helix–helix interactions in membrane proteins. Peptide Science 2007, 88 (2) , 217-232.
    26. Yinan Wei, Dax Fu. Binding and Transport of Metal Ions at the Dimer Interface of the Escherichia coli Metal Transporter YiiP. Journal of Biological Chemistry 2006, 281 (33) , 23492-23502.
    27. Richard B. Jacobsen, Kenneth L. Sale, Marites J. Ayson, Petr Novak, Joohee Hong, Pamela Lane, Nichole L. Wood, Gary H. Kruppa, Malin M. Young, Joseph S. Schoeniger. Structure and dynamics of dark‐state bovine rhodopsin revealed by chemical cross‐linking and high‐resolution mass spectrometry. Protein Science 2006, 15 (6) , 1303-1317.
    28. Mariana Oana Popa, Holger Lerche. Cu 2+ (1,10 phenanthroline) 3 is an open‐channel blocker of the human skeletal muscle sodium channel. British Journal of Pharmacology 2006, 147 (7) , 808-814.
    29. Ligong Chen, Kathleen A. Durkin, John E. Casida. Structural model for γ-aminobutyric acid receptor noncompetitive antagonist binding: Widely diverse structures fit the same site. Proceedings of the National Academy of Sciences 2006, 103 (13) , 5185-5190.
    30. Thue W. Schwartz, Thomas M. Frimurer, Birgitte Holst, Mette M. Rosenkilde, Christian E. Elling. MOLECULAR MECHANISM OF 7TM RECEPTOR ACTIVATION—A GLOBAL TOGGLE SWITCH MODEL. Annual Review of Pharmacology and Toxicology 2006, 46 (1) , 481-519.
    31. Martin B. Ulmschneider, D.Peter Tieleman, Mark S.P. Sansom. The role of extra-membranous inter-helical loops in helix–helix interactions. Protein Engineering, Design and Selection 2005, 18 (12) , 563-570.
    32. Amal K. Bera, Myles H. Akabas. Spontaneous Thermal Motion of the GABAA Receptor M2 Channel-lining Segments. Journal of Biological Chemistry 2005, 280 (42) , 35506-35512.
    33. Anita M. Engh, Merritt Maduke. Cysteine Accessibility in ClC-0 Supports Conservation of the ClC Intracellular Vestibule. The Journal of General Physiology 2005, 125 (6) , 601-617.
    34. Jeffrey Horenstein, Paul Riegelhaupt, Myles H. Akabas. Differential Protein Mobility of the γ-Aminobutyric Acid, Type A, Receptor α and β Subunit Channel-lining Segments. Journal of Biological Chemistry 2005, 280 (2) , 1573-1581.
    35. Julia Adler, Eitan Bibi. Promiscuity in the Geometry of Electrostatic Interactions between the Escherichia coli Multidrug Resistance Transporter MdfA and Cationic Substrates. Journal of Biological Chemistry 2005, 280 (4) , 2721-2729.
    36. Ken Sale, Jean‐Loup Faulon, Genetha A. Gray, Joseph S. Schoeniger, Malin M. Young. Optimal bundling of transmembrane helices using sparse distance constraints. Protein Science 2004, 13 (10) , 2613-2627.
    37. E Padan, T Tzubery, K Herz, L Kozachkov, A Rimon, L Galili. NhaA of Escherichia coli, as a model of a pH-regulated Na+/H+antiporter. Biochimica et Biophysica Acta (BBA) - Bioenergetics 2004, 1658 (1-2) , 2-13.
    38. Kurt Kristiansen. Molecular mechanisms of ligand binding, signaling, and regulation within the superfamily of G-protein-coupled receptors: molecular modeling and mutagenesis approaches to receptor structure and function. Pharmacology & Therapeutics 2004, 103 (1) , 21-80.
    39. Livnat Galili, Katia Herz, Orly Dym, Etana Padan. Unraveling Functional and Structural Interactions between Transmembrane Domains IV and XI of NhaA Na+/H+ Antiporter of Escherichia coli. Journal of Biological Chemistry 2004, 279 (22) , 23104-23113.
    40. Thomas L. Kash, Maria-Johanna F. Dizon, James R. Trudell, Neil L. Harrison. Charged Residues in the β2 Subunit Involved in GABAA Receptor Activation. Journal of Biological Chemistry 2004, 279 (6) , 4887-4893.
    41. David E Paschon, Marc Ostermeier. Construction of Protein Fragment Complementation Libraries Using Incremental Truncation. 2004, 103-116.
    42. Jean‐Loup Faulon, Ken Sale, Malin Young. Exploring the conformational space of membrane protein folds matching distance constraints. Protein Science 2003, 12 (8) , 1750-1761.
    43. Kim Neve, Curtiss DuRand, Martha Teeter. Structural Analysis of the Mammalian D2, D3 and D4 Dopamine Receptors. 2003, 71-128.
    44. Wayne L Hubbell, Christian Altenbach, Cheryl M Hubbell, H.Gobind Khorana. Rhodopsin structure, dynamics, and activation: A perspective from crystallography, site-directed spin labeling, sulfhydryl reactivity, and disulfide cross-linking. 2003, 243-290.
    45. Jan Saam, Emad Tajkhorshid, Shigehiko Hayashi, Klaus Schulten. Molecular Dynamics Investigation of Primary Photoinduced Eventsin the Activation of Rhodopsin. Biophysical Journal 2002, 83 (6) , 3097-3112.
    46. Arlene D. Albert, Philip L. Yeagle. Structural studies on rhodopsin. Biochimica et Biophysica Acta (BBA) - Biomembranes 2002, 1565 (2) , 183-195.
    47. Marı́a L. López-Rodrı́guez, Bruno Vicente, Xavier Deupi, Sergio Barrondo, Mireia Olivella, M. José Morcillo, Bellinda Behamú, Juan A. Ballesteros, Joan Sallés, Leonardo Pardo. Design, Synthesis and Pharmacological Evaluation of 5-Hydroxytryptamine 1a Receptor Ligands to Explore the Three-Dimensional Structure of the Receptor. Molecular Pharmacology 2002, 62 (1) , 15-21.
    48. Tip W. Loo, David M. Clarke. Vanadate trapping of nucleotide at the ATP-binding sites of human multidrug resistance P-glycoprotein exposes different residues to the drug-binding site. Proceedings of the National Academy of Sciences 2002, 99 (6) , 3511-3516.
    49. Carol Deutsch. Potassium Channel Ontogeny. Annual Review of Physiology 2002, 64 (1) , 19-46.
    50. Philip L. Yeagle, Arlene D. Albert. Use of nuclear magnetic resonance to study the three-dimensional structure of rhodopsin. 2002, 223-231.
    51. Sadashiva S. Karnik. Analysis of structure-function from expression of G protein-coupled receptor fragments. 2002, 248-259.
    52. Irache Visiers, Juan A. Ballesteros, Harel Weinstein. Three-dimensional representations of G protein-coupled receptor structures and mechanisms. 2002, 329-371.
    53. Elaine C Meng, Henry R Bourne. Receptor activation: what does the rhodopsin structure tell us?. Trends in Pharmacological Sciences 2001, 22 (11) , 587-593.
    54. Tip W. Loo, David M. Clarke. Determining the Dimensions of the Drug-binding Domain of Human P-glycoprotein Using Thiol Cross-linking Compounds as Molecular Rulers. Journal of Biological Chemistry 2001, 276 (40) , 36877-36880.
    55. Jeffrey Horenstein, David A. Wagner, Cynthia Czajkowski, Myles H. Akabas. Protein mobility and GABA-induced conformational changes in GABAA receptor pore-lining M2 segment. Nature Neuroscience 2001, 4 (5) , 477-485.
    56. David E. Metzler, Carol M. Metzler, David J. Sauke. Lipids, Membranes, and Cell Coats. 2001, 379-453.
    57. Najmoutin G. Abdulaev, Tony Ngo, Ruiwu Chen, Zhijian Lu, Kevin D. Ridge. Functionally Discrete Mimics of Light-activated Rhodopsin Identified through Expression of Soluble Cytoplasmic Domains. Journal of Biological Chemistry 2000, 275 (50) , 39354-39363.
    58. Natalie S Olesnicky, Andrew J Brown, Yoichi Honda, Susan L Dyos, Simon J Dowell, Lorna A Casselton. Self-Compatible B Mutants in Coprinus With Altered Pheromone-Receptor Specificities. Genetics 2000, 156 (3) , 1025-1033.
    59. Roanna C. Padre, James T. Stull. Functional Assembly of Fragments from Bisected Smooth Muscle Myosin Light Chain Kinase. Journal of Biological Chemistry 2000, 275 (35) , 26665-26673.
    60. Peter Dube, Anthony DeCostanzo, James B. Konopka. Interaction between Transmembrane Domains Five and Six of the α-Factor Receptor. Journal of Biological Chemistry 2000, 275 (34) , 26492-26499.
    61. Christopher M. Topham, Lionel Moulédous, Jean-Claude Meunier. On the spatial disposition of the fifth transmembrane helix and the structural integrity of the transmembrane binding site in the opioid and ORL1 G protein-coupled receptor family. Protein Engineering, Design and Selection 2000, 13 (7) , 477-490.
    62. Jean-Luc Popot, Donald M. Engelman. Helical Membrane Protein Folding, Stability, and Evolution. Annual Review of Biochemistry 2000, 69 (1) , 881-922.
    63. Kiweon Cha, Philip J. Reeves, H. Gobind Khorana. Structure and function in rhodopsin: Destabilization of rhodopsin by the binding of an antibody at the N-terminal segment provides support for involvement of the latter in an intradiscal tertiary structure. Proceedings of the National Academy of Sciences 2000, 97 (7) , 3016-3021.
    64. Ulrik Gether. Uncovering Molecular Mechanisms Involved in Activation of G Protein-Coupled Receptors. Endocrine Reviews 2000, 21 (1) , 90-113.
    65. Arlene D. Albert, Philip L. Yeagle. [8] Domain approach to three-dimensional structure of rhodopsin using high-resolution nuclear magnetic resonance. 2000, 107-115.
    66. Mary Struthers, Daniel D. Oprian. [10] Mapping tertiary contacts between amino acid residues within rhodopsin. 2000, 130-143.
    67. Arlene D. Albert, Philip L. Yeagle. Structural aspects of the G-protein receptor, rhodopsin. 2000, 27-51.
    68. W.J. Degrip, K.J. Rothschild. Chapter 1 Structure and mechanism of vertebrate visual pigments. 2000, 1-54.
    69. J. Yao, E. A. Shoubridge. Expression and Functional Analysis of SURF1 in Leigh Syndrome Patients With Cytochrome c Oxidase Deficiency. Human Molecular Genetics 1999, 8 (13) , 2541-2549.
    70. Randal B Bass, Joseph J Falke. The aspartate receptor cytoplasmic domain: in situ chemical analysis of structure, mechanism and dynamics. Structure 1999, 7 (7) , 829-840.
    71. Kevin D. Ridge, Tony Ngo, Stephen S.J. Lee, Najmoutin G. Abdulaev. Folding and Assembly in Rhodopsin. Journal of Biological Chemistry 1999, 274 (30) , 21437-21442.
    72. Søren G.F. Rasmussen, Anne D. Jensen, George Liapakis, Pejman Ghanouni, Jonathan A. Javitch, Ulrik Gether. Mutation of a Highly Conserved Aspartic Acid in the β 2 Adrenergic Receptor: Constitutive Activation, Structural Instability, and Conformational Rearrangement of Transmembrane Segment 6. Molecular Pharmacology 1999, 56 (1) , 175-184.
    73. Fu-Yue Zeng, Amanda Hopp, Andrea Soldner, Jürgen Wess. Use of a Disulfide Cross-linking Strategy to Study Muscarinic Receptor Structure and Mechanisms of Activation. Journal of Biological Chemistry 1999, 274 (23) , 16629-16640.
    74. Harry LeVine. Structural features of heterotrimeric G-protein-coupled receptors and their modulatory proteins. Molecular Neurobiology 1999, 19 (2) , 111-149.
    75. Marc Ostermeier, Andrew E. Nixon, Jae Hoon Shim, Stephen J. Benkovic. Combinatorial protein engineering by incremental truncation. Proceedings of the National Academy of Sciences 1999, 96 (7) , 3562-3567.
    76. Jan Jakubik, Jürgen Wess. Use of a Sandwich Enzyme-linked Immunosorbent Assay Strategy to Study Mechanisms of G Protein-coupled Receptor Assembly. Journal of Biological Chemistry 1999, 274 (3) , 1349-1358.
    77. Jürgen Wess. Molecular Basis of Receptor/G-Protein-Coupling Selectivity. Pharmacology & Therapeutics 1998, 80 (3) , 231-264.
    78. Stathis Frillingos, Miklós Sahin‐Tóth, Jianhua Wu, H. Ronald Kaback. Cys‐scanning mutagenesis: a novel approach to structure—function relationships in polytopic membrane proteins. The FASEB Journal 1998, 12 (13) , 1281-1299.
    79. Karel Konvicka, Frank Guarnieri, Juan A. Ballesteros, Harel Weinstein. A Proposed Structure for Transmembrane Segment 7 of G Protein-Coupled Receptors Incorporating an Asn-Pro/Asp-Pro Motif. Biophysical Journal 1998, 75 (2) , 601-611.
    80. Irina D. Pogozheva, Andrei L. Lomize, Henry I. Mosberg. Opioid Receptor Three-Dimensional Structures from Distance Geometry Calculations with Hydrogen Bonding Constraints. Biophysical Journal 1998, 75 (2) , 612-634.
    81. Ulrik Gether, Brian K. Kobilka. G Protein-coupled Receptors. Journal of Biological Chemistry 1998, 273 (29) , 17979-17982.
    82. Thomas Marti. Refolding of Bacteriorhodopsin from Expressed Polypeptide Fragments. Journal of Biological Chemistry 1998, 273 (15) , 9312-9322.
    83. Sevnur Mandaci, A. Sami Saribas, Fevzi Daldal. Three Dimensional Structure-Based Genetic Modifications of A Bacterial Cytochrome bc1 Complex. 1998, 1487-1492.
    84. William J. Rice, N. Michael Green, David H. MacLennan. Site-directed Disulfide Mapping of Helices M4 and M6 in the Ca2+ Binding Domain of SERCA1a, the Ca2+ ATPase of Fast Twitch Skeletal Muscle Sarcoplasmic Reticulum. Journal of Biological Chemistry 1997, 272 (50) , 31412-31419.
    85. Joyce M Baldwin, Gebhard F.X Schertler, Vinzenz M Unger. An alpha-carbon template for the transmembrane helices in the rhodopsin family of G-protein-coupled receptors 1 1Edited by R. Huber. Journal of Molecular Biology 1997, 272 (1) , 144-164.
    86. A.D Albert, A Watts, P Spooner, G Groebner, J Young, P.L Yeagle. A distance measurement between specific sites on the cytoplasmic surface of bovine rhodopsin in rod outer segment disk membranes. Biochimica et Biophysica Acta (BBA) - Biomembranes 1997, 1328 (1) , 74-82.
    87. Dan Donnelly. The arrangement of the transmembrane helices in the secretin receptor family of G‐protein‐coupled receptors. FEBS Letters 1997, 409 (3) , 431-436.
    88. Henry R Bourne. How receptors talk to trimeric G proteins. Current Opinion in Cell Biology 1997, 9 (2) , 134-142.
    89. CHRISTIAN E. ELLING, KENNETH THIRSTRUP, SØREN M. NIELSEN, SIV A. HJORTH, THUE W. SCHWARTZ. Metal‐Ion Sites as Structural and Functional Probes of Helix–Helix Interactions in 7TM Receptors. Annals of the New York Academy of Sciences 1997, 814 (1) , 142-151.
    90. Jianhua Wu, H. Ronald Kaback. A general method for determining helix packing in membrane proteins in situ : Helices I and II are close to helix VII in the lactose permease of Escherichia coli. Proceedings of the National Academy of Sciences 1996, 93 (25) , 14498-14502.
    91. Tip W. Loo, David M. Clarke. Inhibition of Oxidative Cross-linking between Engineered Cysteine Residues at Positions 332 in Predicted Transmembrane Segments (TM) 6 and 975 in Predicted TM12 of Human P-glycoprotein by Drug Substrates. Journal of Biological Chemistry 1996, 271 (44) , 27482-27487.
    92. Kenneth Thirstrup, Christian E. Elling, Siv A. Hjorth, Thue W. Schwartz. Construction of a High Affinity Zinc Switch in the k-Opioid Receptor. Journal of Biological Chemistry 1996, 271 (14) , 7875-7878.
    93. Kevin D. Ridge, Stephen S.J. Lee, Najmoutin G. Abdulaev. Examining Rhodopsin Folding and Assembly through Expression of Polypeptide Fragments. Journal of Biological Chemistry 1996, 271 (13) , 7860-7867.

    Pair your accounts.

    Export articles to Mendeley

    Get article recommendations from ACS based on references in your Mendeley library.

    Pair your accounts.

    Export articles to Mendeley

    Get article recommendations from ACS based on references in your Mendeley library.

    You’ve supercharged your research process with ACS and Mendeley!

    STEP 1:
    Click to create an ACS ID

    Please note: If you switch to a different device, you may be asked to login again with only your ACS ID.

    Please note: If you switch to a different device, you may be asked to login again with only your ACS ID.

    Please note: If you switch to a different device, you may be asked to login again with only your ACS ID.

    Your Mendeley pairing has expired. Please reconnect