Determination of protein surface hydration shell free energy of water motion: Theoretical study and molecular dynamics simulation

Journal of Physical Chemistry B

Volumn 114, Issue 49, 2010, Pages 16558-16566

  Sheu, Sheh Yi ^a   Yang, Dah Yen ^b,c  

^a NATIONAL YANG MING UNIVERSITY   (Taiwan)

^b ACADEMIA SINICA   (Taiwan)

^c INSTITUTE FOR MOLECULAR SCIENCE   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

BROWNIAN MOVEMENT; DISTRIBUTION FUNCTIONS; DYNAMICS; FOKKER PLANCK EQUATION; FREE ENERGY; MOLECULAR DYNAMICS; MOLECULAR MECHANICS; MOLECULES; PROTEINS; SHELLS (STRUCTURES); SURFACE WATERS;

ACTIVATION ENTROPIES; BARRIER HEIGHTS; BIOLOGICAL PROCESS; BIOLOGICAL WATER; BULK WATER; DETERMINATION OF PROTEINS; EFFECT OF TEMPERATURE; FRACTIONAL BROWNIAN MOTION; FRACTIONAL FOKKER-PLANCK EQUATION; GAS CONSTANTS; HYDRATION SHELL; HYDRATION WATER; INTRIGUING QUESTIONS; LOW MOBILITY; MEAN FIRST PASSAGE TIME; MECHANISTIC ASPECTS; MOLECULAR DYNAMICS SIMULATIONS; NUMERICAL SIMULATION; PROTEIN SURFACE; PURE WATER; QUANTITATIVE ESTIMATES; RADIAL DISTRIBUTION FUNCTIONS; THEORETICAL STUDY; WATER MOBILITY; WATER MOLECULE; WATER MOTION;

HYDRATION;

EID: 78650146283     PISSN: 15206106     EISSN: 15205207     Source Type: Journal    
DOI: 10.1021/jp105164t     Document Type: Article

References (53)

1. Huber, R.; Kukla, D.; Bode, W.; Schwager, P.; Beartels, K.; Deisenhofer, J.; Steigenmann, W. J. Mol. Biol. 1974, 89, 73
2. Otting, G.; Liepinsh, E.; Wuthrich, K. Science 1991, 254, 974
3. Modig, K.; Liepinsh, E.; Otting, G.; Halle, B. J. Am. Chem. Soc. 2004, 126, 102
4. Halle, B. Philos. Trans. R. Soc. London, Ser. B 2004, 359, 1207
5. Pal, S. K.; Peon, J.; Bagchi, B.; Zewail, A. H. J. Phys. Chem. B 2002, 106, 12376
6. Denisob, V. P.; Halle, B. Faraday Discuss. 1996, 103, 227
7. Nandi, N.; Bhattacharyya, K.; Bagchi, B. Chem. Rev. 2000, 100, 2013
8. Bellissent-Funel, M. G. J. Mol. Liq. 2000, 84, 39
9. Dellerue, S.; Bellissen-Funel, M. C. Chem. Phys. 2000, 258, 315
10. Bagchi, B. Chem. Rev. 2000, 105, 3197
11. Grant, E. H.; Sheppard, R. J.; South, G. P. Dielectric Behavior of Biological Molecules in Solution; Oxford: U.K., 1978.
12. Rocchi, C.; Bizzarri, A. R.; Cannistraro, S. Phys. Rev. E 1998, 57, 3315
13. Pizzitutti, F.; Marchi, M.; Sterpone, F.; Rossky, P. J. J. Phys. Chem. B 2007, 111, 7584
14. Rossky, P. J.; Karplus, M. J. Am. Chem. Soc. 1979, 101, 1913
15. Rezus, Y. L. A.; Bakker, H. J. Phys. Rev. Lett. 2007, 99, 148301
16. Kumar, P.; Yan, Z.; Xu, L.; Mazza, M. G.; Buldyrev, S. V.; Chen, S.-H.; Sastry, S.; Stanley, H. E. Phys. Rev. Lett. 2006, 97, 177802
17. Raschke, T. M. Curr. Opin. Struct. Biol. 2006, 16, 152
18. Makarov, V.; Pettitt, B. M.; Feig, M. Acc. Chem. Res. 2002, 35, 376
19. Makarov, V. A.; Andrews, B. K.; Pettitt, B. M. Biopolymers 1998, 45, 469
20. Austin, R. H.; Beeson, K. W.; Eisenstein, L.; Frauenfelder, H.; Gunsalus, I. C. Biochemistry 1975, 14, 5355
21. Frauenfelder, H. Helv. Phys. Acta 1984, 57, 165
22. Frauenfelder, H.; Steinbach, P. J.; Young, R. D. Chem. Scr. 1989, 29A, 145
23. Young, R. D. Chem. Phys. 1991, 158, 315
24. Frauenfelder, H.; Parak, F.; Young, R. D. Ann. Rev. Biophys. Chem. 1988, 17, 451
25. Frauenfelder, H.; Sligar, S. G.; Wolynes, P. Science 1991, 254, 1598
26. Ansari, A. Proc. Natl. Acad. Sci. U.S.A. 1985, 82, 5000
27. Peon, J.; Pal, S. K.; Zewail, A. H. Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 10964
28. Pal, S. K.; Peon, J.; Zewail, A. H. Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 15297
29. Qiu, W.; Kao, Y.-T.; Zhang, L.; Yang, Y.; Wang, L.; Stites, W. E.; Zhong, D.; Zewail, A. H. Proc. Natl. Acad. Sci. U.S.A. 2006, 103, 13979
30. Quiu, W.; Zhang, L.; Okobiah, O.; Yang, Y.; Wang, L.; Zhong, D.; Zewail, A. H. J. Phys. Chem. B 2006, 110, 10540
31. Bhattacharyya, S. M.; Qang, Z.-G.; Zewail, A. H. J. Phys. Chem. B 2003, 107, 13218
32. Pal, S. K.; Peon, J.; Zewail, A. H. Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 1763
33. Sheu, S. Y.; Schlag, E. W.; Selzle, H. L.; Yang, D. Y. J. Phys. Chem. B 2009, 113, 5318
34. Bicout, D. J.; Szabo, A. Protein Sci. 2000, 9, 452
35. Sheu, S. Y.; Yang, D. Y. J. Chem. Phys. 2000, 112, 408
36. Barkai, E. Phys. Rev. E 2001, 63 046118
37. Metzler, R.; Klafter, J. Chem. Phys. Lett. 2000, 321, 238
38. Dybiec, B.; Gudowska-Nowak, E.; Hanggi, P. Phys. Rev. E 2007, 75, 21109
39. Metzler, R.; Klafter, J. J. Phys. Chem. B 2000, 104, 3851
40. Ansari, A. J. Chem. Phys. 2000, 112, 2516
41. Press, W. H.; Flannery, B. P.; Teukulsky, S. A.; Vetterling, W. T. Numerical Recipes; Cambridge University Press: New York, 1986.
42. Abramowitz, M.; Stegun, I. A. Handbook of Mathematical Functions; Dover Publication: New York, 1965.
43. Brooks, B. R.; Bruccoleri, R. E.; Olafson, B. D.; States, D. J.; Swaminarhan, S.; Karplus, M. J. Comput. Chem. 1983, 4, 187
44. MacKerell, A. D., Jr.; Bashford, D.; Bellott, M.; Dunbrack, R. L., Jr.; 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., III; 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
45. Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D.; Impey, R. W.; Klein, M. L. J. Chem. Phys. 1983, 79, 926
46. Ryckaert, J. P.; Ciccotti, G.; Berendsen, H. J. C. J. Comput. Phys. 1977, 23, 327
47. Essmann, U.; Perera, L.; Berkowitz, M. L.; Darden, T.; Lee, H.; Pedersen, L. G. J. Chem. Phys. 1995, 103, 8577
48. Feller, E. S.; Pastor, R. W.; Rojnuckarin, A.; Bogusz, S.; Brooks, B. R. J. Phys. Chem. 1996, 100, 17011
49. Andersen, H. C. J. Chem. Phys. 1980, 72, 2384
50. Nosé, S. Mol. Phys. 1984, 52, 255; J. Chem. Phys. 1984, 81, 511
51. Hoover, W. G. Phys. Rev. A 1985, 31, 1695
52. Sheu, S. Y.; Yang, D. Y.; Selzle, H. L.; Schlag, E. W. Proc. Natl. Acad. Sci. U.S.A. 2003, 100, 12683
53. Szabo, A.; Schulten, K.; Schulten, Z. J. Chem. Phys. 1980, 72, 4350