Oxygen Activation and Energy Conservation by Cytochrome c OxidaseClick to copy article linkArticle link copied!
- Mårten Wikström*Mårten Wikström*E-mail: [email protected]Institute of Biotechnology, University of Helsinki, P.O. Box 56, Helsinki FI-00014, FinlandMore by Mårten Wikström
- Klaas KrabKlaas KrabDepartment of Molecular Cell Physiology, Vrije Universiteit, P.O. Box 7161, Amsterdam1007 MC, The NetherlandsMore by Klaas Krab
- Vivek SharmaVivek SharmaInstitute of Biotechnology, University of Helsinki, P.O. Box 56, Helsinki FI-00014, FinlandDepartment of Physics, University of Helsinki, P.O. Box 64, Helsinki FI-00014, FinlandMore by Vivek Sharma
Abstract
This review focuses on the type A cytochrome c oxidases (CcO), which are found in all mitochondria and also in several aerobic bacteria. CcO catalyzes the respiratory reduction of dioxygen (O2) to water by an intriguing mechanism, the details of which are fairly well understood today as a result of research for over four decades. Perhaps even more intriguingly, the membrane-bound CcO couples the O2 reduction chemistry to translocation of protons across the membrane, thus contributing to generation of the electrochemical proton gradient that is used to drive the synthesis of ATP as catalyzed by the rotary ATP synthase in the same membrane. After reviewing the structure of the core subunits of CcO, the active site, and the transfer paths of electrons, protons, oxygen, and water, we describe the states of the catalytic cycle and point out the few remaining uncertainties. Finally, we discuss the mechanism of proton translocation and the controversies in that area that still prevail.
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1. Introduction
Figure 1
Figure 1. Thirteen-subunit A-type CcO is shown with subunits I, II, and III in blue, red, and green, respectively. Ten nuclear-coded accessory subunits are shown with transparent ribbon representation. Lipid bilayer boundaries (dotted lines) and electron, proton, and oxygen paths (arrows) are also marked. Low-spin heme (yellow), high-spin heme (orange), and copper atoms (purple) are displayed. Figure was prepared with VMD (17) software.
2. General Thermodynamics



3. Overall Structure of the Core Subunits
3.1. Subunit I
Figure 2
Figure 2. (A) View of the catalytic subunit I from the P side of the membrane. Three helix clusters III–VI, VII–X, and XI, XII, I and II are shown in blue, green, and red, respectively. Two clusters (green and red) hold the redox-active centers. Three pore regions (filled circles) are found in each of the three clusters. (B) Side view of the cylindrically shaped catalytic subunit. TM helices are shown as ribbons, colored according to residue polarity (polar, green; acidic, red; basic, blue; hydrophobic, white). Hemes (yellow) and CuB (orange), buried in the catalytic subunit, are also displayed.
Figure 3
Figure 3. (A) Top view (from the P side of the membrane) showing histidine ligands of heme cofactors. Two TM helices in subunit I (II and X) that carry conserved histidine residues are marked in red. (B) Side view showing the histidine ligands of the CuB center. Two tandem histidines (H290 and H291) originate from helix VII, whereas the His240-Tyr244 cross-link is from helix VI. As before, hemes and CuB are shown in yellow and orange.
3.2. Subunits II and III
Figure 4
Figure 4. (A) Structure of subunit II. (Inset) CuA center and its ligand sphere. (B) Structure of subunit III. α-Helices and β-sheets are shown in purple and yellow, respectively. Amino acid residues are marked with their one letter codes and numbers. Phosphatidylglycerol (PG) and phosphatidylethanolamine (PE) lipid molecules bound to subunit III are displayed in licorice representation.
4. Structure of the Active Site
Figure 5
Figure 5. Proton-pumping elements in HCO of type A. The D channel of proton transfer is displayed, which comprises the proton-uptake site (D91), the asparagine gate (circled with purple dotted line), the serine zone, and a highly conserved acidic residue, Glu-242. Heme propionate region is highly polar and consists of a water cluster (circled with red dotted line), two arginines, and one acidic residue, Asp-364. Water molecules (yellow), hemes (blue, left, heme a; right, heme a3), CuB (orange), Mg ion (brown), and subunit I (green transparent ribbons) are also shown. Nonpolar cavity where water produced at the active site may be released is shown as a pink “cloud”.
subfamily | PDB id | organisma | distanceb | distancec | distanced |
---|---|---|---|---|---|
A | 5B1A | Bt | 19.41 (11.82) | 13.20 (6.77) | 4.83 |
A | 2GSM | Rs | 19.36 (11.82) | 13.22 (6.95) | 4.89 |
A | 3HB3 | Pd | 19.45 (12.06) | 13.27 (6.73) | 4.62 |
A (quinol oxidase) | 1FFT | Ec | 13.69 (7.79) | 5.30 | |
A (caa3 type) | 2YEV | Tt | 19.47 (11.99) | 13.58 (7.11) | 4.85 |
B | 3S8F | Tt | 19.07 (11.97) | 13.70 (7.36) | 4.87 |
C | 3MK7 | Ps | 19.75 (11.65) | 13.05 (6.00) | 4.58 |
cNOR | 3WFD | Pa | 20.45 (13.34) | 13.88 (6.49) | 4.43 |
qNOR | 3AYF | Gs | 13.73 (6.30) | 4.58 |
Bt, Bos taurus; Rs, Rhodobacter sphaeroides; Pd, Paracoccus denitrificans; Ec, Escherichia coli; Tt, Thermus thermophilus; Ps, Pseudomonas stutzeri; Pa, Pseudomonas aeruginosa; Gs, Geobacillus stearothermophilus.
Metal-to-metal (edge-to-edge) distance between CuA and heme a in A- and B-type oxidases, and same distance between heme c and heme b in C-type oxidases and cNORs.
Fe–Fe distance between low-spin and high-spin heme (edge–edge distance in parentheses),
Distance between the two metals of the BNC
4.1. Synthetic Models
5. Paths of Electrons, Protons, Oxygen, and Water
5.1. Oxygen Channels and the Escape of Water
5.2. Electron Transfer Paths
5.3. Proton Transfer Pathways
5.3.1. D Channel
Figure 6
Figure 6. Proton transfer pathways in type A (A), B (B), and C (C) HCOs.
5.3.2. K Channel
6. Catalytic Cycle
6.1. R and A States
Figure 7
Figure 7. Catalytic cycle. Square encompasses the binuclear site with the heme a3, CuB, and the covalently linked tyrosine (HO-tyr). Distal histidine ligand of heme a3 and the three histidine ligands of CuB are not shown for simplicity. Uptake of protons to complete the chemistry of water formation is shown, but proton pumping is not shown. One proton is pumped across the membrane in each of the one-electron reactions, but for the A → F reaction the situation is more complicated: formation of state PR is linked to loading the PLS from the N side of the membrane; its release to the P side is driven by uptake of the chemical proton in formation of state F (see text). Structures of intermediates R, A, PM, PR, and F are well established (see text), whereas those of states OH and EH are still more hypothetical.
Figure 8
Figure 8. Oxygen-splitting A → PM transition. Density functional theory-based geometry optimizations (def2-SVP/TZVP/BP86/disp3/MARIJ) (148−154) and energy calculations (def2-TZVP/B3LYP/disp3/eps4) (148,149,151,152,155−157) were performed with Turbomole (158) software on large model systems of the BNC. Spin density (α, green; β, pink) are plotted at an isosurface value of 0.01 e/Å3.
intermediate | resonance Raman Fe–O vibration (cm–1) | light absorption maxima (nm)a |
---|---|---|
A (Fe[II]–O2) | 571 | 590, 430 |
P (Fe[IV]═O) | 804 | 607, 442 |
F (Fe[IV]═O) | 785 | 580, 442 |
OH (Fe[III]–OH) | 450 | NA, NA |
In a difference spectrum vs the O state. References to this data are found in the main text.
6.2. P and F States
6.3. O and E States
Figure 9
6.4. Redox Potentials
Em (exp) | Em,7 (exp) | Em,7 (exp) (pmf = 0) | –ΔG0′ (exp) | –ΔG0′ (Kaukonen) | –ΔG0′ (Blomberg) | |
---|---|---|---|---|---|---|
PM → F | 375 (pH 7.7) | 417 | 857 | 607 | 798 | 871 |
F → OH | 350 (pH 7.2) | 362 | 802 | 552 | 332 | 477 |
OH → EH | (660) | (410) | 342 | 277 | ||
EH → R | (660) | (410) | 518 | 316 | ||
R → Ab | 0 | –41 | 43 | |||
A → PMc | 220 | 124 | 225 |
Em cyt c = 250 mV; Em O2/H2O= 800 mV; pmf assumed at 220 mV. Experimental observations from ref (162). Conversion to pH = 7 and pmf = 0 (Wikström and Verkhovsky (176)). Computational data from Kaukonen (146) and Blomberg (180) converted with Em (cyt c) = 250 mV and Em (O2) = 800 mV. Note that the Em,7 values for the PM/F, F/OH, OH/EH, and EH/R redox transitions are related to the corresponding values of −ΔG0′ by adding 250 mV (the Em,7 of cyt c). The values in parentheses for the OH → EH and EH → R redox reactions were obtained from the known sum of all of the −ΔG0′ (exp) values (i.e., 2200 meV), from which the experimental and calculated values of the other transitions were subtracted. The obtained sum of −ΔG0′ (exp) values for the OH → EH and EH → R transitions was assumed to be distributed equally between them.
These values are based on the equilibrium constant of O2 binding and differ slightly due to different assumed O2 activities.
This value is obtained from the equilibrium constant as estimated by DFT calculations
Figure 10
Figure 10. Redox potentials. Redox potentials for the four one-electron reactions reducing O2 to water are shown in blue for the reaction in aqueous solution (93) and in red for the reactions catalyzed by cytochrome c oxidase (Table 3). Note that the ordinate may also be the standard change in Gibbs free energy (−ΔG0′, in meV), which is obtained by subtracting 250 mV from the Em,7 values plotted. Red point at 2.5 reaction equivalents is not an Em,7 value but the combined −ΔG0′ value for the reactions R → A and A → PM to which 250 mV was added (cf. Table 3).
7. Proton Translocation
7.1. General Principles
7.2. Proton-Pumping Mechanism in Type A Cytochrome c Oxidases
Figure 11
Figure 11. Proton pump mechanism. Mechanism is depicted as revealed from time-resolved electron injection experiments of the OH → EH transition (172,178) but revised from ref (178) to account for the effect of mutating the K channel lysine, which blocks the 150 μs phase. (98,172) The 150 μs phase includes protonation and movement of lysine-319 closer to the BNC (blue circle below heme a3), which is necessary to allow electron transfer from heme a to heme a3 and the linked uptake to the PLS of the proton to be pumped (blue circle above heme a3) in states marked III and IV, respectively. Red color indicates the position of the injected electron.
7.3. Prevention of Leaks
7.4. Proposed Alternative Mechanisms
7.4.1. Role of the so-Called H-Channel
7.4.2. Linkage of the Proton Pump to the Catalytic Cycle
7.4.3. Linkage of the Proton Pump to Oxidoreduction of Heme a
8. Conclusions in Brief
Biographies
Mårten Wikström
Mårten Wikström received his M.D. and Ph.D. degrees at the University of Helsinki in 1971, after which he spent 1 year as a postdoctoral researcher at the University of Amsterdam with Professor E. C. Slater. In 1975–1976 he was Visiting Associate Professor at the University of Pennsylvania with Professor Britton Chance. He worked as an assistant professor at the University of Helsinki until 1983, when he was appointed to a personal Chair in Medical Chemistry (changed to Physical Biochemistry in 2002). In the period 1996–2006 he was Research Professor of the Academy of Finland and from 1998 to 2013 Research Director of the Structural Biology and Biophysics Program of the Institute of Biotechnology. He retired in 2013 but continues as Emeritus Professor. He was the recipient of the Anniversary Prize of the Federation of European Biochemical Societies (FEBS) in 1977, the Scandinavian Anders Jahre Prize in Medicine in 1984 and 1996, and the David Keilin Prize and Medal (British Biochemical Society) in 1997, and he gave the Peter Mitchell Medal Lecture in 2000. He is an elected member of Societas Scientiarum Fennica (1982), the European Molecular Biology Organization (1985), The Royal Swedish Academy of Sciences (chemistry, 1992), and Academia Europaea (2010). His research interests are in molecular bioenergetics, membrane proteins, electron transfer, proton translocation, and mitochondrial diseases
Klaas Krab
Klaas Krab received his Ph.D. degree at the University of Amsterdam in 1977 in the group of Professor E. C. Slater. Then he spent 2 years as a postdoctoral researcher at the University of Helsinki in the group of Mårten Wikström and 3 years at the Vrije Universiteit Amsterdam in the group of Professor A. H. Stouthamer. From 1983 to his retirement in 2015 he worked first as Assistant Professor and then as Associate Professor in the groups of Professor R. Kraayenhof and Professor H. V. Westerhoff at the same university. Since his retirement he is a guest in the group of Westerhoff.
Vivek Sharma
Vivek Sharma is an Academy of Finland Research Fellow and Principal Investigator at the Department of Physics and also at the Institute of Biotechnology, University of Helsinki. He was earlier an Academy of Finland Postdoctoral Researcher in the group of Professor Ilpo Vattulainen at the Tampere University of Technology, Finland. He completed his doctoral degree in the group of Professor Mårten Wikström. His research interests include determining the molecular mechanism and function of mitochondrial proteins, which he studies with multiscale computational methods.
Acknowledgments
This work was supported by Societas Scientiarum Fennica (MW), the Magnus Ehrnrooth Foundation (MW, VS), and the Academy of Finland (VS). M.W. is grateful to Jonathan P. Hosler, Peter R. Rich, and Denis L. Rousseau for helpful comments and access to unpublished material. V.S. is thankful to the Center for Scientific Computing, Finland, for computational resources.
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- 10Mitchell, P. Coupling of Phosphorylation to Electron and Hydrogen Transfer by a Chemi-Osmotic Type of Mechanism. Nature 1961, 191, 144– 148, DOI: 10.1038/191144a0Google Scholar10https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaF38XjtlarsA%253D%253D&md5=6ef71504f7b06641ddcbe73833a68227Coupling of phosphorylation to electron and hydrogen transfer by a chemiosmotic type of mechanismMitchell, PeterNature (London, United Kingdom) (1961), 191 (), 144-8CODEN: NATUAS; ISSN:0028-0836.A chemiosmotic mechanism dependent on the supramol. organization (membrane structure) of multienzyme systems is proposed in contrast to the orthodox substrate-enzyme type of coupling. The driving force is postulated as due to spatially directed diffusion of the active components. An essential requirement is the presence within an ion-impermeable membrane of an anisotropic reversible adenosine triphosphatase (ATPase) system (active center). In such an active center (e.g. phosphokinase), the hydrolysis equil. in the adenosine triphosphate (ATP)-adenosine diphosphate (ADP) system is detd. by the electrochem. activity of the H2O at the active center, [H2O]c = [H+]R[OH]L = [H+]R[H2O]aq./[H+]L where R (right) and L (left) designate the cytoplasmic and intracellular aq. phases, resp. The electrochem. activity ratio for the enzyme system, including the elements of H2O, is given as: [ATP]/[ADP] = {[P]/K[H2O]} {[H+]L/[H+]R}. At pH 7, K1[H2O]aq. ∼105; where [P] is at physiol. levels (approx. 10-2M), the ratio is: [ATP]/[ADP] equal or nearly equal to {[H+]L/[H+]R} × 10-7. Reversal of enzyme activity is kinetically explained on the basis of the electrochem. activity gradient of H+ and OH- across the active center. The fundamental processes essentially involve dehydroxylation and deprotonation. The [H+] and [OH-] gradients are governed by an anisotropic electron-chain transfer (reoxidn.-redn.) mechanism coupled to the reversible ATPase system of the active center. One ATP mol. is produced per electron transfer when the oxidn.-redn. and phosphorylation systems are in chemiosmotic equil. The energy relation is expressed as [ATP]/[ADP] = {[P]/105} × 10ΔE/60, where ΔE (the oxidn.-redn. span) is equiv. to the free energy change in mv./electron transferred. At inorg. phosphate concns. of 10-2M this would require a min. ΔE of 420 mv. to drive the ATP synthesis. Such energies are readily available through the coenzyme (nucleotides, flavoproteins, ubiquinones) and the carboxylic acid (succinic-fumarate) systems. Diagrammatic representations are shown for the coupling systems. Loose membrane structures (or equiv. uncoupling agents like dinitrophenols) are postulated as disrupting the chemiosmotic coupling mechanism with consequent change in the energy relations of the steady state. The chemiosmotic hypothesis is utilized to explain photophosphorylation and also a number of other facts (absence of energy-rich intermediates; dependence of coupling on membrane structure and its ion impermeability; differential effects of [H+]; action of uncoupling agents; membrane swelling and shrinkage) difficult to reconcile on the basis of classical concepts. In some concluding speculations, membrane transport and metabolism are considered as simply different aspects of a unifying process, termed vectorial metabolism.
- 11Wikstrom, M. K. Proton Pump Coupled to Cytochrome C Oxidase in Mitochondria. Nature 1977, 266, 271– 273, DOI: 10.1038/266271a0Google Scholar11https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaE2sXksl2kur8%253D&md5=317ddc9b5e4f943aa9b253af16cc1fc0Proton pump coupled to cytochrome c oxidase in mitochondriaWikstrom, Marten K. F.Nature (London, United Kingdom) (1977), 266 (5599), 271-3CODEN: NATUAS; ISSN:0028-0836.Oxidn. of Fe(CN)64- by O through cytochrome c and cytochrome oxidase resulted in a net release of H+ by isolated rat liver mitochondria into the extramitochondrial phase. The stoichiometry of the initial phase was 1 H+ released per oxidized Fe(CN)64-, with Fe(CN)64- pulses between 0.13 and 1.35mM. After the initial H+ release, alkalinization due to formation of H2O from H+ and O2 occurred. Negligible H+ ejection was obsd. with Fe(CN)63- or with Fe(CN)64- plus CN-. The redox activity of mitochondrial cytochrome c oxidase is coupled therefore to the translocation of H+ across the inner mitochondrial membrane, decaying as the protonmotive force decayed primarily due to increased internal acidity. Possible arrangements of the H+ pump-cytochrome c oxidase system in mitochondria are discussed.
- 12Kim, Y. C.; Wikström, M.; Hummer, G. Kinetic Models of Redox-Coupled Proton Pumping. Proc. Natl. Acad. Sci. U. S. A. 2007, 104, 2169– 2174, DOI: 10.1073/pnas.0611114104Google Scholar12https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2sXisVWrsLw%253D&md5=023c95fa02c571c14b05224bb4a9602eKinetic models of redox-coupled proton pumpingKim, Young C.; Wikstroem, Marten; Hummer, GerhardProceedings of the National Academy of Sciences of the United States of America (2007), 104 (7), 2169-2174CODEN: PNASA6; ISSN:0027-8424. (National Academy of Sciences)Cytochrome c oxidase, the terminal enzyme of the respiratory chain, pumps protons across the inner mitochondrial membrane against an opposing electrochem. gradient by reducing oxygen to water. To explore the fundamental mechanisms of such redox-coupled proton pumps, we develop kinetic models at the single-mol. level consistent with basic phys. principles. We demonstrate that pumping against potentials > 150 mV can be achieved purely through electrostatic couplings, given an asym. arrangement of charge centers; however, nonlinear gates are essential for highly efficient real enzymes. The fundamental requirements for proton pumping identified here highlight a possible evolutionary origin of cytochrome c oxidase pumping. The general design principles are relevant also for other mol. machines and suggest future applications in biol.-inspired fuel cells.
- 13Rauhamäki, V.; Wikström, M. The Causes of Reduced Proton-Pumping Efficiency in Type B and C Respiratory Heme-Copper Oxidases, and in Some Mutated Variants of Type A. Biochim. Biophys. Acta, Bioenerg. 2014, 1837, 999– 1003, DOI: 10.1016/j.bbabio.2014.02.020Google Scholar13https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2cXktVSqsLw%253D&md5=2f00ce7ae7e0b91cb7dabce6914232b6The causes of reduced proton-pumping efficiency in type B and C respiratory heme-copper oxidases, and in some mutated variants of type ARauhamaki, Virve; Wikstrom, MartenBiochimica et Biophysica Acta, Bioenergetics (2014), 1837 (7), 999-1003CODEN: BBBEB4; ISSN:0005-2728. (Elsevier B. V.)The heme-copper oxidases may be divided into three categories, A, B, and C, which include cytochrome c and quinol-oxidizing enzymes. All three types are known to be proton pumps and are found in prokaryotes, whereas eukaryotes only contain A-type cytochrome c oxidase in their inner mitochondrial membrane. However, the bacterial B- and C-type enzymes have often been reported to pump protons with an H+/e- ratio of only one half of the unit stoichiometry in the A-type enzyme. We will show here that these observations are likely to be the result of difficulties with the measuring technique t;ogether with a higher sensitivity of the B- and C-type enzymes to the protonmotive force that opposes pumping. We find that under optimal conditions the H+/e- ratio is close to unity in all the three heme-copper oxidase subfamilies. A higher tendency for proton leak in the B- and C-type enzymes may result from less efficient gating of a proton pump mechanism that we suggest evolved before the so-called D-channel of proton transfer. There is also a discrepancy between results using whole bacterial cells vs. phospholipid vesicles inlaid with oxidase with respect to the obsd. proton pumping after modification of the D-channel residue asparagine-139 (Rhodobacter sphaeroides numbering) to aspartate in A-type cytochrome c oxidase. This discrepancy might also be explained by a higher sensitivity of proton pumping to protonmotive force in the mutated variant. This article is part of a Special Issue entitled: 18th European Bioenergetic Conference.
- 14Han, H.; Hemp, J.; Pace, L. A.; Ouyang, H.; Ganesan, K.; Roh, J. H.; Daldal, F.; Blanke, S. R.; Gennis, R. B. Adaptation of Aerobic Respiration to Low O2 Environments. Proc. Natl. Acad. Sci. U. S. A. 2011, 108, 14109– 14114, DOI: 10.1073/pnas.1018958108Google Scholar14https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3MXhtFaqt73O&md5=7263ca9503de52c48e9c30ba889642d2Adaptation of aerobic respiration to low O2 environmentsHan, Huazhi; Hemp, James; Pace, Laura A.; Ouyang, Hanlin; Ganesan, Krithika; Roh, Jung Hyeob; Daldal, Fevzi; Blanke, Steven R.; Gennis, Robert B.Proceedings of the National Academy of Sciences of the United States of America (2011), 108 (34), 14109-14114, S14109/1-S14109/2CODEN: PNASA6; ISSN:0027-8424. (National Academy of Sciences)Aerobic respiration in bacteria, archaea, and mitochondria is performed by oxygen reductase members of the heme-copper oxidoreductase superfamily. These enzymes are redox-driven proton pumps which conserve part of the free energy released from O2 redn. to generate a protonmotive force. The oxygen reductases can be divided into 3 main families based on evolutionary and structural analyses (A-, B- and C-families), with the B- and C-families evolving after the A-family. The A-family utilizes 2 proton input channels to transfer protons for pumping and chem., whereas the B- and C-families require only 1. Generally, the B- and C-families also have higher apparent O2 affinities than the A-family. Here, the authors used whole cell proton pumping measurements to demonstrate differential proton pumping efficiencies between representatives of the A-, B-, and C-oxygen reductase families. The A-family had a coupling stoichiometry of 1 H+/e-, whereas the B- and C-families had coupling stoichiometries of 0.5 H+/e-. The differential proton pumping stoichiometries, along with differences in the structures of the proton-conducting channels, place crit. constraints on models of the mechanism of proton pumping. Most significantly, it is proposed that the adaptation of aerobic respiration to low O2 environments results in a concomitant redn. in energy conservation efficiency, with important physiol. and ecol. consequences.
- 15Hendriks, J. H.; Jasaitis, A.; Saraste, M.; Verkhovsky, M. I. Proton and Electron Pathways in the Bacterial Nitric Oxide Reductase†,⊥. Biochemistry 2002, 41, 2331– 2340, DOI: 10.1021/bi0121050Google ScholarThere is no corresponding record for this reference.
- 16Watmough, N. J.; Field, S. J.; Hughes, R. J.; Richardson, D. J. The Bacterial Respiratory Nitric Oxide Reductase; Portland Press Ltd.: London, UK, 2009.Google ScholarThere is no corresponding record for this reference.
- 17Humphrey, W.; Dalke, A.; Schulten, K. Vmd: Visual Molecular Dynamics. J. Mol. Graphics 1996, 14, 33– 38, DOI: 10.1016/0263-7855(96)00018-5Google Scholar17https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaK28Xis12nsrg%253D&md5=1e3094ec3151fb85c5ff05f8505c78d5VDM: visual molecular dynamicsHumphrey, William; Dalke, Andrew; Schulten, KlausJournal of Molecular Graphics (1996), 14 (1), 33-8, plates, 27-28CODEN: JMGRDV; ISSN:0263-7855. (Elsevier)VMD is a mol. graphics program designed for the display and anal. of mol. assemblies, in particular, biopolymers such as proteins and nucleic acids. VMD can simultaneously display any no. of structures using a wide variety of rendering styles and coloring methods. Mols. are displayed as one or more "representations," in which each representation embodies a particular rendering method and coloring scheme for a selected subset of atoms. The atoms displayed in each representation are chosen using an extensive atom selection syntax, which includes Boolean operators and regular expressions. VMD provides a complete graphical user interface for program control, as well as a text interface using the Tcl embeddable parser to allow for complex scripts with variable substitution, control loops, and function calls. Full session logging is supported, which produces a VMD command script for later playback. High-resoln. raster images of displayed mols. may be produced by generating input scripts for use by a no. of photorealistic image-rendering applications. VMD has also been expressly designed with the ability to animate mol. dynamics (MD) simulation trajectories, imported either from files or from a direct connection to a running MD simulation. VMD is the visualization component of MDScope, a set of tools for interactive problem solving in structural biol., which also includes the parallel MD program NAMD, and the MDCOMM software used to connect the visualization and simulation programs, VMD is written in C++, using an object-oriented design; the program, including source code and extensive documentation, is freely available via anonymous ftp and through the World Wide Web.
- 18Dutton, P. L.; Wilson, D. F.; Lee, C.-P. Oxidation-Reduction Potentials of Cytochromes in Mitochondria. Biochemistry 1970, 9, 5077– 5082, DOI: 10.1021/bi00828a006Google Scholar18https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaE3MXkvFGrtw%253D%253D&md5=0b768a5eabd01bd3bf110457b3aeba1dOxidation-reduction ptoentials of cytochromes in mitochondriaDutton, P. Leslie; Wilson, David Franklin; Lee, Chuan-PuBiochemistry (1970), 9 (26), 5077-82CODEN: BICHAW; ISSN:0006-2960.Anaerobic techniques were developed to permit the simultaneous potentiometric and spectrophotometric assay of oxidn.-redn. of cytochromes in the mitochondrial membrane over a continuous potential range from +400 to -200 mV. The oxidn.-redn. midpoint potentials (Em) at pH 7.2 of the cytochromes of beef heart mitochondrial prepns. are as follows: a3, +365 mV; a, +205 mV; c + c1, +227 mV; b, +38 mV. Two other membrane-bound components, which like cytochrome b undergo spectral changes at 430 and 562 nm during oxidn. and redn., have Em values +125 and -103 mV at pH 7.2. In pigeon heart mitochondria cytochrome c + c1 has Em +233 mV at pH 7.2, and 2 b-type cytochromes have Em values -15 and -100 mV at pH 8.1. The Em of sol. cytochrome c is sensitive to the nature of the buffer in which it is dissolved; the Em is lowered by as much as 60 mV on binding inside beef heart submitochondrial particles. Isolated cytochrome c1, Em +225 mV (pH 7.0), has a similar Em to that obsd. in the mitochondrial membrane.
- 19Ndubuizu, O.; LaManna, J. C. Brain Tissue Oxygen Concentration Measurements. Antioxid. Redox Signaling 2007, 9, 1207– 1220, DOI: 10.1089/ars.2007.1634Google Scholar19https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2sXot1Wkt7c%253D&md5=629afd54ba2f16a6a44727d8e03ade42Brain tissue oxygen concentration measurementsNdubuizu, Obinna; LaManna, Joseph C.Antioxidants & Redox Signaling (2007), 9 (8), 1207-1219CODEN: ARSIF2; ISSN:1523-0864. (Mary Ann Liebert, Inc.)A review. Brain function depends exquisitely on oxygen for energy metab. Measurements of brain tissue oxygen tension, by a variety of quant. and qual. techniques, going back for >50 years, have led to a no. of significant conclusions. These conclusions have important consequences for understanding brain physiol. as it is now being explored by techniques such as blood-oxygen-level-dependent functional magnetic resonance imaging (BOLD fMRI) and near-IR spectroscopy (NIRS). It has been known for some time that most of the measured oxygen tensions are less than venous pO2 and are distributed in a spatially and temporally heterogeneous manner on a microregional scale. Although certain large-scale methods can provide reproducible av. brain pO2 measurements, no useful concept of a characteristic oxygen tension or meaningful av. value for brain tissue oxygen can be known on a microregional level. Only an oxygen field exists with large local gradients due to local tissue respiration, and the most useful way to express this is with a pO2 distribution curve or histogram. The neurons of the brain cortex normally exist in a low-oxygen environment and on activation are oxygenated by increases in local capillary blood flow that lead to increases in Hb satn. and tissue oxygen.
- 20Hinkle, P. C. P/O Ratios of Mitochondrial Oxidative Phosphorylation. Biochim. Biophys. Acta, Bioenerg. 2005, 1706, 1– 11, DOI: 10.1016/j.bbabio.2004.09.004Google Scholar20https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2cXhtFGht77I&md5=50aff8ad7c54cfc6eeeae1ec8cc59f56P/O ratios of mitochondrial oxidative phosphorylationHinkle, Peter C.Biochimica et Biophysica Acta, Bioenergetics (2005), 1706 (1-2), 1-11CODEN: BBBEB4; ISSN:0005-2728. (Elsevier B.V.)A review. Mitochondrial mechanistic P/O ratios (the no. of ATP mols. produced per O atom reduced by the respiratory chain) are still in question. The major studies since 1937 are summarized and various systematic errors are discussed. Values of approx. 2.5 with NADH-linked substrates and 1.5 with succinate are consistent with most reports after apparent contradictions have been explained. Variability of coupling may occur under some conditions but is generally not significant. The fractional values result from the coupling ratios of proton transport. An addnl. revision of P/O ratios may be required because of a report of the structure of ATP synthase which suggests that the H+/ATP ratio is 10/3, rather than 3, consistent with P/O ratios of 2.3 with NADH and 1.4 with succinate, values that are also possible.
- 21Chamalaun, R.; Tager, J. Stoicheiometry of Oxidative Phosphorylation with Tetramethyl-P-Phenylenediamine in Rat-Liver Mitochondria. Biochim. Biophys. Acta, Bioenerg. 1969, 180, 204– 206, DOI: 10.1016/0005-2728(69)90211-4Google Scholar21https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaF1MXksVGktLk%253D&md5=ad12d80ffa24f13258d5d63282acf688Stoichiometry of oxidative phosphorylation with tetramethyl-p-phenylenediamine in rat-liver mitochondriaChamalaun, R. A. F. M.; Tager, J. M.Biochimica et Biophysica Acta, Bioenergetics (1969), 180 (1), 204-6CODEN: BBBEB4; ISSN:0005-2728.A study was made of the stoichiometry of O uptake, ascorbate disappearance, and phosphate esterification in the presence of tetramethyl-p-phenylenediamine in rat-liver mitochondria. Measurements were obtained in the presence of arsenite or rotenone to minimize any contribution from endogenous substrate. A mean value of 0.94 was obtained for the P:O ratio. The data suggest that although there is only 1 phosphorylation site in the terminal region of the respiratory chain, another reaction leading to the synthesis of ATP occurred.
- 22Watt, I. N.; Montgomery, M. G.; Runswick, M. J.; Leslie, A. G.; Walker, J. E. Bioenergetic Cost of Making an Adenosine Triphosphate Molecule in Animal Mitochondria. Proc. Natl. Acad. Sci. U. S. A. 2010, 107, 16823– 16827, DOI: 10.1073/pnas.1011099107Google Scholar22https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3cXht1OlsLbF&md5=748ab1724baed460609923cceb3a5827Bioenergetic cost of making an adenosine triphosphate molecule in animal mitochondriaWatt, Ian N.; Montgomery, Martin G.; Runswick, Michael J.; Leslie, Andrew G. W.; Walker, John E.Proceedings of the National Academy of Sciences of the United States of America (2010), 107 (39), 16823-16827, S16823/1-S16823/4CODEN: PNASA6; ISSN:0027-8424. (National Academy of Sciences)The catalytic domain of the F-ATPase in mitochondria protrudes into the matrix of the organelle, and is attached to the membrane domain by central and peripheral stalks. Energy for the synthesis of ATP from ADP and phosphate is provided by the transmembrane proton-motive-force across the inner membrane, generated by respiration. The proton-motive force is coupled mech. to ATP synthesis by the rotation at about 100 times per s of the central stalk and an attached ring of c-subunits in the membrane domain. Each c-subunit carries a glutamate exposed around the midpoint of the membrane on the external surface of the ring. The rotation is generated by protonation and deprotonation successively of each glutamate. Each 360° rotation produces three ATP mols., and requires the translocation of one proton per glutamate by each c-subunit in the ring. In fungi, eubacteria, and plant chloroplasts, ring sizes of c10-c15 subunits have been obsd., implying that these enzymes need 3.3-5 protons to make each ATP, but until now no higher eukaryote has been examd. As shown here in the structure of the bovine FI-c-ring complex, the c-ring has eight c-subunits. As the sequences of c-subunits are identical throughout almost all vertebrates and are highly conserved in invertebrates, their F-ATPases probably contain c8-rings also. Therefore, in about 50,000 vertebrate species, and probably in many or all of the two million invertebrate species, 2.7 protons are required by the F-ATPase to make each ATP mol.
- 23Wikström, M.; Hummer, G. Stoichiometry of Proton Translocation by Respiratory Complex I and Its Mechanistic Implications. Proc. Natl. Acad. Sci. U. S. A. 2012, 109, 4431– 4436, DOI: 10.1073/pnas.1120949109Google Scholar23https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC38XkvF2mtr8%253D&md5=1e4456993c98f20b6c9f837bea837781Stoichiometry of proton translocation by respiratory complex I and its mechanistic implicationsWikstrom, Marten; Hummer, GerhardProceedings of the National Academy of Sciences of the United States of America (2012), 109 (12), 4431-4436CODEN: PNASA6; ISSN:0027-8424. (National Academy of Sciences)Complex I (NADH-ubiquinone reductase) in the respiratory chain of mitochondria and several bacteria functions as a redox-driven proton pump that contributes to the generation of the protonmotive force across the inner mitochondrial or bacterial membrane and thus to the aerobic synthesis of ATP. The stoichiometry of. proton translocation-is thought to be 4 H+ per NADH oxidized (2 e-). Here, the authors show that a H+/2 e- ratio of 3 appears more likely on the basis of the recently detd. H+/ATP ratio of the mitochondrial F0F1-ATP synthase of animal mitochondria and of a set of carefully detd. ATP/2 e- ratios for different segments of the mitochondrial respiratory chain. This lower H+/2 e- ratio of 3 is independently supported by thermodn. analyses of expts. with both mitochondria and submitochondrial particles. A reduced H+/2 e- stoichiometry of 3 has important mechanistic implications for this proton pump. In a rough mechanistic model, the authors suggest a concerted proton translocation mechanism in the 3 homologous and tightly packed antiporter-like subunits L, M, and N of the proton-translocating membrane domain of complex I.
- 24Ludwig, B.; Bender, E.; Arnold, S.; Hüttemann, M.; Lee, I.; Kadenbach, B. Cytochrome C Oxidase and the Regulation of Oxidative Phosphorylation. ChemBioChem 2001, 2, 392– 403, DOI: 10.1002/1439-7633(20010601)2:6<392::AID-CBIC392>3.0.CO;2-NGoogle Scholar24https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A280%3ADC%252BD38%252Fpsl2rtA%253D%253D&md5=b7d00beee960fc18505c7c7fd7fb8391Cytochrome C oxidase and the regulation of oxidative phosphorylationLudwig B; Bender E; Arnold S; Huttemann M; Lee I; Kadenbach BChembiochem : a European journal of chemical biology (2001), 2 (6), 392-403 ISSN:1439-4227.Life of higher organisms is essentially dependent on the efficient synthesis of ATP by oxidative phosphorylation in mitochondria. An important and as yet unsolved question of energy metabolism is how are the variable rates of ATP synthesis at maximal work load during exercise or mental work and at rest or during sleep regulated. This article reviews our present knowledge on the structure of bacterial and eukaryotic cytochrome c oxidases and correlates it with recent results on the regulatory functions of nuclear-coded subunits of the eukaryotic enzyme, which are absent from the bacterial enzyme. A new molecular hypothesis on the physiological regulation of oxidative phosphorylation is proposed, assuming a hormonally controlled dynamic equilibrium in vivo between two states of energy metabolism, a relaxed state with low ROS (reactive oxygen species) formation, and an excited state with elevated formation of ROS, which are known to accelerate aging and to cause degenerative diseases and cancer. The hypothesis is based on the allosteric ATP inhibition of cytochrome c oxidase at high intramitochondrial ATP/ADP ratios ("second mechanism of respiratory control"), which is switched on by cAMP-dependent phosphorylation and switched off by calcium-induced dephosphorylation of the enzyme.
- 25Kadenbach, B.; Hüttemann, M. The Subunit Composition and Function of Mammalian Cytochrome C Oxidase. Mitochondrion 2015, 24, 64– 76, DOI: 10.1016/j.mito.2015.07.002Google Scholar25https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2MXht1CrtbfE&md5=350f63622051dad9ec54d8d8f82d7e5fThe subunit composition and function of mammalian cytochrome c oxidaseKadenbach, Bernhard; Huettemann, MaikMitochondrion (2015), 24 (), 64-76CODEN: MITOCN; ISSN:1567-7249. (Elsevier B.V.)A review. Cytochrome c oxidase (COX) from mammals and birds is composed of 13 subunits. The three catalytic subunits I-III are encoded by mitochondrial DNA, the ten nuclear-coded subunits (IV, Va, Vb, VIa, VIb, VIc, VIIa, VIIb, VIIc, VIII) by nuclear DNA. The nuclear-coded subunits are essentially involved in the regulation of oxygen consumption and proton translocation by COX, since their removal or modification changes the activity and their mutation causes mitochondrial diseases. Respiration, the basis for ATP synthesis in mitochondria, is differently regulated in organs and species by expression of tissue-, developmental-, and species-specific isoforms for COX subunits IV, VIa, VIb, VIIa, VIIb, and VIII, but the holoenzyme in mammals is always composed of 13 subunits. Various proteins and enzymes were shown, e.g., by co-immunopptn., to bind to specific COX subunits and modify its activity, but these interactions are reversible, in contrast to the tightly bound 13 subunits. In addn., the formation of supercomplexes with other oxidative phosphorylation complexes has been shown to be largely variable. The regulatory complexity of COX is increased by protein phosphorylation. Up to now 18 phosphorylation sites have been identified under in vivo conditions in mammals. However, only for a few phosphorylation sites and four nuclear-coded subunits could a specific function be identified. Research on the signaling pathways leading to specific COX phosphorylations remains a great challenge for understanding the regulation of respiration and ATP synthesis in mammalian organisms. This article reviews the function of the individual COX subunits and their isoforms, as well as proteins and small mols. interacting and regulating the enzyme.
- 26Tsukihara, T.; Aoyama, H.; Yamashita, E.; Tomizaki, T.; Yamaguchi, H.; Shinzawa-Itoh, K.; Nakashima, R.; Yaono, R.; Yoshikawa, S. The Whole Structure of the 13-Subunit Oxidized Cytochrome C Oxidase at 2.8 Å. Science 1996, 272, 1136– 1144, DOI: 10.1126/science.272.5265.1136Google Scholar26https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaK28XjtF2gu7k%253D&md5=3795986fdab9000460d93f7d874603acThe whole structure of the 13-subunit oxidized cytochrome c oxidase at 2.8 ÅTsukihara, Tomitake; Aoyama, Hiroshi; Yamashita, Eiki; Tomizaki, Takashi; Yamaguchi, Hiroshi; Shinzawa-Itoh, Kyoko; Nakashima, Ryosuke; Yaono, Rieko; Yoshikawa, ShinyaScience (Washington, D. C.) (1996), 272 (5265), 1136-1144CODEN: SCIEAS; ISSN:0036-8075. (American Association for the Advancement of Science)The crystal structure of bovine heart cytochrome c oxidase at 2.8 Å resoln. with an R value of 19.9 % reveals 13 subunits, each different from the other, five phosphatidyl ethanolamines, three phosphatidyl glycerols and two cholates, two hemes A, and three copper, one magnesium, and one zinc. Of 3606 amino acid residues in the dimer, 3560 have been converged to a reasonable structure by refinement. A hydrogen-bonded system, including a propionate of a heme A (heme a), part of peptide backbone, and an imidazole ligand of CuA, could provide an electron transfer pathway between CuA and heme a. Two possible proton pathways for pumping, each spanning from the matrix to the cytosolic surfaces, were identified, including hydrogen bonds, internal cavities likely to contain water mols., and structures that could form hydrogen bonds with small possible conformational change of amino acid side chains. Possible channels for chem. protons to produce H2O, for removing the produced water, and for O2, resp., were identified.
- 27Sharma, V.; Puustinen, A.; Wikström, M.; Laakkonen, L. Sequence Analysis of the Cbb 3 Oxidases and an Atomic Model for the Rhodobacter Sphaeroides Enzyme. Biochemistry 2006, 45, 5754– 5765, DOI: 10.1021/bi060169aGoogle ScholarThere is no corresponding record for this reference.
- 28Tomson, F. L.; Morgan, J. E.; Gu, G.; Barquera, B.; Vygodina, T.; Gennis, R. B. Substitutions for Glutamate 101 in Subunit Ii of Cytochrome C Oxidase from Rhodobacter Sphaeroides Result in Blocking the Proton-Conducting K-Channel. Biochemistry 2003, 42, 1711– 1717, DOI: 10.1021/bi026750yGoogle ScholarThere is no corresponding record for this reference.
- 29Brändén, M.; Tomson, F.; Gennis, R. B.; Brzezinski, P. The Entry Point of the K-Proton-Transfer Pathway in Cytochrome C Oxidase. Biochemistry 2002, 41, 10794– 10798, DOI: 10.1021/bi026093+Google ScholarThere is no corresponding record for this reference.
- 30Haltia, T.; Saraste, M.; Wikström, M. Subunit III of Cytochrome C Oxidase Is Not Involved in Proton Translocation: A Site-Directed Mutagenesis Study. EMBO J. 1991, 10, 2015Google ScholarThere is no corresponding record for this reference.
- 31Bratton, M. R.; Pressler, M. A.; Hosler, J. P. Suicide Inactivation of Cytochrome C Oxidase: Catalytic Turnover in the Absence of Subunit Iii Alters the Active Site. Biochemistry 1999, 38, 16236– 16245, DOI: 10.1021/bi9914107Google ScholarThere is no corresponding record for this reference.
- 32Gilderson, G.; Salomonsson, L.; Aagaard, A.; Gray, J.; Brzezinski, P.; Hosler, J. Subunit III of Cytochrome C Oxidase of Rhodobacter Sphaeroides Is Required to Maintain Rapid Proton Uptake through the D Pathway at Physiologic pH. Biochemistry 2003, 42, 7400– 7409, DOI: 10.1021/bi0341298Google Scholar32https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD3sXktVKrtbc%253D&md5=f01b71d3f5212c4bc4f9c37f5fce5c2eSubunit III of cytochrome c oxidase of Rhodobacter sphaeroides is required to maintain rapid proton uptake through the D pathway at physiologic pHGilderson, Gwen; Salomonsson, Lina; Aagaard, Anna; Gray, Jimmy; Brzezinski, Peter; Hosler, JonathanBiochemistry (2003), 42 (24), 7400-7409CODEN: BICHAW; ISSN:0006-2960. (American Chemical Society)The catalytic core of cytochrome c oxidase is composed of three subunits where subunits I and II contain all of the redox-active metal centers and subunit III is a seven transmembrane helix protein that binds to subunit I. The N-terminal region of subunit III is adjacent to D132 of subunit I, the initial proton acceptor of the D pathway that transfers protons from the protein surface to the buried active site ∼30 Å distant. The absence of subunit III only slightly alters the initial steady-state activity of the oxidase at pH 6.5, but activity declines sharply with increasing pH, yielding an apparent pKa of 7.2 for steady-state O2 redn. When subunit III is present, cytochrome oxidase is more active at higher pH, and the apparent pKa of steady-state O2 redn. is 8. Single-turnover expts. show that proton uptake through the D pathway at pH 8 slows from >10,000 s-1 in the presence of subunit III to 350 s-1 in its absence. At low pH (5.5) the D pathway of the oxidase lacking subunit III regains its capacity for rapid proton uptake. Anal. of the F → O transition indicates that the apparent pKa of the D pathway in the absence of subunit III is 6.8, similar to that of steady-state O2 redn. (7.2). The pKa of D132 itself may decline in the absence of subunit III since its carboxylate group will be more exposed to solvent water. Alternatively, part of a proton antenna for the D pathway may be lost upon removal of subunit III. It is proposed that one role of subunit III in the normal oxidase is to maintain rapid proton uptake through the D pathway at physiol. pH.
- 33Hosler, J. P. The Influence of Subunit III of Cytochrome C Oxidase on the D Pathway, the Proton Exit Pathway and Mechanism-Based Inactivation in Subunit I. Biochim. Biophys. Acta, Bioenerg. 2004, 1655, 332– 339, DOI: 10.1016/j.bbabio.2003.06.009Google Scholar33https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2cXjt1Cgt7s%253D&md5=63b921de00f9543217addd3b28a93d5bThe influence of subunit III of cytochrome c oxidase on the D pathway, the proton exit pathway and mechanism-based inactivation in subunit IHosler, Jonathan P.Biochimica et Biophysica Acta, Bioenergetics (2004), 1655 (1-3), 332-339CODEN: BBBEB4; ISSN:0005-2728. (Elsevier B.V.)A review. Although subunit III of cytochrome c oxidase (CcO) is part of the catalytic core of the enzyme, its function has remained enigmatic. Comparison of wild-type CcO and forms lacking subunit III has shown that the presence of subunit III maintains rapid proton uptake into the proton pumping D pathway at the pH of the bacterial cytoplasm or mitochondrial matrix, apparently by contributing to the protein environment of Asp-132, the initial proton acceptor of the D pathway. Subunit III also appears to contribute to the conformation of the normal proton exit pathway, allowing this pathway to take up protons from the outer surface of CcO in the presence of ΔΨ and ΔpH. Subunit III prevents turnover-induced inactivation of CcO (suicide inactivation) and the subsequent loss of CuB from the active site. This function of subunit III appears partly related to its ability to maintain rapid proton flow to the active site, thereby shortening the lifetime of reactive O2 redn. intermediates. Anal. of proton pumping by subunit III-depleted CcO forms has led to the proposal that the trapping of 2 protons in the D pathway, one on Glu-286 and one on Asp-132, is required for efficient proton pumping.
- 34Riistama, S.; Puustinen, A.; García-Horsman, A.; Iwata, S.; Michel, H.; Wikström, M. Channelling of Dioxygen into the Respiratory Enzyme. Biochim. Biophys. Acta, Bioenerg. 1996, 1275, 1– 4, DOI: 10.1016/0005-2728(96)00040-0Google Scholar34https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaK28XjvF2ksLw%253D&md5=ddfc249620e4d282e43b0a07953fb878Channeling of dioxygen into the respiratory enzymeRiistama, Sirpa; Puustinen, Anne; Garcia-Horsman, Arturo; Iwata, So; Michel, Hartmut; Wikstroem, MartenBiochimica et Biophysica Acta, Bioenergetics (1996), 1275 (1/2), 1-4CODEN: BBBEB4; ISSN:0005-2728. (Elsevier B.V.)A review, with 9 refs.
- 35Sharma, V.; Ala-Vannesluoma, P.; Vattulainen, I.; Wikström, M.; Róg, T. Role of Subunit III and Its Lipids in the Molecular Mechanism of Cytochrome C Oxidase. Biochim. Biophys. Acta, Bioenerg. 2015, 1847, 690– 697, DOI: 10.1016/j.bbabio.2015.04.007Google Scholar35https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2MXntVeru74%253D&md5=11b7a95fd5958ec247ad6e58cc02b0a5Role of subunit III and its lipids in the molecular mechanism of cytochrome c oxidaseSharma, Vivek; Ala-Vannesluoma, Pauliina; Vattulainen, Ilpo; Wikstrom, Marten; Rog, TomaszBiochimica et Biophysica Acta, Bioenergetics (2015), 1847 (8), 690-697CODEN: BBBEB4; ISSN:0005-2728. (Elsevier B. V.)The terminal respiratory enzyme cytochrome c oxidase (CcO) reduces mol. oxygen to water, and pumps protons across the inner mitochondrial membrane, or the plasma membrane of bacteria. A two-subunit CcO harbors all the elements necessary for oxygen redn. and proton pumping. However, it rapidly undergoes turnover-induced irreversible damage, which is effectively prevented by the presence of subunit III and its tightly bound lipids. We have performed classical atomistic mol. dynamics (MD) simulations on a three-subunit CcO, which show the formation of water wires between the polar head groups of lipid mols. bound to subunit III and the proton uptake site Asp91 (Bos taurus enzyme numbering). Continuum electrostatic calcns. suggest that these lipids directly influence the proton affinity of Asp91 by 1-2 pK units. We surmise that lipids bound to subunit III influence the rate of proton uptake through the D-pathway, and therefore play a key role in preventing turnover-induced inactivation. Atomistic MD simulations show that subunit III is rapidly hydrated in the absence of internally bound lipids, which is likely to affect the rate of O2 diffusion into the active-site. The role of subunit III with its indigenous lipids in the mol. mechanism of CcO is discussed.
- 36Qian, J. Role of the Conserved Arginine Pair in Proton and Electron Transfer in Cytochrome C Oxidase. Biochemistry 2004, 43, 5748– 5756, DOI: 10.1021/bi036279oGoogle ScholarThere is no corresponding record for this reference.
- 37Wikström, M.; Ribacka, C.; Molin, M.; Laakkonen, L.; Verkhovsky, M.; Puustinen, A. Gating of Proton and Water Transfer in the Respiratory Enzyme Cytochrome C Oxidase. Proc. Natl. Acad. Sci. U. S. A. 2005, 102, 10478– 10481, DOI: 10.1073/pnas.0502873102Google ScholarThere is no corresponding record for this reference.
- 38Ribacka, C.; Verkhovsky, M. I.; Belevich, I.; Bloch, D. A.; Puustinen, A.; Wikström, M. An Elementary Reaction Step of the Proton Pump Is Revealed by Mutation of Tryptophan-164 to Phenylalanine in Cytochrome C Oxidase from Paracoccus Denitrificans. Biochemistry 2005, 44, 16502– 16512, DOI: 10.1021/bi0511336Google ScholarThere is no corresponding record for this reference.
- 39Mills, D. A.; Geren, L.; Hiser, C.; Schmidt, B.; Durham, B.; Millett, F.; Ferguson-Miller, S. An Arginine to Lysine Mutation in the Vicinity of the Heme Propionates Affects the Redox Potentials of the Hemes and Associated Electron and Proton Transfer in Cytochrome C Oxidase. Biochemistry 2005, 44, 10457– 10465, DOI: 10.1021/bi050283dGoogle Scholar39https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2MXmtVClsr4%253D&md5=b9ccc9c0ef8267b5dbfdac58007641feAn arginine to lysine mutation in the vicinity of the heme propionates affects the redox potentials of the hemes and associated electron and proton transfer in cytochrome c oxidaseMills, Denise A.; Geren, Lois; Hiser, Carrie; Schmidt, Bryan; Durham, Bill; Millett, Francis; Ferguson-Miller, ShelaghBiochemistry (2005), 44 (31), 10457-10465CODEN: BICHAW; ISSN:0006-2960. (American Chemical Society)Cytochrome c oxidase pumps protons across a membrane using energy from electron transfer and redn. of O2 to H2O. It is postulated that an element of the energy transduction mechanism is the movement of protons to the vicinity of the hemes upon redn., to favor charge neutrality. Possible sites on which protons could reside, in addn. to the conserved carboxylate (Glu-286) in Rhodobacter sphaeroides cytochrome c oxidase, are the propionate groups of heme a and/or heme a3. A highly conserved pair of Arg residues (Arg-481 and Arg-482) interact with these propionates through ionic bonds and H-bonds. This study showed that the conservative mutant, R481K, although as fully active as the wild-type protein under many conditions, exhibited a significant decrease in the midpoint redox potential of heme a relative to CuA (ΔEm) of ≃40 mV, had lowered activity under conditions of high pH or in the presence of a membrane potential, and had a slowed heme a3 redn. with dithionite. Another mutant, D132A, which strongly inhibited proton uptake from the internal side of the membrane, had <4% of the activity of the wild-type protein and appeared to be dependent on proton uptake from the outside. A double mutation, D132A/R481K, was even more strongly inhibited (∼1% of that of the wild-type protein). The more-than-additive effect supported the concept that R481K not only lowered the midpoint potential of heme a but also limited a supply route for protons from the outside of the membrane used by the Asp-132 mutant. The results were consistent with an important role of Arg-481 and heme a/a3 propionates in proton movement in a reversible exit path.
- 40von Ballmoos, C.; Gonska, N.; Lachmann, P.; Gennis, R. B.; Ädelroth, P.; Brzezinski, P. Mutation of a Single Residue in the Ba3 Oxidase Specifically Impairs Protonation of the Pump Site. Proc. Natl. Acad. Sci. U. S. A. 2015, 112, 3397– 3402, DOI: 10.1073/pnas.1422434112Google ScholarThere is no corresponding record for this reference.
- 41Tsukihara, T.; Aoyama, H.; Yamashita, E.; Tomizaki, T.; Yamaguchi, H.; Shinzawa-Itoh, K.; Nakashima, R.; Yaono, R.; Yoshikawa, S. Structures of Metal Sites of Oxidized Bovine Heart Cytochrome C Oxidase at 2.8 A. Science 1995, 269, 1069– 1074, DOI: 10.1126/science.7652554Google Scholar41https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaK2MXns12ms7g%253D&md5=3aed818b216db874a86986807857db7fStructures of metal sites of oxidized bovine heart cytochrome c oxidase at 2.8 ÅTsukihara, Tomitake; Aoyama, Hiroshi; Yamashita, Eiki; Tomizaki, Takashi; Yamaguchi, Hiroshi; Shinzawa-Itoh, Kyoko; Nakashima, Ryosuke; Yaono, Rieko; Yoshikawa, ShinyaScience (Washington, D. C.) (1995), 269 (5227), 1069-74CODEN: SCIEAS; ISSN:0036-8075. (American Association for the Advancement of Science)The high resoln. three-dimensional x-ray structure of the metal sites of bovine heart cytochrome c oxidase is reported. Cytochrome c oxidase is the largest membrane protein yet crystd. and analyzed at at. resoln. Electron d. distribution of the oxidized bovine cytochrome c oxidase at 2.8 Å resoln. indicates a dinuclear copper center with an unexpected structure similar to a [2Fe-2S]-type iron-sulfur center. Previously predicted zinc and magnesium sites have been located, the former bound by a nuclear encoded subunit on the matrix side of the membrane, and the latter situated between heme a3 and CuA, at the interface of subunits I and II. The O2 binding site contains heme a3 iron and copper atoms (CuB) with an interat. distance of 4.5 Å; there is no detectable bridging ligand between them. A hydrogen bond is present between a hydroxyl group of the hydroxyfarnesylethyl side chain of heme a3 and an OH of a tyrosine. The tyrosine phenol plane is immediately adjacent and perpendicular to an imidazole group bonded to CuB, suggesting a possible role in intramol. electron transfer or conformational control, the latter of which could induce the redox-coupled proton pumping. A Ph group located halfway between a pyrrole plane of the heme a3 and an imidazole plane liganded to the other heme (heme a) could also influence electron transfer or conformational control.
- 42Yoshikawa, S. Redox-Coupled Crystal Structural Changes in Bovine Heart Cytochrome C Oxidase. Science 1998, 280, 1723– 1729, DOI: 10.1126/science.280.5370.1723Google Scholar42https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaK1cXjslOhs78%253D&md5=f062033285bb99892adbe95058c8ef3aRedox-coupled crystal structural changes in bovine heart cytochrome c oxidaseYoshikawa, Shinya; Shinzawa-itoh, Kyoko; Nakashima, Ryosuke; Yaono, Rieko; Yamashita, Eiki; Inoue, Noriko; Yao, Min; Fei, Ming Jie; Libeu, Clare Peters; Mizushima, Tsunehiro; Yamaguchi, Hiroshi; Tomizaki, Takashi; Tsukihara, TomitakeScience (Washington, D. C.) (1998), 280 (5370), 1723-1729CODEN: SCIEAS; ISSN:0036-8075. (American Association for the Advancement of Science)Crystal structures of bovine heart cytochrome c oxidase in the fully oxidized, fully reduced, azide-bound, and CO-bound states were detd. at 2.30, 2.35, 2.9, and 2.8 Å resoln., resp. An Asp residue (Asp-51) apart from the O2 redn. site exchanged its effective accessibility to the matrix aq. phase for one to the cytosolic phase concomitantly with a significant decrease in the pKa of its carboxyl group, on redn. of the metal sites. The movement indicated the Asp-51 residue as the proton pumping site. A Tyr residue (Tyr-54) acidified by a covalently linked imidazole N atom is a possible proton donor for O2 redn. by the enzyme.
- 43Qin, L.; Hiser, C.; Mulichak, A.; Garavito, R. M.; Ferguson-Miller, S. Identification of Conserved Lipid/Detergent-Binding Sites in a High-Resolution Structure of the Membrane Protein Cytochrome C Oxidase. Proc. Natl. Acad. Sci. U. S. A. 2006, 103, 16117– 16122, DOI: 10.1073/pnas.0606149103Google Scholar43https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD28Xht1WmsL%252FJ&md5=e3fb024aeaff84aba4268858d6b089daIdentification of conserved lipid/detergent-binding sites in a high-resolution structure of the membrane protein cytochrome c oxidaseQin, Ling; Hiser, Carrie; Mulichak, Anne; Garavito, R. Michael; Ferguson-Miller, ShelaghProceedings of the National Academy of Sciences of the United States of America (2006), 103 (44), 16117-16122CODEN: PNASA6; ISSN:0027-8424. (National Academy of Sciences)Well ordered reproducible crystals of cytochrome c oxidase (CcO) from Rhodobacter sphaeroides yield a previously unreported structure at 2.0 Å resoln. that contains the two catalytic subunits and a no. of alkyl chains of lipids and detergents. Comparison with crystal structures of other bacterial and mammalian CcOs reveals that the positions occupied by native membrane lipids and detergent substitutes are highly conserved, along with amino acid residues in their vicinity, suggesting a more prevalent and specific role of lipid in membrane protein structure than often envisioned. Well defined detergent head groups (maltose) are found assocd. with arom. residues in a manner similar to phospholipid head groups, likely contributing to the success of alkyl glycoside detergents in supporting membrane protein activity and crystallizability. Other significant features of this structure include the following: finding of a previously unreported crystal contact mediated by cadmium and an engineered histidine tag; documentation of the unique His-Tyr covalent linkage close to the active site; remarkable conservation of a chain of waters in one proton pathway (D-path); and discovery of an inhibitory cadmium-binding site at the entrance to another proton path (K-path). These observations provide important insight into CcO structure and mechanism, as well as the significance of bound lipid in membrane proteins.
- 44Qin, L.; Liu, J.; Mills, D. A.; Proshlyakov, D. A.; Hiser, C.; Ferguson-Miller, S. Redox-Dependent Conformational Changes in Cytochrome C Oxidase Suggest a Gating Mechanism for Proton Uptake. Biochemistry 2009, 48, 5121– 5130, DOI: 10.1021/bi9001387Google Scholar44https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD1MXmt1Sjs7Y%253D&md5=27ab7a3a4bf583579ca2304770bb1c1fRedox-Dependent Conformational Changes in Cytochrome c Oxidase Suggest a Gating Mechanism for Proton UptakeQin, Ling; Liu, Jian; Mills, Denise A.; Proshlyakov, Denis A.; Hiser, Carrie; Ferguson-Miller, ShelaghBiochemistry (2009), 48 (23), 5121-5130CODEN: BICHAW; ISSN:0006-2960. (American Chemical Society)A role for conformational change in the coupling mechanism of cytochrome c oxidase is the subject of controversy. Relatively small conformational changes have been reported in comparisons of reduced and oxidized crystal structures of bovine oxidase but none in bacterial oxidases. Comparing the x-ray crystal structures of the reduced (at 2.15 Å resoln.) and oxidized forms of cytochrome c oxidase from Rhodobacter sphaeroides, we observe a displacement of heme a3 involving both the porphyrin ring and the hydroxyl farnesyl tail, accompanied by protein movements in nearby regions, including the mid part of helix VIII of subunit I which harbors key residues of the K proton uptake path, K362 and T359. The conformational changes in the reduced form are reversible upon reoxidn. They result in an opening of the top of the K pathway and more ordered waters being resolved in that region, suggesting an access path for protons into the active site. In all high-resoln. structures of oxidized R. sphaeroides cytochrome c oxidase, a water mol. is obsd. in the hydrophobic region above the top of the D path, strategically positioned to facilitate the connection of residue E286 of subunit I to the active site or to the proton pumping exit path. In the reduced and reduced plus cyanide structures, this water mol. disappears, implying disruption of proton conduction from the D path under conditions when the K path is open, thus providing a mechanism for alternating access to the active site.
- 45Bhagi-Damodaran, A. Why Copper Is Preferred over Iron for Oxygen Activation and Reduction in Haem-Copper Oxidases. Nat. Chem. 2017, 9, 257– 263, DOI: 10.1038/nchem.2643Google Scholar45https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC28XhvVSiurbK&md5=72807d1079586eadc8345584552bdd77Why copper is preferred over iron for oxygen activation and reduction in heme-copper oxidasesBhagi-Damodaran, Ambika; Michael, Matthew A.; Zhu, Qianhong; Reed, Julian; Sandoval, Braddock A.; Mirts, Evan N.; Chakraborty, Saumen; Moenne-Loccoz, Pierre; Zhang, Yong; Lu, YiNature Chemistry (2017), 9 (3), 257-263CODEN: NCAHBB; ISSN:1755-4330. (Nature Publishing Group)Heme-copper oxidases (HCOs) catalyze the natural redn. of O2 to H2O using a heme-copper center. Despite decades of research on HCOs, the role of non-heme metal and the reason for Nature's choice of Cu over other metals such as Fe remains unclear. Here, the authors used a biosynthetic model of HCO in myoglobin that selectively bound different non-heme metals to demonstrate 30-fold and 11-fold enhancements in the oxidase activity of Cu- and Fe-bound HCO mimics, resp., as compared with Zn-bound mimics. Detailed electrochem., kinetic, and vibrational spectroscopic studies, in tandem with theor. DFT calcns., demonstrated that the non-heme metal not only donated electrons to O2 but also activated it for efficient O-O bond cleavage. Furthermore, the higher redox potential of Cu and the enhanced weakening of the O-O bond from the higher electron d. in the d orbital of Cu were central to its higher oxidase activity over Fe. Thus, this work resolves a long-standing question in bioenergetics, and renders a chem.-biol. basis for the design of future O2-redn. catalysts.
- 46Aoyama, H.; Muramoto, K.; Shinzawa-Itoh, K.; Hirata, K.; Yamashita, E.; Tsukihara, T.; Ogura, T.; Yoshikawa, S. A Peroxide Bridge between Fe and Cu Ions in the O2 Reduction Site of Fully Oxidized Cytochrome C Oxidase Could Suppress the Proton Pump. Proc. Natl. Acad. Sci. U. S. A. 2009, 106, 2165– 2169, DOI: 10.1073/pnas.0806391106Google Scholar46https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD1MXitlaqtro%253D&md5=f8d51bef5177b2c7a6e218c334df50c8A peroxide bridge between Fe and Cu ions in the O2 reduction site of fully oxidized cytochrome c oxidase could suppress the proton pumpAoyama, Hiroshi; Muramoto, Kazumasa; Shinzawa-Itoh, Kyoko; Hirata, Kunio; Yamashita, Eiki; Tsukihara, Tomitake; Ogura, Takashi; Yoshikawa, ShinyaProceedings of the National Academy of Sciences of the United States of America (2009), 106 (7), 2165-2169CODEN: PNASA6; ISSN:0027-8424. (National Academy of Sciences)The fully oxidized form of cytochrome c oxidase, immediately after complete oxidn. of the fully reduced form, pumps protons upon each of the initial 2 single-electron redn. steps, whereas protons are not pumped during single-electron redn. of the fully oxidized "as-isolated" form (the fully oxidized form without any redn./oxidn. treatment). For identification of structural differences causing the remarkable functional difference between these 2 distinct fully oxidized forms, the x-ray structure of the fully oxidized as-isolated bovine heart cytochrome c oxidase was detd. at 1.95-Å resoln. by limiting the x-ray dose for each shot and by using many (≈400) single crystals. This minimizes the effects of hydrated electrons induced by the x-ray irradn. The x-ray structure showed a peroxide group bridging the 2 metal sites in the O2 redn. site (Fe3+-O--O--Cu2+), in contrast to a ferric hydroxide (Fe3+-OH-) in the fully oxidized form immediately after complete oxidn. from the fully reduced form, as has been revealed by resonance Raman analyses. The peroxide-bridged structure is consistent with the reductive titrn. results showing that 6 electron equiv. are required for complete redn. of the fully oxidized as-isolated form. The structural difference between the 2 fully oxidized forms suggests that the bound peroxide in the O2 redn. site suppresses the proton pumping function.
- 47Yoshikawa, S.; Shimada, A. Reaction Mechanism of Cytochrome C Oxidase. Chem. Chem. Rev. 2015, 115, 1936– 1989, DOI: 10.1021/cr500266aGoogle ScholarThere is no corresponding record for this reference.
- 48Kaila, V. R.; Oksanen, E.; Goldman, A.; Bloch, D. A.; Verkhovsky, M. I.; Sundholm, D.; Wikström, M. A Combined Quantum Chemical and Crystallographic Study on the Oxidized Binuclear Center of Cytochrome C Oxidase. Biochim. Biophys. Acta, Bioenerg. 2011, 1807, 769– 778, DOI: 10.1016/j.bbabio.2010.12.016Google Scholar48https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3MXmsVajtLk%253D&md5=773e2e5fa37e49264f8ce99a2aa2c8e3A combined quantum chemical and crystallographic study on the oxidized binuclear center of cytochrome c oxidaseKaila, Ville R. I.; Oksanen, Esko; Goldman, Adrian; Bloch, Dmitry A.; Verkhovsky, Michael I.; Sundholm, Dage; Wikstrom, MartenBiochimica et Biophysica Acta, Bioenergetics (2011), 1807 (7), 769-778CODEN: BBBEB4; ISSN:0005-2728. (Elsevier B. V.)Cytochrome c oxidase (CcO) is the terminal enzyme of the respiratory chain. By reducing oxygen to water, it generates a proton gradient across the mitochondrial or bacterial membrane. Recently, two independent X-ray crystallog. studies suggested that a peroxide dianion might be bound to the active site of oxidized CcO. We have investigated this hypothesis by combining quantum chem. calcns. with a re-refinement of the X-ray crystallog. data and optical spectroscopic measurements. Our data suggest that dianionic peroxide, superoxide, and dioxygen all form a similar superoxide species when inserted into a fully oxidized ferric/cupric binuclear site (BNC). We argue that stable peroxides are unlikely to be confined within the oxidized BNC since that would be expected to lead to bond splitting and formation of the catalytic P intermediate. Somewhat surprisingly, we find that binding of dioxygen to the oxidized binuclear site is weakly exergonic, and hence the obsd. structure might have resulted from dioxygen itself or from superoxide generated from O2 by the X-ray beam. We show that the presence of O2 is consistent with the X-ray data. We also discuss how other structures, such as a mixt. of the aq. species (H2O + OH- and H2O) and chloride fit the exptl. data.
- 49Buschmann, S.; Warkentin, E.; Xie, H.; Langer, J. D.; Ermler, U.; Michel, H. The Structure of Cbb3 Cytochrome Oxidase Provides Insights into Proton Pumping. Science 2010, 329, 327– 330, DOI: 10.1126/science.1187303Google Scholar49https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3cXosl2itbc%253D&md5=3a41f9630311f35f4bb709d3d46a654eThe structure of cbb3 cytochrome oxidase provides insights into proton pumpingBuschmann, Sabine; Warkentin, Eberhard; Xie, Hao; Langer, Julian D.; Ermler, Ulrich; Michel, HartmutScience (Washington, DC, United States) (2010), 329 (5989), 327-330CODEN: SCIEAS; ISSN:0036-8075. (American Association for the Advancement of Science)The heme-copper oxidases (HCOs) accomplish the key event of aerobic respiration; they couple O2 redn. and transmembrane proton pumping. To gain new insights into the still enigmatic process, the authors structurally characterized a C-family HCO, essential for the pathogenicity of many bacteria, that differed from the 2 other HCO families, A and B, that have previously been structurally analyzed. The x-ray crystal structure of the C-family cbb3 oxidase from Pseudomonas stutzeri at 3.2 Å resoln. showed an electron supply system different from that of families A and B. Like family-B HCOs, family-C HCOs had only one pathway, which conducted protons via an alternative Tyr-His crosslink. Structural differences around hemes b and b3 suggested a different redox-driven proton-pumping mechanism and provided clues to explain the higher activity of family-C HCOs at low O2 concns.
- 50Hemp, J.; Christian, C.; Barquera, B.; Gennis, R. B.; Martínez, T. J. Helix Switching of a Key Active-Site Residue in the Cytochrome Cbb 3 Oxidases. Biochemistry 2005, 44, 10766– 10775, DOI: 10.1021/bi050464fGoogle ScholarThere is no corresponding record for this reference.
- 51Hemp, J.; Robinson, D. E.; Ganesan, K. B.; Martinez, T. J.; Kelleher, N. L.; Gennis, R. B. Evolutionary Migration of a Post-Translationally Modified Active-Site Residue in the Proton-Pumping Heme-Copper Oxygen Reductases. Biochemistry 2006, 45, 15405– 15410, DOI: 10.1021/bi062026uGoogle Scholar51https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD28XhtlChurjI&md5=8af4ca7024b79076768f0cb32c3cbda5Evolutionary Migration of a Post-Translationally Modified Active-Site Residue in the Proton-Pumping Heme-Copper Oxygen ReductasesHemp, James; Robinson, Dana E.; Ganesan, Krithika B.; Martinez, Todd J.; Kelleher, Neil L.; Gennis, Robert B.Biochemistry (2006), 45 (51), 15405-15410CODEN: BICHAW; ISSN:0006-2960. (American Chemical Society)In the respiratory chains of aerobic organisms, oxygen reductase members of the heme-copper superfamily couple the redn. of O2 to proton pumping, generating an electrochem. gradient. There are three distinct families of heme-copper oxygen reductases: A, B, and C types. The A- and B-type oxygen reductases have an active-site tyrosine that forms a unique cross-linked histidine-tyrosine cofactor. In the C-type oxygen reductases (also called cbb3 oxidases), an analogous active-site tyrosine has recently been predicted by mol. modeling to be located within a different transmembrane helix in comparison to the A- and B-type oxygen reductases. In this work, Fourier-transform mass spectrometry is used to show that the predicted tyrosine forms a histidine-tyrosine cross-linked cofactor in the active site of the C-type oxygen reductases. This is the first known example of the evolutionary migration of a post-translationally modified active-site residue. It also verifies the presence of a unique cofactor in all three families of proton-pumping respiratory oxidases, demonstrating that these enzymes likely share a common reaction mechanism and that the histidine-tyrosine cofactor may be a required component for proton pumping.
- 52Rauhamäki, V.; Baumann, M.; Soliymani, R.; Puustinen, A.; Wikström, M. Identification of a Histidine-Tyrosine Cross-Link in the Active Site of the Cbb3-Type Cytochrome C Oxidase from Rhodobacter Sphaeroides. Proc. Natl. Acad. Sci. U. S. A. 2006, 103, 16135– 16140, DOI: 10.1073/pnas.0606254103Google ScholarThere is no corresponding record for this reference.
- 53Sharma, V.; Wikström, M.; Kaila, V. R. Stabilization of the Peroxy Intermediate in the Oxygen Splitting Reaction of Cytochrome Cbb 3. Biochim. Biophys. Acta, Bioenerg. 2011, 1807, 813– 818, DOI: 10.1016/j.bbabio.2011.02.002Google Scholar53https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3MXmsVajtb8%253D&md5=d55db2259232723e778972d9dc57f54cStabilization of the peroxy intermediate in the oxygen splitting reaction of cytochrome cbb3Sharma, Vivek; Wikstroem, Marten; Kaila, Ville R. I.Biochimica et Biophysica Acta, Bioenergetics (2011), 1807 (7), 813-818CODEN: BBBEB4; ISSN:0005-2728. (Elsevier B. V.)The proton-pumping cbb3-type cytochrome c oxidases catalyze cell respiration in many pathogenic bacteria. For reasons not yet understood, the apparent dioxygen (O2) affinity in these enzymes is very high relative to other members of the heme-copper oxidase (HCO) superfamily. Based on d. functional theory (DFT) calcns. on intermediates of the oxygen scission reaction in active-site models of cbb3- and aa3-type oxidases, we find that a transient peroxy intermediate (IP, Fe[III]-OOH-) is ∼ 6 kcal/mol more stable in the former case, resulting in more efficient kinetic trapping of dioxygen and hence in a higher apparent oxygen affinity. The major mol. basis for this stabilization is a glutamate residue, polarizing the proximal histidine ligand of heme b3 in the active site.
- 54Hino, T.; Matsumoto, Y.; Nagano, S.; Sugimoto, H.; Fukumori, Y.; Murata, T.; Iwata, S.; Shiro, Y. Structural Basis of Biological N2o Generation by Bacterial Nitric Oxide Reductase. Science 2010, 330, 1666– 1670, DOI: 10.1126/science.1195591Google Scholar54https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3cXhsFGms7rF&md5=30023c4075fd45f1cb70a3d5d506b2dcStructural Basis of Biological N2O Generation by Bacterial Nitric Oxide ReductaseHino, Tomoya; Matsumoto, Yushi; Nagano, Shingo; Sugimoto, Hiroshi; Fukumori, Yoshihiro; Murata, Takeshi; Iwata, So; Shiro, YoshitsuguScience (Washington, DC, United States) (2010), 330 (6011), 1666-1670CODEN: SCIEAS; ISSN:0036-8075. (American Association for the Advancement of Science)Nitric oxide reductase (NOR) is an iron-contg. enzyme that catalyzes the redn. of nitric oxide (NO) to generate a major greenhouse gas, nitrous oxide (N2O). Here, we report the crystal structure of NOR from Pseudomonas aeruginosa at 2.7 angstrom resoln. The structure reveals details of the catalytic binuclear center. The non-heme iron (FeB) is coordinated by three His and one Glu ligands, but the His-Tyr covalent linkage common in cytochrome oxidases (COX) is absent. This structural characteristic is crucial for NOR reaction. Although the overall structure of NOR is closely related to COX, neither the D- nor K-proton pathway, which connect the COX active center to the intracellular space, was obsd. Protons required for the NOR reaction are probably provided from the extracellular side.
- 55Matsumoto, Y.; Tosha, T.; Pisliakov, A. V.; Hino, T.; Sugimoto, H.; Nagano, S.; Sugita, Y.; Shiro, Y. Crystal Structure of Quinol-Dependent Nitric Oxide Reductase from Geobacillus Stearothermophilus. Nat. Struct. Mol. Biol. 2012, 19, 238– 245, DOI: 10.1038/nsmb.2213Google Scholar55https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC38XhtVKjtrk%253D&md5=88c572e7800c74f652e7929f4cabcd12Crystal structure of quinol-dependent nitric oxide reductase from Geobacillus stearothermophilusMatsumoto, Yushi; Tosha, Takehiko; Pisliakov, Andrei V.; Hino, Tomoya; Sugimoto, Hiroshi; Nagano, Shingo; Sugita, Yuji; Shiro, YoshitsuguNature Structural & Molecular Biology (2012), 19 (2), 238-245CODEN: NSMBCU; ISSN:1545-9993. (Nature Publishing Group)The structure of quinol-dependent nitric oxide reductase (qNOR) from G. stearothermophilus, which catalyzes the redn. of NO to produce the major ozone-depleting gas N2O, has been characterized at 2.5 Å resoln. The overall fold of qNOR is similar to that of cytochrome C-dependent NOR (cNOR), and some structural features that are characteristic of cNOR, such as the calcium binding site and hydrophilic cytochrome c domain, are obsd. in qNOR, even though it harbors no heme C. The overall fold of qNOR is similar to that of cytochrome C-dependent NOR (cNOR), and some structural features that are characteristic of cNOR, such as the calcium binding site and hydrophilic cytochrome c domain, are obsd. in qNOR, even though it harbors no heme C. Further structural comparison of qNOR with cNOR and aerobic and microaerobic respiratory oxidases elucidates their evolutionary relationship and possible functional conversions.
- 56Hino, T.; Nagano, S.; Sugimoto, H.; Tosha, T.; Shiro, Y. Molecular Structure and Function of Bacterial Nitric Oxide Reductase. Biochim. Biophys. Acta, Bioenerg. 2012, 1817, 680– 687, DOI: 10.1016/j.bbabio.2011.09.021Google Scholar56https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC38Xjtlyjt7s%253D&md5=f9557453da2e55ce963e2a6d41bd10fcMolecular structure and function of bacterial nitric oxide reductaseHino, Tomoya; Nagano, Shingo; Sugimoto, Hiroshi; Tosha, Takehiko; Shiro, YoshitsuguBiochimica et Biophysica Acta, Bioenergetics (2012), 1817 (4), 680-687CODEN: BBBEB4; ISSN:0005-2728. (Elsevier B. V.)A review. The crystal structure of the membrane-integrated nitric oxide reductase cNOR from Pseudomonas aeruginosa was detd. The smaller NorC subunit of cNOR is comprised of 1 trans-membrane helix and a hydrophilic domain, where the heme c is located, while the larger NorB subunit consists of 12 trans-membrane helixes, which contain heme b and the catalytically active binuclear center (heme b3 and non-heme FeB). The roles of the 5 well-conserved glutamates in NOR are discussed, based on the recently solved structure. Glu211 and Glu280 appear to play an important role in the catalytic redn. of NO at the binuclear center by functioning as a terminal proton donor, while Glu215 probably contributes to the electro-neg. environment of the catalytic center. Glu135, a ligand for Ca2+ sandwiched between two heme propionates from heme b and b3, and the nearby Glu138 appears to function as a structural factor in maintaining a protein conformation that is suitable for electron-coupled proton transfer from the periplasmic region to the active site. On the basis of these observations, the possible mol. mechanism for the redn. of NO by cNOR is discussed. This article is part of a Special Issue entitled: Respiratory Oxidases.
- 57ter Beek, J.; Krause, N.; Ädelroth, P. Investigating the Proton Donor in the NO Reductase from Paracoccus denitrificans. PLoS One 2016, 11, e0152745, DOI: 10.1371/journal.pone.0152745Google ScholarThere is no corresponding record for this reference.
- 58Blomberg, M. R.; Ädelroth, P. The Mechanism for Oxygen Reduction in Cytochrome C Dependent Nitric Oxide Reductase (Cnor) as Obtained from a Combination of Theoretical and Experimental Results. Biochim. Biophys. Acta, Bioenerg. 2017, 1858, 884– 894, DOI: 10.1016/j.bbabio.2017.08.005Google Scholar58https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2sXhtlWks77E&md5=6d7694e06648de62b9bd6411da4a8ae7The mechanism for oxygen reduction in cytochrome c dependent nitric oxide reductase (cNOR) as obtained from a combination of theoretical and experimental resultsBlomberg, Margareta R. A.; Aedelroth, PiaBiochimica et Biophysica Acta, Bioenergetics (2017), 1858 (11), 884-894CODEN: BBBEB4; ISSN:0005-2728. (Elsevier B.V.)Bacterial NO-reductases (NOR) belong to the heme-copper oxidase (HCuO) superfamily, in which most members are O2-reducing, proton-pumping enzymes. This study is one in a series aiming to elucidate the reaction mechanisms of the HCuOs, including the mechanisms for cellular energy conservation. One approach towards this goal is to compare the mechanisms for the different types of HCuOs, cytochrome c oxidase (CcO) and NOR, reducing the two substrates O2 and NO. Specifically in this study, we describe the mechanism for oxygen redn. in cytochrome c dependent NOR (cNOR). Hybrid d. functional calcns. were performed on large cluster models of the cNOR binuclear active site. Our results are used, together with published exptl. information, to construct a free energy profile for the entire catalytic cycle. Although the overall reaction is quite exergonic, we show that during the redn. of mol. oxygen in cNOR, two of the redn. steps are endergonic with high barriers for proton uptake, which is in contrast to oxygen redn. in CcO, where all redn. steps are exergonic. This difference between the two enzymes is suggested to be important for their differing capabilities for energy conservation. An addnl. result from this study is that at least three of the four redn. steps are initiated by proton transfer to the active site, which is in contrast to CcO, where electrons always arrive before the protons to the active site. The roles of the non-heme metal ion and the redox-active tyrosine in the active site are also discussed.
- 59Collman, J. P.; Devaraj, N. K.; Decréau, R. A.; Yang, Y.; Yan, Y.-L.; Ebina, W.; Eberspacher, T. A.; Chidsey, C. E. A Cytochrome C Oxidase Model Catalyzes Oxygen to Water Reduction under Rate-Limiting Electron Flux. Science 2007, 315, 1565– 1568, DOI: 10.1126/science.1135844Google Scholar59https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2sXivVSnsb4%253D&md5=9e226c8e59f5108db8c9e4bc88d8f5d9A Cytochrome c Oxidase Model Catalyzes Oxygen to Water Reduction Under Rate-Limiting Electron FluxCollman, James P.; Devaraj, Neal K.; Decreau, Richard A.; Yang, Ying; Yan, Yi-Long; Ebina, Wataru; Eberspacher, Todd A.; Chidsey, Christopher E. D.Science (Washington, DC, United States) (2007), 315 (5818), 1565-1568CODEN: SCIEAS; ISSN:0036-8075. (American Association for the Advancement of Science)We studied the selectivity of a functional model of cytochrome c oxidase's active site that mimics the coordination environment and relative locations of Fea3, CuB, and Tyr244. To control electron flux, we covalently attached this model and analogs lacking copper and phenol onto self-assembled monolayer-coated gold electrodes. When the electron transfer rate was made rate limiting, both copper and phenol were required to enhance selective redn. of oxygen to water. This finding supports the hypothesis that, during steady-state turnover, the primary role of these redox centers is to rapidly provide all the electrons needed to reduce oxygen by four electrons, thus preventing the release of toxic partially reduced oxygen species.
- 60Kim, E.; Chufán, E. E.; Kamaraj, K.; Karlin, K. D. Synthetic Models for Heme– Copper Oxidases. Chem. Rev. 2004, 104, 1077– 1134, DOI: 10.1021/cr0206162Google ScholarThere is no corresponding record for this reference.
- 61Nanthakumar, A. Oxo-and Hydroxo-Bridged (Porphyrin) Iron (Iii)-Copper (Ii) Species as Cytochrome C Oxidase Models: Acid-Base Interconversions and X-Ray Structure of the Fe (Iii)-(O2-)-Cu (Ii) Complex. J. Am. Chem. Soc. 1993, 115, 8513– 8514, DOI: 10.1021/ja00071a097Google ScholarThere is no corresponding record for this reference.
- 62Karlin, K. D.; Nanthakumar, A.; Fox, S.; Murthy, N. N.; Ravi, N.; Huynh, B. H.; Orosz, R. D.; Day, E. P. X-Ray Structure and Physical-Properties of the Oxo-Bridged Complex ((F-8-Tpp) Fe-O-Cu (Tmpa))(+), F-8-Tpp Equals Tetrakis (2, 6-Difluorophenyl) Porphyrinate (2-), Tmpa Equals Tris (2-Pyridylmethyl) Amine-Modeling the Cytochrome-C-Oxidase Fe-Cu Heterodinuclear Active-Site. J. Am. Chem. Soc. 1994, 116, 4753– 4763, DOI: 10.1021/ja00090a023Google ScholarThere is no corresponding record for this reference.
- 63Sharma, V.; Karlin, K. D.; Wikström, M. Computational Study of the Activated Oh State in the Catalytic Mechanism of Cytochrome C Oxidase. Proc. Natl. Acad. Sci. U. S. A. 2013, 110, 16844– 16849, DOI: 10.1073/pnas.1220379110Google Scholar63https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3sXhslejsbrO&md5=bde20c7969a5852d7bf17e26e5f10f3eComputational study of the activated OH state in the catalytic mechanism of cytochrome c oxidaseSharma, Vivek; Karlin, Kenneth D.; Wikstrom, MartenProceedings of the National Academy of Sciences of the United States of America (2013), 110 (42), 16844-16849, S16844/1-S16844/8CODEN: PNASA6; ISSN:0027-8424. (National Academy of Sciences)Complex IV/cytochrome c oxidase in the respiratory chain of mitochondria and bacteria catalyzes the redn. of O2 to H2O, and conserves much of the liberated free energy as an electrochem. proton gradient which is used for the synthesis of ATP. Photochem. electron injection expts. have shown that redn. of the ferric/cupric state of the enzyme's binuclear heme a3/CuB center is coupled to proton pumping across the membrane, but only if oxidn. of the reduced enzyme by O2 immediately precedes electron injection. In contrast redn. of the binuclear center in the "as-isolated" ferric/cupric enzyme is sluggish and without linkage to proton translocation. During turnover, the binuclear center apparently shuttles via a metastable but activated ferric/cupric state (OH), which may decay into a more stable catalytically incompetent form (O) in the absence of electron donors. The structural basis for the difference between these 2 states has remained elusive, and is addressed here using computational methodol. The results supported the notion that CuB(II) is either 3-coordinated in the OH state or shares an OH- ligand with heme a3 in a strained μ-hydroxo structure. Relaxation to state O is initiated by hydration of the binuclear site. The redox potential of CuB was expected, and found by DFT calcns., to be substantially higher in the OH state than in state O. These calcns. also suggested that the neutral radical form of the crosslinked Tyr residue in the binuclear site may be more significant in the catalytic cycle than suspected so far.
- 64Blomberg, M. R.; Siegbahn, P. E. How Cytochrome c Oxidase Can Pump Four Protons Per Oxygen Molecule at High Electrochemical Gradient. Biochim. Biophys. Acta, Bioenerg. 2015, 1847, 364– 376, DOI: 10.1016/j.bbabio.2014.12.005Google Scholar64https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2MXltVygtQ%253D%253D&md5=31c303c208de159ba91770d4abe9df26How cytochrome c oxidase can pump four protons per oxygen molecule at high electrochemical gradientBlomberg, Margareta R. A.; Siegbahn, Per E. M.Biochimica et Biophysica Acta, Bioenergetics (2015), 1847 (3), 364-376CODEN: BBBEB4; ISSN:0005-2728. (Elsevier B. V.)Expts. have shown that the A-family cytochrome c oxidases pump 4 protons per O2 mol., also at a high electrochem. gradient. This has been considered a puzzle, since 2 of the redn. potentials involved, Cu(II) and Fe(III), were estd. from expts. to be too low to afford proton pumping at a high gradient. The present quantum mech. study (using hybrid DFT) suggests a soln. to this puzzle. First, the calcns. show that the charge compensated Cu(II) potential for CuB is actually much higher than estd. from expt., of the same order as the redn. potentials for the tyrosyl radical and the ferryl group, which are also involved in the catalytic cycle. The reason for the discrepancy between theory and expt. is the very large uncertainty in the exptl. observations used to est. the equil. potentials, mainly caused by the lack of methods for direct detn. of reduced CuB. Second, the calcns. show that a high energy metastable state, labeled EH, is involved during catalytic turnover. The EH state mixes the low redn. potential of Fe(III) in heme a3 with another, higher potential, here suggested to be that of the tyrosyl radical, resulting in enough exergonicity to allow proton pumping at a high gradient. In contrast, the corresponding metastable oxidized state, OH, is not significantly higher in energy than the resting state, O. Finally, to secure the involvement of the high energy EH state it is suggested that only one proton is taken up via the K-channel during catalytic turnover.
- 65Han Du, W.-G.; Noodleman, L. Broken Symmetry DFT Calculations/Analysis for Oxidized and Reduced Dinuclear Center in Cytochrome C Oxidase: Relating Structures, Protonation States, Energies, and Mössbauer Properties in ba3 Thermus thermophilus. Inorg. Chem. 2015, 54, 7272, DOI: 10.1021/acs.inorgchem.5b00700Google Scholar65https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2MXht1SgsLbE&md5=61955f37c10c7495e7936cce7fa3ffd2Broken symmetry DFT calculations/analysis for oxidized and reduced dinuclear center in cytochrome c oxidase: Relating structures, protonation states, energies, and Mossbauer properties in ba3 Thermus thermophilusHan Du, Wen-Ge; Noodleman, LouisInorganic Chemistry (2015), 54 (15), 7272-7290CODEN: INOCAJ; ISSN:0020-1669. (American Chemical Society)The Fea33+···CuB2+ dinuclear center (DNC) structure of the as-isolated oxidized ba3 cytochrome c oxidase (CcO) from T. thermophilus (Tt) is still not fully understood. When proteins are initially crystd. in the oxidized state, they typically become radiolyticly reduced through x-ray irradn. Several x-ray crystal structures of reduced ba3 CcO from Tt are available. However, depending on whether the crystals were prepd. in a lipidic cubic phase environment or in detergent micelles, and whether the CcO's were chem. or radiolyticly reduced, the x-ray diffraction anal. of the crystals showed different Fea32+···CuB+ DNC structures. On the other hand, Mossbauer spectroscopic expts. on reduced and oxidized ba3 CcOs from Tt have revealed multiple 57Fea32+ and 57Fea33+ components. Moreover, one of the 57Fea33+ components obsd. at 4.2 K transformed from a proposed "low-spin" state to a different high-spin species when the temp. was increased above 190 K, whereas the other high-spin 57Fea33+ component remained unchanged. Here, in order to understand the heterogeneities of the DNC in both Mossbauer spectra and x-ray crystal structures, the spin crossover of one of the 57Fea33+ components, and how the coordination and spin states of the Fea33+/2+ and Cu2+/1+ sites relate to the heterogeneity of the DNC structures, the authors applied DFT OLYP calcns. to the DNC clusters established based on the different x-ray crystal structures of ba3 CcO from Tt. As a result, specific oxidized and reduced DNC structures related to the obsd. Mossbauer spectra and to spectral changes with temp. were proposed. The authors' calcns. also showed that, in certain intermediate states, the His-233 and His-283 ligand side-chains may dissoc. from the CuB+ site, and they may become potential proton loading sites during the catalytic cycle.
- 66Morgan, J. E.; Verkhovsky, M. I.; Palmer, G.; Wikström, M. Role of the Pr Intermediate in the Reaction of Cytochrome C Oxidase with O2. Biochemistry 2001, 40, 6882– 6892, DOI: 10.1021/bi010246wGoogle Scholar66https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD3MXjsVGjt70%253D&md5=b5ccd68b118c32639595540c59b0383fRole of the PR Intermediate in the Reaction of Cytochrome c Oxidase with O2Morgan, Joel E.; Verkhovsky, Michael I.; Palmer, Graham; Wikstroem, MartenBiochemistry (2001), 40 (23), 6882-6892CODEN: BICHAW; ISSN:0006-2960. (American Chemical Society)The first discernible intermediate when fully reduced cytochrome c oxidase reacts with O2 is a dioxygen adduct (compd. A) of the binuclear heme iron-copper center. The subsequent decay of compd. A is assocd. with transfer of an electron from the low-spin heme a to this center. This reaction eventually produces the ferryl state (F) of this center, but whether an intermediate state may be obsd. between A and F has been the subject of some controversy. Here we show, using both optical and EPR spectroscopy, that such an intermediate (PR) indeed exists and that it exhibits spectroscopic properties quite distinct from F. The optical spectrum of PR is similar or identical to the spectrum of the PM intermediate that is formed after compd. A when two-electron-reduced enzyme reacts with O2. An unusual EPR spectrum with features of a CuB(II) ion that interacts magnetically with a nearby paramagnet can be uniquely assigned to the PR intermediate, not being found in either the PM or F intermediate. The binuclear center in the PR state may be assigned as having an Fea3(IV):O CuB(II) structure, as in both the PM and F states. The spectroscopic differences between these three intermediates are evaluated. The PR state has a key role as an initiator of proton translocation by the enzyme, and the thermodn. and electrostatic bases for this are discussed.
- 67Poiana, F.; von Ballmoos, C.; Gonska, N.; Blomberg, M. R.; Ädelroth, P.; Brzezinski, P. Splitting of the O–O Bond at the Heme-Copper Catalytic Site of Respiratory Oxidases. Sci. Adv. 2017, 3, e1700279, DOI: 10.1126/sciadv.1700279Google Scholar67https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1cXmvFOmtL8%253D&md5=d52615c109b1b5f4aa07c044ac709b47Splitting of the O-O bond at the heme-copper catalytic site of respiratory oxidasesPoiana, Federica; von Ballmoos, Christoph; Gonska, Nathalie; Blomberg, Margareta R. A.; Adelroth, Pia; Brzezinski, PeterScience Advances (2017), 3 (6), e1700279/1-e1700279/10CODEN: SACDAF; ISSN:2375-2548. (American Association for the Advancement of Science)Heme-copper oxidases catalyze the four-electron redn. of O2 to H2O at a catalytic site that is composed of a heme group, a copper ion (CuB), and a tyrosine residue. Results from earlier exptl. studies have shown that the O-O bond is cleaved simultaneously with electron transfer from a low-spin heme (heme a/b), forming a ferryl state (PR;Fe4+ = O2-, CuB2+-OH-). We show that with the Thermus thermophilus ba3 oxidase, at low temp. (10°C, pH 7), electron transfer from the low-spin heme b to the catalytic site is faster by a factor of ∼10 (τt 11 μs) than the formation of the PR ferryl (t ≃ 110 μs), which indicates that O2 is reduced before the splitting of the O-O bond. Application of d. functional theory indicates that the electron acceptor at the catalytic site is a high-energy peroxy state [Fe3+-O--O-(H+)], which is formed before the PR ferryl. The rates of heme b oxidn. and PR ferryl formation were more similar at pH 10, indicating that the formation of the high-energy peroxy state involves proton transfer within the catalytic site, consistent with theory. The combined exptl. and theor. data suggest a general mechanism for O2 redn. by heme-copper oxidases.
- 68Blomberg, M. R.; Siegbahn, P. E.; Wikström, M. Metal-Bridging Mechanism for O– O Bond Cleavage in Cytochrome C Oxidase. Inorg. Chem. 2003, 42, 5231– 5243, DOI: 10.1021/ic034060sGoogle ScholarThere is no corresponding record for this reference.
- 69Hematian, S.; Garcia-Bosch, I.; Karlin, K. D. Synthetic Heme/Copper Assemblies: Toward an Understanding of Cytochrome C Oxidase Interactions with Dioxygen and Nitrogen Oxides. Acc. Chem. Res. 2015, 48, 2462– 2474, DOI: 10.1021/acs.accounts.5b00265Google Scholar69https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2MXht1yrs7vE&md5=52dc6668a3c36fa7107c09d12117a60dSynthetic Heme/Copper Assemblies: Toward an Understanding of Cytochrome c Oxidase Interactions with Dioxygen and Nitrogen OxidesHematian, Shabnam; Garcia-Bosch, Isaac; Karlin, Kenneth D.Accounts of Chemical Research (2015), 48 (8), 2462-2474CODEN: ACHRE4; ISSN:0001-4842. (American Chemical Society)A review. Our long-time niche in synthetic biol. inorg. chem. has been to design ligands and generate coordination complexes of copper or iron ions or both, those reacting with dioxygen (O2) or nitrogen oxides (e.g., nitric oxide (NO(g)) and nitrite (NO2-)) or both. As inspiration for this work, we turn to mitochondrial cytochrome c oxidase (CcO), which is responsible for dioxygen consumption and is also the predominant target for NO(g) and nitrite within mitochondria. In this Account, we highlight recent advances in studying synthetic heme/Cu complexes in two respects. First, there is the design, synthesis, and characterization of new O2 adducts whose further study will add insights into O2 reductive cleavage chem. Second, we describe how related heme/Cu constructs reduce nitrite ion to NO(g) or the reverse, oxidize NO(g) to nitrite. The reactions of nitrogen oxides occur as part of CcO's function, which is intimately tied to cellular O2 balance. We had first discovered that reduced heme/Cu compds. react with O2, giving μ-oxo heme-FeIII-O-CuII(L) products; their properties are discussed. The O-atom is derived from dioxygen, and interrogations of these systems led to the construction and characterization of three distinctive classes of heme-peroxo complexes, two high-spin and one low-spin species. Recent investigations include a new approach to the synthesis of low-spin heme-peroxo-Cu complexes, employing a "naked" synthon, where the copper ligand denticity and geometric types can be varied. The result is a collection of such complexes; spectroscopic and structural features (by DFT calcns.) are described. Some of these compds. are reactive toward reductants/protons effecting subsequent O-O cleavage. This points to how subtle improvements in ligand environment lead to a desired local structure and resulting optimized reactivity, as known to occur at enzyme active sites. The other sector of research is focused on heme/Cu assemblies mediating the redox interplay between nitrite and NO(g). In the nitrite reductase chem., the cupric center serves as a Lewis acid, while the heme is the redox active center providing the electron. The orientation of nitrite in approaching the ferrous heme center and N-atom binding are important. Also, detailed spectroscopic and kinetic studies of the NO(g) oxidase chem., in excellent agreement with theor. calcns., reveal the intermediates and key mechanistic steps. Thus, we suggest that both chem. and biochem. heme/Cu-mediated nitrite reductase and NO(g) oxidase chem. require N-atom binding to a ferrous heme along with cupric ion O-atom coordination, proceeding via a three-membered O-Fe-N chelate ring transition state. These important mechanistic features of heme/Cu systems interconverting NO(g) and nitrite are discussed for the first time.
- 70Chatterjee, S.; Sengupta, K.; Hematian, S.; Karlin, K. D.; Dey, A. Electrocatalytic O2-Reduction by Synthetic Cytochrome C Oxidase Mimics: Identification of a “Bridging Peroxo” Intermediate Involved in Facile 4e–/4h+ O2-Reduction. J. Am. Chem. Soc. 2015, 137, 12897– 12905, DOI: 10.1021/jacs.5b06513Google Scholar70https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2MXhs1ajsb7N&md5=065689b47af0dbee72385ed45cd7c595Electrocatalytic O2-Reduction by Synthetic Cytochrome c Oxidase Mimics: Identification of a "Bridging Peroxo" Intermediate Involved in Facile 4e-/4H+ O2-ReductionChatterjee, Sudipta; Sengupta, Kushal; Hematian, Shabnam; Karlin, Kenneth D.; Dey, AbhishekJournal of the American Chemical Society (2015), 137 (40), 12897-12905CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)A synthetic heme-Cu CcO model complex shows selective and highly efficient electrocatalytic 4e-/4H+ O2-redn. to H2O with a large catalytic rate (>105 M-1 s-1). While the heme-Cu model (FeCu) shows almost exclusive 4e-/4H+ redn. of O2 to H2O (detected using ring disk electrochem. and rotating ring disk electrochem.), when imidazole is bound to the heme (Fe(Im)Cu), this same selective O2-redn. to H2O occurs only under slow electron fluxes. Surface enhanced resonance Raman spectroscopy coupled to dynamic electrochem. data suggests the formation of a bridging peroxide intermediate during O2-redn. by both complexes under steady state reaction conditions, indicating that O-O bond heterolysis probably is the rate-detg. step (RDS) at the mass transfer limited region. The O-O vibrational frequencies at 819 cm-1 in 16O2 (759 cm-1 in 18O2) for the FeCu complex and at 847 cm-1 (786 cm-1) for the Fe(Im)Cu complex, indicate the formation of side-on and end-on bridging Fe-peroxo-Cu intermediates, resp., during O2-redn. in an aq. environment. Probably side-on bridging peroxide intermediates are involved in fast and selective O2-redn. in these synthetic complexes. The greater amt. of H2O2 prodn. by the imidazole bound complex under fast electron transfer is due to 1e-/1H+ O2-redn. by the distal Cu where O2 binding to the H2O bound low spin FeII complex is inhibited.
- 71Adam, S. M.; Garcia-Bosch, I.; Schaefer, A. W.; Sharma, S. K.; Siegler, M. A.; Solomon, E. I.; Karlin, K. D. Critical Aspects of Heme–Peroxo–Cu Complex Structure and Nature of Proton Source Dictate Metal–Operoxo Breakage Versus Reductive O–O Cleavage Chemistry. J. Am. Chem. Soc. 2017, 139, 472– 481, DOI: 10.1021/jacs.6b11322Google Scholar71https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC28XitFGht7nP&md5=f42cbeb35ea052dfc4801b163e6fe2ffCritical Aspects of Heme-Peroxo-Cu Complex Structure and Nature of Proton Source Dictate Metal-Operoxo Breakage versus Reductive O-O Cleavage ChemistryAdam, Suzanne M.; Garcia-Bosch, Isaac; Schaefer, Andrew W.; Sharma, Savita K.; Siegler, Maxime A.; Solomon, Edward I.; Karlin, Kenneth D.Journal of the American Chemical Society (2017), 139 (1), 472-481CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)The 4H+/4e- redn. of O2 to H2O, a key fuel-cell reaction also carried out in biol. by oxidase enzymes, includes the crit. O-O bond reductive cleavage step. Mechanistic studies on active-site model compds., which were synthesized by rational design to incorporate systematic variations, can focus on and resolve answers to fundamental questions, including protonation and/or H-bonding aspects which accompany electron transfer. Here, the authors describe the nature and comparative reactivity of two low-spin heme-peroxo-Cu complexes, LS-4DCHIm, [(DCHIm)F8FeIII-(O22-)-CuII(DCHIm)4]+, and LS-3DCHIm, [(DCHIm)F8FeIII-(O22-)-CuII(DCHIm)3]+, (F8 = tetrakis(2,6-difluorophenyl)porphyrinate; DCHIm = 1,5-dicyclohexylimidazole) toward different proton (4-nitrophenol and [DMF·H+](CF3SO3-)) or electron (decamethylferrocene (Fc*)) sources. Spectroscopic reactivity studies show that differences in structure and electronic properties of LS-3DCHIm and LS-4DCHIm lead to significant differences in behavior. LS-3DCHIm is resistant to redn., is unreactive toward weakly acidic 4-NO2-phenol, and stronger acids cleave the metal-O bonds, releasing H2O2. By contrast, LS-4DCHIm forms an adduct with 4-NO2-phenol which includes an H-bond to the peroxo O atom distal to Fe (resonance Raman (rR) spectroscopy and DFT). With addn. of Fc* (2 equiv overall required) O-O reductive cleavage occurs, giving H2O, Fe(III), and Cu(II) products, however a kinetic study reveals a 1-electron rate detg. process, ket = 1.6M-1 s-1 (-90°). The intermediacy of a high-valent [(DCHIm)F8FeIV=O] species is thus implied, and sep. expts. show that one electron redn.-protonation of [(DCHIm)F8FeIV=O] occurs faster (ket2 = 5.0M-1 s-1), consistent with the overall postulated mechanism. The importance of the H-bonding interaction as a prerequisite for reductive cleavage is highlighted.
- 72Schaefer, A. W.; Kieber-Emmons, M. T.; Adam, S. M.; Karlin, K. D.; Solomon, E. I. Phenol-Induced O–O Bond Cleavage in a Low-Spin Heme-Peroxo-Copper Complex: Implications for O2 Reduction in Heme-Copper Oxidases. J. Am. Chem. Soc. 2017, 139, 7958– 7973, DOI: 10.1021/jacs.7b03292Google ScholarThere is no corresponding record for this reference.
- 73Yoshioka, Y.; Kawai, H.; Yamaguchi, K. Theoretical Study of Role of H 2 O Molecule on Initial Stage of Reduction of O2 Molecule in Active Site of Cytochrome C Oxidase. Chem. Phys. Lett. 2003, 374, 45– 52, DOI: 10.1016/S0009-2614(03)00683-3Google ScholarThere is no corresponding record for this reference.
- 74Al-Abdul-Wahid, M. S.; Evanics, F.; Prosser, R. S. Dioxygen Transmembrane Distributions and Partitioning Thermodynamics in Lipid Bilayers and Micelles. Biochemistry 2011, 50, 3975– 3983, DOI: 10.1021/bi200168nGoogle Scholar74https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3MXkvFWrtL8%253D&md5=fffa771772b2d3201ec76603d579804fDioxygen Transmembrane Distributions and Partitioning Thermodynamics in Lipid Bilayers and MicellesAl-Abdul-Wahid, M. Sameer; Evanics, Ferenc; Prosser, R. ScottBiochemistry (2011), 50 (19), 3975-3983CODEN: BICHAW; ISSN:0006-2960. (American Chemical Society)Cellular respiration, mediated by the passive diffusion of oxygen across lipid membranes, is key to many basic cellular processes. In this work, we report the detailed distribution of oxygen across lipid bilayers and examine the thermodn. of oxygen partitioning via NMR studies of lipids in a small unilamellar vesicle (SUV) morphol. Dissolved oxygen gives rise to paramagnetic chem. shift perturbations and relaxation rate enhancements, both of which report on local oxygen concn. From SUVs contg. the phospholipid sn-2-perdeuterio-1-myristelaidoyl, 2-myristoyl-sn-glycero-3-phosphocholine (MLMPC), an analog of 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC), we deduced the complete trans-bilayer oxygen distribution by measuring 13C paramagnetic chem. shifts perturbations for 18 different sites on MLMPC arising from oxygen at a partial pressure of 30 bar. The overall oxygen soly. at 45 °C spans a factor of 7 between the bulk water (23.7 mM) and the bilayer center (170 mM) and is lowest in the vicinity of the phosphocholine headgroup, suggesting that oxygen diffusion across the glycerol backbone should be the rate-limiting step in diffusion-mediated passive transport of oxygen across the lipid bilayer. Lowering of the temp. from 45 to 25 °C gave rise to a slight decrease of the oxygen soly. within the hydrocarbon interior of the membrane. An anal. of the temp. dependence of the oxygen soly. profile, as measured by 1H paramagnetic relaxation rate enhancements, reveals that oxygen partitioning into the bilayer is entropically favored (ΔS° = 54 ± 3 J K-1 mol-1) and must overcome an enthalpic barrier (ΔH° = 12.0 ± 0.9 kJ mol-1).
- 75Möller, M. N.; Li, Q.; Chinnaraj, M.; Cheung, H. C.; Lancaster, J. R., Jr; Denicola, A. Solubility and Diffusion of Oxygen in Phospholipid Membranes. Biochim. Biophys. Acta, Biomembr. 2016, 1858, 2923– 2930, DOI: 10.1016/j.bbamem.2016.09.003Google Scholar75https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC28XhsVyitbvM&md5=0f2879bb62f0f9060f26e885b63cc4a3Solubility and diffusion of oxygen in phospholipid membranesMoller, Matias N.; Li, Qian; Chinnaraj, Mathivanan; Cheung, Herbert C.; Lancaster, Jack R.; Denicola, AnaBiochimica et Biophysica Acta, Biomembranes (2016), 1858 (11), 2923-2930CODEN: BBBMBS; ISSN:0005-2736. (Elsevier B.V.)The transport of O2 and other nonelectrolytes across lipid membranes is known to depend on both diffusion and soly. in the bilayer, and to be affected by changes in the phys. state and by the lipid compn., esp. the content of cholesterol and unsatd. fatty acids. However, it is not known how these factors affect diffusion and soly. sep. Here, the authors measured the partition coeff. of O2 in liposome membranes of dilauroyl-, dimyristoyl- and dipalmitoylphosphatidylcholine in buffer at different temps. using the equil.-shift method with electrochem. detection. The apparent diffusion coeff. was measured following the fluorescence quenching of 1-pyrenedodecanoate inserted in the liposome bilayers under the same conditions. The partition coeff. varied with the temp. and the phys. state of the membrane, from <1 in the gel state to >2.8 in the liq.-cryst. state in DMPC and DPPC membranes. The partition coeff. was directly proportional to the partial molar volume and was then assocd. to the increase in free-vol. in the membrane as a function of temp. The apparent diffusion coeffs. were cor. by the partition coeffs. and found to be nearly the same, with a null dependence on viscosity and phys. state of the membrane, probably because the pyrene is disturbing the surrounding lipids and thus becoming insensitive to changes in membrane viscosity. Combining these results with those of others, it is apparent that both soly. and diffusion increase when increasing the temp. or when comparing a membrane in the gel to one in the fluid state.
- 76Cordeiro, R. M. Reactive Oxygen Species at Phospholipid Bilayers: Distribution, Mobility and Permeation. Biochim. Biophys. Acta, Biomembr. 2014, 1838, 438– 444, DOI: 10.1016/j.bbamem.2013.09.016Google Scholar76https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3sXhvFOlsrvL&md5=849ee1f846bbcc3525464d4580028be3Reactive oxygen species at phospholipid bilayers: Distribution, mobility and permeationCordeiro, Rodrigo M.Biochimica et Biophysica Acta, Biomembranes (2014), 1838 (1PB), 438-444CODEN: BBBMBS; ISSN:0005-2736. (Elsevier B.V.)Reactive oxygen species (ROS) are involved in biochem. processes such as redox signaling, aging, carcinogenesis and neurodegeneration. Although biomembranes are targets for reactive oxygen species attack, little is known about the role of their specific interactions. Here, mol. dynamics (MD) simulations were employed to det. the distribution, mobility and residence times of various reactive oxygen species at the membrane-water interface. Simulations showed that mol. oxygen (O2) accumulated at the membrane interior. The applicability of this result to singlet oxygen (1O2) was discussed. Conversely, superoxide (O2-) radicals and hydrogen peroxide (H2O2) remained at the aq. phase. Both hydroxyl (HO) and hydroperoxyl (HO2) radicals were able to penetrate deep into the lipid headgroups region. Due to membrane fluidity and disorder, these radicals had access to potential peroxidn. sites along the lipid hydrocarbon chains, without having to overcome the permeation free energy barrier. Strikingly, HO2 radicals were an order of magnitude more concd. in the headgroups region than in water, implying a large shift in the acid-base equil. between HO2 and O2-. In comparison with O2, both HO and HO2 radicals had lower lateral mobility at the membrane. Simulations revealed that there were intermittent interruptions in the H-bond network around the HO radicals at the headgroups region. This effect is expected to be unfavorable for the H-transfer mechanism involved in HO diffusion. The implications for lipid peroxidn. and for the effectiveness of membrane antioxidants were evaluated.
- 77Shinzawa-Itoh, K. Structures and Physiological Roles of 13 Integral Lipids of Bovine Heart Cytochrome c Oxidase. EMBO J. 2007, 26, 1713– 1725, DOI: 10.1038/sj.emboj.7601618Google Scholar77https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2sXjt1Wktrc%253D&md5=e3766c3ed5bfbaffefaa252e938a983eStructures and physiological roles of 13 integral lipids of bovine heart cytochrome c oxidaseShinzawa-Itoh, Kyoko; Aoyama, Hiroshi; Muramoto, Kazumasa; Terada, Hirohito; Kurauchi, Tsuyoshi; Tadehara, Yoshiki; Yamasaki, Akiko; Sugimura, Takashi; Kurono, Sadamu; Tsujimoto, Kazuo; Mizushima, Tsunehiro; Yamashita, Eiki; Tsukihara, Tomitake; Yoshikawa, ShinyaEMBO Journal (2007), 26 (6), 1713-1725CODEN: EMJODG; ISSN:0261-4189. (Nature Publishing Group)All 13 lipids, including two cardiolipins, one phosphatidylcholine, three phosphatidylethanolamines, four phosphatidylglycerols and three triglycerides, were identified in a cryst. bovine heart cytochrome c oxidase (CcO) prepn. The chain lengths and unsatd. bond positions of the fatty acid moieties detd. by mass spectrometry suggest that each lipid head group identifies its specific binding site within CcOs. The X-ray structure demonstrates that the flexibility of the fatty acid tails facilitates their effective space-filling functions and that the four phospholipids stabilize the CcO dimer. Binding of dicyclohexylcarbodiimide to the O2 transfer pathway of CcO causes two palmitate tails of phosphatidylglycerols to block the pathway, suggesting that the palmitates control the O2 transfer process. The phosphatidylglycerol with vaccenate (cis-Δ11-octadecenoate) was found in CcOs of bovine and Paracoccus denitrificans, the ancestor of mitochondrion, indicating that the vaccenate is conserved in bovine CcO in spite of the abundance of oleate (cis-Δ9-octadecenoate). The X-ray structure indicates that the protein moiety selects cis-vaccenate near the O2 transfer pathway against trans-vaccenate. These results suggest that vaccenate plays a crit. role in the O2 transfer mechanism.
- 78Svensson-Ek, M.; Abramson, J.; Larsson, G.; Törnroth, S.; Brzezinski, P.; Iwata, S. The X-Ray Crystal Structures of Wild-Type and Eq (I-286) Mutant Cytochrome C Oxidases from Rhodobacter Sphaeroides. J. Mol. Biol. 2002, 321, 329– 339, DOI: 10.1016/S0022-2836(02)00619-8Google ScholarThere is no corresponding record for this reference.
- 79Luna, V. M.; Chen, Y.; Fee, J. A.; Stout, C. D. Crystallographic Studies of Xe and Kr Binding within the Large Internal Cavity of Cytochrome Ba 3 from Thermus Thermophilus: Structural Analysis and Role of Oxygen Transport Channels in the Heme– Cu Oxidases. Biochemistry 2008, 47, 4657– 4665, DOI: 10.1021/bi800045yGoogle ScholarThere is no corresponding record for this reference.
- 80Luna, V. M.; Fee, J. A.; Deniz, A. A.; Stout, C. D. Mobility of Xe Atoms within the Oxygen Diffusion Channel of Cytochrome Ba 3 Oxidase. Biochemistry 2012, 51, 4669– 4676, DOI: 10.1021/bi3003988Google ScholarThere is no corresponding record for this reference.
- 81Schmidt, B.; McCracken, J.; Ferguson-Miller, S. A Discrete Water Exit Pathway in the Membrane Protein Cytochrome C Oxidase. Proc. Natl. Acad. Sci. U. S. A. 2003, 100, 15539– 15542, DOI: 10.1073/pnas.2633243100Google Scholar81https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2cXhtVCisA%253D%253D&md5=eb3710596efd38c6a4176726b201a9ffA discrete water exit pathway in the membrane protein cytochrome c oxidaseSchmidt, Bryan; McCracken, John; Ferguson-Miller, ShelaghProceedings of the National Academy of Sciences of the United States of America (2003), 100 (26), 15539-15542CODEN: PNASA6; ISSN:0027-8424. (National Academy of Sciences)By using the non-redox-active Mg2+/Mn2+ site of cytochrome c oxidase as a probe, water access from the outside of the enzyme and water escape from the buried active site were studied. Water movement was time-resolved by monitoring the magnetic interaction of the oxygen isotope 17O with the Mn2+ by using a rapid freeze-quench-electron spin echo envelope modulation technique. Rapid (msec) access of water from the bulk phase to the Mn2+ was demonstrated by mixing cytochrome c oxidase with H217O. To det. whether a channel involving the Mn2+ was used for water exit from the active site, samples incubated in 17O2 were allowed to turn over approx. five times before freezing. The 17O, now in the form of H217O, was detected at the Mn2+. The significant broadening of the Mn2+ signal after the limited no. of turnovers strongly suggests that the water exits the protein by means of one discrete pathway, not by random diffusion.
- 82Sharma, V.; Enkavi, G.; Vattulainen, I.; Róg, T.; Wikström, M. Proton-Coupled Electron Transfer and the Role of Water Molecules in Proton Pumping by Cytochrome C Oxidase. Proc. Natl. Acad. Sci. U. S. A. 2015, 112, 2040– 2045, DOI: 10.1073/pnas.1409543112Google Scholar82https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2MXhvFCgtr4%253D&md5=9beae0315c7257f542717f6e091a1a33Proton-coupled electron transfer and the role of water molecules in proton pumping by cytochrome c oxidaseSharma, Vivek; Enkavi, Giray; Vattulainen, Ilpo; Rog, Tomasz; Wikstrom, MartenProceedings of the National Academy of Sciences of the United States of America (2015), 112 (7), 2040-2045CODEN: PNASA6; ISSN:0027-8424. (National Academy of Sciences)Mol. oxygen (O2) acts as the terminal electron sink in the respiratory chains of aerobic organisms. Cytochrome c oxidase (CcO) in the inner membrane of mitochondria and the plasma membrane of bacteria catalyzes the redn. of oxygen to water, and couples the free energy of the reaction to proton pumping across the membrane. The proton-pumping activity contributes to the proton electrochem. gradient, which drives the synthesis of ATP. Based on kinetic expts. on the O-O bond splitting transition of the catalytic cycle (A → PR), it has been proposed that the electron transfer to the binuclear iron-copper center of O2 redn. initiates the proton pump mechanism. This key electron transfer event is coupled to an internal proton transfer from a conserved glutamic acid to the proton-loading site (PLS) of the pump. However, the proton may instead be transferred to the binuclear center to complete the oxygen redn. chem., which would constitute a short-circuit. Based on atomistic mol. dynamics simulations of cytochrome c oxidase in an explicit membrane-solvent environment, complemented by related free-energy calcns., we propose that this short-circuit is effectively prevented by a redox-state-dependent organization of water mols. within the protein structure that gates the proton transfer pathway.
- 83Moser, C. C.; Farid, T. A.; Chobot, S. E.; Dutton, P. L. Electron Tunneling Chains of Mitochondria. Biochim. Biophys. Acta, Bioenerg. 2006, 1757, 1096– 1109, DOI: 10.1016/j.bbabio.2006.04.015Google Scholar83https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD28XhtVanurvJ&md5=53f26760dadb7080907851bc55be2dd6Electron tunneling chains of mitochondriaMoser, Christopher C.; Farid, Tammer A.; Chobot, Sarah E.; Dutton, P. LeslieBiochimica et Biophysica Acta, Bioenergetics (2006), 1757 (9-10), 1096-1109CODEN: BBBEB4; ISSN:0005-2728. (Elsevier B.V.)The single, simple concept that natural selection adjusts distances between redox cofactors goes a long way towards encompassing natural electron transfer protein design. Distances are short or long as required to direct or insulate promiscuously tunneling single electrons. Along a chain, distances are usually 14 Å or less. Shorter distances are needed to allow climbing of added energetic barriers at paired-electron catalytic centers in which substrate and the required no. of cofactors form a compact cluster. When there is a short-circuit danger, distances between shorting centers are relatively long. Distances much longer than 14Å will support only very slow electron tunneling, but could act as high impedance signals useful in regulation. Tunneling simulations of the respiratory complexes provide clear illustrations of this simple engineering.
- 84Blumberger, J. Recent Advances in the Theory and Molecular Simulation of Biological Electron Transfer Reactions. Chem. Rev. 2015, 115, 11191– 11238, DOI: 10.1021/acs.chemrev.5b00298Google Scholar84https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2MXhs1OrsL3E&md5=cadcc0a7ef37f98feeae7878dc7cbaa0Recent advances in the theory and molecular simulation of biological electron transfer reactionsBlumberger, JochenChemical Reviews (Washington, DC, United States) (2015), 115 (20), 11191-11238CODEN: CHREAY; ISSN:0009-2665. (American Chemical Society)A review. The author's aim is to provide a crit, account of both anal. and numerical methods that have been developed to investigate, characterize, quantify, and explain biol. electron transfer reactions.
- 85Moser, C. C.; Keske, J. M.; Warncke, K.; Farid, R. S.; Dutton, P. L. Nature of Biological Electron Transfer. Nature 1992, 355, 796, DOI: 10.1038/355796a0Google Scholar85https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaK38XhsVKhu78%253D&md5=c7725760b5efee0b5572df1cbe714afdNature of biological electron transferMoser, Christopher C.; Keske, Jonathan M.; Warncke, Kurt; Farid, Ramy S.; Dutton, P. LeslieNature (London, United Kingdom) (1992), 355 (6363), 796-802CODEN: NATUAS; ISSN:0028-0836.Factors which govern long-range electron transfer in biol. systems are examd. A powerful first-order anal. of intraprotein electron transfer is developed from electron-transfer measurements both in biol. and chem. systems. The anal. provides guidelines basic to the understanding of the design and engineering of respiratory and photosynthetic electron-transfer chains and other redox proteins.
- 86Winkler, J. R.; Gray, H. B. Electron Flow through Metalloproteins. Chem. Rev. 2014, 114, 3369, DOI: 10.1021/cr4004715Google Scholar86https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3sXhvVCmur%252FN&md5=784dc3f774bde08e216f97288ea84d6aElectron flow through metalloproteinsWinkler, Jay R.; Gray, Harry B.Chemical Reviews (Washington, DC, United States) (2014), 114 (7), 3369-3380CODEN: CHREAY; ISSN:0009-2665. (American Chemical Society)A review. Electron flow through proteins and protein assemblies in the photosynthetic and respiratory machinery commonly occurs between metal centers or other redox cofactors that are sepd. by relatively large mol. distances, often in the 10-20 Å range. Here, long-range electron transfer in metalloproteins is discussed. A key finding from these studies is that macromol. structures tune thermodn. properties and electronic coupling interactions to facilitate electron flow through biol. redox chains.
- 87Tan, M.-L.; Balabin, I.; Onuchic, J. N. Dynamics of Electron Transfer Pathways in Cytochrome c Oxidase. Biophys. J. 2004, 86, 1813– 1819, DOI: 10.1016/S0006-3495(04)74248-4Google ScholarThere is no corresponding record for this reference.
- 88Shimada, S. Complex Structure of Cytochrome c–Cytochrome c oxidase Reveals a Novel Protein–Protein Interaction Mode. EMBO J. 2017, 36, 291– 300, DOI: 10.15252/embj.201695021Google Scholar88https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC28XitVyit7rP&md5=272334509c6e57daed5d2bfb31c730ebComplex structure of cytochrome c-cytochrome c oxidase reveals a novel protein-protein interaction modeShimada, Satoru; Shinzawa-Itoh, Kyoko; Baba, Junpei; Aoe, Shimpei; Shimada, Atsuhiro; Yamashita, Eiki; Kang, Jiyoung; Tateno, Masaru; Yoshikawa, Shinya; Tsukihara, TomitakeEMBO Journal (2017), 36 (3), 291-300CODEN: EMJODG; ISSN:0261-4189. (Wiley-VCH Verlag GmbH & Co. KGaA)Mitochondrial cytochrome c oxidase (CcO) transfers electrons from cytochrome c (Cyt.c) to O2 to generate H2O, a process coupled to proton pumping. To elucidate the mechanism of electron transfer, we detd. the structure of the mammalian Cyt.c-CcO complex at 2.0-Å resoln. and identified an electron transfer pathway from Cyt.c to CcO. The specific interaction between Cyt.c and CcO is stabilized by a few electrostatic interactions between side chains within a small contact surface area. Between the two proteins are three water layers with a long intermol. span, one of which lies between the other two layers without significant direct interaction with either protein. Cyt.c undergoes large structural fluctuations, using the interacting regions with CcO as a fulcrum. These features of the protein-protein interaction at the docking interface represent the first known example of a new class of protein-protein interaction, which we term "soft and specific". This interaction is likely to contribute to the rapid assocn./dissocn. of the Cyt.c-CcO complex, which facilitates the sequential supply of four electrons for the O2 redn. reaction.
- 89Witt, H.; Malatesta, F.; Nicoletti, F.; Brunori, M.; Ludwig, B. Tryptophan 121 of Subunit Ii Is the Electron Entry Site to Cytochrome-C Oxidase in Paracoccus Denitrificans Involvement of a Hydrophobic Patch in the Docking Reaction. J. Biol. Chem. 1998, 273, 5132– 5136, DOI: 10.1074/jbc.273.9.5132Google ScholarThere is no corresponding record for this reference.
- 90Witt, H.; Malatesta, F.; Nicoletti, F.; Brunori, M.; Ludwig, B. Cytochrome-C– Binding Site on Cytochrome Oxidase in Paracoccus Denitrificans. Eur. J. Biochem. 1998, 251, 367– 373, DOI: 10.1046/j.1432-1327.1998.2510367.xGoogle Scholar90https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaK1cXnvV2qtw%253D%253D&md5=a81701993b5da2e6f3c7bf94eb964846Cytochrome-c-binding site on cytochrome oxidase in Paracoccus denitrificansWitt, Heike; Malatesta, Francesco; Nicoletti, Flavia; Brunori, Maurizio; Ludwig, BerndEuropean Journal of Biochemistry (1998), 251 (1/2), 367-373CODEN: EJBCAI; ISSN:0014-2956. (Springer-Verlag)To monitor the docking site for cytochrome c on cytochrome oxidase from P. denitrificans, a series of site-directed mutants in acidic residues exposed on the 3 largest subunits was constructed, and the purified enzymes were assayed for their steady-state kinetic parameters, their ionic strength dependence, and their fast electron entry kinetics by stopped-flow measurements. Increasing the ionic strength, the max. of the bell-shaped dependence of the steady-state rate obsd. for wild type shifted the max. to lower ionic strength in most of the mutants. The Km detd. in steady-state expts. under different conditions was largely increased for most of the subunit II and one of the subunit I mutants, giving evidence that binding was impaired, whereas subunit III residues did not seem to contribute significantly. In addn., the bimol. rate const. for cytochrome c oxidn. under presteady state conditions was measured using stopped flow spectroscopy. Taken together, the results demonstrated that the initial interaction of cytochrome c and oxidase is mediated through Glu and Asp residues mainly located in subunit II. The crystal structure of oxidase revealed that the participating residues are clustered, creating an extended, neg. charged patch. This clustering is proposed to be a decisive factor in the recognition of pos. charged patches on the surface of cytochrome c.
- 91Flöck, D.; Helms, V. Protein–Protein Docking of Electron Transfer Complexes: Cytochrome C Oxidase and Cytochrome C. Proteins: Struct., Funct., Genet. 2002, 47, 75– 85, DOI: 10.1002/prot.10066Google ScholarThere is no corresponding record for this reference.
- 92Lyons, J. A.; Nissen, P. Brief Encounters of Cytochrome C. EMBO J. 2017, 36, 250– 251, DOI: 10.15252/embj.201696124Google Scholar92https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2sXoslarsw%253D%253D&md5=cece82eb51adf34705236925c559c2c9Brief encounters of cytochrome cLyons, Joseph A.; Nissen, PoulEMBO Journal (2017), 36 (3), 250-251CODEN: EMJODG; ISSN:0261-4189. (Wiley-VCH Verlag GmbH & Co. KGaA)A review. The research of C. Y. Zou et al. (ibid., doi: 10.15252/embj.201695021) is reviewed with commentary and refs. Transient protein interactions are paramount to life where fast and efficient transfer of information and cargo are often integral to pathways and networks. However, complexes formed by transient protein interactions are often times resistant to direct structural characterization due to their inherent, dynamic nature, so our knowledge to date typically derives from biochem., biophys. and computational methods. In this issue, Shimada and co-authors present the crystal structure of the mammalian cytochrome c oxidase in complex with its electron donor cytochrome c, identifying a new class of protein-protein interaction termed "soft and specific".
- 93Kaila, V. R.; Verkhovsky, M. I.; Wikström, M. Wikström, M. Proton-Coupled Electron Transfer in Cytochrome Oxidase. Chem. Rev. 2010, 110, 7062– 7081, DOI: 10.1021/cr1002003Google ScholarThere is no corresponding record for this reference.
- 94Mitchell, R.; Rich, P. R. Proton Uptake by Cytochrome C Oxidase on Reduction and on Ligand Binding. Biochim. Biophys. Acta, Bioenerg. 1994, 1186, 19– 26, DOI: 10.1016/0005-2728(94)90130-9Google Scholar94https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaK2cXlsFajs7o%253D&md5=30af5518841f3645afc5cb82e7be9c70Proton uptake by cytochrome c oxidase on reduction and on ligand bindingMitchell, Roy; Rich, Peter R.Biochimica et Biophysica Acta, Bioenergetics (1994), 1186 (1-2), 19-26CODEN: BBBEB4; ISSN:0005-2728.On redn., cytochrome oxidase was found to take up 2.4 protons in the pH range 7.2-8.5, of which 2 are assocd. with the binuclear center, and the remaining fractional proton with heme a/CuA. Ligation to oxidized cytochrome oxidase of the azide, formate, fluoride or cyanide anions is accompanied by uptake of one proton. Cyanide binding to reduced oxidase is accompanied by uptake of a proton. These findings are discussed in terms of the authors' previously-published proposal for the ligand chem. of the binuclear site. The results overall suggest a principle of electroneutrality of redox and ligand state changes of the binuclear center, with charge compensations provided only by protonation reactions.
- 95Verkhovsky, M. I.; Jasaitis, A.; Wikström, M. Ultrafast Haem–Haem Electron Transfer in Cytochrome C Oxidase. Biochim. Biophys. Acta, Bioenerg. 2001, 1506, 143– 146, DOI: 10.1016/S0005-2728(01)00220-1Google Scholar95https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD38XkvFCg&md5=9219053bd1ac7758604ef576da213036Ultrafast haem-haem electron transfer in cytochrome c oxidaseVerkhovsky, Michael I.; Jasaitis, Audrius; Wikstrom, MartenBiochimica et Biophysica Acta, Bioenergetics (2001), 1506 (3), 143-146CODEN: BBBEB4; ISSN:0005-2728. (Elsevier B.V.)Electron transfer between the redox centers is essential for the function of the heme-copper oxidases. To date, the fastest rate of electron transfer between the heme groups has been detd. to be ca. 3×105 s-1. Here, we show by optical spectroscopy that about one half of this electron transfer actually occurs at least three orders of magnitude faster, after photolysis of carbon monoxide from the half-reduced bovine heart enzyme. We ascribe this to the true heme-heme electron tunneling rate between the heme groups.
- 96Jasaitis, A.; Johansson, M. P.; Wikström, M.; Vos, M. H.; Verkhovsky, M. I. Nanosecond Electron Tunneling between the Hemes in Cytochrome Bo3. Proc. Natl. Acad. Sci. U. S. A. 2007, 104, 20811– 20814, DOI: 10.1073/pnas.0709876105Google ScholarThere is no corresponding record for this reference.
- 97Belevich, I.; Verkhovsky, M. I.; Wikström, M. Proton-Coupled Electron Transfer Drives the Proton Pump of Cytochrome C Oxidase. Nature 2006, 440, 829– 832, DOI: 10.1038/nature04619Google Scholar97https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD28XjtFKjsLY%253D&md5=8e269192f1893c085024c230b0a59dcfProton-coupled electron transfer drives the proton pump of cytochrome c oxidaseBelevich, Ilya; Verkhovsky, Michael I.; Wikstroem, MartenNature (London, United Kingdom) (2006), 440 (7085), 829-832CODEN: NATUAS; ISSN:0028-0836. (Nature Publishing Group)Electron transfer in cell respiration is coupled to proton translocation across mitochondrial and bacterial membranes, which is a primary event of biol. energy transduction. The resulting electrochem. proton gradient is used to power energy-requiring reactions, such as ATP synthesis. Cytochrome c oxidase (I) is a key component of the respiratory chain, which harnesses O2 as a sink for electrons and links O2 redn. to proton pumping. Electrons from cytochrome c are transferred sequentially to the O2 redn. site of I via 2 other metal centers, CuA and heme a, and this is coupled to vectorial proton transfer across the membrane by a hitherto unknown mechanism. On the basis of the kinetics of proton uptake and release on the 2 aq. sides of the membrane, it was recently suggested that proton pumping by I is not mechanistically coupled to internal electron transfer. Here, the authors monitored the translocation of elec. charge equiv as well as electron transfer within I in real time. The results showed that electron transfer from heme a to the O2 redn. site initiates the proton pump mechanism by being kinetically linked to an internal vectorial proton transfer. This reaction drives the proton pump and occurs before the relaxation steps in which protons are taken up from the aq. space on one side of the membrane and released on the other.
- 98Wikström, M.; Sharma, V.; Kaila, V. R.; Hosler, J. P.; Hummer, G. New Perspectives on Proton Pumping in Cellular Respiration. Chem. Chem. Rev. 2015, 115, 2196– 2221, DOI: 10.1021/cr500448tGoogle ScholarThere is no corresponding record for this reference.
- 99Tsukihara, T. The Low-Spin Heme of Cytochrome C Oxidase as the Driving Element of the Proton-Pumping Process. Proc. Natl. Acad. Sci. U. S. A. 2003, 100, 15304– 15309, DOI: 10.1073/pnas.2635097100Google Scholar99https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2cXhtVeksw%253D%253D&md5=59fa9a04a5c5f24e8b9847f229142fc9The low-spin heme of cytochrome c oxidase as the driving element of the proton-pumping processTsukihara, Tomitake; Shimokata, Kunitoshi; Katayama, Yukie; Shimada, Hideo; Muramoto, Kazumasa; Aoyama, Hiroshi; Mochizuki, Masao; Shinzawa-itoh, Kyoko; Yamashita, Eiki; Yao, Min; Ishimura, Yuzuru; Yoshikawa, ShinyaProceedings of the National Academy of Sciences of the United States of America (2003), 100 (26), 15304-15309CODEN: PNASA6; ISSN:0027-8424. (National Academy of Sciences)Mitochondrial cytochrome c oxidase (I) plays an essential role in aerobic cellular respiration, reducing O2 to water in a process coupled with the pumping of protons across the mitochondrial inner membrane. Asp-51, located near the enzyme surface, was found to undergo a redox-coupled x-ray structural change, which was suggestive of a role for this residue in redox-driven proton pumping. However, functional or mechanistic evidence for the involvement of this residue in proton pumping has not yet been obtained. Here, the authors report that the Asp-51 → Asn mutation (D51N mutant) of bovine I abolished its proton-pumping function without impairment of the O2 redn. activity. Improved x-ray crystal structures (at 1.8/1.9-Å resoln. in both the fully oxidized and reduced states) showed that the net pos. charge created upon oxidn. of the low-spin heme of I drives the active proton transport from the interior of the mitochondria to Asp-51 across the enzyme via a water channel and a H-bond network, located in tandem, and that the enzyme redn. induces proton ejection from the Asp residue to the mitochondrial exterior. A peptide bond in the H-bond network critically inhibits reverse proton transfer through the network. A redox-coupled change in the capacity of the water channel, induced by the hydroxyfarnesylethyl group of the low-spin heme, suggested that the channel functions as an effective proton-collecting region. IR results indicated that the conformation of Asp-51 is controlled only by the oxidn. state of the low-spin heme. These results indicate that the low-spin heme in I drives the proton-pumping process.
- 100Umena, Y.; Kawakami, K.; Shen, J.-R.; Kamiya, N. Crystal Structure of Oxygen-Evolving Photosystem Ii at a Resolution of 1.9 Å. Nature 2011, 473, 55– 60, DOI: 10.1038/nature09913Google Scholar100https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3MXkslCmtLg%253D&md5=ed60c19fbfdfa3b11aa4c49887173f0dCrystal structure of oxygen-evolving photosystem II at a resolution of 1.9 ÅUmena, Yasufumi; Kawakami, Keisuke; Shen, Jian-Ren; Kamiya, NobuoNature (London, United Kingdom) (2011), 473 (7345), 55-60CODEN: NATUAS; ISSN:0028-0836. (Nature Publishing Group)Photosystem II is the site of photosynthetic water oxidn. and contains 20 subunits with a total mol. mass of 350 kDa. The structure of photosystem II has been reported at resolns. from 3.8 to 2.9 Å. These resolns. have provided much information on the arrangement of protein subunits and cofactors but are insufficient to reveal the detailed structure of the catalytic center of water splitting. Here we report the crystal structure of photosystem II at a resoln. of 1.9 Å. From our electron d. map, we located all of the metal atoms of the Mn4CaO5 cluster, together with all of their ligands. We found that five oxygen atoms served as oxo bridges linking the five metal atoms, and that four water mols. were bound to the Mn4CaO5 cluster; some of them may therefore serve as substrates for dioxygen formation. We identified more than 1,300 water mols. in each photosystem II monomer. Some of them formed extensive hydrogen-bonding networks that may serve as channels for protons, water or oxygen mols. The detn. of the high-resoln. structure of photosystem II will allow us to analyze and understand its functions in great detail.
- 101Fetter, J. R. Possible Proton Relay Pathways in Cytochrome C Oxidase. Proc. Natl. Acad. Sci. U. S. A. 1995, 92, 1604– 1608, DOI: 10.1073/pnas.92.5.1604Google Scholar101https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaK2MXktFWku7s%253D&md5=1932fac29a5018a136c17228a22369a7Possible proton relay pathways in cytochrome c oxidaseFetter, John R.; Qian, Jie; Shapleigh, James; Thomas, Jeffrey W.; Garcia-Horsman, Arturo; Schmidt, Einhardt; Hosler, Jonathan; Babcock, Gerald T.; Gennis, Robert B.; Ferguson-Miller, ShelaghProceedings of the National Academy of Sciences of the United States of America (1995), 92 (5), 1604-8CODEN: PNASA6; ISSN:0027-8424. (National Academy of Sciences)As the final electron acceptor in the respiratory chain of eukaryotic and many prokaryotic organisms, cytochrome c oxidase (EC 1.9.3.1) catalyzes the redn. of oxygen to water and generates a proton gradient. To test for proton pathways through the oxidase, site-directed mutagenesis was applied to subunit I of the Rhodobacter sphaeroides enzyme. Mutants were characterized in three highly conserved regions of the peptide, comprising possible proton loading, unloading, and transfer sites: an interior loop between helixes II and III (Asp132Asn/Ala), an exterior loop between helixes IX and X (His411Ala, Asp412Asn, Thr413Asn, Tyr414Phe), and the predicted transmembrane helix VIII (Thr352Ala, Pro358Ala, Thr359Ala, Lys362Met). Most of the mutants had lower activity than wild type, but only mutants at residue 132 lost proton pumping while retaining electron transfer activity. Although electron transfer was substantially inhibited, no major structural alteration appears to have occurred in D132 mutants, since resonance Raman and visible absorbance spectra were normal. However, lower CO binding (70-85% of wild type) suggests some minor change to the binuclear center. In addn., the activity of the reconstituted Asp132 mutants was inhibited rather than stimulated by ionophores or uncoupler. The inhibition was not obsd. with the purified enzyme and a direct pH effect was ruled out, suggesting an altered response to the elec. or pH gradient. The results support an important role for the conserved III-III loop in the proton pumping process and are consistent with the possibility of involvement of residues in helix VIII and the IX-X loop.
- 102Hosler, J. P. Polar Residues in Helix Viii of Subunit I of Cytochrome C Oxidase Influence the Activity and the Structure of the Active Site. Biochemistry 1996, 35, 10776– 10783, DOI: 10.1021/bi9606511Google Scholar102https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaK28XksFyjurk%253D&md5=b1401915491cf9c125dfcaae1bc63075Polar residues in helix VIII of subunit I of cytochrome c oxidase influence the activity and the structure of the active siteHosler, Jonathan P.; Shapleigh, James P.; Mitchell, David M.; Kim, Younkyoo; Pressler, Michelle A.; Georgiou, Christos; Babcock, Gerald T.; Alben, James O.; Ferguson-Miller, Shelagh; Gennis, Robert B.Biochemistry (1996), 35 (33), 10776-10783CODEN: BICHAW; ISSN:0006-2960. (American Chemical Society)The aa3-type cytochrome c oxidase from Rhodobacter sphaeroides is closely related to eukaryotic cytochrome c oxidases. Previous anal. of site-directed mutants identified the ligands of heme a, heme a3, and CuB, which have been confirmed by high-resoln. structures of homologous oxidases. Since the protons used to form water originate from the inner side of the membrane, and the heme a3-CuB center is located near the outer surface, the protein must convey these substrate protons to the O2 redn. site. Transmembrane helix VIII in subunit I is close to this site and contains several conserved polar residues that could function in a rate-detg. proton relay system. To test this role, apolar residues were substituted for THr-352, THr-359, and Lys-362 in helix VIII and the mutants were characterized in terms of activity and structure. Mutation of Thr-352, near CuB, strongly decreased enzyme activity and disrupted the spectral properties of the heme a3-CuB center. Mutation of Thr-359, below heme a3, substantially reduced oxidase activity with only minor effects on metal center structure. Two mutations of Lys-362, ∼15 Å below the axial ligand of heme a3, were inactive, made heme a3 difficult to reduce, and caused changes in the resonance Raman signal specific for the Fe-histidine bond to heme a3. The results were consistent with a key role for Thr-352, Thr-359, and Lys-362 in oxidase activity and with the involvement of Thr-359 and Lys-362 in proton transfer through a relay system now plausibly identified in the crystal structure. However, the characteristics of the Lys-362 mutants raise some questions about the assignment of this as the substrate proton channel.
- 103Konstantinov, A. A.; Siletsky, S.; Mitchell, D.; Kaulen, A.; Gennis, R. B. The Roles of the Two Proton Input Channels in Cytochrome C Oxidase from Rhodobacter Sphaeroides Probed by the Effects of Site-Directed Mutations on Time-Resolved Electrogenic Intraprotein Proton Transfer. Proc. Natl. Acad. Sci. U. S. A. 1997, 94, 9085– 9090, DOI: 10.1073/pnas.94.17.9085Google Scholar103https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaK2sXls1Kmu7w%253D&md5=099893b6fcbfe7221fa65d42771ccbd9The roles of the two proton input channels in cytochrome c oxidase from Rhodobacter sphaeroides probed by the effects of site-directed mutations on time-resolved electrogenic intraprotein proton transferKonstantinov, Alexander A.; Siletsky, Sergey; Mitchell, David; Kaulen, Andrey; Gennis, Robert B.Proceedings of the National Academy of Sciences of the United States of America (1997), 94 (17), 9085-9090CODEN: PNASA6; ISSN:0027-8424. (National Academy of Sciences)The crystal structures of cytochrome c oxidase from both bovine and Paracoccus denitrificans reveal two putative proton input channels that connect the heme-copper center, where dioxygen is reduced, to the internal aq. phase. In this work we have examd. the role of these two channels, looking at the effects of site-directed mutations of residues obsd. in each of the channels of the cytochrome c oxidase from Rhodobacter sphaeroides. A photoelec. technique was used to monitor the time-resolved electrogenic proton transfer steps assocd. with the photo-induced redn. of the ferryl-oxo form of heme a3 (Fe4+ = O2-) to the oxidized form (Fe3+OH-). This redox step requires the delivery of a "chem." H+ to protonate the reduced oxygen atom and is also coupled to proton pumping. It is found that mutations in the K channel (K362M and T359A) have virtually no effect on the ferryl-oxo-to-oxidized (F-to-Ox) transition; although, steady-state turnover is severely limited. In contrast, electrogenic proton transfer at this step is strongly suppressed by mutations in the D channel. The results strongly suggest that the functional roles of the two channels are not the sep. delivery of chem. or pumped protons, as proposed recently [Iwata, S., Ostermeier, C., Ludwig, B. & Michel, H. (1995) Nature (London) 376, 660-669]. The D channel is likely to be involved in the uptake of both "chem." and "pumped" protons in the F-to-Ox transition, whereas the K channel is probably idle at this partial reaction and is likely to be used for loading the enzyme with protons at some earlier steps of the catalytic cycle. This conclusion agrees with different redox states of heme a3 in the K362M and E286Q mutants under aerobic steady-state turnover conditions.
- 104Lee, H.-m.; Das, T. K.; Rousseau, D. L.; Mills, D.; Ferguson-Miller, S.; Gennis, R. B. Mutations in the Putative H-Channel in the Cytochrome C Oxidase from Rhodobacter Sphaeroides Show That This Channel Is Not Important for Proton Conduction but Reveal Modulation of the Properties of Heme A. Biochemistry 2000, 39, 2989– 2996, DOI: 10.1021/bi9924821Google Scholar104https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD3cXht1yjs7o%253D&md5=640c2c31846bed2fcbf94e2fccff3508Mutations in the Putative H-Channel in the Cytochrome c Oxidase from Rhodobacter sphaeroides Show That This Channel Is Not Important for Proton Conduction but Reveal Modulation of the Properties of Heme aLee, Hang-mo; Das, Tapan Kanti; Rousseau, Denis L.; Mills, Denise; Ferguson-Miller, Shelagh; Gennis, Robert B.Biochemistry (2000), 39 (11), 2989-2996CODEN: BICHAW; ISSN:0006-2960. (American Chemical Society)As the final electron acceptor in the respiratory chain of eukaryotic and many prokaryotic organisms, cytochrome c oxidase catalyzes the redn. of oxygen to water, concomitantly generating a proton gradient. X-ray structures of two cytochrome c oxidases have been reported, and in each structure three possible pathways for proton translocation are indicated: the D-, K-, and H-channels. The putative H-channel is most clearly delineated in the bovine heart oxidase and has been proposed to be functionally important for the translocation of pumped protons in the mammalian oxidase [Yoshikawa et al. (1998) Science 280, 1723-1729]. In the present work, the functional importance of residues lining the putative H-channel in the oxidase from Rhodobacter sphaeroides are examd. by site-directed mutagenesis. Mutants were generated in eight different sites and the enzymes have been purified and characterized. The results suggest that the H-channel is not functionally important in the prokaryotic oxidase, in agreement with the conclusion from previous work with the oxidase from Paracoccus denitrificans [Pfitzner et al. (1998) J. Biomembr. Bioenerg. 30, 89-93]. Except for mutations involving one residue, each of the mutants in R. sphaeroides is enzymically active and pumps protons in reconstituted proteoliposomes. This includes H456A, which is of interest since in the P. denitrificans oxidase a leucine substituted for the corresponding residue resulted in an inactive enzyme. The only mutations that result in completely inactive enzyme in the set examd. in the R. sphaeroides oxidase involve R52, a residue that along with Q471 appears to be hydrogen-bonded to the formyl group of heme a in the X-ray structures. Resonance Raman spectra of the R52 mutants were obtained in order to characterize the interactions between R52 and the heme group,. The frequency of the heme a formyl stretching mode in the R52A mutant is characteristic of that seen in non-hydrogen-bonded model heme a complexes. The data thus confirm the presence of hydrogen bonding between the heme a formyl group and the R52 side chain, as suggested from crystallog. data. In the R52K mutant, hydrogen bonding is maintained by the lysine residue, and this mutant enzyme retains near wild-type activity. The heme a formyl frequency is also affected by mutation of Q471, confirming the X-ray models that show this residue also has hydrogen-bonding interactions with the formyl group. However, unlike R52, Q471 does not appear to be crit. for the enzyme function.
- 105Wikström, M.; Jasaitis, A.; Backgren, C.; Puustinen, A.; Verkhovsky, M. I. The Role of the D-and K-Pathways of Proton Transfer in the Function of the Haem–Copper Oxidases. Biochim. Biophys. Acta, Bioenerg. 2000, 1459, 514– 520, DOI: 10.1016/S0005-2728(00)00191-2Google Scholar105https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD3cXlslWru7Y%253D&md5=0a7d2410535a422b2984de3d7d93550fThe role of the D- and K-pathways of proton transfer in the function of the heme-copper oxidasesWikstrom, M.; Jasaitis, A.; Backgren, C.; Puustinen, A.; Verkhovsky, M. I.Biochimica et Biophysica Acta, Bioenergetics (2000), 1459 (2-3), 514-520CODEN: BBBEB4; ISSN:0005-2728. (Elsevier B.V.)A review with 37 refs. The X-ray structures of several heme-copper oxidases now at hand have given important constraints on how these enzymes function. Yet, dynamic data are required to elucidate the mechanisms of electron and proton transfer, the activation of O2 and its redn. to water, as well as the still enigmatic mechanism by which these enzymes couple the redox reaction to proton translocation. Here, some recent observations are briefly reviewed with special emphasis on the functioning of the so-called D- and K-pathways of proton transfer. It turns out that only one of the eight protons taken up by the enzyme during its catalytic cycle is transferred via the K-pathway. The D-pathway is probably responsible for the transfer of all other protons, including the four that are pumped across the membrane. The unique K-pathway proton may be specifically required to aid O-O bond scission by the heme-copper oxidases.
- 106Jünemann, S.; Meunier, B.; Gennis, R. B.; Rich, P. R. Effects of Mutation of the Conserved Lysine-362 in Cytochrome C Oxidase from Rhodobacter Sphaeroides. Biochemistry 1997, 36, 14456– 14464, DOI: 10.1021/bi971458pGoogle Scholar106https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaK2sXntFWkur0%253D&md5=4e686d60a692565b562e99556f4fe277Effects of Mutation of the Conserved Lysine-362 in Cytochrome c Oxidase from Rhodobacter sphaeroidesJuenemann, Susanne; Meunier, Brigitte; Gennis, Robert B.; Rich, Peter R.Biochemistry (1997), 36 (47), 14456-14464CODEN: BICHAW; ISSN:0006-2960. (American Chemical Society)We describe the effects of a mutation, K362M, of the conserved lysine in cytochrome c oxidase from Rhodobacter sphaeroides, a residue located in a putative proton channel that may convey substrate protons to the binuclear center. Spectra of the "as prepd.", ferricyanide-oxidized, and dithionite-reduced forms of the mutant protein confirm that the redox centers remain intact. Ligand binding kinetics of the ferricyanide-oxidized enzyme and of the dithionite-reducible fraction are similar to those of the wild type, indicating that the K channel is not the major route for CO, cyanide, formate, or peroxide entry into the structure. Protonation of the lysine residue is not redox-linked to heme a or CuB as judged from the essentially unaltered midpoint potentials of these centers in the cyanide-ligated enzyme. A difficulty in electron transfer from heme a to the binuclear center is indicated by the slow and only partial redn. of heme a3 by dithionite or ferrocytochrome c and by the presence of some reduced heme a in the as prepd. mutant enzyme and under steady-state conditions. Further characterization of the K362M enzyme in the steady state shows that up to one electron, but not two, can enter the binuclear center easily. It is this inability to form the two-electron-reduced, oxygen-reactive R state that prevents activity. A model is proposed where the K channel serves as a dielec. well of high dielec. strength and low proton cond., rather than as a pathway for proton entry to the binuclear center. The function of this structure would be to decrease the cost of introducing a transiently uncompensated charge into the binuclear center prior to formation of a stable, charge-compensated R-state.
- 107Rich, P. R.; Maréchal, A. Functions of the Hydrophilic Channels in Protonmotive Cytochrome C Oxidase. J. R. Soc., Interface 2013, 10, 20130183, DOI: 10.1098/rsif.2013.0183Google Scholar107https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3sXhsVyqsrbJ&md5=9d737160e831a770272fe226712a6ec6Functions of the hydrophilic channels in protonmotive cytochrome c oxidaseRich, Peter R.; Marechal, AmandineJournal of the Royal Society, Interface (2013), 10 (86), 20130183/1-20130183/14CODEN: JRSICU; ISSN:1742-5689. (Royal Society)A review. The structure and function of hydrophilic channels in electron-transferring membrane proteins are discussed. A distinction is made between proton channels that can conduct protons and dielec. channels that are nonconducting but can dielec. polarize in response to the introduction of charge changes in buried functional centers. The functions of the K, D, and H channels found in A1-type cytochrome c oxidases are reviewed in relation to these ideas. Possible control of function by dielec. channels and their evolutionary relation to proton channels is explored.
- 108Agmon, N. The Grotthuss Mechanism. Chem. Phys. Lett. 1995, 244, 456– 462, DOI: 10.1016/0009-2614(95)00905-JGoogle Scholar108https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaK2MXos1Wls7o%253D&md5=d285f388a62674436db3a2f55ea74984The Grotthuss mechanismAgmon, NoamChemical Physics Letters (1995), 244 (5,6), 456-62CODEN: CHPLBC; ISSN:0009-2614. (Elsevier)Suggested mechanisms for proton mobility are confronted with exptl. findings and quantum mech. calcns., indicating that no model is consistent with the existing data. It is suggested that the mol. mechanism behind prototropic mobility involves a periodic series of isomerizations between H9O4+ and H5O2+, the first triggered by hydrogen-bond cleavage of a second-shell water mol. and the second by the reverse, hydrogen-bond formation process.
- 109Henry, R. M.; Yu, C.-H.; Rodinger, T.; Pomès, R. Functional Hydration and Conformational Gating of Proton Uptake in Cytochrome C Oxidase. J. Mol. Biol. 2009, 387, 1165– 1185, DOI: 10.1016/j.jmb.2009.02.042Google Scholar109https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD1MXktF2qt7o%253D&md5=2cdf0514a4154239c434b1df772b8ab7Functional Hydration and Conformational Gating of Proton Uptake in Cytochrome c OxidaseHenry, Rowan M.; Yu, Ching-Hsing; Rodinger, Tomas; Pomes, RegisJournal of Molecular Biology (2009), 387 (5), 1165-1185CODEN: JMOBAK; ISSN:0022-2836. (Elsevier Ltd.)Cytochrome c oxidase (CcO) couples the redn. of dioxygen to proton pumping against an electrochem. gradient. The D-channel, a 25-Å-long cavity, provides the principal pathway for the uptake of chem. and pumped protons. A water chain is thought to mediate the relay of protons via a Grotthuss mechanism through the D-channel, but it is interrupted at N139 in all available crystallog. structures. We use free-energy simulations to examine the proton uptake pathway in the wild type and in single-point mutants N139V and N139A, in which redox and pumping activities are compromised. We present a general approach for the calcn. of water occupancy in protein cavities and demonstrate that combining efficient sampling algorithms with long simulation times (hundreds of nanoseconds) is required to achieve statistical convergence of equil. properties in the protein interior. The relative population of different conformational and hydration states of the D-channel is characterized. Results shed light on the role of N139 in the mechanism of proton uptake and clarify the phys. basis for inactive phenotypes. The conformational isomerization of the N139 side chain is shown to act as a gate controlling the formation of a functional water chain or "proton wire.". In the closed state of N139, the spatial distribution of water in the D-channel is consistent with available crystallog. models. However, a metastable state of N139 opens up a narrow bottleneck in which 50% occupancy by a water mol. establishes a proton pathway throughout the D-channel. Results for N139V suggest that blockage of proton uptake resulting from persistent interruption of the water pathway is the cause of this mutant's marginal oxidase activity. In contrast, results for N139A indicate that the D-channel is a continuously hydrated cavity, implying that the decoupling of oxidase activity from proton pumping measured in this mutant is not due to interruption of the proton relay chain.
- 110Liang, R.; Swanson, J. M.; Wikström, M.; Voth, G. A. Understanding the Essential Proton-Pumping Kinetic Gates and Decoupling Mutations in Cytochrome C Oxidase. Proc. Natl. Acad. Sci. U. S. A. 2017, 114, 5924– 5929, DOI: 10.1073/pnas.1703654114Google Scholar110https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2sXot1yrsbc%253D&md5=96ba3e0b5de57c9c0c0defff62a73e5cUnderstanding the essential proton-pumping kinetic gates and decoupling mutations in cytochrome c oxidaseLiang, Ruibin; Swanson, Jessica M. J.; Wikstrom, Marten; Voth, Gregory A.Proceedings of the National Academy of Sciences of the United States of America (2017), 114 (23), 5924-5929CODEN: PNASA6; ISSN:0027-8424. (National Academy of Sciences)Cytochrome c oxidase (CcO) catalyzes the redn. of O2 to H2O and uses the released free energy to pump protons against the transmembrane proton gradient. To better understand the proton-pumping mechanism of wild-type (WT) CcO, much attention has been given to the mutation of amino acid residues along the proton translocating D-channel that impair, and sometimes decouple, proton pumping from the chem. catalysis. Although their influence has been clearly demonstrated exptl., the underlying mol. mechanisms of these mutants remain unknown. Here, we report multiscale reactive mol. dynamics simulations that characterize the free-energy profiles of explicit proton transport through several important D-channel mutants. The results elucidated the mechanisms by which proton pumping is impaired, thus revealing key kinetic gating features in CcO. In the N139T and N139C mutants, proton back-leakage through the D-channel was kinetically favored over proton pumping due to the loss of a kinetic gate in the Asn-139 region. In the N139L mutant, the bulky Leu-139 side-chain inhibited timely reprotonation of Glu-286 through the D-channel, which impaired both proton pumping and the chem. reaction. In the S200V/S201V double mutant, the proton affinity of Glu-286 was increased, which slowed down both proton pumping and chem. catalysis. Thus, this work not only provides insight into the decoupling mechanisms of CcO mutants, but also explains how kinetic gating in the D-channel is imperative to achieving high proton-pumping efficiency in the WT CcO.
- 111Han, D.; Namslauer, A.; Pawate, A.; Morgan, J. E.; Nagy, S.; Vakkasoglu, A. S.; Brzezinski, P.; Gennis, R. B. Replacing Asn207 by Aspartate at the Neck of the D Channel in the Aa3-Type Cytochrome C Oxidase from Rhodobacter Sphaeroides Results in Decoupling the Proton Pump. Biochemistry 2006, 45, 14064– 14074, DOI: 10.1021/bi061465qGoogle ScholarThere is no corresponding record for this reference.
- 112Pfitzner, U.; Hoffmeier, K.; Harrenga, A.; Kannt, A.; Michel, H.; Bamberg, E.; Richter, O.-M.; Ludwig, B. Tracing the D-Pathway in Reconstituted Site-Directed Mutants of Cytochrome C Oxidase from Paracoccus Denitrificans. Biochemistry 2000, 39, 6756– 6762, DOI: 10.1021/bi992235xGoogle ScholarThere is no corresponding record for this reference.
- 113Siegbahn, P. E. M.; Blomberg, M. R. A. Mutations in the D-Channel of Cytochrome C Oxidase Causes Leakage of the Proton Pump. FEBS Lett. 2014, 588, 545– 548, DOI: 10.1016/j.febslet.2013.12.020Google Scholar113https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2cXhtFSmsrc%253D&md5=9611aba33dcecafd4cac8a24f9caee55Mutations in the D-channel of cytochrome c oxidase causes leakage of the proton pumpSiegbahn, Per E. M.; Blomberg, Margareta R. A.FEBS Letters (2014), 588 (4), 545-548CODEN: FEBLAL; ISSN:0014-5793. (Elsevier B.V.)It has exptl. been found that certain mutations close to the entry point of the proton transfer channel in cytochrome c oxidase stop proton translocation but not the O2 redn. chem. This effect is termed uncoupling. Since the mutations are 20 Å away from the catalytic center, this is very surprising. A new explanation for this phenomenon is suggested here, involving a local effect at the entry point of the proton channel, rather than the long range effects suggested earlier.
- 114Pomès, R.; Hummer, G.; Wikström, M. Structure and Dynamics of a Proton Shuttle in Cytochrome C Oxidase. Biochim. Biophys. Acta, Bioenerg. 1998, 1365, 255– 260, DOI: 10.1016/S0005-2728(98)00077-2Google Scholar114https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaK1cXksFKitr0%253D&md5=98f6b8f749f92125a63625447caf95a5Structure and dynamics of a proton shuttle in cytochrome c oxidasePomes, Regis; Hummer, Gerhard; Wikstrom, MartenBiochimica et Biophysica Acta, Bioenergetics (1998), 1365 (1-2), 255-260CODEN: BBBEB4; ISSN:0005-2728. (Elsevier B.V.)Protein-assisted transport of protons across the bioenergetic membrane is mediated by hydrogen-bonded networks. These networks involve titratable amino acid residues of membrane-spanning protein assemblies as well as internal water mols. In cytochrome c oxidase, the so-called D-channel defines such a network for the uptake of protons from the cytoplasmic side of the membrane. It has been proposed that conformational changes of a Glu residue are required for the establishment of a proton linkage from the channel into the active site. The thermodn. basis for the conformational isomerization of this residue is investigated using simulated annealing and free energy mol. dynamics simulations. The results support the existence of metastable conformations of the side chain, and their interchange through local structural fluctuations of neighboring residues and nearby internal chains of water mols. The conformational isomerization of both protonated and unprotonated states of Glu, coupled with the reorganization of hydrogen bonds, suggests a kinetically competent mechanism for proton shuttling.
- 115Hofacker, I.; Schulten, K. Oxygen and Proton Pathways in Cytochrome C Oxidase. Proteins: Struct., Funct., Genet. 1998, 30, 100– 107, DOI: 10.1002/(SICI)1097-0134(199801)30:1<100::AID-PROT9>3.0.CO;2-SGoogle Scholar115https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaK1cXjsVarug%253D%253D&md5=f6c116db7752e0851335df3a345fd685Oxygen and proton pathways in cytochrome c oxidaseHofacker, Ivo; Schulten, KlausProteins: Structure, Function, and Genetics (1998), 30 (1), 100-107CODEN: PSFGEY; ISSN:0887-3585. (Wiley-Liss, Inc.)Cytochrome c oxidase is a redox-driven proton pump, which couples the redn. of O2 to water to the translocation of protons across the membrane. The recently solved x-ray structures of cytochrome c oxidase permit mol. dynamics simulations of the underlying transport processes. To eventually establish the proton pump mechanism, the authors investigated the transport of the substrates, O2 and protons, through the enzyme. Mol. dynamics simulations of O2 diffusion through the protein revealed a well-defined pathway to the O2-binding site starting at a hydrophobic cavity near the membrane-exposed surface of subunit I, close to the interface to subunit III. A large no. of water sites were predicted within the protein, which could play an essential role for the transfer of protons in cytochrome c oxidase. The water mols. formed 2 channels along which protons could enter from the cytoplasmic (matrix) side of the protein and reach the binuclear center. A possible pumping mechanism was proposed that involves a shuttling motion of a Glu side-chain, which could then transfer a proton to a propionate group of heme α3.
- 116Wikström, M.; Verkhovsky, M. I.; Hummer, G. Water-Gated Mechanism of Proton Translocation by Cytochrome C Oxidase. Biochim. Biophys. Acta, Bioenerg. 2003, 1604, 61– 65, DOI: 10.1016/S0005-2728(03)00041-0Google Scholar116https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD3sXjvFahs7s%253D&md5=e63522f3b583853576bd74c496ee049dWater-gated mechanism of proton translocation by cytochrome c oxidaseWikstrom, Marten; Verkhovsky, Michael I.; Hummer, GerhardBiochimica et Biophysica Acta, Bioenergetics (2003), 1604 (2), 61-65CODEN: BBBEB4; ISSN:0005-2728. (Elsevier B.V.)Cytochrome c oxidase is essential for aerobic life as a membrane-bound energy transducer. O2 redn. at the heme a3-CuB center consumes electrons transferred via heme a from cytochrome c outside the membrane. Protons are taken up from the inside, both to form water and to be pumped across the membrane (M.K.F. Wikstrom, Nature 266 (1977) 271 ; M. Wikstrom, K. Krab, M. Saraste, Cytochrome Oxidase, A Synthesis, Academic Press, London, 1981 ). The resulting electrochem. proton gradient drives ATP synthesis (P. Mitchell, Chemiosmotic Coupling in Oxidative and Photosynthetic Phosphorylation, Glynn Research, Bodmin, UK, 1966 ). Here we present a mol. mechanism for proton pumping coupled to oxygen redn. that is based on the unique properties of water in hydrophobic cavities. An array of water mols. conducts protons from a conserved glutamic acid, either to the Δ-propionate of heme a3 (pumping), or to heme a3-CuB (water formation). Switching between these pathways is controlled by the redox-state-dependent elec. field between heme a and heme a3-CuB, which dets. the water-dipole orientation, and therefore the proton transfer direction. Proton transfer via the propionate provides a gate to O2 redn. This pumping mechanism explains the unique arrangement of the metal cofactors in the structure. It is consistent with the large body of biochem. data, and is shown to be plausible by mol. dynamics simulations.
- 117Zheng, X.; Medvedev, D. M.; Swanson, J.; Stuchebrukhov, A. A. Computer Simulation of Water in Cytochrome C Oxidase. Biochim. Biophys. Acta, Bioenerg. 2003, 1557, 99– 107, DOI: 10.1016/S0005-2728(03)00002-1Google Scholar117https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD3sXhs1Klu78%253D&md5=859e0a9b9e25e5fd1aae89db758d9dd7Computer simulation of water in cytochrome c oxidaseZheng, Xuehe; Medvedev, Dmitry M.; Swanson, Jessica; Stuchebrukhov, Alexei A.Biochimica et Biophysica Acta, Bioenergetics (2003), 1557 (1-3), 99-107CODEN: BBBEB4; ISSN:0005-2728. (Elsevier B.V.)Statistical mechanics and mol. dynamics simulations have been carried out to study the distribution and dynamics of internal water mols. in bovine heart cytochrome c oxidase (CcO). CcO is found to be capable of holding plenty of water, which in subunit I alone amts. to about 165 mols. The dynamic characterization of these water mols. is carried out. The nascent water mols. produced in the redox reaction at the heme a3-CuB binuclear site form an intriguing chain structure. The chain begins at the position of Glu242 at the end of the D channel, and has a fork structure, one branch of which leads to the binuclear center, and the other to the propionate d of heme a3. The branch that leads to the binuclear center has dynamic access both to the site where the formation of water occurs, and to delta-nitrogen of His291. From the binuclear center, the chain continues to run into the K channel. The stability of this hydrogen bond network is examd. dynamically. The catalytic site is located at the hydrophobic region, and the nascent water mols. are produced at the top of the energy hill. The energy gradient is utilized as the mechanism of water removal from the protein. The water exit channels are explored using high-temp. dynamics simulations. Two putative channels for water exit from the catalytic site have been identified. One is leading directly toward Mg2+ site. However, this channel is only open when His291 is dissocd. from CuB. If His291 is bound to CuB, the only channel for water exit is the one that originates at E242 and leads toward the middle of the membrane. This is the same channel that is presumably used for oxygen supply.
- 118Liang, R.; Swanson, J. M. J.; Peng, Y.; Wikström, M.; Voth, G. A. Multiscale Simulations Reveal Key Features of the Proton-Pumping Mechanism in Cytochrome C Oxidase. Proc. Natl. Acad. Sci. U. S. A. 2016, 113, 7420– 7425, DOI: 10.1073/pnas.1601982113Google Scholar118https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC28XhtFCrsbfM&md5=065aa8ebbada113673b188f23a7fcd94Multiscale simulations reveal key features of the proton-pumping mechanism in cytochrome c oxidaseLiang, Ruibin; Swanson, Jessica M. J.; Peng, Yuxing; Wikstrom, Marten; Voth, Gregory A.Proceedings of the National Academy of Sciences of the United States of America (2016), 113 (27), 7420-7425CODEN: PNASA6; ISSN:0027-8424. (National Academy of Sciences)Cytochrome c oxidase (CcO) reduces oxygen to water and uses the released free energy to pump protons across the membrane. We have used multiscale reactive mol. dynamics simulations to explicitly characterize (with free-energy profiles and calcd. rates) the internal proton transport events that enable proton pumping during first steps of oxidn. of the fully reduced enzyme. Our results show that proton transport from amino acid residue E286 to both the pump loading site (PLS) and to the binuclear center (BNC) are thermodynamically driven by electron transfer from heme a to the BNC, but that the former (i.e., pumping) is kinetically favored whereas the latter (i.e., transfer of the chem. proton) is rate-limiting. The calcd. rates agree with exptl. measurements. The backflow of the pumped proton from the PLS to E286 and from E286 to the inside of the membrane is prevented by large free-energy barriers for the backflow reactions. Proton transport from E286 to the PLS through the hydrophobic cavity and from D132 to E286 through the D-channel are found to be strongly coupled to dynamical hydration changes in the corresponding pathways, and importantly, vice versa.
- 119Riistama, S.; Hummer, G.; Puustinen, A.; Dyer, R. B.; Woodruff, W. H.; Wikström, M. Bound Water in the Proton Translocation Mechanism of the Haem-Copper Oxidases. FEBS Lett. 1997, 414, 275– 280, DOI: 10.1016/S0014-5793(97)01003-XGoogle ScholarThere is no corresponding record for this reference.
- 120Maréchal, A.; Rich, P. R. Water Molecule Reorganization in Cytochrome C Oxidase Revealed by FTIR Spectroscopy. Proc. Natl. Acad. Sci. U. S. A. 2011, 108, 8634– 8638, DOI: 10.1073/pnas.1019419108Google Scholar120https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3MXntVGqtb0%253D&md5=d266abbbda11121a1de7916f73406994Water molecule reorganization in cytochrome c oxidase revealed by FTIR spectroscopyMarechal, Amandine; Rich, Peter R.Proceedings of the National Academy of Sciences of the United States of America (2011), 108 (21), 8634-8638, S8634/1-S8634/2CODEN: PNASA6; ISSN:0027-8424. (National Academy of Sciences)Although internal electron transfer and oxygen redn. chem. in cytochrome c oxidase are fairly well understood, the assocd. groups and pathways that couple these processes to gated proton translocation across the membrane remain unclear. Several possible pathways have been identified from crystallog. structural models; these involve hydrophilic residues in combination with structured waters that might reorganize to form transient proton transfer pathways during the catalytic cycle. To date, however, comparisons of at. structures of different oxidases in different redox or ligation states have not provided a consistent answer as to which pathways are operative or the details of their dynamic changes during catalysis. In order to provide an exptl. means to address this issue, FTIR spectroscopy in the 3560-3800 cm-1 range has been used to detect weakly H-bonded water mols. in bovine cytochrome c oxidase that might change during catalysis. Full redox spectra exhibited at least four signals at 3674(+), 3638(+), 3620(-), and 3607(+) cm-1. A more complex set of signals was obsd. in spectra of photolysis of the ferrous-CO compd., a reaction that mimics the catalytic oxygen binding step, and their D2O and H218O sensitivities confirmed that they arose from water mol. rearrangements. Fitting with Gaussian components indicated the involvement of up to eight waters in the photolysis transition. Similar signals were also obsd. in photolysis spectra of the ferrous-CO compd. of bacterial CcO from Paracoccus denitrificans. Such water changes are discussed in relation to roles in hydrophilic channels and proton/electron coupling mechanism.
- 121Ghosh, N.; Prat-Resina, X.; Gunner, M.; Cui, Q. Microscopic pKa Analysis of Glu286 in Cytochrome C Oxidase (Rhodobacter sphaeroides): Toward a Calibrated Molecular Model. Biochemistry 2009, 48, 2468– 2485, DOI: 10.1021/bi8021284Google ScholarThere is no corresponding record for this reference.
- 122Woelke, A. L.; Galstyan, G.; Galstyan, A.; Meyer, T.; Heberle, J.; Knapp, E.-W. Exploring the Possible Role of Glu286 in C C O by Electrostatic Energy Computations Combined with Molecular Dynamics. J. Phys. Chem. B 2013, 117, 12432– 12441, DOI: 10.1021/jp407250dGoogle ScholarThere is no corresponding record for this reference.
- 123Wikström, M.; Verkhovsky, M. I. The D-Channel of Cytochrome Oxidase: An Alternative View. Biochim. Biophys. Acta, Bioenerg. 2011, 1807, 1273– 1278, DOI: 10.1016/j.bbabio.2011.05.013Google Scholar123https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A280%3ADC%252BC3MjlsFKnsQ%253D%253D&md5=3f7b665c473fe6ff4b57706ba3688a4bThe D-channel of cytochrome oxidase: an alternative viewWikstrom Marten; Verkhovsky Michael IBiochimica et biophysica acta (2011), 1807 (10), 1273-8 ISSN:0006-3002.The D-pathway in A-type cytochrome c oxidases conducts protons from a conserved aspartate on the negatively charged N-side of the membrane to a conserved glutamic acid at about the middle of the membrane dielectric. Extensive work in the past has indicated that all four protons pumped across the membrane on reduction of O(2) to water are transferred via the D-pathway, and that it is also responsible for transfer of two out of the four "chemical protons" from the N-side to the binuclear oxygen reduction site to form product water. The function of the D-pathway has been discussed in terms of an apparent pK(a) of the glutamic acid. After reacting fully reduced enzyme with O(2), the rate of formation of the F state of the binuclear heme-copper active site was found to be independent of pH up to pH~9, but to drop off at higher pH with an apparent pK(a) of 9.4, which was attributed to the glutamic acid. Here, we present an alternative view, according to which the pH-dependence is controlled by proton transfer into the aspartate residue at the N-side orifice of the D-pathway. We summarise experimental evidence that favours a proton pump mechanism in which the proton to be pumped is transferred from the glutamic acid to a proton-loading site prior to proton transfer for completion of oxygen reduction chemistry. The mechanism is discussed by which the proton-pumping activity is decoupled from electron transfer by structural alterations of the D-pathway. This article is part of a Special Issue entitled: Allosteric cooperativity in respiratory proteins.
- 124Maréchal, A.; Meunier, B.; Lee, D.; Orengo, C.; Rich, P. R. Yeast Cytochrome C Oxidase: A Model System to Study Mitochondrial Forms of the Haem–Copper Oxidase Superfamily. Biochim. Biophys. Acta, Bioenerg. 2012, 1817, 620– 628, DOI: 10.1016/j.bbabio.2011.08.011Google Scholar124https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC38XjtlOnt74%253D&md5=ddccb2581faf5111cb37835620f87559Yeast cytochrome c oxidase: A model system to study mitochondrial forms of the heme-copper oxidase superfamilyMarechal, Amandine; Meunier, Brigitte; Lee, David; Orengo, Christine; Rich, Peter R.Biochimica et Biophysica Acta, Bioenergetics (2012), 1817 (4), 620-628CODEN: BBBEB4; ISSN:0005-2728. (Elsevier B. V.)A review. The known subunits of yeast mitochondrial cytochrome c oxidase are reviewed. The structures of all 11 of its subunits are explored by building homol. models based on the published structures of the homologous bovine subunits and similarities and differences are highlighted, particularly of the core functional subunit I. Yeast genetic techniques to enable introduction of mutations into the 3 core mitochondrially-encoded subunits are reviewed.
- 125Iwata, S.; Ostermeier, C.; Ludwig, B.; Michel, H. Structure at 2.8 Angstrom Resolution of Cytochrome C Oxidase from Paracoccus Denitrificans. Nature 1995, 376, 660– 669, DOI: 10.1038/376660a0Google ScholarThere is no corresponding record for this reference.
- 126Koepke, J.; Olkhova, E.; Angerer, H.; Müller, H.; Peng, G.; Michel, H. High Resolution Crystal Structure of Paracoccus Denitrificans Cytochrome C Oxidase: New Insights into the Active Site and the Proton Transfer Pathways. Biochim. Biophys. Acta, Bioenerg. 2009, 1787, 635– 645, DOI: 10.1016/j.bbabio.2009.04.003Google Scholar126https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD1MXntVSitr8%253D&md5=c75b27fc8c97dc0304504621839c249bHigh resolution crystal structure of Paracoccus denitrificans cytochrome c oxidase: New insights into the active site and the proton transfer pathwaysKoepke, Juergen; Olkhova, Elena; Angerer, Heike; Mueller, Hannelore; Peng, Guohong; Michel, HartmutBiochimica et Biophysica Acta, Bioenergetics (2009), 1787 (6), 635-645CODEN: BBBEB4; ISSN:0005-2728. (Elsevier B. V.)The structure of the 2-subunit cytochrome c oxidase from P. denitrificans was refined using x-ray cryo-data to 2.25 Å resoln. in order to gain further insights into its mechanism of action. The refined structural model showed a no. of new features including many addnl. solvent and detergent mols. The electron d. bridging the heme a3 Fe and CuB atoms of the active site was fitted best by a peroxo-group or a Cl- ion. Two waters or OH- groups did not fit, one water (or OH-) did not provide sufficient electron d. The anal. of crystals of cytochrome c oxidase isolated in the presence of Br- instead of Cl- appeared to exclude Cl- as the bridging ligand. In the D-pathway, a H-bonded chain of 6 water mols. connected Asn-131 and Glu-278, but the access for protons to this water chain was blocked by Asn-113, Asn-131, and Asn-199. The K-pathway contained 2 firmly bound water mols., and an addnl. water chain seemed to form its entrance. Above the hemes, a cluster of 13 water mols. was obsd. which potentially form multiple exit pathways for pumped protons. The H-bond pattern excluded that the CuB ligand, His-326, was present in the imidazolate form.
- 127Soulimane, T.; Buse, G.; Bourenkov, G. P.; Bartunik, H. D.; Huber, R.; Than, M. E. Structure and Mechanism of the Aberrant Ba3-Cytochrome C Oxidase from Thermus Thermophilus. EMBO J. 2000, 19, 1766– 1776, DOI: 10.1093/emboj/19.8.1766Google Scholar127https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD3cXivVKlsbg%253D&md5=8871a053de5c01ae950b0c75bbd541dfStructure and mechanism of the aberrant ba3-cytochrome c oxidase from Thermus thermophilusSoulimane, Tewfik; Buse, Gerhard; Bourenkov, Gleb P.; Bartunik, Hans D.; Huber, Robert; Than, Manuel E.EMBO Journal (2000), 19 (8), 1766-1776CODEN: EMJODG; ISSN:0261-4189. (Oxford University Press)Cytochrome c oxidase is a respiratory enzyme catalyzing the energy-conserving redn. of mol. oxygen to water. The crystal structure of the ba3-cytochrome c oxidase from Thermus thermophilus has been detd. to 2.4 Å resoln. using multiple anomalous dispersion (MAD) phasing and led to the discovery of a novel subunit IIa. A structure-based sequence alignment of this phylogenetically very distant oxidase with the other structurally known cytochrome oxidases leads to the identification of sequence motifs and residues that seem to be indispensable for the function of the heme copper oxidases, e.g. a new electron transfer pathway leading directly from CuA to CuB. Specific features of the ba3-oxidase include an extended oxygen input channel, which leads directly to the active site, the presence of only one oxygen atom (O2-, OH- or H2O) as bridging ligand at the active site and the mainly hydrophobic character of the interactions that stabilize the electron transfer complex between this oxidase and its substrate cytochrome c. New aspects of the proton pumping mechanism could be identified.
- 128Tiefenbrunn, T.; Liu, W.; Chen, Y.; Katritch, V.; Stout, C. D.; Fee, J. A.; Cherezov, V. High Resolution Structure of the Ba3 Cytochrome C Oxidase from Thermus Thermophilus in a Lipidic Environment. PLoS One 2011, 6, e22348, DOI: 10.1371/journal.pone.0022348Google Scholar128https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3MXhtVGhtL7N&md5=9b19f713508d448e17b8067d92c6c8edHigh resolution structure of the ba3 cytochrome c oxidase from Thermus thermophilus in a lipidic environmentTiefenbrunn, Theresa; Liu, Wei; Chen, Ying; Katritch, Vsevolod; Stout, C. David; Fee, James A.; Cherezov, VadimPLoS One (2011), 6 (7), e22348CODEN: POLNCL; ISSN:1932-6203. (Public Library of Science)The fundamental chem. underpinning aerobic life on Earth involves the redn. of O2 to H2O with concomitant proton translocation. This process is catalyzed by members of the heme-copper oxidase (HCO) superfamily. Despite the availability of crystal structures for all types of HCOs, the mode of action for this enzyme is not understood at the at. level, namely how vectorial H+ and e- transport are coupled. Toward addressing this problem, The authors report wild-type and A120F mutant structures of ba3-type cytochrome c oxidase of T. thermophilus at 1.8 Å resoln. The enzyme was crystd. from the lipidic cubic phase, which mimicked the biomembrane environment. The structures revealed 20 ordered lipid mols. that occupied binding sites on the protein surface or mediated crystal packing interfaces. The interior of the protein enclosed 53 water mols., including 3 trapped in the designated K-path of proton transfer and 8 in a cluster seen also in A-type enzymes that likely functions in egress of product H2O and proton translocation. The hydrophobic O2-uptake channel, connecting the active site to the lipid bilayer, contained a single H2O mol. nearest the CuB atom but otherwise exhibited no residual electron d. The active site contained strong electron d. for a pair of bonded atoms bridging the heme Fea3 and CuB atoms that was best modeled as peroxide. The structure of the ba3 cytochrome c oxidase revealed new information about the positioning of the enzyme within the membrane and the nature of its interactions with lipid mols. The at. resoln. details provided insight into the mechanisms of electron transfer, O2 diffusion into the active site, redn. of O2 to H2O, and the pumping of protons across the membrane. The development of a robust system for prodn. of ba3 cytochrome c oxidase crystals diffracting to high resoln., together with an established expression system for generating mutants, opens the door for systematic structure-function studies.
- 129Chang, H.-Y.; Hemp, J.; Chen, Y.; Fee, J. A.; Gennis, R. B. The Cytochrome Ba3 Oxygen Reductase from Thermus Thermophilus Uses a Single Input Channel for Proton Delivery to the Active Site and for Proton Pumping. Proc. Natl. Acad. Sci. U. S. A. 2009, 106, 16169– 16173, DOI: 10.1073/pnas.0905264106Google Scholar129https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD1MXht1OjsbbF&md5=ae2b7e9c6afab23f9eb1ed3b0b12b61fThe cytochrome ba3 oxygen reductase from Thermus thermophilus uses a single input channel for proton delivery to the active site and for proton pumpingChang, Hsin-Yang; Hemp, James; Chen, Ying; Fee, James A.; Gennis, Robert B.Proceedings of the National Academy of Sciences of the United States of America (2009), 106 (38), 16169-16173, S16169/1-S16169/20CODEN: PNASA6; ISSN:0027-8424. (National Academy of Sciences)The heme-copper oxygen reductases are redox-driven proton pumps that generate a proton motive force in both prokaryotes and mitochondria. These enzymes have been divided into 3 evolutionarily related groups: the A-, B- and C-families. Most exptl. work on proton-pumping mechanisms has been performed with members of the A-family. These enzymes require 2 proton input pathways (D- and K-channels) to transfer protons used for oxygen redn. chem. and for proton pumping, with the D-channel transporting all pumped protons. In this work, site-directed mutagenesis was used to demonstrate that the ba3 oxygen reductase from Thermus thermophilus, a representative of the B-family, does not contain a D-channel. Rather, it utilizes only 1 proton input channel, analogous to that of the A-family K-channel, and it delivers protons to the active site for both O2 chem. and proton pumping. Comparison of available subunit I sequences reveals that the only structural elements conserved within the oxygen reductase families that could perform these functions are active-site components, namely the covalently linked histidine-tyrosine, the Cu8 and its ligands, and the active-site heme and its ligands. Therefore, the data suggest that all oxygen reductases perform the same chem. reactions for oxygen redn. and comprise the essential elements of the proton-pumping mechanism (e.g., the proton-loading and kinetic-grating sites). These sites, however, cannot be located within the D-channel. These results along with structural considerations point to the A-propionate region of the active-site heme and surrounding water mols. as the proton-loading site.
- 130Lee, H. J.; Gennis, R. B.; Ädelroth, P. Entrance of the Proton Pathway in Cbb3-Type Heme-Copper Oxidases. Proc. Natl. Acad. Sci. U. S. A. 2011, 108, 17661– 17666, DOI: 10.1073/pnas.1107543108Google Scholar130https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3MXhsVGrtb7E&md5=729100c9063687935211e5219732502bEntrance of the proton pathway in cbb3-type heme-copper oxidasesLee, Hyun Ju; Gennis, Robert B.; Aedelroth, PiaProceedings of the National Academy of Sciences of the United States of America (2011), 108 (43), 17661-17666, S17661/1-S17661/3CODEN: PNASA6; ISSN:0027-8424. (National Academy of Sciences)Heme-copper oxidases (HCuOs) are the last components of the respiratory chain in mitochondria and many bacteria. They catalyze O2 redn. and couple it to the maintenance of a proton-motive force across the membrane in which they are embedded. In the mitochondrial-like, A family of HCuOs, there are two well established proton transfer pathways leading from the cytosol to the active site, the D and the K pathways. In the C family (cbb3) HCuOs, recent work indicated the use of only one pathway, analogous to the K pathway. In this work, we have studied the functional importance of the suggested entry point of this pathway, the Glu-25 (Rhodobacter sphaeroides cbb3 numbering) in the accessory subunit CcoP (E25P). We show that catalytic turnover is severely slowed in variants lacking the protonatable Glu-25. Furthermore, proton uptake from soln. during oxidn. of the fully reduced cbb3 by O2 is specifically and severely impaired when Glu-25 was exchanged for Ala or Gln, with rate consts. 100-500 times slower than in wild type. Thus, our results support the role of E25P as the entry point to the proton pathway in cbb3 and that this pathway is the main proton pathway. This is in contrast to the A-type HCuOs, where the D (and not the K) pathway is used during O2 redn. The cbb3 is in addn. to O2 redn. capable of NO redn., an activity that was largely retained in the E25P variants, consistent with a scenario where NO redn. in cbb3 uses protons from the periplasmic side of the membrane.
- 131Sharma, V.; Wikström, M.; Kaila, V. R. Dynamic Water Networks in Cytochrome cbb3 Oxidase. Biochim. Biophys. Acta, Bioenerg. 2012, 1817, 726– 734, DOI: 10.1016/j.bbabio.2011.09.010Google Scholar131https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC38XlsVSjur0%253D&md5=6ccb5a0b742506a3074a941570cc18bbDynamic water networks in cytochrome cbb3 oxidaseSharma, Vivek; Wikstrom, Marten; Kaila, Ville R. I.Biochimica et Biophysica Acta, Bioenergetics (2012), 1817 (5), 726-734CODEN: BBBEB4; ISSN:0005-2728. (Elsevier B. V.)Heme-copper oxidases (HCOs) are terminal electron acceptors in aerobic respiration. They catalyze the redn. of mol. oxygen to water with concurrent pumping of protons across the mitochondrial and bacterial membranes. Protons required for oxygen redn. chem. and pumping are transferred through proton uptake channels. Recently, the crystal structure of the first C-type member of the HCO superfamily was resolved [Buschmann et al. Science 329 (2010) 327-330], but crystallog. water mols. could not be identified. Here, we have used mol. dynamics (MD) simulations, continuum electrostatic approaches, and quantum chem. cluster calcns. to identify proton transfer pathways in cytochrome cbb3. In MD simulations, we observe formation of stable water chains that connect the highly conserved Glu323 residue on the proximal side of heme b3 both with the N- and the P-sides of the membrane. We propose that such pathways could be utilized for redox-coupled proton pumping in the C-type oxidases. Electrostatics and quantum chem. calcns. suggest an increased proton affinity of Glu323 upon redn. of high-spin heme b3. Protonation of Glu323 provides a mechanism to tune the redox potential of heme b3 with possible implications for proton pumping.
- 132Sharma, V.; Wikström, M. A Structural and Functional Perspective on the Evolution of the Heme–Copper Oxidases. FEBS Lett. 2014, 588, 3787– 3792, DOI: 10.1016/j.febslet.2014.09.020Google ScholarThere is no corresponding record for this reference.
- 133Brochier-Armanet, C.; Talla, E.; Gribaldo, S. The Multiple Evolutionary Histories of Dioxygen Reductases: Implications for the Origin and Evolution of Aerobic Respiration. Mol. Biol. Evol. 2009, 26, 285– 297, DOI: 10.1093/molbev/msn246Google ScholarThere is no corresponding record for this reference.
- 134Richter, O. M.; Dürr, K. L.; Kannt, A.; Ludwig, B.; Scandurra, F. M.; Giuffre, A.; Sarti, P.; Hellwig, P. Probing the Access of Protons to the K Pathway in the Paracoccus Denitrificans Cytochrome C Oxidase. FEBS J. 2005, 272, 404– 412, DOI: 10.1111/j.1742-4658.2004.04480.xGoogle ScholarThere is no corresponding record for this reference.
- 135Woelke, A. L.; Galstyan, G.; Knapp, E.-W. Lysine 362 in Cytochrome C Oxidase Regulates Opening of the K-Channel Via Changes in Pk a and Conformation. Biochim. Biophys. Acta, Bioenerg. 2014, 1837, 1998– 2003, DOI: 10.1016/j.bbabio.2014.08.003Google Scholar135https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2cXhsVars73P&md5=6c7de5238a2108927cabbf7847ca3473Lysine 362 in cytochrome c oxidase regulates opening of the K-channel via changes in pKA and conformationWoelke, Anna Lena; Galstyan, Gegham; Knapp, Ernst-WalterBiochimica et Biophysica Acta, Bioenergetics (2014), 1837 (12), 1998-2003CODEN: BBBEB4; ISSN:0005-2728. (Elsevier B. V.)The metab. of aerobic life uses the conversion of mol. oxygen to water as an energy source. This reaction is catalyzed by cytochrome c oxidase (CcO) consuming four electrons and four protons, which move along specific routes. While all four electrons are transferred via the same cofactors to the binuclear reaction center (BNC), the protons take two different routes in the A-type CcO, i.e., two of the four chem. protons consumed in the reaction arrive via the D-channel in the oxidative first half starting after oxygen binding. The other two chem. protons enter via the K-channel in the reductive second half of the reaction cycle. To date, the mechanism behind these sep. proton transport pathways has not been understood.In this study, we propose a model that can explain the reaction-step specific opening and closing of the K-channel by conformational and pKA changes of its central lysine 362. Mol. dynamics simulations reveal an upward movement of Lys362 towards the BNC, which had already been supposed by several exptl. studies. Redox state-dependent pKA calcns. provide evidence that Lys362 may protonate transiently, thereby opening the K-channel only in the reductive second half of the reaction cycle. From our results, we develop a model that assigns a key role to Lys362 in the proton gating between the two proton input channels of the A-type CcO.
- 136Sharma, V.; Wikström, M. The Role of the K-Channel and the Active-Site Tyrosine in the Catalytic Mechanism of Cytochrome C Oxidase. Biochim. Biophys. Acta, Bioenerg. 2016, 1857, 1111– 1115, DOI: 10.1016/j.bbabio.2016.02.008Google Scholar136https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC28XivFyitro%253D&md5=08e50de78127be585c4d39826ac5415eThe role of the K-channel and the active-site tyrosine in the catalytic mechanism of cytochrome c oxidaseSharma, Vivek; Wikstrom, MartenBiochimica et Biophysica Acta, Bioenergetics (2016), 1857 (8), 1111-1115CODEN: BBBEB4; ISSN:0005-2728. (Elsevier B. V.)The active site of cytochrome c oxidase (CcO) comprises an oxygen-binding heme, a nearby copper ion (CuB), and a tyrosine residue that is covalently linked to one of the histidine ligands of CuB. Two proton-conducting pathways are obsd. in CcO, namely the D- and the K-channels, which are used to transfer protons either to the active site of oxygen redn. (substrate protons) or for pumping. Proton transfer through the D-channel is very fast, and its role in efficient transfer of both substrate and pumped protons is well established. However, it has not been fully clear why a sep. K-channel is required, apparently for the supply of substrate protons only. In this work, we have analyzed the available exptl. and computational data, based on which we provide new perspectives on the role of the K-channel. Our anal. suggests that proton transfer in the K-channel may be gated by the protonation state of the active-site tyrosine (Tyr244) and that the neutral radical form of this residue has a more general role in the CcO mechanism than thought previously. This article is part of a Special Issue entitled 'EBEC 2016: 19th European Bioenergetics Conference, Riva del Garda, Italy, July 2-6, 2016', edited by Prof. Paolo Bernardi.
- 137Lyons, J. A.; Aragão, D.; Slattery, O.; Pisliakov, A. V.; Soulimane, T.; Caffrey, M. Structural Insights into Electron Transfer in Caa3-Type Cytochrome Oxidase. Nature 2012, 487, 514– 518, DOI: 10.1038/nature11182Google Scholar137https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC38XhtFWjtrzL&md5=6c3166585662879e0bab0d51df20e405Structural insights into electron transfer in caa3-type cytochrome oxidaseLyons, Joseph A.; Aragao, David; Slattery, Orla; Pisliakov, Andrei V.; Soulimane, Tewfik; Caffrey, MartinNature (London, United Kingdom) (2012), 487 (7408), 514-518CODEN: NATUAS; ISSN:0028-0836. (Nature Publishing Group)Cytochrome c oxidase is a member of the haem copper oxidase superfamily (HCO). HCOs function as the terminal enzymes in the respiratory chain of mitochondria and aerobic prokaryotes, coupling mol. oxygen redn. to transmembrane proton pumping. Integral to the enzyme's function is the transfer of electrons from cytochrome c to the oxidase via a transient assocn. of the two proteins. Electron entry and exit are proposed to occur from the same site on cytochrome c. Here we report the crystal structure of the caa3-type cytochrome oxidase from Thermus thermophilus, which has a covalently tethered cytochrome c domain. Crystals were grown in a bicontinuous mesophase using a synthetic short-chain monoacylglycerol as the hosting lipid. From the electron d. map, at 2.36 Å resoln., a novel integral membrane subunit and a native glycoglycerophospholipid embedded in the complex were identified. Contrary to previous electron transfer mechanisms obsd. for sol. cytochrome c, the structure reveals the architecture of the electron transfer complex for the fused cupredoxin/cytochrome c domain, which implicates different sites on cytochrome c for electron entry and exit. Support for an alternative to the classical proton gate characteristic of this HCO class is presented.
- 138Blomberg, M. R.; Siegbahn, P. E. Proton Pumping in Cytochrome C Oxidase: Energetic Requirements and the Role of Two Proton Channels. Biochim. Biophys. Acta, Bioenerg. 2014, 1837, 1165– 1177, DOI: 10.1016/j.bbabio.2014.01.002Google Scholar138https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2cXhtF2ntL0%253D&md5=e2796d4b0a3e6c482b7aebce3b50cd87Proton pumping in cytochrome c oxidase: Energetic requirements and the role of two proton channelsBlomberg, Margareta R. A.; Siegbahn, Per E. M.Biochimica et Biophysica Acta, Bioenergetics (2014), 1837 (7), 1165-1177CODEN: BBBEB4; ISSN:0005-2728. (Elsevier B. V.)Cytochrome c oxidase is a superfamily of membrane-bound enzymes catalyzing the exergonic redn. of O2 to H2O, producing an electrochem. gradient across the membrane. The gradient is formed both by the electrogenic chem., taking electrons and protons from opposite sides of the membrane, and by proton pumping across the entire membrane. In the most efficient subfamily, the A-family of oxidases, one proton is pumped in each redn. step, which is surprising considering the fact that two of the redn. steps most likely are only weakly exergonic. Based on a combination of quantum chem. calcns. and exptl. information, it is here shown that from both a thermodn. and a kinetic point of view, it should be possible to pump one proton per electron also with such an uneven distribution of the free energy release over the redn. steps, at least up to half the max. gradient. A previously suggested pumping mechanism was developed further to suggest a reason for the use of 2 proton transfer channels in the A-family. Since the rate of proton transfer to the binuclear center through the D-channel is redox-dependent, it might become too slow for the steps with low exergonicity. Therefore, a 2nd channel, the K-channel, where the rate is redox-independent is needed. A redox-dependent leakage possibility was also suggested, which might be important for efficient energy conservation at a high gradient. A mechanism for the variation in proton pumping stoichiometry over the different subfamilies of cytochrome oxidase was also suggested.
- 139Carvalheda, C. A.; Pisliakov, A. V. Insights into Proton Translocation in cbb3 Oxidase from MD Simulations. Biochim. Biophys. Acta, Bioenerg. 2017, 1858, 396– 406, DOI: 10.1016/j.bbabio.2017.02.013Google Scholar139https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2sXkt1Ogsro%253D&md5=7cb34f0add60963b8c6e6cc6a56496f6Insights into proton translocation in cbb3 oxidase from MD simulationsCarvalheda, Catarina A.; Pisliakov, Andrei V.Biochimica et Biophysica Acta, Bioenergetics (2017), 1858 (5), 396-406CODEN: BBBEB4; ISSN:0005-2728. (Elsevier B.V.)Heme-copper oxidases are membrane protein complexes that catalyze the final step of the aerobic respiration, namely the redn. of oxygen to water. The energy released during catalysis is coupled to the active translocation of protons across the membrane, which contributes to the establishment of an electrochem. gradient that is used for ATP synthesis. The distinctive C-type (or cbb3) cytochrome c oxidases, which are mostly present in proteobacteria, exhibit a no. of unique structural and functional features, including high catalytic activity at low oxygen concns. At the moment, the functioning mechanism of C-type oxidases, in particular the proton transfer/pumping mechanism presumably via a single proton channel, is still poorly understood. In this work we used all-atom mol. dynamics simulations and continuum electrostatics calcns. to obtain at.-level insights into the hydration and dynamics of a cbb3 oxidase. We provide the details of the water dynamics and proton transfer pathways for both the "chem." and "pumped" protons, and show that formation of protonic connections is strongly affected by the protonation state of key residues, namely H243, E323 and H337.
- 140Woelke, A. L.; Wagner, A.; Galstyan, G.; Meyer, T.; Knapp, E.-W. Proton Transfer in the K-Channel Analog of B-Type Cytochrome C Oxidase from Thermus Thermophilus. Biophys. J. 2014, 107, 2177– 2184, DOI: 10.1016/j.bpj.2014.09.010Google Scholar140https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2cXhs1Klu77M&md5=bfeb71ee98d1201c0451c26897ebcc99Proton Transfer in the K-Channel Analog of B-Type Cytochrome c Oxidase from Thermus thermophilusWoelke, Anna Lena; Wagner, Anke; Galstyan, Gegham; Meyer, Tim; Knapp, Ernst-WalterBiophysical Journal (2014), 107 (9), 2177-2184CODEN: BIOJAU; ISSN:0006-3495. (Cell Press)A key enzyme in aerobic metab. is cytochrome c oxidase (CcO), which catalyzes the redn. of mol. oxygen to water in the mitochondrial and bacterial membranes. Substrate electrons and protons are taken up from different sides of the membrane and protons are pumped across the membrane, thereby generating an electrochem. gradient. The well-studied A-type CcO uses two different entry channels for protons: the D-channel for all pumped and two consumed protons, and the K-channel for the other two consumed protons. In contrast, the B-type CcO uses only a single proton input channel for all consumed and pumped protons. It has the same location as the A-type K-channel (and thus is named the K-channel analog) without sharing any significant sequence homol. In this study, we performed mol. dynamics (MD) simulations and electrostatic calcns. to characterize the K-channel analog in terms of its energetic requirements and functionalities. The function of Glu-15B as a proton sink at the channel entrance is demonstrated by its rotational movement out of the channel when it is deprotonated and by its high pKA value when it points inside the channel. Tyr-244 in the middle of the channel is identified as the valve that ensures unidirectional proton transfer, as it moves inside the hydrogen bond gap of the K-channel analog only while being deprotonated. The electrostatic energy landscape was calcd. for all proton transfer steps in the K-channel analog, which functions via proton-hole transfer. Overall, the K-channel analog has a very stable geometry without large energy barriers.
- 141Babcock, G. T.; Wikstrom, M. Oxygen Activation and the Conservation of Energy in Cell Respiration. Nature 1992, 356, 301, DOI: 10.1038/356301a0Google Scholar141https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaK38XksVaktbc%253D&md5=af4d7aefec71fda95b758a968131b582Oxygen activation and the conservation of energy in cell respirationBabcock, Gerald T.; Wikstrom, MartenNature (London, United Kingdom) (1992), 356 (6367), 301-9CODEN: NATUAS; ISSN:0028-0836.A review, with 100 refs., of O activation by membrane-assocd. cytochrome and quinol oxidases of plants and animals, and the linkage of respiratory redn. of O to the conservation of energy in cell respiration through coupling with H+ translocation across the membranes.
- 142Ferguson-Miller, S.; Babcock, G. T. Heme/Copper Terminal Oxidases. Chem. Rev. 1996, 96, 2889– 2908, DOI: 10.1021/cr950051sGoogle Scholar142https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaK28Xmt1Gmsr8%253D&md5=cae63bc0c12f47ef8bba2d0e1e61de5dHeme/Copper Terminal OxidasesFerguson-Miller, Shelagh; Babcock, Gerald T.Chemical Reviews (Washington, D. C.) (1996), 96 (7), 2889-2907CODEN: CHREAY; ISSN:0009-2665. (American Chemical Society)A review, with 122 refs. The authors review here structure and functions of heme/copper terminal oxidases.
- 143Lindsay, J. G.; Wilson, D. F. Reaction of Cytochrome c Oxidase with CO: Involvement of the Invisible Copper. FEBS Lett. 1974, 48, 45– 49, DOI: 10.1016/0014-5793(74)81058-6Google ScholarThere is no corresponding record for this reference.
- 144Chance, B.; Saronio, C.; Leigh, J. Functional Intermediates in the Reaction of Membrane-Bound Cytochrome Oxidase with Oxygen. J. Biol. Chem. 1975, 250, 9226– 9237Google ScholarThere is no corresponding record for this reference.
- 145Kitagawa, T.; Ogura, T. Oxygen Activation Mechanism at the Binuclear Site of Heme–Copper Oxidase Superfamily as Revealed by Time-Resolved Resonance Raman Spectroscopy; John Wiley & Sons, Inc.: Hoboken, NJ, 1996.Google ScholarThere is no corresponding record for this reference.
- 146Kaukonen, M. Calculated Reaction Cycle of Cytochrome C Oxidase. J. Phys. Chem. B 2007, 111, 12543– 12550, DOI: 10.1021/jp070578wGoogle Scholar146https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2sXhtFehu7fL&md5=6035e83c89df254559fe59202cda6712Calculated Reaction Cycle of Cytochrome c OxidaseKaukonen, MarkusJournal of Physical Chemistry B (2007), 111 (43), 12543-12550CODEN: JPCBFK; ISSN:1520-6106. (American Chemical Society)The catalytic cycle of cytochrome c oxidase has been simulated by means of quantum mech. calcns. The exptl. energetics of the catalytic cycle is nearly reproduced. The at. structures of the intermediates are suggested. In particular, the structures of nonactive "resting" intermediates are proposed.
- 147Blomberg, M. R.; Siegbahn, P. E.; Babcock, G. T.; Wikström, M. Modeling Cytochrome Oxidase: A Quantum Chemical Study of the O– O Bond Cleavage Mechanism. J. Am. Chem. Soc. 2000, 122, 12848– 12858, DOI: 10.1021/ja002745aGoogle ScholarThere is no corresponding record for this reference.
- 148Schäfer, A.; Horn, H.; Ahlrichs, R. Fully Optimized Contracted Gaussian Basis Sets for Atoms Li to Kr. J. Chem. Phys. 1992, 97, 2571– 2577, DOI: 10.1063/1.463096Google ScholarThere is no corresponding record for this reference.
- 149Schäfer, A.; Huber, C.; Ahlrichs, R. Fully Optimized Contracted Gaussian Basis Sets of Triple Zeta Valence Quality for Atoms Li to Kr. J. Chem. Phys. 1994, 100, 5829– 5835, DOI: 10.1063/1.467146Google ScholarThere is no corresponding record for this reference.
- 150Sierka, M.; Hogekamp, A.; Ahlrichs, R. Fast Evaluation of the Coulomb Potential for Electron Densities Using Multipole Accelerated Resolution of Identity Approximation. J. Chem. Phys. 2003, 118, 9136– 9148, DOI: 10.1063/1.1567253Google Scholar150https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD3sXjs1Gkurw%253D&md5=6230812b9a569f78764d98e156fda7d6Fast evaluation of the Coulomb potential for electron densities using multipole accelerated resolution of identity approximationSierka, Marek; Hogekamp, Annika; Ahlrichs, ReinhartJournal of Chemical Physics (2003), 118 (20), 9136-9148CODEN: JCPSA6; ISSN:0021-9606. (American Institute of Physics)A new computational approach is presented that allows for an accurate and efficient treatment of the electronic Coulomb term in d. functional methods. This multipole accelerated resoln. of identity for J (MARI-J) method partitions the Coulomb interactions into the near- and far-field parts. The calcn. of the far-field part is performed by a straightforward application of the multipole expansions and the near-field part is evaluated employing expansion of mol. electron densities in atom-centered auxiliary basis sets (RI-J approxn.). Compared to full RI-J calcns., up to 6.5-fold CPU time savings are reported for systems with about 1000 atoms without any significant loss of accuracy. Other multipole-based methods are compared with regard to redn. of the CPU times vs. the conventional treatment of the Coulomb term. The MARI-J approach compares favorably and offers speedups approaching two orders of magnitude for mols. with about 400 atoms and more than 5000 basis functions. Our new method shows scalings as favorable as N1.5, where N is the no. of basis functions, for a variety of systems including dense three-dimensional mols. Calcns. on mols. with up to 1000 atoms and 7000 to 14 000 basis functions, depending on symmetry, can now be easily performed on single processor work stations. Details of the method implementation in the quantum chem. program TURBOMOLE are discussed.
- 151Weigend, F.; Ahlrichs, R. Balanced Basis Sets of Split Valence, Triple Zeta Valence and Quadruple Zeta Valence Quality for H to Rn: Design and Assessment of Accuracy. Phys. Chem. Chem. Phys. 2005, 7, 3297– 3305, DOI: 10.1039/b508541aGoogle Scholar151https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2MXpsFWgu7o%253D&md5=a820fb6055c993b50c405ba0fc62b194Balanced basis sets of split valence, triple zeta valence and quadruple zeta valence quality for H to Rn: Design and assessment of accuracyWeigend, Florian; Ahlrichs, ReinhartPhysical Chemistry Chemical Physics (2005), 7 (18), 3297-3305CODEN: PPCPFQ; ISSN:1463-9076. (Royal Society of Chemistry)Gaussian basis sets of quadruple zeta valence quality for Rb-Rn are presented, as well as bases of split valence and triple zeta valence quality for H-Rn. The latter were obtained by (partly) modifying bases developed previously. A large set of more than 300 mols. representing (nearly) all elements-except lanthanides-in their common oxidn. states was used to assess the quality of the bases all across the periodic table. Quantities investigated were atomization energies, dipole moments and structure parameters for Hartree-Fock, d. functional theory and correlated methods, for which we had chosen Moller-Plesset perturbation theory as an example. Finally recommendations are given which type of basis set is used best for a certain level of theory and a desired quality of results.
- 152Grimme, S.; Antony, J.; Ehrlich, S.; Krieg, H. A Consistent and Accurate Ab Initio Parametrization of Density Functional Dispersion Correction (Dft-D) for the 94 Elements H-Pu. J. Chem. Phys. 2010, 132, 154104, DOI: 10.1063/1.3382344Google Scholar152https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3cXkvVyks7o%253D&md5=2bca89d904579d5565537a0820dc2ae8A consistent and accurate ab initio parametrization of density functional dispersion correction (DFT-D) for the 94 elements H-PuGrimme, Stefan; Antony, Jens; Ehrlich, Stephan; Krieg, HelgeJournal of Chemical Physics (2010), 132 (15), 154104/1-154104/19CODEN: JCPSA6; ISSN:0021-9606. (American Institute of Physics)The method of dispersion correction as an add-on to std. Kohn-Sham d. functional theory (DFT-D) has been refined regarding higher accuracy, broader range of applicability, and less empiricism. The main new ingredients are atom-pairwise specific dispersion coeffs. and cutoff radii that are both computed from first principles. The coeffs. for new eighth-order dispersion terms are computed using established recursion relations. System (geometry) dependent information is used for the first time in a DFT-D type approach by employing the new concept of fractional coordination nos. (CN). They are used to interpolate between dispersion coeffs. of atoms in different chem. environments. The method only requires adjustment of two global parameters for each d. functional, is asymptotically exact for a gas of weakly interacting neutral atoms, and easily allows the computation of at. forces. Three-body nonadditivity terms are considered. The method has been assessed on std. benchmark sets for inter- and intramol. noncovalent interactions with a particular emphasis on a consistent description of light and heavy element systems. The mean abs. deviations for the S22 benchmark set of noncovalent interactions for 11 std. d. functionals decrease by 15%-40% compared to the previous (already accurate) DFT-D version. Spectacular improvements are found for a tripeptide-folding model and all tested metallic systems. The rectification of the long-range behavior and the use of more accurate C6 coeffs. also lead to a much better description of large (infinite) systems as shown for graphene sheets and the adsorption of benzene on an Ag(111) surface. For graphene it is found that the inclusion of three-body terms substantially (by about 10%) weakens the interlayer binding. We propose the revised DFT-D method as a general tool for the computation of the dispersion energy in mols. and solids of any kind with DFT and related (low-cost) electronic structure methods for large systems. (c) 2010 American Institute of Physics.
- 153Becke, A. D. Density-Functional Exchange-Energy Approximation with Correct Asymptotic Behavior. Phys. Rev. A: At., Mol., Opt. Phys. 1988, 38, 3098, DOI: 10.1103/PhysRevA.38.3098Google Scholar153https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaL1cXmtlOhsLo%253D&md5=d4d219c134a5a90f689a8abed04d82ccDensity-functional exchange-energy approximation with correct asymptotic behaviorBecke, A. D.Physical Review A: Atomic, Molecular, and Optical Physics (1988), 38 (6), 3098-100CODEN: PLRAAN; ISSN:0556-2791.Current gradient-cor. d.-functional approxns. for the exchange energies of at. and mol. systems fail to reproduce the correct 1/r asymptotic behavior of the exchange-energy d. A gradient-cor. exchange-energy functional is given with the proper asymptotic limit. This functional, contg. only one parameter, fits the exact Hartree-Fock exchange energies of a wide variety of at. systems with remarkable accuracy, surpassing the performance of previous functionals contg. two parameters or more.
- 154Perdew, J. P. Density-Functional Approximation for the Correlation Energy of the Inhomogeneous Electron Gas. Phys. Rev. B: Condens. Matter Mater. Phys. 1986, 33, 8822, DOI: 10.1103/PhysRevB.33.8822Google Scholar154https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A280%3ADC%252BC2sfgsFSktA%253D%253D&md5=fb343a074cf09acda3e96d7f13ec2c7eDensity-functional approximation for the correlation energy of the inhomogeneous electron gasPerdewPhysical review. B, Condensed matter (1986), 33 (12), 8822-8824 ISSN:0163-1829.There is no expanded citation for this reference.
- 155Becke, A. D. Density-Functional Thermochemistry. Iii. The Role of Exact Exchange. J. Chem. Phys. 1993, 98, 5648– 5652, DOI: 10.1063/1.464913Google Scholar155https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaK3sXisVWgtrw%253D&md5=291bbfc119095338bb1624f0c21c7ca8Density-functional thermochemistry. III. The role of exact exchangeBecke, Axel D.Journal of Chemical Physics (1993), 98 (7), 5648-52CODEN: JCPSA6; ISSN:0021-9606.Despite the remarkable thermochem. accuracy of Kohn-Sham d.-functional theories with gradient corrections for exchange-correlation, the author believes that further improvements are unlikely unless exact-exchange information is considered. Arguments to support this view are presented, and a semiempirical exchange-correlation functional (contg. local-spin-d., gradient, and exact-exchange terms) is tested for 56 atomization energies, 42 ionization potentials, 8 proton affinities, and 10 total at. energies of first- and second-row systems. This functional performs better than previous functionals with gradient corrections only, and fits expt. atomization energies with an impressively small av. abs. deviation of 2.4 kcal/mol.
- 156Lee, C.; Yang, W.; Parr, R. G. Development of the Colle-Salvetti Correlation-Energy Formula into a Functional of the Electron Density. Phys. Rev. B: Condens. Matter Mater. Phys. 1988, 37, 785, DOI: 10.1103/PhysRevB.37.785Google Scholar156https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaL1cXktFWrtbw%253D&md5=ee7b59267a2ff72e15171a481819ccf8Development of the Colle-Salvetti correlation-energy formula into a functional of the electron densityLee, Chengteh; Yang, Weitao; Parr, Robert G.Physical Review B: Condensed Matter and Materials Physics (1988), 37 (2), 785-9CODEN: PRBMDO; ISSN:0163-1829.A correlation-energy formula due to R. Colle and D. Salvetti (1975), in which the correlation energy d. is expressed in terms of the electron d. and a Laplacian of the 2nd-order Hartree-Fock d. matrix, is restated as a formula involving the d. and local kinetic-energy d. On insertion of gradient expansions for the local kinetic-energy d., d.-functional formulas for the correlation energy and correlation potential are then obtained. Through numerical calcns. on a no. of atoms, pos. ions, and mols., of both open- and closed-shell type, it is demonstrated that these formulas, like the original Colle-Salvetti formulas, give correlation energies within a few percent.
- 157Klamt, A.; Schüürmann, G. Cosmo: A New Approach to Dielectric Screening in Solvents with Explicit Expressions for the Screening Energy and Its Gradient. J. Chem. Soc., Perkin Trans. 2 1993, 2, 799– 805, DOI: 10.1039/P29930000799Google ScholarThere is no corresponding record for this reference.
- 158Ahlrichs, R.; Bär, M.; Häser, M.; Horn, H.; Kölmel, C. Electronic Structure Calculations on Workstation Computers: The Program System Turbomole. Chem. Phys. Lett. 1989, 162, 165– 169, DOI: 10.1016/0009-2614(89)85118-8Google Scholar158https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaK3cXkt1yrtg%253D%253D&md5=b6aa32e6226a8e11b511e4d09cc60dc8Electronic structure calculations on workstation computers: the program system TURBOMOLEAhlrichs, Reinhart; Baer, Michael; Haeser, Marco; Horn, Hans; Koelmel, ChristophChemical Physics Letters (1989), 162 (3), 165-9CODEN: CHPLBC; ISSN:0009-2614.The basic structure of the program system TURBOMOLE for SCF - including first and second anal. derivs. with respect to nuclear coordinates - and MP2 calcns. is briefly described. The program takes full advantage of all discrete point group symmetries and has only modest - and (partially) adjustable - I/O and background storage requirements. The performance of TURBOMOLE is documented for demonstrative applications.
- 159Verkhovsky, M. I.; Morgan, J. E.; Wikstroem, M. Oxygen Binding and Activation: Early Steps in the Reaction of Oxygen with Cytochrome C Oxidase. Biochemistry 1994, 33, 3079– 3086, DOI: 10.1021/bi00176a042Google ScholarThere is no corresponding record for this reference.
- 160Verkhovsky, M. I.; Morgan, J. E.; Puustinen, A.; Wikstrom, M. Kinetic Trapping of Oxygen in Cell Respiration. Nature 1996, 380, 268– 270, DOI: 10.1038/380268a0Google ScholarThere is no corresponding record for this reference.
- 161Blomberg, M. R. A.; Borowski, T.; Himo, F.; Liao, R.-Z.; Siegbahn, P. E. M. Quantum Chemical Studies of Mechanisms for Metalloenzymes. Chem. Rev. 2014, 114, 3601– 3658, DOI: 10.1021/cr400388tGoogle Scholar161https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2cXotVCqtg%253D%253D&md5=1ea41ed44644916eff67769e6ca21826Quantum chemical studies of mechanisms for metalloenzymesBlomberg, Margareta R. A.; Borowski, Tomasz; Himo, Fahmi; Liao, Rong-Zhen; Siegbahn, Per E. M.Chemical Reviews (Washington, DC, United States) (2014), 114 (7), 3601-3658CODEN: CHREAY; ISSN:0009-2665. (American Chemical Society)A review. The status of high-accuracy, mainly DFT, studies of redox-active metalloenzymes is described. This area has during the past 15 yr gradually grown to become at least of equal importance in comparison to traditional spectroscopic studies. By far most of the studies of redox mechanisms until now have used the cluster model approach, but there are also a significant no. where the QM/MM approach has been used, in particular for cytochrome P 450.
- 162Wikström, M. Energy-Dependent Reversal of the Cytochrome Oxidase Reaction. Proc. Natl. Acad. Sci. U. S. A. 1981, 78, 4051– 4054, DOI: 10.1073/pnas.78.7.4051Google ScholarThere is no corresponding record for this reference.
- 163Gorbikova, E. A.; Belevich, I.; Wikström, M.; Verkhovsky, M. I. The Proton Donor for Oo Bond Scission by Cytochrome C Oxidase. Proc. Natl. Acad. Sci. U. S. A. 2008, 105, 10733– 10737, DOI: 10.1073/pnas.0802512105Google ScholarThere is no corresponding record for this reference.
- 164Blomberg, M. R.; Borowski, T.; Himo, F.; Liao, R.-Z.; Siegbahn, P. E. Quantum Chemical Studies of Mechanisms for Metalloenzymes. Chem. Rev. 2014, 114, 3601– 3658, DOI: 10.1021/cr400388tGoogle Scholar164https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2cXotVCqtg%253D%253D&md5=1ea41ed44644916eff67769e6ca21826Quantum chemical studies of mechanisms for metalloenzymesBlomberg, Margareta R. A.; Borowski, Tomasz; Himo, Fahmi; Liao, Rong-Zhen; Siegbahn, Per E. M.Chemical Reviews (Washington, DC, United States) (2014), 114 (7), 3601-3658CODEN: CHREAY; ISSN:0009-2665. (American Chemical Society)A review. The status of high-accuracy, mainly DFT, studies of redox-active metalloenzymes is described. This area has during the past 15 yr gradually grown to become at least of equal importance in comparison to traditional spectroscopic studies. By far most of the studies of redox mechanisms until now have used the cluster model approach, but there are also a significant no. where the QM/MM approach has been used, in particular for cytochrome P 450.
- 165Rich, P. Towards an Understanding of the Chemistry of Oxygen Reduction. Aust. J. Plant Physiol. 1995, 22, 479– 486, DOI: 10.1071/PP9950479Google Scholar165https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaK2MXnt1Ortrg%253D&md5=33eba02dc31dd3e0f5c8632f5d1594f4Towards an understanding of the chemistry of oxygen reduction and proton translocation in the iron-copper respiratory oxidasesRich, P. R.Australian Journal of Plant Physiology (1995), 22 (3), 479-86CODEN: AJPPCH; ISSN:0310-7841. (Commonwealth Scientific and Industrial Research Organization)A review, with 58 refs. Advances in understanding of the structure and the catalytic cycle of oxygen redn. of the protonmotive heme-copper terminal oxidases are reviewed. This information has been combined with the recent recognition of the need for electroneutrality of stable catalytic intermediates to produce a new working model of the essential elements of the chemiosmotic mechanism of coupling of oxygen redn. chem. to vectorial proton translocation.
- 166Jünemann, S.; Heathcote, P.; Rich, P. R. The Reactions of Hydrogen Peroxide with Bovine Cytochrome C Oxidase. Biochim. Biophys. Acta, Bioenerg. 2000, 1456, 56– 66, DOI: 10.1016/S0005-2728(99)00105-XGoogle Scholar166https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD3cXotFKhsA%253D%253D&md5=9253162be73fb1d20c3cf6c56b074b70The reactions of hydrogen peroxide with bovine cytochrome c oxidaseJunemann, Susanne; Heathcote, Peter; Rich, Peter R.Biochimica et Biophysica Acta, Bioenergetics (2000), 1456 (1), 56-66CODEN: BBBEB4; ISSN:0005-2728. (Elsevier B.V.)Oxidized bovine heart cytochrome c oxidase is known to react with 2 mols. of H2O2 to form consecutively 607 nm peroxy (P) and 580-nm ferryl (F) species. These are widely used as model compds. for the equiv. P and F intermediates of the catalytic cycle. However, kinetic anal. of the reaction with H2O2 in the pH range of 6.0-9.0 revealed a more complex situation. In particular, as the pH was lowered, a 580-nm compd. could be formed by reaction with a single H2O2 mol. This species, termed F*, was spectrally similar, but not identical, to F. The reactions were equiv. to those previously reported for the cytochrome bo-type quinol oxidase from Escherichia coli where it was proposed that F was produced directly from P. However, in bovine cytochrome c oxidase, F did not appear in samples of the 607-nm form, PM, produced by CO/O2 treatment, even at low pH, although this form was shown to be identical to the H2O2-derived P state, PH, on the basis of spectral characteristics and kinetics of reaction with H2O2. Furthermore, lowering the pH of a sample of PM or PH generated at high pH resulted in F formation only on a time scale of minutes. It was concluded that P and F are not in a rapid, pH-dependent equil., but instead are formed by distinct pathways and cannot interconvert in a simple manner, and that the crucial difference between them lies in their patterns of protonation.
- 167Tommos, C.; Babcock, G. T. Proton and Hydrogen Currents in Photosynthetic Water Oxidation. Biochim. Biophys. Acta, Bioenerg. 2000, 1458, 199– 219, DOI: 10.1016/S0005-2728(00)00069-4Google Scholar167https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD3cXjsV2jsL4%253D&md5=b98d534584cbd637648c877801c87226Proton and hydrogen currents in photosynthetic water oxidationTommos, C.; Babcock, G. T.Biochimica et Biophysica Acta, Bioenergetics (2000), 1458 (1), 199-219CODEN: BBBEB4; ISSN:0005-2728. (Elsevier B.V.)A review with 137 refs. considering the means by which photosystem II (PSII) catalyzes the high electron/proton flux assocd. with water oxidn. and the functional implications that these currents have for the oxygen-evolving process. The photosynthetic processes that lead to water oxidn. involve an evolution in time from photon dynamics to photochem.-driven electron transfer to coupled electron/proton chem. The redox-active tyrosine, YZ, is the component at which the proton currents necessary for water oxidn. are switched on. The thermodn. and kinetic implications of this function for YZ are discussed. These considerations also provide insight into the related roles of YZ in preserving the high photochem. quantum efficiency in PSII and of conserving the highly oxidizing conditions generated by the photochem. in the PSII reaction center. The oxidn. of YZ by P680+ can be described well by a treatment that invokes proton coupling within the context of nonadiabatic electron transfer. The redn. of YZ•, however, appears to proceed by an adiabatic process that may have hydrogen-atom transfer character.
- 168Siletsky, S. A.; Belevich, I.; Jasaitis, A.; Konstantinov, A. A.; Wikström, M.; Soulimane, T.; Verkhovsky, M. I. Time-Resolved Single-Turnover of Ba 3 Oxidase from Thermus Thermophilus. Biochim. Biophys. Acta, Bioenerg. 2007, 1767, 1383– 1392, DOI: 10.1016/j.bbabio.2007.09.010Google Scholar168https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2sXhtlyhsrbM&md5=e0de59b67f8de13e67e6186c1293aaf4Time-resolved single-turnover of ba3 oxidase from Thermus thermophilusSiletsky, Sergey A.; Belevich, Ilya; Jasaitis, Audrius; Konstantinov, Alexander A.; Wikstroem, Marten; Soulimane, Tewfik; Verkhovsky, Michael I.Biochimica et Biophysica Acta, Bioenergetics (2007), 1767 (12), 1383-1392CODEN: BBBEB4; ISSN:0005-2728. (Elsevier Ltd.)The kinetics of the oxidn. of fully-reduced ba3 cytochrome c oxidase from Thermus thermophilus by oxygen were followed by time-resolved optical spectroscopy and electrometry. Four catalytic intermediates were resolved during this reaction. The chem. nature and the spectral properties of three intermediates (compds. A, P and O) reproduce the general features of aa3-type oxidases. However, the F intermediate in ba3 oxidase has a spectrum identical to the P state. This indicates that the proton taken up during the P → F transition does not reside in the binuclear site but is rather transferred to the covalently cross-linked tyrosine near that site. The total charge translocation assocd. with the F → O transition in ba3 oxidase is close to that obsd. during the F → O transition in the aa3 oxidases. However, the PR → F transition is characterized by significantly lower charge translocation, which probably reflects the overall lower measured pumping efficiency during multiple turnovers.
- 169von Ballmoos, C.; Ädelroth, P.; Gennis, R. B.; Brzezinski, P. Proton Transfer in Ba 3 Cytochrome C Oxidase from Thermus Thermophilus. Biochim. Biophys. Acta, Bioenerg. 2012, 1817, 650– 657, DOI: 10.1016/j.bbabio.2011.11.015Google Scholar169https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC38XjtlOmtrY%253D&md5=65ece85e73c2ce34ece73dc22bf34f64Proton transfer in ba3 cytochrome c oxidase from Thermus thermophilusvon Ballmoos, Christoph; Aedelroth, Pia; Gennis, Robert B.; Brzezinski, PeterBiochimica et Biophysica Acta, Bioenergetics (2012), 1817 (4), 650-657CODEN: BBBEB4; ISSN:0005-2728. (Elsevier B. V.)A review. The respiratory heme-copper oxidases catalyze redn. of O2 to H2O, linking this process to transmembrane proton pumping. These oxidases have been classified according to the architecture, location and no. of proton pathways. Most structural and functional studies to date have been performed on the A-class oxidases, which includes those that are found in the inner mitochondrial membrane and bacteria such as Rhodobacter sphaeroides and Paracoccus denitrificans (aa3-type oxidases in these bacteria). These oxidases pump protons with a stoichiometry of one proton per electron transferred to the catalytic site. The bacterial A-class oxidases use two proton pathways (denoted by letters D and K, resp.), for the transfer of protons to the catalytic site, and protons that are pumped across the membrane. The B-type oxidases such as, for example, the ba3 oxidase from Thermus thermophilus, pump protons with a lower stoichiometry of 0.5 H+/electron and use only one proton pathway for the transfer of all protons. This pathway overlaps in space with the K pathway in the A class oxidases without showing any sequence homol. though. Here, we review the functional properties of the A- and the B-class ba3 oxidases with a focus on mechanisms of proton transfer and pumping. This article is part of a Special Issue entitled: Respiratory Oxidases.
- 170Andersson, R. Serial Femtosecond Crystallography Structure of Cytochrome C Oxidase at Room Temperature. Sci. Rep. 2017, 7, 4518, DOI: 10.1038/s41598-017-04817-zGoogle Scholar170https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A280%3ADC%252BC1cjkt1CktA%253D%253D&md5=89c56ec1051fdd56ad9fe4d7e4d634c2Serial femtosecond crystallography structure of cytochrome c oxidase at room temperatureAndersson Rebecka; Safari Cecilia; Dods Robert; Bath Petra; Dunevall Elin; Bosman Robert; Neutze Richard; Branden Gisela; Nango Eriko; Tanaka Rie; Yamashita Ayumi; Iwata So; Nango Eriko; Iwata So; Nakane Takanori; Nureki Osamu; Tono Kensuke; Joti YasumasaScientific reports (2017), 7 (1), 4518 ISSN:.Cytochrome c oxidase catalyses the reduction of molecular oxygen to water while the energy released in this process is used to pump protons across a biological membrane. Although an extremely well-studied biological system, the molecular mechanism of proton pumping by cytochrome c oxidase is still not understood. Here we report a method to produce large quantities of highly diffracting microcrystals of ba 3-type cytochrome c oxidase from Thermus thermophilus suitable for serial femtosecond crystallography. The room-temperature structure of cytochrome c oxidase is solved to 2.3 ÅA resolution from data collected at an X-ray Free Electron Laser. We find overall agreement with earlier X-ray structures solved from diffraction data collected at cryogenic temperature. Previous structures solved from synchrotron radiation data, however, have shown conflicting results regarding the identity of the active-site ligand. Our room-temperature structure, which is free from the effects of radiation damage, reveals that a single-oxygen species in the form of a water molecule or hydroxide ion is bound in the active site. Structural differences between the ba 3-type and aa 3-type cytochrome c oxidases around the proton-loading site are also described.
- 171Hirata, K. Determination of Damage-Free Crystal Structure of an X-Ray-Sensitive Protein Using an Xfel. Nat. Nat. Methods 2014, 11, 734– 736, DOI: 10.1038/nmeth.2962Google Scholar171https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2cXnslGqtrg%253D&md5=6bf5611134041976ef8c1e69302664cbDetermination of damage-free crystal structure of an X-ray-sensitive protein using an XFELHirata, Kunio; Shinzawa-Itoh, Kyoko; Yano, Naomine; Takemura, Shuhei; Kato, Koji; Hatanaka, Miki; Muramoto, Kazumasa; Kawahara, Takako; Tsukihara, Tomitake; Yamashita, Eiki; Tono, Kensuke; Ueno, Go; Hikima, Takaaki; Murakami, Hironori; Inubushi, Yuichi; Yabashi, Makina; Ishikawa, Tetsuya; Yamamoto, Masaki; Ogura, Takashi; Sugimoto, Hiroshi; Shen, Jian-Ren; Yoshikawa, Shinya; Ago, HideoNature Methods (2014), 11 (7), 734-736CODEN: NMAEA3; ISSN:1548-7091. (Nature Publishing Group)We report a method of femtosecond crystallog. for solving radiation damage-free crystal structures of large proteins at sub-angstrom spatial resoln., using a large single crystal and the femtosecond pulses of an X-ray free-electron laser (XFEL). We demonstrated the performance of the method by detg. a 1.9-Å radiation damage-free structure of bovine cytochrome c oxidase, a large (420-kDa), highly radiation-sensitive membrane protein.
- 172Bloch, D.; Belevich, I.; Jasaitis, A.; Ribacka, C.; Puustinen, A.; Verkhovsky, M. I.; Wikström, M. The Catalytic Cycle of Cytochrome C Oxidase Is Not the Sum of Its Two Halves. Proc. Natl. Acad. Sci. U. S. A. 2004, 101, 529– 533, DOI: 10.1073/pnas.0306036101Google Scholar172https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2cXmsFGnsg%253D%253D&md5=e374dd61b273639495a1a01c39812d0cThe catalytic cycle of cytochrome c oxidase is not the sum of its two halvesBloch, Dmitry; Belevich, Ilya; Jasaitis, Audrius; Ribacka, Camilla; Puustinen, Anne; Verkhovsky, Michael I.; Wikstroem, MartenProceedings of the National Academy of Sciences of the United States of America (2004), 101 (2), 529-533CODEN: PNASA6; ISSN:0027-8424. (National Academy of Sciences)Membrane-bound cytochrome c oxidase catalyzes cell respiration in aerobic organisms and is a primary energy transducer in biol. The two halves of the catalytic cycle may be studied sep.; in an oxidative phase, the enzyme is oxidized by O2, and in a reductive phase, the oxidized enzyme is reduced before binding the next O2 mol. Here we show by time-resolved membrane potential and pH measurements with cytochrome oxidase liposomes that with both phases in succession, two protons are translocated during each phase, one during each individual electron transfer step. However, when the reductive phase is not immediately preceded by oxidn., it follows a different reaction pathway no longer coupled to proton pumping. Metastable states with altered redox properties of the metal centers are accessed during turnover and relax when external electron donors are exhausted but recover after enzyme redn. and reoxidn. by O2. The efficiency of ATP synthesis might be regulated by switching between the two catalytic pathways.
- 173Verkhovsky, M. I.; Jasaitis, A.; Verkhovskaya, M. L.; Morgan, J. E.; Wikström, M. Proton Translocation by Cytochrome C Oxidase. Nature 1999, 400, 480– 483, DOI: 10.1038/22813Google Scholar173https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaK1MXltVGqtb0%253D&md5=d40507a3ca009653caa22723f68545e2Proton translocation by cytochrome c oxidaseVerkhovsky, Michael I.; Jasaitis, Audrius; Verkhovskaya, Marina L.; Morgan, Joel E.; Wikstrom, MartenNature (London) (1999), 400 (6743), 480-483CODEN: NATUAS; ISSN:0028-0836. (Macmillan Magazines)Cell respiration in mitochondria and some bacteria is catalyzed by cytochrome c oxidase, which reduces O2 to water, coupled with translocation of four protons across the mitochondrial or bacterial membrane. The enzyme's catalytic cycle consists of a reductive phase, in which the oxidized enzyme receives electrons from cytochrome c, and an oxidative phase, in which the reduced enzyme is oxidized by O2. Previous studies indicated that proton translocation is coupled energetically only to the oxidative phase, but this has been challenged. Here, with the purified enzyme inlaid in liposomes, we report time-resolved measurements of membrane potential, which show that half of the elec. charges due to proton-pumping actually cross the membrane during redn. after a preceding oxidative phase. PH measurements confirm that proton translocation also occurs during redn., but only when immediately preceded by an oxidative phase. We conclude that all the energy for proton translocation is conserved in the enzyme during its oxidn. by O2. One half of it is utilized for proton-pumping during oxidn., but the other half is unlatched for this purpose only during re-redn. of the enzyme.
- 174Han, S.; Takahashi, S.; Rousseau, D. L. Time Dependence of the Catalytic Intermediates in Cytochromec Oxidase. J. Biol. Chem. 2000, 275, 1910– 1919, DOI: 10.1074/jbc.275.3.1910Google ScholarThere is no corresponding record for this reference.
- 175Ishigami, I.; Hikita, M.; Egawa, T.; Yeh, S.-R.; Rousseau, D. L. Proton Translocation in Cytochrome C Oxidase: Insights from Proton Exchange Kinetics and Vibrational Spectroscopy. Biochim. Biophys. Acta, Bioenerg. 2015, 1847, 98– 108, DOI: 10.1016/j.bbabio.2014.09.008Google Scholar175https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2cXhs1Kltb%252FN&md5=e8897a6d19a5bb9c312f3ba7a62a615bProton translocation in cytochrome c oxidase: Insights from proton exchange kinetics and vibrational spectroscopyIshigami, Izumi; Hikita, Masahide; Egawa, Tsuyoshi; Yeh, Syun-Ru; Rousseau, Denis L.Biochimica et Biophysica Acta, Bioenergetics (2015), 1847 (1), 98-108CODEN: BBBEB4; ISSN:0005-2728. (Elsevier B. V.)A review. Cytochrome c oxidase is the terminal enzyme in the electron transfer chain. It reduces O2 to H2O and harnesses the released energy to translocate protons across the inner mitochondrial membrane. The mechanism by which the oxygen chem. is coupled to proton translocation is not yet resolved owing to the difficulty of monitoring dynamic proton transfer events. Here, the authors summarize several postulated mechanisms for proton translocation, which have been supported by a variety of vibrational spectroscopic studies. The authors recently proposed a proton translocation model involving proton accessibility to the regions near the propionate groups of the heme a and heme a3 redox centers of the enzyme based by H/D exchange Raman scattering studies. To advance the understanding of this model and to refine the proton accessibility to the hemes, the H/D exchange dependence of the heme propionate group vibrational modes on temp. and pH has been measured. The H/D exchange detected at the propionate groups of heme a3 takes place within a few seconds under all conditions. In contrast, that detected at the heme a propionates occurs in the oxidized but not the reduced enzyme and the H/D exchange is pH-dependent with a pKa of ∼8.0 (faster at high pH). Anal. of the thermodn. parameters has revealed that, as the pH is varied, entropy/enthalpy compensation holds the free energy of activation in a narrow range. The redox dependence of the possible proton pathways to the heme groups is discussed.
- 176Wikström, M.; Verkhovsky, M. I. Towards the Mechanism of Proton Pumping by the Haem-Copper Oxidases. Biochim. Biophys. Acta, Bioenerg. 2006, 1757, 1047– 1051, DOI: 10.1016/j.bbabio.2006.01.010Google Scholar176https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A280%3ADC%252BD28rnvVWmuw%253D%253D&md5=763734333a48bac285437f7d5ab0bab4Towards the mechanism of proton pumping by the haem-copper oxidasesWikstrom Marten; Verkhovsky Michael IBiochimica et biophysica acta (2006), 1757 (8), 1047-51 ISSN:0006-3002.The haem-copper oxidases comprise a large family of enzymes that is widespread among aerobic organisms. These remarkable membrane-bound proteins catalyse the respiratory reduction of dioxygen to water, and conserve free energy from this reaction by operating as proton pumps. The mechanism of redox-dependent proton translocation has been elusive despite the availability of high resolution crystal structures from several oxidases. Here, we discuss some recent as well as some older results that may shed light on this mechanism. We conclude that proton-pumping is initiated by vectorial proton transfer from a conserved glutamic acid (Glu242 in the bovine enzyme) to a proton acceptor above the haem groups, and that this primary event is mechanistically coupled to electron transfer from haem a to the binuclear haem a3/CuB centre. Subsequently, Glu242 is reprotonated from the negatively charged side of the membrane. Next this proton is transferred to the binuclear site to complete the chemistry, Glu242 is reprotonated once more, and the "prepumped" proton is ejected on the opposite side of the membrane. The different kinetics of electron-coupled proton transfer in different steps of the catalytic cycle may be related to differences in the driving force due to different Em values of the electron acceptor in the binuclear site.
- 177Gorbikova, E. A.; Vuorilehto, K.; Wikström, M.; Verkhovsky, M. I. Redox Titration of All Electron Carriers of Cytochrome C Oxidase by Fourier Transform Infrared Spectroscopy. Biochemistry 2006, 45, 5641– 5649, DOI: 10.1021/bi060257vGoogle Scholar177https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD28Xjt1KmsLw%253D&md5=184a3677dfdcbb27d8c2a418a67236ceRedox Titration of All Electron Carriers of Cytochrome c Oxidase by Fourier Transform Infrared SpectroscopyGorbikova, Elena A.; Vuorilehto, Kai; Wikstroem, Marten; Verkhovsky, Michael I.Biochemistry (2006), 45 (17), 5641-5649CODEN: BICHAW; ISSN:0006-2960. (American Chemical Society)Electrochem. redox titrns. of cytochrome c oxidase from Paracoccus denitrificans were performed by attenuated total reflectance Fourier transform IR (ATR-FTIR) spectroscopy. The majority of the differential IR absorption features may be divided into four groups, which correlate with the redox transitions of the four redox centers of the enzyme. IR spectroscopy has the advantage of allowing one to measure independent alterations in redox centers, which are not well sepd., or even obsd., by other spectroscopic techniques. We found 12 IR bands that titrated with the highest obsd. midpoint redox potential (Em = 412 mV at pH 6.5) and which had a pH dependence of 52 mV per pH unit in the alk. region. These bands were assigned to be linked to the CuB center. We assigned bands to the CuA center that showed a pH-independent Em of 250 mV. Two other groups of IR differential bands reflected redox transitions of the two heme groups and showed a more complex behavior. Each of them included two parts, corresponding to high- and low-potential redox transitions. For the bands representing heme a, the ratio of high- to low-potential components was ca. 3:2; for heme a3 this ratio was ca. 2:3. Taking into account the redox interactions between the hemes, these ratios yielded a difference in Em of 9 mV between the hemes (359 mV for heme a; 350 mV for heme a3 at pH 8.0). The extent of the redox interaction between the hemes (-115 mV at pH 8.0) was found to be pH-dependent. The pH dependence of the Em values for the two hemes was the same and about two times smaller than the theor. one, suggesting that an acid/base group binds a proton upon redn. of either heme. The applied approach allowed assignment of IR bands in each of the four groups to vibrations of the hemes, ligands of the redox centers, amino acid residues, and/or protein backbone. For example, the well-known band shift at 1737/1746 cm-1 corresponding to the protonated glutamic acid E278 correlated with oxidoredn. of heme a.
- 178Belevich, I.; Bloch, D. A.; Belevich, N.; Wikström, M.; Verkhovsky, M. I. Exploring the Proton Pump Mechanism of Cytochrome C Oxidase in Real Time. Proc. Natl. Acad. Sci. U. S. A. 2007, 104, 2685– 2690, DOI: 10.1073/pnas.0608794104Google Scholar178https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2sXisVWru7g%253D&md5=5e6cb01e6542a50a4a286e741a59bab6Exploring the proton pump mechanism of cytochrome c oxidase in real timeBelevich, Ilya; Bloch, Dmitry A.; Belevich, Nikolai; Wikstrom, Marten; Verkhovsky, Michael I.Proceedings of the National Academy of Sciences of the United States of America (2007), 104 (8), 2685-2690CODEN: PNASA6; ISSN:0027-8424. (National Academy of Sciences)Cytochrome c oxidase catalyzes most of the biol. O2 consumption on Earth, a process responsible for energy supply in aerobic organisms. This remarkable membrane-bound enzyme also converts free energy from O2 redn. to an electrochem. proton gradient by functioning as a redox-linked proton pump. Although the structures of several oxidases are known, the mol. mechanism of redox-linked proton translocation has remained elusive. Here, correlated internal electron and proton transfer reactions were tracked in real time by spectroscopic and electrometric techniques after laser-activated electron injection into the oxidized enzyme. The obsd. kinetics established the long-sought reaction sequence of the proton pump mechanism and described some of its thermodn. properties. The 10-μs electron transfer to heme a raised the pKa of a "pump site," which was loaded by a proton from the inside of the membrane in 150 μs. This loading increased the redox potentials of both hemes a and a3, which allowed electron equilibration between them at the same rate. Then, in 0.8 ms, another proton was transferred from the inside to the heme a3/CuB center, and the electron was transferred to CuB. Finally, in 2.6 ms, the preloaded proton was released from the pump site to the opposite side of the membrane.
- 179Kaila, V. R.; Johansson, M. P.; Sundholm, D.; Laakkonen, L.; Wikström, M. The Chemistry of the Cu B Site in Cytochrome C Oxidase and the Importance of Its Unique His–Tyr Bond. Biochim. Biophys. Acta, Bioenerg. 2009, 1787, 221– 233, DOI: 10.1016/j.bbabio.2009.01.002Google Scholar179https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD1MXivVeltr8%253D&md5=893079f2442a26c89bf3724b1f600a34The chemistry of the CuB site in cytochrome c oxidase and the importance of its unique His-Tyr bondKaila, Ville R. I.; Johansson, Mikael P.; Sundholm, Dage; Laakkonen, Liisa; Wikstrom, MartenBiochimica et Biophysica Acta, Bioenergetics (2009), 1787 (4), 221-233CODEN: BBBEB4; ISSN:0005-2728. (Elsevier B. V.)The CuB metal center is at the core of the active site of the heme-copper oxidases, comprising a copper atom ligating three histidine residues one of which is covalently bonded to a tyrosine residue. Using quantum chem. methodol., we have studied the CuB site in several redox and ligand states proposed to be intermediates of the catalytic cycle. The importance of the His-Tyr crosslink was investigated by comparing energetics, charge, and spin distributions between systems with and without the crosslink. The His-Tyr bond was shown to decrease the proton affinity and increase the electron affinity of both Tyr-244 and the copper. A previously unnoticed internal electronic equil. between the copper atom and the tyrosine was obsd., which seems to be coupled to the unique structure of the system. In certain states the copper and Tyr-244 compete for the unpaired electron, the localization of which is detd. by the oxygenous ligand of the copper. This electronic equil. was found to be sensitive to the presence of a pos. charge 10 Å away from the center, simulating the effect of Lys-319 in the K-pathway of proton transfer. The combined results provide an explanation for why the heme-copper oxidases need two pathways of proton uptake, and why the K-pathway is active only in the second half of the reaction cycle.
- 180Blomberg, M. R. Mechanism of Oxygen Reduction in Cytochrome C Oxidase and the Role of the Active Site Tyrosine. Biochemistry 2016, 55, 489– 500, DOI: 10.1021/acs.biochem.5b01205Google Scholar180https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2MXitVCrsbnF&md5=ea2165942763e22c35e8eb40f39907cdMechanism of Oxygen Reduction in Cytochrome c Oxidase and the Role of the Active Site TyrosineBlomberg, Margareta R. A.Biochemistry (2016), 55 (3), 489-500CODEN: BICHAW; ISSN:0006-2960. (American Chemical Society)Cytochrome c oxidase, the terminal enzyme in the respiratory chain, reduces mol. oxygen to water and stores the released energy through electrogenic chem. and proton pumping across the membrane. Apart from the heme-copper binuclear center, there is a conserved tyrosine residue in the active site (BNC). The tyrosine delivers both an electron and a proton during the O-O bond cleavage step, forming a tyrosyl radical. The catalytic cycle then occurs in four redn. steps, each taking up one proton for the chem. (water formation) and one proton to be pumped. It is here suggested that in three of the redn. steps the chem. proton enters the center of the BNC, leaving the tyrosine unprotonated with radical character. The reproprotonation of the tyrosine occurs first in the final redn. step before binding the next oxygen mol. It is also suggested that this redn. mechanism and the presence of the tyrosine are essential for the proton pumping. D. functional theory calcns. on large cluster models of the active site show that only the intermediates with the proton in the center of the BNC and with an unprotonated tyrosyl radical have a high electron affinity of similar size as the electron donor, which is essential for the ability to take up two protons per electron and thus for the proton pumping. This type of redn. mechanism is also the only one that gives a free energy profile in accordance with exptl. observations for the amt. of proton pumping in the working enzyme.
- 181Blomberg, M. R.; Siegbahn, P. E. Protonation of the Binuclear Active Site in Cytochrome C Oxidase Decreases the Reduction Potential of Cub. Biochim. Biophys. Acta, Bioenerg. 2015, 1847, 1173– 1180, DOI: 10.1016/j.bbabio.2015.06.008Google Scholar181https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2MXhtVWqs7%252FI&md5=69cce2260ed3ec3484305c09ef0529b9Protonation of the binuclear active site in cytochrome c oxidase decreases the reduction potential of CuBBlomberg, Margareta R. A.; Siegbahn, Per E. M.Biochimica et Biophysica Acta, Bioenergetics (2015), 1847 (10), 1173-1180CODEN: BBBEB4; ISSN:0005-2728. (Elsevier B. V.)One of the remaining mysteries regarding the respiratory enzyme cytochrome c oxidase is how proton pumping can occur in all redn. steps in spite of the low redn. potentials obsd. in equil. titrn. expts. for two of the active site cofactors, CuB(II) and Fea3(III). It has been speculated that, at least the copper cofactor can acquire two different states, one metastable activated state occurring during enzyme turnover, and one relaxed state with lower energy, reached only when the supply of electrons stops. The activated state should have a transiently increased CuB(II) redn. potential, allowing proton pumping. The relaxed state should have a lower redn. potential, as measured in the titrn. expts. However, the structures of these two states are not known. Quantum mech. calcns. show that the proton coupled redn. potential for CuB is inherently high in the active site as it appears after reaction with oxygen, which explains the obsd. proton pumping. It is suggested here that, when the flow of electrons ceases, a relaxed resting state is formed by the uptake of one extra proton, on top of the charge compensating protons delivered in each redn. step. The extra proton in the active site decreases the proton coupled redn. potential for CuB by almost half a volt, leading to agreement with titrn. expts. Furthermore, the structure for the resting state with an extra proton has a hydroxo-bridge between CuB(II) and Fea3(III), yielding a magnetic coupling that can explain the exptl. obsd. EPR silence.
- 182Wikström, M. Identification of the Electron Transfers in Cytochrome Oxidase That Are Coupled to Proton-Pumping. Nature 1989, 338, 776– 778, DOI: 10.1038/338776a0Google Scholar182https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaL1MXktVehsLk%253D&md5=750653864e65c0e73805a4cecb8d097eIdentification of the electron transfers in cytochrome oxidase that are coupled to proton-pumpingWikstrom, MartenNature (London, United Kingdom) (1989), 338 (6218), 776-8CODEN: NATUAS; ISSN:0028-0836.The effects of protonmotive force and membrane potential on 2 equil. involving intermediates of the bimetallic center of cytochrome oxidase at different levels of O2 redn. are reported. Only 2 of the electron transfers, to the peroxy and oxyferryl intermediates of the bimetallic center, are linked to proton translocation, a finding which strongly constrains candidate mechanisms for proton-pumping.
- 183Wikström, M.; Krab, K. Proton-Pumping Cytochrome c Oxidase. Biochim. Biophys. Acta, Rev. Bioenerg. 1979, 549, 177– 222, DOI: 10.1016/0304-4173(79)90014-4Google Scholar183https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A280%3ADyaL3c%252FgtVGjuw%253D%253D&md5=fad1c52da0bb38ae91a4bf0f23f156efProton-pumping cytochrome c oxidaseWikstrom M; Krab KBiochimica et biophysica acta (1979), 549 (2), 177-22 ISSN:0006-3002.There is no expanded citation for this reference.
- 184Morgan, J. E.; Verkhovsky, M. I.; Wikström, M. The Histidine Cycle: A New Model for Proton Translocation in the Respiratory Heme-Copper Oxidases. J. Bioenerg. Biomembr. 1994, 26, 599– 608, DOI: 10.1007/BF00831534Google ScholarThere is no corresponding record for this reference.
- 185Siletsky, S. A.; Konstantinov, A. A. Cytochrome C Oxidase: Charge Translocation Coupled to Single-Electron Partial Steps of the Catalytic Cycle. Biochim. Biophys. Acta, Bioenerg. 2012, 1817, 476– 488, DOI: 10.1016/j.bbabio.2011.08.003Google Scholar185https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC38XjtlOkt78%253D&md5=07fd578deaf0c51299ce8145e1f8e914Cytochrome c oxidase: Charge translocation coupled to single-electron partial steps of the catalytic cycleSiletsky, Sergey A.; Konstantinov, Alexander A.Biochimica et Biophysica Acta, Bioenergetics (2012), 1817 (4), 476-488CODEN: BBBEB4; ISSN:0005-2728. (Elsevier B. V.)A review. The authors present a survey of time-resolved studies of charge translocation by cytochrome c oxidase coupled to transfer of the 1st, 2nd, 3rd, and 4th electrons in the catalytic cycle. Single-electron photoredn. expts. carried out with the A-class cytochrome c oxidases of the aa3 type from mitochondria, Rhodobacter sphaeroides, and Paracoccus denitrificans as well as with the ba3-type oxidase from Thermus thermophilus indicate that the protonmotive mechanisms, although similar, may not be identical for different partial steps in the same enzyme species, as well as for the same single-electron transition in different oxidases. The pattern of charge translocation coupled to transfer of a single electron in the A-class oxidases confirms major predictions of the original model of proton pumping by cytochrome oxidase. The intermediates and partial electrogenic steps obsd. in the single-electron photoredn. expts. may be very different from those obsd. during oxidn. of the fully reduced oxidase by O2 in the "flow-flash" studies.
- 186Popović, D. M.; Stuchebrukhov, A. A. Proton Pumping Mechanism and Catalytic Cycle of Cytochrome C Oxidase: Coulomb Pump Model with Kinetic Gating. FEBS Lett. 2004, 566, 126– 130, DOI: 10.1016/j.febslet.2004.04.016Google ScholarThere is no corresponding record for this reference.
- 187Siletsky, S. A.; Pawate, A. S.; Weiss, K.; Gennis, R. B.; Konstantinov, A. A. Transmembrane Charge Separation During the Ferryl-Oxo→ Oxidized Transition in a Nonpumping Mutant of Cytochrome C Oxidase. J. Biol. Chem. 2004, 279, 52558– 52565, DOI: 10.1074/jbc.M407549200Google ScholarThere is no corresponding record for this reference.
- 188Wikström, M.; Bogachev, A.; Finel, M.; Morgan, J. E.; Puustinen, A.; Raitio, M.; Verkhovskaya, M.; Verkhovsky, M. I. Mechanism of Proton Translocation by the Respiratory Oxidases. The Histidine Cycle. Biochim. Biophys. Acta, Bioenerg. 1994, 1187, 106– 111, DOI: 10.1016/0005-2728(94)90093-0Google ScholarThere is no corresponding record for this reference.
- 189Quenneville, J.; Popović, D. M.; Stuchebrukhov, A. A. Redox-Dependent P K a of Cub Histidine Ligand in Cytochrome C Oxidase. J. Phys. Chem. B 2004, 108, 18383– 18389, DOI: 10.1021/jp0467797Google ScholarThere is no corresponding record for this reference.
- 190Wikström, M.; Verkhovsky, M. I. Mechanism and Energetics of Proton Translocation by the Respiratory Heme-Copper Oxidases. Biochim. Biophys. Acta, Bioenerg. 2007, 1767, 1200– 1214, DOI: 10.1016/j.bbabio.2007.06.008Google Scholar190https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A280%3ADC%252BD2srpslKisw%253D%253D&md5=5310d1397c7dfdc28dc23651f9619338Mechanism and energetics of proton translocation by the respiratory heme-copper oxidasesWikstrom Marten; Verkhovsky Michael IBiochimica et biophysica acta (2007), 1767 (10), 1200-14 ISSN:0006-3002.Recent time-resolved optical and electrometric experiments have provided a sequence of events for the proton-translocating mechanism of cytochrome c oxidase. These data also set limits for the mechanistic, kinetic, and thermodynamic parameters of the proton pump, which are analysed here in some detail. The analysis yields limit values for the pK of the "pump site", its modulation during the proton-pumping process, and suggests its identity in the structure. Special emphasis is made on side-reactions that may short-circuit the pump, and the means by which these may be avoided. We will also discuss the most prominent proton pumping mechanisms proposed to date in relation to these data.
- 191Kaila, V. R.; Sharma, V.; Wikström, M. The Identity of the Transient Proton Loading Site of the Proton-Pumping Mechanism of Cytochrome C Oxidase. Biochim. Biophys. Acta, Bioenerg. 2011, 1807, 80– 84, DOI: 10.1016/j.bbabio.2010.08.014Google Scholar191https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3cXhsVagurjP&md5=2d994f9d16ba437b6171143cd8e3021cThe identity of the transient proton loading site of the proton-pumping mechanism of cytochrome c oxidaseKaila, Ville R. I.; Sharma, Vivek; Wikstroem, MartenBiochimica et Biophysica Acta, Bioenergetics (2011), 1807 (1), 80-84CODEN: BBBEB4; ISSN:0005-2728. (Elsevier B. V.)Cellular respiration is driven by cytochrome c oxidase (CcO), which reduces oxygen to water and couples the released energy to proton pumping across the mitochondrial or bacterial membrane. Proton pumping in CcO involves proton transfer from the neg. charged side of the membrane to a transient proton-loading or pump site (PLS), before it is ejected to the opposite side. Although many details of the reaction mechanism are known, the exact location of the PLS has remained elusive. Here, results from combined classical mol. dynamics simulations and continuum electrostatic calcns. are reported, which show that the hydrogen-bonded system around the A-propionate of heme a3 dissocs. reversibly upon redn. of heme a. The dissocn. increases the pKa value of the propionate to a value above ∼ 9, making it accessible for redox-state dependent protonation. The redox state of heme a is of key importance in controlling proton leaks by polarizing the PLS both statically and dynamically. These findings suggest that the propionate region of heme a3 fulfills the criteria of the pump site in the proton translocation mechanism of CcO.
- 192Siegbahn, P. E.; Blomberg, M. R.; Blomberg, M. L. Theoretical Study of the Energetics of Proton Pumping and Oxygen Reduction in Cytochrome Oxidase. J. Phys. Chem. B 2003, 107, 10946– 10955, DOI: 10.1021/jp035486vGoogle ScholarThere is no corresponding record for this reference.
- 193Supekar, S.; Gamiz-Hernandez, A. P.; Kaila, V. R. I. A Protonated Water Cluster as a Transient Proton-Loading Site in Cytochrome C Oxidase. Angew. Chem., Int. Ed. 2016, 55, 11940– 11944, DOI: 10.1002/anie.201603606Google Scholar193https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC28XhtlOrtb%252FO&md5=3da43f98bda023b2629917e7b558b94cA protonated water cluster as a transient proton-loading site in cytochrome c oxidaseSupekar, Shreyas; Gamiz-Hernandez, Ana P.; Kaila, Ville R. I.Angewandte Chemie, International Edition (2016), 55 (39), 11940-11944CODEN: ACIEF5; ISSN:1433-7851. (Wiley-VCH Verlag GmbH & Co. KGaA)Cytochrome c oxidase (CcO) is a redox-driven proton pump that powers aerobic respiratory chains. Here, the authors show by multi-scale mol. dynamics simulations that a protonated water cluster near the active site is likely to serve as the transient proton-loading site (PLS) that stores a proton during the pumping process. The pKa of this water cluster was sensitive to the redox states of the enzyme, showing distinct similarities to other energy-converting proton pumps.
- 194Lu, J.; Gunner, M. R. Characterizing the Proton Loading Site in Cytochrome C Oxidase. Proc. Natl. Acad. Sci. U. S. A. 2014, 111, 12414– 12419, DOI: 10.1073/pnas.1407187111Google Scholar194https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2cXhtlCju7bI&md5=509158a2ffbb497f0d7d3dfdeb036ce7Characterizing the proton loading site in cytochrome c oxidaseLu, Jianxun; Gunner, M. R.Proceedings of the National Academy of Sciences of the United States of America (2014), 111 (34), 12414-12419CODEN: PNASA6; ISSN:0027-8424. (National Academy of Sciences)Cytochrome c oxidase (CcO) uses the energy released by redn. of O2 to H2O to drive 8 charges from the high pH to low pH side of the membrane, increasing the electrochem. gradient. Four electrons and protons are used for chem., while 4 more protons are pumped. Proton pumping requires that residues on a pathway change proton affinity through the reaction cycle to load and then release protons. Here, the protonation states of all residues in CcO were detd. in MultiConformational Continuum Electrostatics simulations with the protonation and redox states of heme a, a3, CuB, Tyr-288, and Glu-286 used to define the catalytic cycle. One proton was found to be loaded and released from residues identified as the proton loading site (PLS) on the P-side of the protein in each of the 4 CcO redox states. Thus, the same proton pumping mechanism can be used each time CcO is reduced. Calcns. with structures of Rhodobacter sphaeroides, Paracoccus denitrificans, and bovine mitochondrial CcO derived by crystallog. and mol. dynamics showed that the PLS functions similarly in different CcO species. The PLS is a cluster rather than a single residue, as different structures showed 1-4 residues loaded and released protons. However, the proton affinity of the heme a3 propionic acids primarily dets. the no. of protons loaded into the PLS; if their proton affinity is too low, less than one proton is loaded.
- 195Ädelroth, P.; Gennis, R. B.; Brzezinski, P. Role of the Pathway through K (I-362) in Proton Transfer in Cytochrome C Oxidase from R. Biochemistry 1998, 37, 2470– 2476, DOI: 10.1021/bi971813bGoogle ScholarThere is no corresponding record for this reference.
- 196Lepp, H.; Salomonsson, L.; Zhu, J.-P.; Gennis, R. B.; Brzezinski, P. Impaired Proton Pumping in Cytochrome C Oxidase Upon Structural Alteration of the D Pathway. Biochim. Biophys. Acta, Bioenerg. 2008, 1777, 897– 903, DOI: 10.1016/j.bbabio.2008.04.013Google Scholar196https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD1cXnsFCmurg%253D&md5=ef108d05dd0daa70a036d6461cd92ccfImpaired proton pumping in cytochrome c oxidase upon structural alteration of the D pathwayLepp, Hakan; Salomonsson, Lina; Zhu, Jia-Peng; Gennis, Robert B.; Brzezinski, PeterBiochimica et Biophysica Acta, Bioenergetics (2008), 1777 (7-8), 897-903CODEN: BBBEB4; ISSN:0005-2728. (Elsevier Ltd.)Cytochrome c oxidase is a membrane-bound enzyme, which catalyzes the one-electron oxidn. of four mols. of cytochrome c and the four-electron redn. of O2 to water. Electron transfer through the enzyme is coupled to proton pumping across the membrane. Protons that are pumped as well as those that are used for O2 redn. are transferred though a specific intraprotein (D) pathway. Results from earlier studies have shown that replacement of residue Asn139 by an Asp, at the beginning of the D pathway, results in blocking proton pumping without slowing uptake of substrate protons used for O2 redn. Furthermore, introduction of the acidic residue results in an increase of the apparent pK a of E286, an internal proton donor to the catalytic site, from 9.4 to ∼ 11. In this study we have investigated intramol. electron and proton transfer in a mutant cytochrome c oxidase in which a neutral residue, Thr, was introduced at the 139 site. The mutation results in uncoupling of proton pumping from O2 redn., but a decrease in the apparent pK a of E286 from 9.4 to 7.6. The data provide insights into the mechanism by which cytochrome c oxidase pumps protons and the structural elements involved in this process.
- 197Faxén, K.; Gilderson, G.; Ädelroth, P.; Brzezinski, P. A Mechanistic Principle for Proton Pumping by Cytochrome C Oxidase. Nature 2005, 437, 286, DOI: 10.1038/nature03921Google Scholar197https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2MXpslekur8%253D&md5=18276fd29508da07f7383b05c7e5e836A mechanistic principle for proton pumping by cytochrome c oxidaseFaxen, Kristina; Gilderson, Gwen; Aedelroth, Pia; Brzezinski, PeterNature (London, United Kingdom) (2005), 437 (7056), 286-289CODEN: NATUAS; ISSN:0028-0836. (Nature Publishing Group)In aerobic organisms, cellular respiration involves electron transfer to O2 through a series of membrane-bound protein complexes. The process maintains a transmembrane electrochem. proton gradient that is used, e.g., in the synthesis of ATP. In mitochondria and many bacteria, the last enzyme complex in the electron transfer chain is cytochrome c oxidase (I), which catalyzes the 4-electron redn. of O2 to H2O using electrons delivered by a water-sol. donor, cytochrome c. The electron transfer through I, accompanied by proton uptake to form H2O, drives the phys. movement (pumping) of 4 protons across the membrane per reduced O2 mol. So far, the mol. mechanism of such proton pumping driven by electron transfer has not been detd. in any biol. system. Here, the authors show that proton pumping in I is mechanistically coupled to proton transfer to O2 at the catalytic site, rather than to internal electron transfer. This scenario suggests a principle by which redox-driven proton pumps might operate and places considerable constraints on possible mol. mechanisms by which I translocates protons.
- 198Siegbahn, P. E.; Blomberg, M. R. Energy Diagrams and Mechanism for Proton Pumping in Cytochrome C Oxidase. Biochim. Biophys. Acta, Bioenerg. 2007, 1767, 1143– 1156, DOI: 10.1016/j.bbabio.2007.06.009Google Scholar198https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2sXpvFWmtLo%253D&md5=c96552aff3f2079eb8e5ccac1b363610Energy diagrams and mechanism for proton pumping in cytochrome c oxidaseSiegbahn, Per E. M.; Blomberg, Margareta R. A.Biochimica et Biophysica Acta, Bioenergetics (2007), 1767 (9), 1143-1156CODEN: BBBEB4; ISSN:0005-2728. (Elsevier Ltd.)The powerful technique of energy diagrams has been used to analyze the mechanism for proton pumping in cytochrome c oxidase. Energy levels and barriers are derived starting out from recent kinetic expts. for the O to E transition, and are then refined using general criteria and a few addnl. exptl. facts. Both allowed and non-allowed pathways were obtained in this way. A useful requirement was that the forward and backward rates should approach each other for the full membrane gradient. A key finding was that an electron on heme a (or the binuclear center) must have a significant lowering effect on the barrier for proton uptake, in order to prevent backflow from the pump-site to the N-side. While there is no structural gating in the present mechanism, there is thus an electronic gating provided by the electron on heme a. A quant. anal. of the energy levels in the diagrams, leads to propionate-A of heme a3 as the most likely position for the pump site, and the Glu-278 region as the place for the transition state for proton uptake. Variations of key redox potentials and pKa values during the pumping process were derived for comparison to expts.
- 199Brzezinski, P.; Larsson, G. Redox-Driven Proton Pumping by Heme-Copper Oxidases. Biochim. Biophys. Acta, Bioenerg. 2003, 1605, 1– 13, DOI: 10.1016/S0005-2728(03)00079-3Google Scholar199https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD3sXlvFyitrg%253D&md5=83a71d9902300cb13bc7fdc4afd0dd1dRedox-driven proton pumping by heme-copper oxidasesBrzezinski, Peter; Larsson, GiselaBiochimica et Biophysica Acta, Bioenergetics (2003), 1605 (1-3), 1-13CODEN: BBBEB4; ISSN:0005-2728. (Elsevier B.V.)A review. One of the key problems of mol. bioenergetics is the understanding of the function of redox-driven proton pumps on a mol. level. One such class of proton pumps are the heme-copper oxidases. These enzymes are integral membrane proteins in which proton translocation across the membrane is driven by electron transfer from a low-potential donor, such as, e.g. cytochrome c, to a high-potential acceptor, O2. Proton pumping is assocd. with distinct exergonic reaction steps that involve gradual redn. of oxygen to water. During the process of O2 redn., unprotonated high pKa proton acceptors are created at the catalytic site. Initially, these proton acceptors become protonated as a result of intramol. proton transfer from a residue(s) located in the membrane-spanning part of the enzyme, but removed from the catalytic site. This residue is then reprotonated from the bulk soln. In cytochrome c oxidase from Rhodobacter sphaeroides, the proton is initially transferred from a glutamate, E(I-286), which has an apparent pKa of 9.4. According to a recently published structure of the enzyme, the deprotonation of E(I-286) is likely to result in minor structural changes that propagate to protonatable groups on the proton output (pos.) side of the protein. We propose that in this way, the free energy available from the O2 redn. is conserved during the proton transfer. On the basis of the observation of these structural changes, a possible proton-pumping model is presented in this paper. Initially, the structural changes assocd. with deprotonation of E(I-286) result in the transfer of a proton to an acceptor for pumped protons from the input (neg.) side of the membrane. After reprotonation of E(I-286) this acceptor releases a proton to the output side of the membrane.
- 200Yang, S.; Cui, Q. Glu-286 Rotation and Water Wire Reorientation Are Unlikely the Gating Elements for Proton Pumping in Cytochrome C Oxidase. Biophys. J. 2011, 101, 61– 69, DOI: 10.1016/j.bpj.2011.05.004Google ScholarThere is no corresponding record for this reference.
- 201Kaila, V. R.; Verkhovsky, M. I.; Hummer, G.; Wikström, M. Glutamic Acid 242 Is a Valve in the Proton Pump of Cytochrome C Oxidase. Proc. Natl. Acad. Sci. U. S. A. 2008, 105, 6255– 6259, DOI: 10.1073/pnas.0800770105Google Scholar201https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD1cXlsFyht7w%253D&md5=fbde16bae5b9d046325e6d078f15f229Glutamic acid 242 is a valve in the proton pump of cytochrome c oxidaseKaila, Ville R. I.; Verkhovsky, Michael I.; Hummer, Gerhard; Wikstrom, MartenProceedings of the National Academy of Sciences of the United States of America (2008), 105 (17), 6255-6259CODEN: PNASA6; ISSN:0027-8424. (National Academy of Sciences)Aerobic life is based on a mol. machinery that utilizes O2 a as terminal electron sink. Membrane-bound cytochrome c oxidase (CcO) catalyzes the redn. of O2 to H2O in mitochondria and many bacteria. The energy released in this reaction is conserved by pumping protons across the mitochondrial or bacterial membrane, creating an electrochem. proton gradient that drives the prodn. of ATP. A crucial question is how the protons pumped by CcO are prevented from flowing backwards during the process. Here, the authors show by mol. dynamics simulations that the conserved Glu-242 near the active site of CcO undergoes a protonation state-dependent conformational change, which provides a valve in the pumping mechanism. The valve ensures that at any point in time, the proton pathway across the membrane is effectively discontinuous, thereby preventing thermodynamically favorable proton back-leakage while maintaining an overall high efficiency of proton translocation. Suppression of proton leakage is particularly important in mitochondria under physiol. conditions, where prodn. of ATP takes place in the presence of a high electrochem. proton gradient.
- 202Pawate, A. S.; Morgan, J.; Namslauer, A.; Mills, D.; Brzezinski, P.; Ferguson-Miller, S.; Gennis, R. B. A Mutation in Subunit I of Cytochrome Oxidase from Rhodobacter Sphaeroides Results in an Increase in Steady-State Activity but Completely Eliminates Proton Pumping. Biochemistry 2002, 41, 13417– 13423, DOI: 10.1021/bi026582+Google Scholar202https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD38Xnslamt7w%253D&md5=7c07b833f6a4c1ff3f5ad0293391af70A Mutation in Subunit I of Cytochrome Oxidase from Rhodobacter sphaeroides Results in an Increase in Steady-State Activity but Completely Eliminates Proton PumpingPawate, Ashtamurthy S.; Morgan, Joel; Namslauer, Andreas; Mills, Denise; Brzezinski, Peter; Ferguson-Miller, Shelagh; Gennis, Robert B.Biochemistry (2002), 41 (45), 13417-13423CODEN: BICHAW; ISSN:0006-2960. (American Chemical Society)The heme-copper oxidases convert the free energy liberated in the redn. of O2 to water into a transmembrane proton electrochem. potential (protonmotive force). One of the essential structural elements of the enzyme is the D-channel, which is thought to be the input pathway, both for protons which go to form H2O ("chem. protons") and for protons that get translocated across the lipid membrane ("pumped protons"). The D-channel contains a chain of water mols. extending about 25 Å from an aspartic acid (D132 in the Rhodobacter sphaeroides oxidase) near the cytoplasmic ("inside") enzyme surface to a glutamic acid (E286) in the protein interior. Mutations in which either of these acidic residues is replaced by their corresponding amides (D132N or E286Q) result in severe inhibition of enzyme activity. In the current work, an asparagine located in the D-channel has been replaced by the corresponding acid (N139 to D; N98 in bovine enzyme) with dramatic consequences. The N139D mutation not only completely eliminates proton pumping but, at the same time, confers a substantial increase (150-300%) in the steady-state cytochrome oxidase activity. The N139D mutant of the R. sphaeroides oxidase was further characterized by examg. the rates of individual steps in the catalytic cycle. Under anaerobic conditions, the rate of redn. of heme a3 in the fully oxidized enzyme, prior to the reaction with O2, is identical to that of the wild-type oxidase and is not accelerated. However, the rate of reaction of the fully reduced enzyme with O2 is accelerated by the N139D mutation, as shown by a more rapid F → O transition. Whereas the rates of formation and decay of the oxygenated intermediates are altered, the nature of the oxygenated intermediates is not perturbed by the N139D mutation.
- 203Vakkasoglu, A. S.; Morgan, J. E.; Han, D.; Pawate, A. S.; Gennis, R. B. Mutations Which Decouple the Proton Pump of the Cytochrome C Oxidase from Rhodobacter Sphaeroides Perturb the Environment of Glutamate 286. FEBS Lett. 2006, 580, 4613– 4617, DOI: 10.1016/j.febslet.2006.07.036Google ScholarThere is no corresponding record for this reference.
- 204Johansson, A.-L.; Carlsson, J.; Högbom, M.; Hosler, J. P.; Gennis, R. B.; Brzezinski, P. Proton Uptake and P K a Changes in the Uncoupled Asn139cys Variant of Cytochrome C Oxidase. Biochemistry 2013, 52, 827– 836, DOI: 10.1021/bi301597aGoogle ScholarThere is no corresponding record for this reference.
- 205Han, D.; Namslauer, A.; Pawate, A.; Morgan, J. E.; Nagy, S.; Vakkasoglu, A. S.; Brzezinski, P.; Gennis, R. B. Replacing Asn207 by Aspartate at the Neck of the D Channel in the Aa3-Type Cytochrome C Oxidase from Rhodobacter Sphaeroides Results in Decoupling the Proton Pump. Biochemistry 2006, 45, 14064, DOI: 10.1021/bi061465qGoogle ScholarThere is no corresponding record for this reference.
- 206Yoshikawa, S.; Muramoto, K.; Shinzawa-Itoh, K. Proton-Pumping Mechanism of Cytochrome C Oxidase. Annu. Rev. Biophys. 2011, 40, 205– 223, DOI: 10.1146/annurev-biophys-042910-155341Google Scholar206https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3MXnvFaitbc%253D&md5=7c6296b4e05ae500761b58d56a3269cbProton-pumping mechanism of cytochrome c oxidaseYoshikawa, Shinya; Muramoto, Kazumasa; Shinzawa-Itoh, KyokoAnnual Review of Biophysics (2011), 40 (), 205-223CODEN: ARBNCV; ISSN:1936-122X. (Annual Reviews Inc.)A review. Cytochrome c oxidase (I), as the terminal oxidase of cellular respiration, coupled with a proton-pumping process, reduces O2 to H2O. This intriguing and highly organized chem. process represents one of the most crit. aspects of cellular respiration. I employs transition metals (Fe and Cu) at the O2-redn. site and has been considered one of the most challenging research subjects in life science. Extensive x-ray structural and mutational analyses have provided 2 different proposals with regard to the mechanism of proton pumping. One mechanism is based on bovine I and includes an independent pathway for the pumped protons. The 2nd mechanistic proposal includes a common pathway for the pumped and chem. protons and is based upon bacterial I. Here, recent progress in exptl. evaluations of these proposals is reviewed and strategies for improving the understanding of the mechanism of this physiol. important process are discussed.
- 207Shimada, A. A Nanosecond Time-Resolved Xfel Analysis of Structural Changes Associated with Co Release from Cytochrome C Oxidase. Sci. Adv. 2017, 3, e1603042, DOI: 10.1126/sciadv.1603042Google Scholar207https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1cXntVOkur0%253D&md5=2843c282032c7b151c4e6ac263293fc7A nanosecond time-resolved XFEL analysis of structural changes associated with CO release from cytochrome c oxidaseShimada, Atsuhiro; Kubo, Minoru; Baba, Seiki; Yamashita, Keitaro; Hirata, Kunio; Ueno, Go; Nomura, Takashi; Kimura, Tetsunari; Shinzawa-Itoh, Kyoko; Baba, Junpei; Hatano, Keita; Eto, Yuki; Miyamoto, Akari; Murakami, Hironori; Kumasaka, Takashi; Owada, Shigeki; Tono, Kensuke; Yabashi, Makina; Yamaguchi, Yoshihiro; Yanagisawa, Sachiko; Sakaguchi, Miyuki; Ogura, Takashi; Komiya, Ryo; Yan, Jiwang; Yamashita, Eiki; Yamamoto, Masaki; Ago, Hideo; Yoshikawa, Shinya; Tsukihara, TomitakeScience Advances (2017), 3 (7), e1603042/1-e1603042/12CODEN: SACDAF; ISSN:2375-2548. (American Association for the Advancement of Science)Bovine cytochrome c oxidase (CcO), a 420-kDa membrane protein, pumps protons using electrostatic repulsion between protons transferred through a water channel and net pos. charges created by oxidn. of heme α (Fe) for redn. of O2 at heme α3 (Feα3). For this process to function properly, timing is essential: The channel must be closed after collection of the protons to be pumped and before Fe oxidn. If the channel were to remain open, spontaneous backflow of the collected protons would occur. For elucidation of the channel closure mechanism, the opening of the channel, which occurs upon release of CO from CcO, is investigated by newly developed time-resolved x-ray free-electron laser and IR techniques with nanosecond time resoln. The opening process indicates that CuB senses completion of proton collection and binds O2 before binding to Feα3 to close the water channel using a conformational relay system, which includes CuB, heme α3, and a transmembrane helix, to block backflow of the collected protons.
- 208Papa, S.; Capitanio, G.; Papa, F. The Mechanism of Coupling between Oxido-Reduction and Proton Translocation in Respiratory Chain Enzymes. Biol. Rev. 2017, 12347, DOI: 10.1111/brv.12347Google ScholarThere is no corresponding record for this reference.
- 209Egawa, T.; Yeh, S.-R.; Rousseau, D. L. Redox-Controlled Proton Gating in Bovine Cytochrome C Oxidase. PLoS One 2013, 8, e63669, DOI: 10.1371/journal.pone.0063669Google ScholarThere is no corresponding record for this reference.
- 210Salje, J.; Ludwig, B.; Richter, O. M. H. Is a Third Proton-Conducting Pathway Operative in Bacterial Cytochrome c Oxidase?. Biochem. Soc. Trans. 2005, 33, 829, DOI: 10.1042/BST0330829Google Scholar210https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2MXmvFSmsLc%253D&md5=a893953bc4d6a53821beceed6ab67518Is a third proton-conducting pathway operative in bacterial cytochrome c oxidase?Salje, J.; Ludwig, B.; Richter, O.-M. H.Biochemical Society Transactions (2005), 33 (4), 829-831CODEN: BCSTB5; ISSN:0300-5127. (Portland Press Ltd.)A review. Despite the existence of several 3-dimensional structures of cytochrome c oxidases, a detailed understanding of pathways involved in proton movements through the complex remains largely elusive. Next to the 2 well-established pathways (termed D and K), an addnl. proton-conducting network (H-channel) has been proposed for the bovine heart enzyme. However, the authors' recent mutational studies on corresponding residues of the Paracoccus denitrificans cytochrome c oxidase provided no clues that such a pathway operates in the prokaryotic enzyme.
- 211Rich, P. R. Cytochrome c Oxidase: Insight into Functions from Studies of the Yeast S. Cerevisiae Homologue; World Scientific Publishers: London, UK, 2017.Google ScholarThere is no corresponding record for this reference.
- 212Yoshikawa, S.; Muramoto, K.; Shinzawa-Itoh, K.; Mochizuki, M. Structural Studies on Bovine Heart Cytochrome C Oxidase. Biochim. Biophys. Acta, Bioenerg. 2012, 1817, 579– 589, DOI: 10.1016/j.bbabio.2011.12.012Google Scholar212Structural studies on bovine heart cytochrome c oxidaseYoshikawa, Shinya; Muramoto, Kazumasa; Shinzawa-Itoh, Kyoko; Mochizuki, MasaoBiochimica et Biophysica Acta, Bioenergetics (2012), 1817 (4), 579-589CODEN: BBBEB4; ISSN:0005-2728. (Elsevier B. V.)A review. Among the X-ray structures of bovine heart cytochrome c oxidase (CcO), reported thus far, the highest resoln. is 1.8 Å. CcO includes 13 different protein subunits, 7 species of phospholipids, 7 species of triglycerides, 4 redox-active metal sites (CuA, heme a (Fea), CuB, heme a3 (Fea3)) and 3 redox-inactive metal sites (Mg2+, Zn2+ and Na+). The effects of various O2 analogs on the X-ray structure suggest that O2 mols. are transiently trapped at the CuB site before binding to Fea32+ to provide O2-. This provides three possible electron transfer pathways from CuB, Fea3 and Tyr244 via a water mol. These pathways facilitate non-sequential 3 electron redn. of the bound O2- to break the OO bond without releasing active oxygen species. Bovine heart CcO has a proton conducting pathway that includes a hydrogen-bond network and a water-channel which, in tandem, connect the pos. side phase with the neg. side phase. The hydrogen-bond network forms two addnl. hydrogen-bonds with the formyl and propionate groups of heme a. Thus, upon oxidn. of heme a, the pos. charge created on Fea is readily delocalized to the heme peripheral groups to drive proton-transport through the hydrogen-bond network. A peptide bond in the hydrogen-bond network and a redox-coupled conformational change in the water channel are expected to effectively block reverse proton transfer through the H-pathway. These functions of the pathway have been confirmed by site-directed mutagenesis of bovine CcO express