Simulating redox coupled proton transfer in cytochrome c oxidase: Looking for the proton bottleneck

FEBS Letters

Volumn 579, Issue 10, 2005, Pages 2026-2034

  Olsson, Mats H M ^a   Sharma, Pankaz K ^a   Warshel, Arieh ^a  

^a UNIVERSITY OF SOUTHERN CALIFORNIA   (United States)

Author keywords

Coupled ET PT; Cytochrome c oxidase; EVB; Proton pumping

Indexed keywords

CYTOCHROME C OXIDASE; PROTON PUMP;

ARTICLE; BIOENERGY; CHANNEL GATING; ELECTRON TRANSPORT; ENERGY TRANSFER; ENZYME ACTIVITY; ENZYME STRUCTURE; KINETICS; MOLECULAR DYNAMICS; OXIDATION REDUCTION REACTION; PRIORITY JOURNAL; PROTON TRANSPORT; SIMULATION;

EID: 16344363592     PISSN: 00145793     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.febslet.2005.02.051     Document Type: Article

References (38)

1. M.K.F. Wikström Proton pump coupled to cytochrome c oxidase in mitochondria Nature 266 1977 271 273
2. H. Michel, J. Behr, A. Harrenga, and A. Kannt Cytochrome c oxidase: structure and spectroscopy Ann. Rev. Biophys. Biomol. Struct. 27 1998 329 356
3. D.A. Mills, and S. Ferguson-Miller Influence of structure, pH and membrane potential on proton movement in cytochrome oxidase Biochim. Biophys. Acta 1555 2002 96 100
4. C. Ostermeier, A. Harrenga, U. Ermler, and H. Michel Structure at 2.7 Å resolution of the Paracoccus denitrificans two-subunit cytochrome c oxidase complexed with an antibody FV fragment Proc. Natl. Acad. Sci. USA 94 1997 10547 10553
5. S. Yoshikawa, K. Shinzawa-Itoh, R. Nakashima, R. aono, E. Yamashita, N. Inoue, M. Yao, M.J. Fei, C.P. Libeu, T. Mizushima, Y. Yamaguchi, T. Tomizaki, and T. Tsukihara Redox-coupled crystal structural changes in bovine heart cytochrome c oxidase Science 280 1998 1723 1729
6. S. Ferguson-Miller, and G.T. Babcock Heme/copper terminal oxidases Chem. Rev. 96 1996 2889 2907
7. P. Brzezinski, and G. Larsson Redox-driven proton pumping by heme-copper oxidases Biochim. Biophys. Acta 1605 2003 1 13
8. M. Wikstrom, M.I. Verkhovsky, and G. Hummer ater-gated mechanism of proton translocation by cytochrome c oxidase Biochim. Biophys. Acta 1604 2003 61 65
9. E. Olkhova, M.C. Hutter, M.A. Lill, V. Helms, and H. Michel Dynamic water networks in cytochrome c oxidase from Paracoccus denitrificans investigated by molecular dynamics simulations Biophys. J. 86 2004 1873 1889
10. I. Hofacker, and K. Schulten Oxygen and proton pathways in cytochrome c oxidase Proteins 30 1998 100 107
11. P.E.M. Siegbahn, M.R.A. lomberg, and M.L. Blomberg Theoretical study of the energetics of proton pumping and oxygen reduction in cytochrome oxidase J. Phys. Chem. B 107 2003 10946 10955
12. D.A. Mills, and S. Ferguson-Miller Understanding the mechanism of proton movement linked to oxygen reduction in cytochrome c oxidase: lessons from other proteins FEBS Lett. 545 2003 47 51
13. A. Namslauer, and P. Brzezinski Structural elements involved in electron-coupled proton transfer in cytochrome c oxidase FEBS Lett. 567 2004 103 110
14. A. Warshel Conversion of light energy to electrostatic energy in the proton pump of Halobacterium halobium Photochem. Photobiol. 30 1979 285 290
15. Y. Sham, I. Muegge, and A. Warshel Simulating proton translocations in proteins: probing proton transfer pathways in the Rhodobacter sphaeroides reaction center Proteins 36 1999 484 500
16. A. Burykin, and A. Warshel What really prevents proton transport throughAquaporin? Charge self-energy versus proton wire proposals Biophys. J. 85 2003 3696 3706
17. A. Warshel, and D.W. Schlosser Electrostatic control of the efficiency of light-induced electron transfer across membranes Proc. Natl. Acad. Sci. USA 78 1981 5564 5568
18. A. Warshel, and W.W. Parson Computer simulations of electron-transfer reactions in solution and in photosynthetic reaction centers Ann. Rev. Phys. Chem. 42 1991 279 309
19. A. Warshel Computer Simulations of Chemical Reactions in Enzymes and Solution 1991 John Wiley & Sons New York
20. C.N. Schutz, and A. Warshel What are the dielectric "constants" of proteins and how to validate electrostatic models Proteins 44 2001 400 417
21. S. Braun-Sand, M. Strajbl, and A. Warshel Studies of proton transocations in biological systems: simulating proton transport in carbonic anhydrase by EVB based models Biophys. J. 87 2004 2221 2239
22. A. Warshel, and J.K. Hwang Simulation of the dynamics of electron-transfer reactions in polar solvents: semiclassical trajectories and dispersed polaron approaches J. Chem. Phys. 84 1986 4938 4957
23. M.H.M. Olsson, P.E.M. Siegbahn, and A. Warshel Simulations of the large kinetic isotope effect and the temperature dependence of the hydrogen atom transfer in Lipoxygenase J. Am. Chem. Soc. 126 2004 2820 2828
24. A. Warshel, and W.W. Parson Dynamics of biochemical and biophysical reactions: insight from computer simulations Quart. Rev. Biophys. 34 2001 563 670
25. A.K. Churg, and A. Warshel Control of redox potential of cytochrome c and microscopic dielectric effects in proteins Biochemistry 25 1986 1675 1681
26. I. Muegge, P.X. Qi, A.J. Wand, Z.T. Chu, and A. Warshel The reorganization energy of cytochrome c revisited J. Phys. Chem. B 101 1997 825 836
27. Chu, T.Z., Villà, J., Strajbl, M., Schutz, C., Shurki, A. and Warshel, A. (2002) Los Angeles
28. M.H.M. Olsson, G. Hong, and A. Warshel Frozen density functional free energy simulations of redox proteins: computational studies of the reduction potential of Plastocyanin andRusticyanin J. Am. Chem. Soc. 125 2003 5025 5039
29. M. Svensson-Ek, J. Abramson, G. Larsson, S. Tornroth, P. Brzezinski, and S. Iwata The X-ray crystal structures of wild-type and EQ(I-286) mutant cytochrome c oxidases from Rhodobacter sphaeroides J. Mol. Biol. 321 2002 329 339
30. R. Langen, G.D. Brayer, A.M. Berghuis, G. McLendon, F. Sherman, and A. Warshel Effect of the Asn52-Ile mutation on the redox potential of yeast cytochrome c J. Mol. Biol. 224 1992 589 600
31. J. Qian Role of the conserved arginine pair in proton and electron transfer in cytochrome c oxidase Biochemistry 43 2004 5748 5756
32. A. Kannt, R.D. Lancaster, and H. Michel The coupling of electron transfer and proton translocation: electrostatic calculations on Paracoccus dentrificans cytochrome c oxidase Biophys. J. 74 1998 708 721
33. J. Åqvist, and V. Luzhkov Ion permeation mechanism of the potassium channel Nature 404 2000 881 884
34. A. Burykin, M. Kato, and A. Warshel Exploring the origin of the ion selectivity of the KcsA potassium channel Proteins 52 2003 412 426
35. A. Warshel, and R.M. Weiss Energetics of heme-protein interactions in Hemoglobin J. Am. Chem. Soc. 103 1981 446 451
36. I. Muegge, T. Schweins, and A. Warshel Electrostatic contributions to protein-protein binding affinities: application to Rap/Raf interaction Proteins 30 1998 407 423
37. D.M. Popovic, and A.A. Stuchebrukhov Electrostatic study of the proton pumping mechanism in bovine heart cytochrome c oxidase J. Am. Chem. Soc. 126 2004 1858 1871
38. J.K. Lanyi Bacteriorhodopsin Annu. Rev. Physiol. 66 2004 665 688