51
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Roy A, Taraphder S. Identification of Proton-Transfer Pathways in Human Carbonic Anhydrase II. J Phys Chem B 2007; 111:10563-76. [PMID: 17691838 DOI: 10.1021/jp073499t] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We investigate the probable proton-transfer pathways from the surface of human carbonic anhydrase II into the active site cavity through His-64 that has been widely implicated as a key residue along the proton-transfer path. A recursive analysis of hydrogen-bonded clusters in the static crystallographic structure shows that there is no complete path through His-64 in either of its experimentally detected conformations. Side chain conformational fluctuation of His-64 from its outward conformation toward the active site is found to provide a crucial dynamic connectivity needed to complete the path coupled to local reorganization of the protein structure and hydration. The energy and free energy barriers along the detected pathway have been estimated to derive the mechanism of His-64 rotation toward the active site. We also investigate a dynamical connectivity map that highlights networks of disordered water molecules that may promote a direct (and probably transient) access of the solvent to the active site. Our studies reveal how such solvent access channels may be related to the putative proton shuttle mediated by His-64. The paths thus identified can be potentially used as reaction coordinates for further studies on the molecular mechanism of enzyme action.
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Affiliation(s)
- Arijit Roy
- Department of Chemistry, Indian Institute of Technology, Kharagpur 721302, India
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52
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Chen H, Wu Y, Voth GA. Proton transport behavior through the influenza A M2 channel: insights from molecular simulation. Biophys J 2007; 93:3470-9. [PMID: 17693473 PMCID: PMC2072055 DOI: 10.1529/biophysj.107.105742] [Citation(s) in RCA: 94] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The structural properties of the influenza A virus M2 transmembrane channel in dimyristoylphosphatidylcholine bilayer for each of the four protonation states of the proton-gating His-37 tetrad and their effects on proton transport for this low-pH activated, highly proton-selective channel are studied by classical molecular dynamics with the multistate empirical valence-bond (MS-EVB) methodology. The excess proton permeation free energy profile and maximum ion conductance calculated from the MS-EVB simulation data combined with the Poisson-Nernst-Planck theory indicates that the triply protonated His-37 state is the most likely open state via a significant side-chain conformational change of the His-37 tetrad. This proposed open state of M2 has a calculated proton permeation free energy barrier of 7 kcal/mol and a maximum conductance of 53 pS compared to the experimental value of 6 pS. By contrast, the maximum conductance for Na(+) is calculated to be four orders of magnitude lower, in reasonable agreement with the experimentally observed proton selectivity. The pH value to activate the channel opening is estimated to be 5.5 from dielectric continuum theory, which is also consistent with experimental results. This study further reveals that the Ala-29 residue region is the primary binding site for the antiflu drug amantadine (AMT), probably because that domain is relatively spacious and hydrophobic. The presence of AMT is calculated to reduce the proton conductance by 99.8% due to a significant dehydration penalty of the excess proton in the vicinity of the channel-bound AMT.
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Affiliation(s)
- Hanning Chen
- Center for Biophysical Modeling and Simulation, Department of Chemistry, University of Utah, Salt Lake City, Utah 84112-0850, USA
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53
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Marx D. Proton transfer 200 years after von Grotthuss: insights from ab initio simulations. Chemphyschem 2007; 7:1848-70. [PMID: 16929553 DOI: 10.1002/cphc.200600128] [Citation(s) in RCA: 613] [Impact Index Per Article: 36.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
In the last decade, ab initio simulations and especially Car-Parrinello molecular dynamics have significantly contributed to the improvement of our understanding of both the physical and chemical properties of water, ice, and hydrogen-bonded systems in general. At the heart of this family of in silico techniques lies the crucial idea of computing the many-body interactions by solving the electronic structure problem "on the fly" as the simulation proceeds, which circumvents the need for pre-parameterized potential models. In particular, the field of proton transfer in hydrogen-bonded networks greatly benefits from these technical advances. Here, several systems of seemingly quite different nature and of increasing complexity, such as Grotthuss diffusion in water, excited-state proton-transfer in solution, phase transitions in ice, and protonated water networks in the membrane protein bacteriorhodopsin, are discussed in the realms of a unifying viewpoint.
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Affiliation(s)
- Dominik Marx
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, 44780 Bochum, Germany
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54
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Swanson JMJ, Maupin CM, Chen H, Petersen MK, Xu J, Wu Y, Voth GA. Proton solvation and transport in aqueous and biomolecular systems: insights from computer simulations. J Phys Chem B 2007; 111:4300-14. [PMID: 17429993 PMCID: PMC2548316 DOI: 10.1021/jp070104x] [Citation(s) in RCA: 239] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The excess proton in aqueous media plays a pivotal role in many fundamental chemical (e.g., acid-base chemistry) and biological (e.g., bioenergetics and enzyme catalysis) processes. Understanding the hydrated proton is, therefore, crucial for chemistry, biology, and materials sciences. Although well studied for over 200 years, excess proton solvation and transport remains to this day mysterious, surprising, and perhaps even misunderstood. In this feature article, various efforts to address this problem through computer modeling and simulation will be described. Applications of computer simulations to a number of important and interesting systems will be presented, highlighting the roles of charge delocalization and Grotthuss shuttling, a phenomenon unique in many ways to the excess proton in water.
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Affiliation(s)
- Jessica M J Swanson
- Center for Biophysical Modeling and Simulation and Department of Chemistry, University of Utah, 315 South 1400 East, Room 2020, Salt Lake City, Utah 84112-0850, USA
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55
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Di Costanzo L, Pique ME, Christianson DW. Crystal structure of human arginase I complexed with thiosemicarbazide reveals an unusual thiocarbonyl mu-sulfide ligand in the binuclear manganese cluster. J Am Chem Soc 2007; 129:6388-9. [PMID: 17469833 PMCID: PMC2593847 DOI: 10.1021/ja071567j] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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56
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Gu W, Frigato T, Straatsma T, Helms V. Dynamisches Protonierungsgleichgewicht der in Wasser gelösten Essigsäure. Angew Chem Int Ed Engl 2007. [DOI: 10.1002/ange.200603583] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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57
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Gu W, Frigato T, Straatsma TP, Helms V. Dynamic Protonation Equilibrium of Solvated Acetic Acid. Angew Chem Int Ed Engl 2007; 46:2939-43. [PMID: 17366497 DOI: 10.1002/anie.200603583] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Wei Gu
- Zentrum für Bioinformatik, Universität des Saarlandes, 66041 Saarbrücken, Germany
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58
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Olsson MHM, Siegbahn PEM, Blomberg MRA, Warshel A. Exploring pathways and barriers for coupled ET/PT in cytochrome c oxidase: a general framework for examining energetics and mechanistic alternatives. BIOCHIMICA ET BIOPHYSICA ACTA 2007; 1767:244-60. [PMID: 17350588 PMCID: PMC2025695 DOI: 10.1016/j.bbabio.2007.01.015] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2006] [Revised: 01/19/2007] [Accepted: 01/24/2007] [Indexed: 11/28/2022]
Abstract
Gaining a detailed understanding of the energetics of the proton pumping process in cytochrome c oxidase (CcO) is one of the challenges of modern biophysics. Although there are several current mechanistic proposals, most of these ideas have not been subjected to consistent structure-function considerations. In particular most works have not related the activation barriers for different mechanistic proposals to the protein structure. The present work describes a general approach for exploring the energetics of different feasible models of the action of CcO, using the observed protein structure, established simulation methods and a modified Marcus' formulation. We start by reviewing our methods for evaluation of the energy diagrams for different proton translocation paths and then present a systematic analysis of various constraints that should be imposed on any energy diagram for the pumping process. After the general analysis we turn to the actual computational study, where we construct energy diagrams for forward and backward paths, using the estimated calculated reduction potentials and pK(a) values of all the relevant sites (including internal water molecules). We then explore the relationship between the calculated energy diagrams and key experimental constraints. This comparison allows us to identify some barriers that are not fully consistent with the overall requirement for an efficient pumping. In particular we identify back leakage channels, which are hard to block without stopping the forward channels. This helps to identify open problems that will require further experimental and theoretical studies. We also consider reasonable adjustments of the calculated barriers that may lead to a working pump. Although the present analysis does not establish a unique and workable model for the mechanism of CcO, it presents what is probably the most consistent current analysis of the barriers for different feasible pathways. Perhaps more importantly, the framework developed here should provide a general way for examining any proposal for the action of CcO as well as for the analysis of further experimental findings about the action of this fascinating system.
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Affiliation(s)
- Mats H M Olsson
- University of Southern California, 3620 McClintock Avenue, Department of Chemistry, SGM 418, Los Angeles, CA 90089-1062, USA.
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59
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Shimokata K, Katayama Y, Murayama H, Suematsu M, Tsukihara T, Muramoto K, Aoyama H, Yoshikawa S, Shimada H. The proton pumping pathway of bovine heart cytochrome c oxidase. Proc Natl Acad Sci U S A 2007; 104:4200-5. [PMID: 17360500 PMCID: PMC1820732 DOI: 10.1073/pnas.0611627104] [Citation(s) in RCA: 104] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
X-ray structures of bovine heart cytochrome c oxidase have suggested that the enzyme, which reduces O(2) in a process coupled with a proton pumping process, contains a proton pumping pathway (H-pathway) composed of a hydrogen bond network and a water channel located in tandem across the enzyme. The hydrogen bond network includes the peptide bond between Tyr-440 and Ser-441, which could facilitate unidirectional proton transfer. Replacement of a possible proton-ejecting aspartate (Asp-51) at one end of the H-pathway with asparagine, using a stable bovine gene expression system, abolishes the proton pumping activity without influencing the O(2) reduction function. Blockage of either the water channel by a double mutation (Val386Leu and Met390Trp) or proton transfer through the peptide by a Ser441Pro mutation was found to abolish the proton pumping activity without impairment of the O(2) reduction activity. These results significantly strengthen the proposal that H-pathway is involved in proton pumping.
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Affiliation(s)
- Kunitoshi Shimokata
- *Department of Biochemistry and Integrative Medical Biology, School of Medicine, Keio University, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
- Japan Biological Informatics Consortium, 2-45 Aomi, Koto-ku, Tokyo 135-8073, Japan
| | - Yukie Katayama
- *Department of Biochemistry and Integrative Medical Biology, School of Medicine, Keio University, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
- Japan Biological Informatics Consortium, 2-45 Aomi, Koto-ku, Tokyo 135-8073, Japan
| | - Haruka Murayama
- *Department of Biochemistry and Integrative Medical Biology, School of Medicine, Keio University, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Makoto Suematsu
- *Department of Biochemistry and Integrative Medical Biology, School of Medicine, Keio University, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Tomitake Tsukihara
- Institute for Protein Research, Osaka University, 3-2 Yamada-oka, Suita, Osaka 565-0871, Japan
| | - Kazumasa Muramoto
- Department of Life Science, University of Hyogo, 3-2-1 Koto, Kamighori, Akoh, Hyogo 678-1297, Japan; and
| | | | - Shinya Yoshikawa
- Department of Life Science, University of Hyogo, 3-2-1 Koto, Kamighori, Akoh, Hyogo 678-1297, Japan; and
- To whom correspondence may be addressed. E-mail:
or
| | - Hideo Shimada
- *Department of Biochemistry and Integrative Medical Biology, School of Medicine, Keio University, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
- To whom correspondence may be addressed. E-mail:
or
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60
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Xu J, Sharpe MA, Qin L, Ferguson-Miller S, Voth GA. Storage of an excess proton in the hydrogen-bonded network of the d-pathway of cytochrome C oxidase: identification of a protonated water cluster. J Am Chem Soc 2007; 129:2910-3. [PMID: 17309257 PMCID: PMC2556150 DOI: 10.1021/ja067360s] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The mechanism of proton transport in the D-pathway of cytochrome c oxidase (CcO) is further elucidated through examining a protonated water/hydroxyl cluster inside the channel. The second generation multi-state empirical valence bond (MS-EVB2) model was employed in a molecular dynamics study based on a high-resolution X-ray structure to simulate the interaction of the excess proton with the channel environment. Our results indicate that a hydrogen-bonded network consisting of about 5 water molecules surrounded by three side chains and two backbone groups (S197, S200, S201, F108) is involved in storage and translocation of an excess proton to the extracellular side of CcO.
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Affiliation(s)
- Jiancong Xu
- Department of Chemistry and Center for Biophysical Modeling and Simulation, 315 South 1400 East Room 2020, University of Utah, Salt Lake City, UT 84112-0850, USA
| | - Martyn A. Sharpe
- Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, Michigan 48824-1319, USA
| | - Ling Qin
- Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, Michigan 48824-1319, USA
| | - Shelagh Ferguson-Miller
- Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, Michigan 48824-1319, USA
| | - Gregory A. Voth
- Department of Chemistry and Center for Biophysical Modeling and Simulation, 315 South 1400 East Room 2020, University of Utah, Salt Lake City, UT 84112-0850, USA
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61
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Kariev AM, Znamenskiy VS, Green ME. Quantum mechanical calculations of charge effects on gating the KcsA channel. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2007; 1768:1218-29. [PMID: 17336921 PMCID: PMC1989151 DOI: 10.1016/j.bbamem.2007.01.021] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2006] [Revised: 01/01/2007] [Accepted: 01/24/2007] [Indexed: 12/01/2022]
Abstract
A series of ab initio (density functional) calculations were carried out on side chains of a set of amino acids, plus water, from the (intracellular) gating region of the KcsA K(+) channel. Their atomic coordinates, except hydrogen, are known from X-ray structures [D.A. Doyle, J.M. Cabral, R.A. Pfuetzner, A. Kuo, J.M. Gulbis, S.L. Cohen, B.T. Chait, R. MacKinnon, The structure of the potassium channel: molecular basis of K(+) conduction and selectivity, Science 280 (1998) 69-77; R. MacKinnon, S.L. Cohen, A. Kuo, A. Lee, B.T. Chait, Structural conservation in prokaryotic and eukaryotic potassium channels, Science 280 (1998) 106-109; Y. Jiang, A. Lee, J. Chen, M. Cadene, B.T. Chait, R. MacKinnon, The open pore conformation of potassium channels. Nature 417 (2001) 523-526], as are the coordinates of some water oxygen atoms. The 1k4c structure is used for the starting coordinates. Quantum mechanical optimization, in spite of the starting configuration, places the atoms in positions much closer to the 1j95, more tightly closed, configuration. This state shows four water molecules forming a "basket" under the Q119 side chains, blocking the channel. When a hydrated K(+) approaches this "basket", the optimized system shows a strong set of hydrogen bonds with the K(+) at defined positions, preventing further approach of the K(+) to the basket. This optimized structure with hydrated K(+) added shows an ice-like 12 molecule nanocrystal of water. If the water molecules exchange, unless they do it as a group, the channel will remain blocked. The "basket" itself appears to be very stable, although it is possible that the K(+) with its hydrating water molecules may be more mobile, capable of withdrawing from the gate. It is also not surprising that water essentially freezes, or forms a kind of glue, in a nanometer space; this agrees with experimental results on a rather different, but similarly sized (nm dimensions) system [K.B. Jinesh, J.W.M. Frenken, Capillary condensation in atomic scale friction: how water acts like a glue, Phys. Rev. Lett. 96 (2006) 166103/1-4]. It also agrees qualitatively with simulations on channels [A. Anishkin, S. Sukharev, Water dynamics and dewetting transitions in the small mechanosensitive channel MscS, Biophys. J. 86 (2004) 2883-2895; O. Beckstein, M.S.P. Sansom, Liquid-vapor oscillations of water in hydrophobic nanopores, Proc. Natl Acad. Sci. U. S. A. 100 (2003) 7063-7068] and on featureless channel-like systems [J. Lu, M.E. Green, Simulation of water in a pore with charges: application to a gating mechanism for ion channels, Prog. Colloid Polym. Sci. 103 (1997) 121-129], in that it forms a boundary on water that is not obvious from the liquid state. The idea that a structure is stable, even if individual molecules exchange, is well known, for example from the hydration shell of ions. We show that when charges are added in the form of protons to the domains (one proton per domain), the optimized structure is open. No stable water hydrogen bonds hold it together; an opening of 11.0 A appears, measured diagonally between non-neighboring domains as glutamine 119 carbonyl O-O distance. This is comparable to the opening in the MthK potassium channel structure that is generally agreed to be open. The appearance of the opening is in rather good agreement with that found by Perozo and coworkers. In contrast, in the uncharged structure this diagonal distance is 6.5 A, and the water "basket" constricts the uncharged opening still further, with the ice-like structure that couples the K(+) ion to the gating region freezing the entrance to the channel. Comparison with our earlier model for voltage gated channels suggests that a similar mechanism may apply in those channels.
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Affiliation(s)
| | | | - Michael E. Green
- *To whom correspondence should be addressed Tel: (212)650-6034, Fax: (212)650-6107,
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62
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Abstract
A series of metalloprotein complexes embedded in a mitochondrial or bacterial membrane utilize electron transfer reactions to pump protons across the membrane and create an electrochemical potential (DeltamuH+). Current understanding of the principles of electron-driven proton transfer is discussed, mainly with respect to the wealth of knowledge available from studies of cytochrome c oxidase. Structural, experimental, and theoretical evidence supports the model of long-distance proton transfer via hydrogen-bonded water chains in proteins as well as the basic concept that proton uptake and release in a redox-driven pump are driven by charge changes at the membrane-embedded centers. Key elements in the pumping mechanism may include bound water, carboxylates, and the heme propionates, arginines, and associated water above the hemes. There is evidence for an important role of subunit III and proton backflow, but the number and nature of gating mechanisms remain elusive, as does the mechanism of physiological control of efficiency.
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Affiliation(s)
- Jonathan P. Hosler
- Department of Biochemistry, University of Mississippi Medical Center, Jackson, Mississippi 39216;
| | - Shelagh Ferguson-Miller
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824; ,
| | - Denise A. Mills
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824; ,
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64
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Liu Y, Hill BC. Formamide probes a role for water in the catalytic cycle of cytochrome c oxidase. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2007; 1767:45-55. [PMID: 17184725 DOI: 10.1016/j.bbabio.2006.10.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2006] [Revised: 09/18/2006] [Accepted: 10/12/2006] [Indexed: 11/26/2022]
Abstract
Formamide is a slow-onset inhibitor of mitochondrial cytochrome c oxidase that is proposed to act by blocking water movement through the protein. In the presence of formamide the redox level of mitochondrial cytochrome c oxidase evolves over the steady state as the apparent electron transfer rate from cytochrome a to cytochrome a(3) slows. At maximal inhibition cytochrome a and cytochrome c are fully reduced, whereas cytochrome a(3) and Cu(B) remain fully oxidized consistent with the idea that formamide interferes with electron transfer between cytochrome a and the oxygen reaction site. However, transient kinetic studies show that intrinsic rates of electron transfer are unchanged in the formamide-inhibited enzyme. Formamide inhibition is demonstrated for another member of the heme-oxidase family, cytochrome c oxidase from Bacillus subtilis, but the onset of inhibition is much quicker than for mitochondrial oxidase. If formamide inhibition arises from a steric blockade of water exchange during catalysis then water exchange in the smaller bacterial oxidase is more open. Subunit III removal from the mitochondrial oxidase hastens the onset of formamide inhibition suggesting a role for subunit III in controlling water exchange during the cytochrome c oxidase reaction.
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Affiliation(s)
- Yu Liu
- Department of Biochemistry, Queen's University, Kingston, ON, Canada
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65
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Chen H, Ilan B, Wu Y, Zhu F, Schulten K, Voth GA. Charge delocalization in proton channels, I: the aquaporin channels and proton blockage. Biophys J 2006; 92:46-60. [PMID: 17056733 PMCID: PMC1697834 DOI: 10.1529/biophysj.106.091934] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The explicit contribution to the free energy barrier and proton conductance from the delocalized nature of the excess proton is examined in aquaporin channels using an accurate all-atom molecular dynamics computer simulation model. In particular, the channel permeation free energy profiles are calculated and compared for both a delocalized (fully Grotthuss shuttling) proton and a classical (nonshuttling) hydronium ion along two aquaporin channels, Aqp1 and GlpF. To elucidate the effects of the bipolar field thought to arise from two alpha-helical macrodipoles on proton blockage, free energy profiles were also calculated for computational mutants of the two channels where the bipolar field was eliminated by artificially discharging the backbone atoms. Comparison of the free energy profiles between the proton and hydronium cases indicates that the magnitude of the free energy barrier and position of the barrier peak for the fully delocalized and shuttling proton are somewhat different from the case of the (localized) classical hydronium. The proton conductance through the two aquaporin channels is also estimated using Poisson-Nernst-Planck theory for both the Grotthuss shuttling excess proton and the classical hydronium cation.
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Affiliation(s)
- Hanning Chen
- Center for Biophysical Modeling and Simulation, Department of Chemistry, University of Utah, Salt Lake City, Utah, USA
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66
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Song Y, Michonova-Alexova E, Gunner MR. Calculated proton uptake on anaerobic reduction of cytochrome C oxidase: is the reaction electroneutral? Biochemistry 2006; 45:7959-75. [PMID: 16800622 PMCID: PMC2727075 DOI: 10.1021/bi052183d] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cytochrome c oxidase is a transmembrane proton pump that builds an electrochemical gradient using chemical energy from the reduction of O(2). Ionization states of all residues were calculated with Multi-Conformation Continuum Electrostatics (MCCE) in seven anaerobic oxidase redox states ranging from fully oxidized to fully reduced. One long-standing problem is how proton uptake is coupled to the reduction of the active site binuclear center (BNC). The BNC has two cofactors: heme a(3) and Cu(B). If the protein needs to maintain electroneutrality, then 2 protons will be bound when the BNC is reduced by 2 electrons in the reductive half of the reaction cycle. The effective pK(a)s of ionizable residues around the BNC are evaluated in Rhodobacter sphaeroides cytochrome c oxidase. At pH 7, only a hydroxide coordinated to Cu(B) shifts its pK(a) from below 7 to above 7 and so picks up a proton when heme a(3) and Cu(B) are reduced. Glu I-286, Tyr I-288, His I-334, and a second hydroxide on heme a(3) all have pK(a)s above 7 in all redox states, although they have only 1.6-3.5 DeltapK units energy cost for deprotonation. Thus, at equilibrium, they are protonated and cannot serve as proton acceptors. The propionic acids near the BNC are deprotonated with pK(a)s well below 7. They are well stabilized in their anionic state and do not bind a proton upon BNC reduction. This suggests that electroneutrality in the BNC is not maintained during the anaerobic reduction. Proton uptake on reduction of Cu(A), heme a, heme a(3), and Cu(B) shows approximately 2.5 protons bound per 4 electrons, in agreement with prior experiments. One proton is bound by a hydroxyl group in the BNC and the rest to groups far from the BNC. The electrochemical midpoint potential (E(m)) of heme a is calculated in the fully oxidized protein and with 1 or 2 electrons in the BNC. The E(m) of heme a shifts down when the BNC is reduced, which agrees with prior experiments. If the BNC reduction is electroneutral, then the heme a E(m) is independent of the BNC redox state.
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Affiliation(s)
| | | | - M. R. Gunner
- To whom correspondence should be addressed. Telephone: 212-650-5557. Fax: 212-650-6940. E-mail:
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67
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Wraight CA. Chance and design—Proton transfer in water, channels and bioenergetic proteins. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2006; 1757:886-912. [PMID: 16934216 DOI: 10.1016/j.bbabio.2006.06.017] [Citation(s) in RCA: 286] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2006] [Revised: 06/07/2006] [Accepted: 06/13/2006] [Indexed: 12/17/2022]
Abstract
Proton transfer and transport in water, gramicidin and some selected channels and bioenergetic proteins are reviewed. An attempt is made to draw some conclusions about how Nature designs long distance, proton transport functionality. The prevalence of water rather than amino acid hydrogen bonded chains is noted, and the possible benefits of waters as the major component are discussed qualitatively.
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Affiliation(s)
- Colin A Wraight
- Center for Biophysics and Computational Biology, University of Illinois, Urbana, IL 61801, USA.
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68
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Xu J, Voth GA. Free energy profiles for H+ conduction in the D-pathway of Cytochrome c Oxidase: a study of the wild type and N98D mutant enzymes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2006; 1757:852-9. [PMID: 16815239 DOI: 10.1016/j.bbabio.2006.05.028] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2006] [Revised: 05/11/2006] [Accepted: 05/15/2006] [Indexed: 11/29/2022]
Abstract
The molecular mechanism for proton conduction in the D-pathway of Cytochrome c Oxidase (CcO) is investigated through the free energy profile, i.e., potential of mean force (PMF) calculations of both the native enzyme and the N98D mutant. The multistate empirical valence bond (MS-EVB) model was applied to simulate the interaction of an excess proton with the channel environment. In the study of the wild type enzyme, the PMF reveals the previously proposed proton trap inside the channel; it also shows a high free energy barrier against the passage of proton at the entry of the channel, where two conserved asparagines (ASN80/98) may be essential for the gating of proton uptake. We also present data from an investigation of the N98D mutant, which has been previously shown to completely eliminate proton pumping but significantly enhance the oxidase activity in Rhodobacter sphaeroides. These results suggest that mutating Asn98 to negatively charged aspartate will create an unfavorable energy barrier sufficiently high to prevent the overall proton uptake through the D-pathway, whereas with a protonated aspartic acid the proton conduction was found to be accelerated. Plausible explanations for the origin of the uncoupling of proton pumping from the oxidase activity will be discussed.
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Affiliation(s)
- Jiancong Xu
- Department of Chemistry, University of Utah, Salt Lake City, 84112-0850, USA
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Brändén G, Gennis RB, Brzezinski P. Transmembrane proton translocation by cytochrome c oxidase. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2006; 1757:1052-63. [PMID: 16824482 DOI: 10.1016/j.bbabio.2006.05.020] [Citation(s) in RCA: 90] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2006] [Revised: 05/11/2006] [Accepted: 05/12/2006] [Indexed: 10/24/2022]
Abstract
Respiratory heme-copper oxidases are integral membrane proteins that catalyze the reduction of molecular oxygen to water using electrons donated by either quinol (quinol oxidases) or cytochrome c (cytochrome c oxidases, CcOs). Even though the X-ray crystal structures of several heme-copper oxidases and results from functional studies have provided significant insights into the mechanisms of O2 -reduction and, electron and proton transfer, the design of the proton-pumping machinery is not known. Here, we summarize the current knowledge on the identity of the structural elements involved in proton transfer in CcO. Furthermore, we discuss the order and timing of electron-transfer reactions in CcO during O2 reduction and how these reactions might be energetically coupled to proton pumping across the membrane.
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Affiliation(s)
- Gisela Brändén
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, Stockholm, Sweden
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70
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Olsson MHM, Warshel A. Monte Carlo simulations of proton pumps: on the working principles of the biological valve that controls proton pumping in cytochrome c oxidase. Proc Natl Acad Sci U S A 2006; 103:6500-5. [PMID: 16614069 PMCID: PMC1458913 DOI: 10.1073/pnas.0510860103] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Gaining a detailed understanding of the proton-pumping process in cytochrome c oxidase (COX) is one of the challenges of modern biophysics. Recent mutation experiments have highlighted this challenge by showing that a single mutation (the N139D mutation) blocks the overall pumping while continuing to channel protons to the binuclear center without inhibiting the oxidase activity. Rationalizing this result has been a major problem because the mutation is quite far from E286, which is believed to serve as the branching point for the proton transport in the pumping process. In the absence of a reasonable explanation for this important observation, we have developed a Monte Carlo simulation method that can convert mutation and structural information to pathways for proton translocation and simulate the pumping process in COX on a millisecond and even subsecond time scale. This tool allows us to reproduce and propose a possible explanation to the effect of the N139D mutation and to offer a consistent model for the origin of the "valve effect" in COX, which is crucial for maintaining uphill proton pumping. Furthermore, obtaining the first structure-based simulation of proton pumping in COX, or in any other protein, indicates that our approach should provide a powerful tool for verification of mechanistic hypotheses about the action of proton transport proteins.
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Affiliation(s)
- Mats H. M. Olsson
- Department of Chemistry, University of Southern California, 3620 McClintock Avenue, SGM418, Los Angeles, CA 90089-1062
- *To whom correspondence may be addressed. E-mail:
or
| | - Arieh Warshel
- Department of Chemistry, University of Southern California, 3620 McClintock Avenue, SGM418, Los Angeles, CA 90089-1062
- *To whom correspondence may be addressed. E-mail:
or
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Popovic DM, Stuchebrukhov AA. Two conformational states of Glu242 and pKas in bovine cytochrome c oxidase. Photochem Photobiol Sci 2006; 5:611-20. [PMID: 16761090 DOI: 10.1039/b600096g] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Cytochrome c oxidase (CcO) is the terminal enzyme in the respiratory electron transport chain of aerobic organisms. It catalyses the reduction of atmospheric oxygen to water, and couples this reaction to proton pumping across the membrane; this process generates the electrochemical gradient that subsequently drives the synthesis of ATP. The molecular details of the mechanism by which electron transfer is coupled to proton pumping in CcO is poorly understood. Recent calculations from our group indicate that His291, a ligand of the Cu(B) center of the enzyme, may play the role of the pumping element. In this paper we describe calculations in which a DFT/continuum electrostatic method is used to explore the coupling of the conformational changes of Glu242 residue, the main proton donor of both chemical and pump protons, to its pKa, and the pKa of His291, a putative proton loading site of our pumping model. The computations are done for several redox states of metal centers, different protonation states of Glu242 and His291, and two well-defined conformations of the Glu242 side chain. Thus, in addition to equilibrium redox/protonation states of the catalytic cycle, we also examine the transient and intermediate states. Different dielectric models are employed to investigate the robustness of the results, and their viability in the light of the proposed proton pumping mechanism of CcO. The main results are in agreement with the experimental measurements and support the proposed pumping mechanism. Additionally, the present calculations indicate a possibility of gating through conformational changes of Glu242; namely, in the pumping step, we find that Glu242 needs to be reprotonated before His291 can eject a proton to the P-site of membrane. As a result, the reprotonation of Glu can control proton release from the proton loading site.
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Affiliation(s)
- Dragan M Popovic
- Department of Chemistry, University of California-Davis, One Shields Avenue, Davis, CA 95616, USA.
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