Simulating the proton transfer in gramicidin a by a sequential dynamical Monte Carlo method

Journal of Physical Chemistry B

Volumn 112, Issue 42, 2008, Pages 13401-13410

  Till, Mirco S ^a   Essigke, Timm ^a   Becker, Torsten ^a   Ullmann, G Matthias ^a  

^a UNIVERSITÄT BAYREUTH   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL SYSTEMS; BIOMOLECULES; CHARGE TRANSFER; DETOXIFICATION; HYDROGEN; HYDROGEN BONDS; ION EXCHANGE; MASS TRANSFER; MOLECULAR BIOLOGY; MOLECULES; MONTE CARLO METHODS; PH; PH EFFECTS; PROTONS; RANDOM PROCESSES; ROTATION; SEQUENTIAL SWITCHING; SYSTEMS ANALYSIS; SYSTEMS ENGINEERING;

BIOCHEMICAL PROCESSES; BIOLOGICAL ENERGIES; CHALLENGING TASKS; ELECTROSTATIC CALCULATIONS; ELEMENTARY STEPS; ENERGETIC PARAMETERS; EXPERIMENTAL DATUMS; GRAMICIDIN A; IN DEPENDENCES; MASTER EQUATIONS; MEMBRANE POTENTIALS; MICROSTATES; MOLECULAR LEVELS; MONTE CARLO; PENTIUM 4; PH VALUES; PROTON CHANNELS; PROTON FLUXES; PROTON UPTAKES; PROTONATION PATTERNS; REACTIVE SYSTEMS; SIMULATION METHODS; STOCHASTIC PROCESSES; TIME SCALES; TRANSMEMBRANE; WATER MOLECULES;

PROTON TRANSFER;

EID: 55649114895     PISSN: 15206106     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp801477b     Document Type: Article

References (51)

1. Krishtalik, L. I. Biochim. Biophys. Acta 2000, 7458, 6-27.
2. Nagle, J. F.; Morowitz, H. J. Proc. Natl. Acad. Sci. U.S.A. 1978, 75, 298-302.
3. Agmon, N. Chem. Phys. Lett. 1995, 244, 456-462.
4. Braun-Sand, S.; Burykin, A.; Chu, Z. T.; Warshel, A. J. Phys. Chem. B 2005, 109, 583-592.
5. Warshel, A. Acc. Chem. Res. 2002, 35, 385-395.
6. Warshel, A. Chem. Rev. 1993, 93, 2523-2544.
7. Voth, O. A. Acc. Chem. Res. 2006, 39, 143-150.
8. Braun-Sand, S.; Strajbl, M.; Warshel, A. Biophys. J. 2004, 87, 2221-2239.
9. Warshel, A.; Weiss, R. M. J. Am. Chem. Soc. 1980, 102, 6218-6226.
10. Schmitt, U. W.; Volh, G. A. J. Chem. Phys. 1999, 111, 9361-9381.
11. Friedman, R.; Nachliel, E.; Gutman, M. Biochim. Biophys. Acta 2005, 1710, 67-77.
12. Marx, D. Com. Phys. Commun. 2006, 7, 1848-1870.
13. Lill, M. A.; Helms, V. J. Chem. Phys. 2001, 115, 7993-8005.
14. Ferreira, A.; Bashford, D. J. Am. Chem. Soc. 2006, 128, 16778-16790.
15. Becker, T.; Ullmann, R. T.; Ullmann, G. M. J. Phys. Chem. B 2007, 111, 2957-2968.
16. Gillespie, D. T. J. Phys. Chem. 1977, 81, 2340-2361.
17. Fichthorn, K. A.; Weinberg, W. H. J. Chem. Phys. 1991, 95, 1090-1096.
18. Burkhart, B. M.; Li, N.; Langs, D. A.; Pangborn, W. A.; Duax, W. L. Proc. Natl. Acad. Sci. U.S.A. 1998, 95, 12950-12955.
19. Eisenman, G.; Enos, B.; Hagglund, J.; Sandblom, J. Ann. N.Y. Acad. Sci. 1980, 339, 8-20.
20. Andersen, O. S.; Koeppe, R. E.; B. R. IEEE Trans. Nanobiosci. 2005, 4, 10-20.
21. Pomes, R.; Roux, B. Biophys. J. 2002, 82, 2304-2316.
22. de Groot, B. L.; Tieleman, D. P.; Pohl, P.; Grubmüller, H. Biophys. J. 2002, 82, 2934-2942.
23. Chernyshev, A.; Cukierman, S. Biophys. J. 2006, 91, 580-587.
24. Cukierman, S. Biophys. J. 2000, 78, 1825-1834.
25. Akeson, M.; Deamer, D. W. Biophys. J. 1991, 60, 101-109.
26. Cukierman, S.; Quigley, E. P.; Crumrine, D. S. Biophys. J. 1997, 73, 2489-2502.
27. Homeyer, N.; Essigke, T.; Ullmann, G.; Sticht, H. Biochemistry 2007, 46, 12314-12326.
28. Klingen, A. R.; Bombarda, E.; Ullmann, G. M. Photochem. Photobiol. Sci. 2006, 5, 588-596.
29. Ullmann, G. J. Phys. Chem. B 2003, 107, 1263-1271.
30. Ullmann, G. M.; Knapp, E.-W. Eur. Biophys. J. 1999, 28, 533-551.
31. Bombarda, E.; Becker, T.; Ullmann, G. M. J. Am. Chem. Soc. 2006, 128, 12129-12139.
32. Landau, D. P.; Binder, K. A Guide to Monte Carlo Simulations in Statistical Physics; Cambridge University Press: New York, 2000.
33. Prados, A.; Brey, J.; SanchezRey, B. J. Stat. Phys. 1997, 89, 709-734.
34. Sadhukhan, S.; Munoz, D.; Adamo, C.; Scuseria, G. E. Chem, Phys. Lett. 1999, 306, 83-87.
35. Pavese, M.; Chawla, S.; Lu, D. S.; Lobaugh, J.; Voth, G. A. J. Chem. Phys. 1997, 107, 7428-7432.
36. Lill, M. A.; Helms, V. J. Chem. Phys. 2001, 115, 7985-7992.
37. Barroso, M.; Arnaut, L. G.; Formosinho, S. J. J. Phys. Chem. A 2007, 111, 591-602.
38. Cherepanov, D. A.; Junge, W.; Mulkidjanian, A. Y. Biophys. J. 2004, 86, 665-680.
39. Mulkidjanian, A. Y.; Heberle, J.; Cherepanov, D. A. Biochim. Biophys. Acta 2006, 1757, 913-930.
40. Espinosa, E.; Molins, E.; Lecomte, C. Chem. Phys. Lett. 1998, 285, 170-173.
41. Woutersen, S.; Emmerichs, U.; Bakker, H. J. Science 1997, 278 (5338), 658-660.
42. Townsley, L. E.; Tucker, A, W.; Sham, S.; Hinton, F, J. Biochemistry 2001, 40, 11676-11686.
43. Brooks, B. R.; Bruccoleri, R. E.; Olafson, B. D.; States, D. J.; Swaminatha, S.; Karplus, M. J. Comput. Chem. 1983, 4, 187-217.
44. Swart, M.; Van Duijnen, P. T.; Snijders, J. G. J. Chem. Phys. 2001, 22, 79-88.
45. Guerra, C. F.; Snijders, J. G.; te Velde, G.; Baerends, E. J. Theor. Chem. Acc. 1998, 99, 391-403.
46. Bashford, D.; Gerwert, K. J. Mol. Biol. 1992, 224, 473-486.
47. MacKerell, A. D.; Bashford, D.; Bellott, M.; Dunbrack, R. L.; Evanseck, J. D.; Field, M. J.; Fischer, S.; Gao, J.; Guo, H.; Ha, S.; Joseph-McCarthy, D.; Kuchnir, L.; Kuczera, K.; Lau, F. T. K.; Mattos, C.; Michnick, S.; Ngo, T.; Nguyen, D. T.; Prodhom, B.; Reiher, W. E.; Roux, B.; Schlenkrich, M.; Smith, J. C.; Stote, R.; Straub, J.; Watanabe, M.; Wiorkiewicz-Kuczera, J.; Yin, D.; Karplus, M. J. Phys. Chem. B 1998, 102, 3586-3616.
48. Im, W.; Beglov, D.; Roux, B. Com. Phys. Commun. 1998, 111, 59-75.
49. Roux, B. Biophys. J. 1997, 73, 2980-2989.
50. de Groot, B. L.; Frigato, T.; Helms, V.; Grubmüller, H. J. Mol. Biol. 2003, 333, 279-293.
51. Jensen, M. O.; Tajkhorshid, E.; Schulten, K. Biophys. J. 2003, 85, 2884-2899.