Simulation of electron-proton coupling with a Monte Carlo method: Application to cytochrome c3 using continuum electrostatics

Biophysical Journal

Volumn 76, Issue 6, 1999, Pages 2978-2998

  Baptista, António M ^a   Martel, Paulo J ^a   Soares, Cláudio M ^a  

^a INSTITUTO DE TECNOLOGIA QUÍMICA E BIOLÓGICA   (Portugal)

Author keywords

[No Author keywords available]

Indexed keywords

CYTOCHROME C3;

ARTICLE; DESULFOVIBRIO VULGARIS; ELECTRICITY; ELECTRON; NONHUMAN; OXIDATION REDUCTION POTENTIAL; OXIDATION REDUCTION STATE; SIMULATION; SYSTEM ANALYSIS; THERMODYNAMICS;

DESULFOVIBRIO VULGARIS; DESULFOVIBRIO VULGARIS SUBSP. VULGARIS STR. HILDENBOROUGH;

EID: 0033001692     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0006-3495(99)77452-7     Document Type: Article

References (82)

1. Alden, R. G., W. W. Parson, Z. T. Chu, and A. Warshel. 1995. Calculations of electrostatic energies in photosynthetic reaction centers. J. Am. Chem. Soc. 117:12284-12298.
2. Alexov, E. G., and M. R. Gunner. 1997. Incorporating protein conformational flexibility into the calculation of pH-dependent protein properties. Biophys. J. 72:2075-2093.
3. Allen, M. P., and D. J. Tildesley. 1987. Computer Simulation of Liquids. Clarendon, Oxford.
4. Antosiewicz, J., J. A. McCammon, and M. K. Gilson. 1994. Prediction of pH-dependent properties of proteins. J. Mol. Biol. 238:415-436.
5. Antosiewicz, J., and D. Porschke. 1989. The nature of protein dipole moments: experimental and calculated permanent dipole of α-chymotrypsin. Biochemistry. 28:10072-10078.
6. Apostolakis, J., I. Muegge, U. Ermler, G. Fritzsch, and E. W. Knapp. 1996. Free energy computations on the shift of the special pair redox potential: mutants of the reaction center of Rhodobacter sphaeroides. J. Am. Chem. Soc. 118:3743-3752.
7. Badziong, W., and R. K. Thauer. 1978. Growth yields and growth rates of Desulfovibrio vulgaris (Marburg) growing on hydrogen plus sulfate and hydrogen plus thiosulfate as the sole energy source. Arch. Microbiol. 117:209-214.
8. Badziong, W., R. K. Thauer, and J. G. Zeikus. 1978. Isolation and characterization of Desulfovibrio growing on hydrogen plus sulfate as the sole energy source. Arch. Microbiol. 116:41-49.
9. Baptista, A. M., P. J. Martel, and S. B. Petersen. 1997. Simulation of protein conformational freedom as a function of pH: constant-pH molecular dynamics using implicit titration. Proteins. 27:523-544.
10. a values in myoglobin and comparison with NMR data for histidines. Biochemistry. 32:8045-8056.
11. a values of ionizable groups in bacteriorhodopsin. J. Mol. Biol. 224: 473-486.
12. a's of ionizable groups in proteins: atomic detail from a continuum electrostatic model. Biochemistry. 29: 10219-10225.
13. Bashford, D., M. Karplus, and G. W. Canters. 1988. Electrostatic effects of charge perturbations introduced by metal oxidation in proteins. J. Mol. Biol. 203:507-510.
14. Ben-Naim, A. 1992. Statistical Thermodynamics for Chemists and Biochemists. Plenum Press, New York.
15. Beroza, P., D. R. Fredkin, M. Y. Okamura, and G. Feher. 1991. Protonation of interacting residues in a protein by a Monte Carlo method: application to lysozyme and the photosynthetic reaction center of Rhodobacter sphaeroides. Proc. Natl. Acad. Sci. USA. 88:5804-5808.
16. Bertrand, P., O. Mbarki, M. Asso, L. Blanchard, F. Guerlesquin, and M. Tegoni. 1995. Control of the redox potential in c-type cytochromes: importance of the entropic contribution. Biochemistry. 34:11071-11079.
17. Beveridge, D. L., and F. M. DiCapua. 1989. Free energy via molecular simulation: application to chemical and biomolecular systems. Annu. Rev. Biophys. Biophys. Chem. 18:431-492.
18. Churg, A. K., and A. Warshel. 1986. Control of the redox potential of cytochrome c and microscopic dielectric effects in proteins. Biochemistry. 25:1675-1681.
19. 3 from Desulfovibrio gigas. Eur. J. Biochem. 202: 1101-1106.
20. Cutler, R. L., A. M. Davies, S. Creighton, A. Warshel, G. R. Moore, M. Smith, and A. G. Mauk. 1989. Role of arginine-38 in regulation of the cytochrome c oxidation-reduction equilibrium. Biochemistry. 28: 3188-3197.
21. 3 from Desulfovibrio desulfuricans Norway at 1.7 A resolution. J. Mol. Biol. 243:653-667.
22. de Groot, S. R., and P. Mazur. 1962. Non-Equilibrium Thermodynamics. North-Holland, Amsterdam.
23. as of ionizable residues in proteins: an explicit solvent calculation for lysozyme. Proteins. 20:85-97.
24. as of ionizable groups in proteins. J. Phys. Chem. 100:17373-17387.
25. Gilson, M. K., and B. H. Honig. 1986. The dielectric constant of a folded protein. Biopolymers. 25:2097-2119.
26. Gilson, M. K., and B. Honig. 1988. Energetics of charge-charge interactions in proteins. Proteins. 3:32-52.
27. Gilson, M. K., K. A. Sharp, and B. Honig. 1987. Calculating the electrostatic potential of proteins in solution: method and error assessment. J. Comput. Chem. 9:327-335.
28. Gunner, M. R., and B. Honig. 1991. Electrostatic control of midpoint potentials in the cytochrome subunit of the Rhodopseudomonas viridis reaction center. Proc. Natl. Acad. Sci. USA. 88:9151-9155.
29. Harbury, H. A., J. R. Cronin, M. W. Fanger, T. P. Hettinger, A. J. Murphy, Y. P. Myer, and S. N. Vinogradov. 1965. Complex formation between methionine and a heme peptide from cytochrome c. Proc. Natl. Acad. Sci. USA. 54:1658-1664.
30. Hastings, W. K. 1970. Monte Carlo sampling methods using Markov chains and their applications. Biometrika. 57:97-109.
31. 3 at 1.8 Å resolution. J. Mol. Biol. 172:109-139.
32. Hill, T. L. 1960. An Introduction to Statistical Thermodynamics. Addison-Wesley, Reading, MA.
33. Honig, B., and A. Nicholls. 1995. Classical electrostatics in biology and chemistry. Science. 268:1144-1149.
34. Hooft, R. W. W., C. Sander, and G. Vriend. 1996. Positioning hydrogen atoms by optimizing hydrogen-bond networks in protein structures. Proteins. 26:363-376.
35. Kannt, A., C. R. D. Lancaster, and H. Michel. 1998. The coupling of electron transfer and proton translocation: electrostatic calculations on Paracocus denitrificans cytochrome c oxidase. Biophys. J. 74:708-721.
36. Lancaster, C. R. D., H. Michel, B. Honig, and M. R. Gunner. 1996. Calculated coupling of electron and proton transfer in the photosynthetic reaction center of Rhodopseudomonas viridis. Biophys. J. 70: 2469-2492.
37. Langen, R., G. M. Jensen, U. Jacob, P. J. Stephens, and A. Warshel. 1992. Protein control of iron-sulfur cluster redox potentials. J. Biol. Chem. 267:25625-25627.
38. Lee, F. S., Z. T. Chu, and A. Warshel. 1993. Microscopic and semimicroscopic calculations of electrostatic energies in proteins by the POLARIS and ENZYMIX programs. J. Comput. Chem. 14:161-185.
39. Levy, R. M., M. Belhadj, and D. B. Kitchen. 1991. Gaussian fluctuation formula for electrostatic free-energy changes in solution. J. Chem. Phys. 95:3627-3633.
40. 3 coupled to hydrogenase works as a "proton thruster" in Desulfovibrio vulgaris. J. Biol. Inorg. Chem. 2:488-491.
41. 3 from Desulfovibrio vulgaris: a model for energy transduction mechanism. J. Biol. Inorg. Chem. 1:34-38.
42. Mark, A. E., and W. F. van Gunsteren. 1994. Decomposition of the free energy of a system in terms of specific interactions. J. Mol. Biol. 240:167-176.
43. 3 from several Desulfovibrio species using continuum electrostatic methods. J. Biol. Inorg. Chem. (in press).
44. 3 from Desulfovibrio vulgaris Hildenborough at 1.9 A resolution. J. Mol. Biol. 234:680-699.
45. 3 from Desulfovibrio gigas: crystal structure at 1.8 Å resolution and evidence for a specific calcium-binding site. Protein Sci. 5:1342-1354.
46. McQuarrie, D. A. 1976. Statistical Mechanics. Harper, New York.
47. 3: structural basis for functional cooperativity. J. Mol. Biol. 281:719-739.
48. Metropolis, N., A. W. Rosenbluth, M. N. Rosenbluth, A. H. Teller, and E. Teller. 1953. Equation of state calculations by fast computing machines. J. Chem. Phys. 21:1087-1092.
49. Mezei, M., and D. L. Beveridge. 1986. Free energy simulations. Ann. N.Y. Acad. Sci. 482:1-23.
50. Mood, A. M., F. A. Graybill, and D. C. Boes. 1974. Introduction to the Theory of Statistics, 3rd Ed. McGraw-Hill, New York.
51. Morais, J., P. N. Palma, C. Frazão, J. Caldeira, J. LeGall, I. Moura, J. J. Moura, and M. A. Carrondo. 1995. Structure of the tetraheme cytochrome from Desulfovibrio desulfuricans ATCC 27774: x-ray diffraction and electron paramagnetic resonance studies. Biochemistry. 34: 12830-12841.
52. Muegge, I., P. X. Qi, A. J. Wand, Z. T. Chu, and A. Warshel. 1997. The reorganization energy of cytochrome c revisited. J. Chem. Phys. B. 101:825-836.
53. Nozaki, Y., and C. Tanford. 1967. Examination of titration behavior. Methods Enzymol. 11:715-734.
54. Papa, S., F. Guerrieri, and G. Izzo. 1979. Redox Bohr-effects in the cytochrome system in mitochondria. FEBS Lett. 105:213-216.
55. 3 from D. vulgaris Miyazaki F. Biochim. Biophys. Acta. 1293:45-54.
56. Reif, F. 1965. Fundamentals of Statistical and Thermal Physics. McGraw-Hill, New York.
57. Russell, S. T., and A. Warshel. 1985. Calculations of electrostatic energies in proteins. The energetics of ionized groups in bovine pancreatic trypsin inhibitor. J. Mol. Biol. 185:389-404.
58. 3. J. Biol. Inorg. Chem. 2:343-349.
59. 3 by 2D-NMR. FEBS Lett. 314:155-158.
60. 3. Eur. J. Biochem. 141:283-296.
61. 3 of Desulfovibrio vulgaris (Hildenborough). Biochemistry. 37:12160-12165.
62. Schellman, J. A. 1975. Macromolecular binding. Biopolymers. 14: 999-1018.
63. Sharp, K. A., and B. Honig. 1990. Electrostatic interactions in macromolecules: theory and applications. Annu. Rev. Biophys. Biophys. Chem. 19:301-332.
64. Smith, L. J., A. E. Mark, C. M. Dobson, and W. F. van Gunsteren. 1995. Comparison of MD simulations and NMR experiments for hen lysozyme: analysis of local fluctuations, cooperative motions and global changes. Biochemistry, 34:10918-10931.
65. 3 from Desulfovibrio vulgaris Hildenborough. J. Biol. Inorg. Chem. 2:714-727.
66. 3: studying the reduction processes using free energy calculations. Biophys. J. 74:1708-1721.
67. Tanford, C., and J. G. Kirkwood. 1957. Theory of protein titration curves. I. General equations for impenetrable spheres. J. Am. Chem. Soc. 79: 5333-5339.
68. 3 from Desulfovibrio vulgaris. Biochim. Biophys. Acta. 1187: 232-235.
69. 3 from Desulfovibrio vulgaris. Eur. J. Biochem. 241:723-731.
70. van Gunsteren, W. F., and H. J. C. Berendsen. 1987. Groningen Molecular Simulation (GROMOS) Library Manual. Biomos, Groningen, the Netherlands.
71. Vorobjev, Y. N., H. A. Scheraga, B. Hitz, and B. Honig. 1994. Theoretical modeling of electrostatic effects of titrable side-chain groups on protein conformation in a polar ionic solution. 1. Potential of mean force between charged lysine residues and titration of poly(L-lysine) in 95% methanol solution. J. Phys. Chem. 98:10940-10948.
72. Vriend, G. 1990. WHAT IF: a molecular modeling and drug design program. J. Mol. Graph. 8:52-56.
73. a, proton transfer reactions, and general acid catalysis reactions in enzymes. Biochemistry. 20:3167-3177.
74. Warshel, A., and J. Aqvist. 1991. Electrostatic energy and macromolecular function. Annu. Rev. Biophys. Biophys. Chem. 20:267-298.
75. Warshel, A., and A. Papazyan. 1998. Electrostatic effects in macromolecules: fundamental concepts and practical modeling. Curr. Opin. Struct. Biol. 8:211-217.
76. Warshel, A., and S. T. Russell. 1984. Calculations of electrostatic interactions in biological systems and in solutions. Q. Rev. Biophys. 17: 283-422.
77. Warshel, A., F. Sussman, and G. King. 1986. Free energy of charges in solvated proteins: microscopic calculations using a reversible charging process. Biochemistry. 25:8368-8372.
78. Weast, R. C., editor. 1984. Handbook of Chemistry and Physics. CRC Press, Boca Raton, FL.
79. Wyman, J., Jr. 1964. Linked functions and reciprocal effects in hemoglobin: a second look. Adv. Protein Chem. 19:223-286.
80. Xavier, A. V. 1985. In Frontiers in Bioinorganic Chemistry. A. V. Xavier, editor. VCH Publishers, Weinheim, Germany. 722-725.
81. a's in proteins. Proteins. 15:252-265.
82. Zwanzig, R. W. 1954. High-temperature equation of state by a perturbation method. I. Nonpolar gases. J. Chem. Phys. 22:1420-1426.