Model for proton transport coupled to protein conformational change: Application to proton pumping in the bacteriorhodopsin photocycle

Journal of the American Chemical Society

Volumn 128, Issue 51, 2006, Pages 16778-16790

  Ferreira, Antonio M ^a   Bashford, Donald ^a  

^a ST JUDE CHILDREN S RESEARCH HOSPITAL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CONFORMATIONS; FREE ENERGY; IONIZATION; MATHEMATICAL MODELS; PROTEINS;

CONFORMERS; MACROSCOPIC DIELECTRICS; PROTON PUMPS; PROTONATION MICROSTATES;

PROTONS;

BACTERIORHODOPSIN;

ANALYTIC METHOD; ARTICLE; CALCULATION; CONFORMATIONAL TRANSITION; DIELECTRIC CONSTANT; IONIZATION; MASTER EQUATION MODEL; MATHEMATICAL MODEL; PKA; PROTEIN CONFORMATION; PROTON MOTIVE FORCE; PROTON TRANSPORT; REPRODUCIBILITY;

BACTERIORHODOPSINS; ION TRANSPORT; MODELS, BIOLOGICAL; MODELS, MOLECULAR; PHOTOCHEMISTRY; PHOTOSYNTHESIS; PROTEIN CONFORMATION; PROTON PUMPS; PROTONS;

EID: 33846021303     PISSN: 00027863     EISSN: None     Source Type: Journal    
DOI: 10.1021/ja060742d     Document Type: Article

References (78)

1. Mitchell, P. Nature 1961, 191, 144-148.
2. Heberle, J. Biochim. Biophys. Acta 2000, 1458, 135-147.
3. Neutze, R.; Pebay-Peyroula, E.; Edman, K.; Royant, A.; Navarro, J.; Landau, E. M. Biochim. Biophys. Acta 2002, 1565, 144-167.
4. Lanyi, J. K.; Pohorille, A. Trends Biotechnol. 2001, 19, 140-144.
5. Balashov, S. P. Biochim. Biophys. Acta 2000, 1460, 75-94.
6. Betancourt, F. M. H.; Glaeser, R. M. Biochim. Biophys. Acta 2000, 1460, 106-118.
7. Haupts, U.; Tittor, J.; Oesterhelt, D. Annu. Rev. Biophys. Biomol. Struct. 1999, 28, 367-399.
8. Hirai, T.; Subramaniam, S. FEBS Lett. 2003, 545, 2-8.
9. Lanyi, J. K.; Luecke, H. Curr. Opin. Struct. Biol. 2001, 11, 415-419.
10. Subramaniam, S. Curr. Opin. Struct. Biol. 1999, 9, 462-468.
11. Rothschild, K. J. J. Bioenerg. Biomembr. 1992, 24, 147-167.
12. Maeda, A. Isr. J. Chem. 1995, 35, 387-400.
13. Kötting, C.; Gerwert, K. ChemPhysChem 2005, 6, 881-888.
14. Henderson, R.; Baldwin, J. M.; Ceska, T. A.; Zemlin, F.; Beckmann, E.; Downing, K. H. J. Mol. Biol. 1990, 213, 899-929.
15. Pebay-Peyroula, E.; Rummel, G.; Rosenbusch, J. P.; Landau, E. M. Science 1997, 277, 1676-1681.
16. Luecke, H.; Richter, H.-T.; Lanyi, J. K. Science 1998, 280, 1934-1937.
17. Essen, L.-O.; Sietjert, R.; Lehmann, W. D.; Oesterhelt, D. Proc. Natl. Acad. Sci. U.S.A. 1998, 95, 11673-11678.
18. Belrhali, H.; Nollert, P.; Royant, A.; Menzel, C.; Rosenbusch, J. P.; Landau, E. M.; Pebay-Peyroula, E. Struct. Fold. Des. 1999, 7, 909-917.
19. Luecke, H.; Schobert, B.; Richter, H.-T.; Cartailler, J.-P.; Lanyi, J. K. J. Mol. Biol. 1999, 291, 899-911.
20. Luecke, H.; Schobert, B.; Richter, H.-T.; Cartailler, J. P.; Lanyi, J. K. Science 1999, 286, 255-261.
21. Edman, K.; Mollert, P.; Royant, A.; Belrhali, H.; Pebay-Peyroula, E.; Hajdu, J.; Neutze, R.; Landau, E. M. Nature 1999, 401, 822-826.
22. Sass, H. J.; Büldt, G.; Gessenich, R.; Hehn, D.; Neff, D.; Schlesinger, R.; Berendzen, J.; Ormos, P. Nature 2000, 406, 649-653.
23. Luecke, H.; Schobert, B.; Cartailler, J.-P.; Hans-Thomas, R.; Rosengarth, A.; Needleman, R.; Lanyi, J. K. J. Mol. Biol. 2000, 300, 1237-1255.
24. Subramaniam, S.; Henderson, R. Nature 2000, 406, 653-657.
25. Royant, A.; Edman, K.; Ursby, T.; Pebay-Peyroula, E.; EM, L.; Neutze, R. Nature 2000, 406, 645-648.
26. Facciotti, M. T.; Rouhani, S.; Burkard, F. T.; Betancourt, F. M.; Downing. K. H.; Rose, R. B.; McDermott, G.; M. G. R. Biophys. J. 2001, 81, 3442-55.
27. Rouhani, S.; Cartailler, J.; Facciotti, M.; Walian, P.; Needleman, R. Lanyi, J.; Glaeser, R.; Luecke, H. J. Mol. Biol. 2001, 313, 615-628.
28. Schobert, B.; Cupp-Vickery, J.; Hornak, V.; Smith, S. O.; Lanyi, J. K. J. Mol. Biol. 2002, 321, 715-726.
29. Lanyi, J. K.; Schobert, B. J. Mol. Biol. 2002, 321, 727-737.
30. Lanyi, J. K.; Schobert, B. J. Mol. Biol. 2003, 328, 439-450.
31. Schobert, B.; Brown, L. S.; Lanyi, J. K. J. Mol. Biol. 2003, 330, 553-570.
32. Ormos, P. Proc. Natl. Acad. Sci. U.S.A. 1991, 88, 473-477.
33. Richter, H.-T.; Brown, L. S.; Needleman, R.; Lanyi, J. K. Biochemistry 1996, 35, 4054-4062.
34. Brown, L. S.; Dioumaev, A. K.; Needleman, R.; Lanyi, J. K. Biophys. J. 1998, 75, 1455-1465.
35. Spassov, V. Z.; Luecke, H.; Gerwert, K.; Bashford, D. J. Mol. Biol. 2001, 312, 203-219.
36. Baudry, J.; Tajkhorshid, E.; Molnar, F.; Phillips, J.; Schulten, K. J. Phys. Chem. B 2001, 105, 905-918.
37. Rajamani, R.; Gao, J. L. J. Comput. Chem. 2002, 23, 96-105.
38. Vreven, T.; Morokuma, K. Theor. Chem. Acc. 2003, 109, 125-132.
39. Hayashi, S.; Tajkhorshid, E.; Schulten, K. Biophys. J. 2002, 83, 1281-1297.
40. Hayashi, S.; Tajkhorshid, E.; Schulten, K. Biophys. J. 2003, 85, 1440-1449.
41. Grudinin, S.; Büldt, G.; Gordeliy, V.; Baumgaertner, A. Biophys. J. 2005, 88, 3257-3261.
42. Bondar, A.-N.; Elstner, M.; Suhai, S.; Smith, J. C.; Fischer, S. Structure 2004, 12, 1281-1288.
43. Bashford, D.; Gerwert, K. J. Mol. Biol. 1992, 224, 473-486.
44. Sampogna, R. V.; Honig, B. Biophys. J. 1994, 66, 1341-1352.
45. Engels, M.; Gerwert, K.; Bashford, D. Biophys. Chem. 1995, 56, 95-104.
46. Rammelsberg, R.; Huhn, G.; Lübben, M.; Gerwert, K. Biochemistry 1998, 37, 5001-5009.
47. Song, Y.; Mao, J.; Gunner, M. R. Biochemistry 2003, 42, 9875-9888.
48. Onufriev, A.; Smondyrev, A.; Bashford, D. J. Mol. Biol. 2003, 332, 1183-1193.
49. van Kampen, N. G. Stochastic Processes in Physics and Chemistry; North-Holland: Amsterdam, 1981; Chapter V.
50. Pilling, M. J.; Robertson, S. H. Ann. Rev. Phys. Chem. 2003, 54, 245-275.
51. Barker, J. R.; Golden, D. M. Chem. Rev. 2003, 103, 4577-4591.
52. Mattis, D. C.; Glasser, M. L. Rev. Mod. Phys. 1998, 70, 979-1001.
53. Sham, Y. Y.; Muegge, I.; Warshel, A. Proteins: Struct. Funct. Genet. 1999, 36, 484-500.
54. Bashford, D.; Karplus, M. Biochemistry 1990, 29, 10219-10225.
55. Spassov, V. Z.; Bashford, D. J. Comput. Chem. 1999, 20, 1091-1111.
56. Tanford, C.; Kirkwood, J. G. J. Am. Chem. Soc. 1957, 79, 5333-5339.
57. Yang, A.-S.; Gunner, M. R.; Sampogna, R.; Sharp, K.; Honig, B. Proteins 1993, 15, 252-265.
58. Frankcombe, T. J.; Smith, S. C. J. Comput. Chem. 2000, 21, 592-606.
59. Frankcombe, T. J.; Smith, S. C. J. Theor. Comput. Chem. 2003, 2, 179-191.
60. Zscherp, C.; Schlesinger, R.; Tutor, J.; Oesterhelt, D.; Heberle, J. Proc. Natl. Acad. Sci. U.S.A. 1999, 96, 5498-5503.
61. Wang, J.; El-Sayed, M. A. J. Phys. Chem. A 2000, 104, 4333-4337.
62. Garczarek, F.; Brown, L. S.; Lanyi, J. K.; Gerwert, K. Proc. Natl. Acad. Sci. U.S.A. 2005, 102, 3564-3569.
63. Tavan, P.; Schulten, K.; Oesterhelt, D. Biophys. J. 1985, 47, 415-430.
64. Bashford, D. An object-oriented programming suite for electrostatic effects in biological molecules. In Scientific Computing in Object-Oriented Parallel Environments, Vol. 1343; Ishikawa, Y., Oldehoeft, R. R., Reynders, J. V. W., Tholburn, M., Eds.; Springer: Berlin, 1997.
65. Abola, E. E.; Sussman, J. L.; Prilusky, J.; Manning, N. O. Methods Enzymol. 1997, 277.
66. Abola, E. E.; Bernstein, F. C.; Bryant, S. H.; Koetzle, T. F.; Weng, J. Protein data bank. In Crystallographic Databases-Informaton Content, Software Systems, Scientific Applications; Allan, F. H., Bergerhoff, G., Sievers, R., Eds.; Data Comminssion of the International Union of Crystallography: Bonn/Cambridge/Chester, 1987.
67. Okumura, H.; Murakami, M.; Kouyama, T. J. Mol. Biol. 2005, 351, 481-495.
68. Ludmann, K.; Gergely, C.; Váró, G. Biophys. J. 1998, 75, 3110-3119.
69. Beazley, D. Python Essential Reference. 2 ed.; New Riders: Indianapolis, 2001; see also http://www.python.org.
70. Ascher, D.; Dubois, P. F.; Hinsen, K.; Hugunin, J.; Oliphant, T. Numerical python. Lawrence Livermore National Lab: 2001; http://numeric.scipy. org.
71. Anderson, E.; Bai, Z.; Bischof, C.; Blackford, S.; Demmel, J.; Dongarra, J.; Du Croz, J.; Greenbaum, A.; Hammarling, S.; McKenney, A.; Sorensen, D. LAPACK Users' Guide, 3rd ed.; Society for Industrial and Applied Mathematics: Philadelphia, 1999.
72. Gansner, E. R.; North, S. C. Software Pract. Exp. 2000, 30, 1203-1233; http://www.graphviz.org.
73. Onufriev, A.; Case, D. A.; Ullmann, G. M. Biochemistry 2001, 40, 3413-3419.
74. Balashov, S. P.; Imasheva, E. S.; Govindjee, R.; Ebrey, T. G. Biophys. J. 1996, 70, 473-481.
75. Balashov, S. P.; Lu, M.; Imasheva, E. S.; Govindjee, R.; Ebrey, T. G.; Othersen III, B.; Chen, Y.; Crouch, R. K.; Menick, D. R. Biochemistry 1999, 38, 2026-39.
76. Misra, S.; Govindjee, R.; Ebrey, T. G.; Chen, N.; Ma, J.-X.; Crouch, R. K. Biochemistry 1997, 36, 4875-4883.
77. Váró, G.; Lanyi, J. K. Biochemistry 1991, 30, 5008-5015.
78. Stuchebrukhov, A. A. J. Theor. Comp. Chem. 2003, 2, 91-118.