Vibrational energy relaxation in proteins

Proceedings of the National Academy of Sciences of the United States of America

Volumn 102, Issue 19, 2005, Pages 6726-6731

  Fujisaki, Hiroshi ^a   Straub, John E ^a  

^a Boston University ^*  (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CYTOCHROME C; PROTEIN;

ANALYTIC METHOD; CIRCULAR DICHROISM; ENERGY TRANSFER; MATHEMATICAL MODEL; NONLINEAR SYSTEM; PRIORITY JOURNAL; PROTEIN INTERACTION; QUANTUM MECHANICS; REVIEW; SIMULATION; VIBRATION;

ADENOSINE TRIPHOSPHATE; BIOPHYSICS; CIRCULAR DICHROISM; CYTOCHROMES C; ELECTROSTATICS; LIGANDS; MODELS, MOLECULAR; MODELS, STATISTICAL; MOLECULAR CONFORMATION; PROTEIN CONFORMATION; PROTEINS; QUANTUM THEORY; SPECTROPHOTOMETRY; TEMPERATURE; VIBRATION;

EID: 18744380061     PISSN: 00278424     EISSN: None     Source Type: Journal    
DOI: 10.1073/pnas.0409083102     Document Type: Review

References (71)

1. Berne, B. J., Borkovec, M. & Straub, J. E. (1988) J. Phys. Chem. 92, 3711-3725.
2. Gruebele, M. & Wolynes, P. G. (2004) Acc. Chem. Res. 37, 261-267.
3. Dian, B. C., Longarte, A. & Zwier, T. S. (2002) Science 296, 2369-2373.
4. Lian, T., Locke, B., Kholodenko, Y. & Hochstrasser, R. M. (1994) J. Phys. Chem. 98, 11648-11656.
5. Lim, M. H., Jackson, T. A. & Anfinrud, P. A. (1996) J. Phys. Chem. 100, 12043-12051.
6. Mizutani, Y. & Kitagawa, T. (1997) Science 278, 443-446.
7. Sagnella, D. E., Straub, J. E., Jackson, T. A., Lim, M. & Anfinrud, P. A. (1999) Proc. Natl. Acad. Sci. USA 96, 14324-14329.
8. Rosca, F., Kumar, A. T. N., Ye, X., Sjodin, T., Demidov, A. A. & Champion, P. M. (2000) J. Phys. Chem. A 104, 4280-4290.
9. Wang, W., Ye, X., Demidov, A. A., Rosca, F., Sjodin, T., Cao, W., Sheeran, M. & Champion, P. M. (2000) J. Phys. Chem. B 104, 10789-10801.
10. Xie, A., van der Meer, L., Hoff, W. & Austin, R. H. (2000) Phys. Rev. Lett. 84, 5435-5438.
11. Fayer, M. D. (2001) Annu. Rev. Phys. Chem. 52, 315-356.
12. Chin, J. K., Jimenez, R. & Romesberg, F. E. (2001) J. Am. Chem. Soc. 123, 2426-2427.
13. Chin, J. K., Jimenez, R. & Romesberg, F. E. (2002) J. Am. Chem. Soc. 124, 1846-1847.
14. Ye, X., Demidov, A. & Champion, P. M. (2002) J. Am. Chem. Soc. 124, 5914-5924.
15. Xie, A., van der Meer, A. F. G. & Austin, R. H. (2002) Phys. Rev. Lett. 88, 018102-1-4.
16. Merchant, K. A., Noid, W. G., Thompson, D. E., Akiyama, R., Loring, R. F. & Fayer, M. D. (2003) J. Phys. Chem. B 107, 4-7.
17. Sagle, L. B., Zimmermann, J., Dawson, P. E. & Romesberg, F. E. (2004) J. Am. Chem. Soc. 126, 3384-3385.
18. Leitner, D. M. (2005) Adv. Chem. Phys., in press.
19. Fujisaki, H., Bu, L. & Straub, J. E. (2005) Adv. Chem. Phys., in press.
20. Fujisaki, H., Bu, L. & Straub, J. E. (2005) in Normal Mode Analysis: Theory and Applications to Biological and Chemical Systems, eds. Cui, Q. & Bahar, I., in press.
21. Whitnell, R. E., Wilson, K. R. & Hynes, J. T. (1992) J. Chem. Phys. 96, 5354-5369.
22. Sagnella, D. E. & Straub, J. E. (1999) Biophys. J. 77, 70-84.
23. Skinner, J. L. & Park, K. (2001) J. Phys. Chem. B 105, 6716-6721.
24. Bader, J. S. & Berne, B. J. (1994) J. Chem. Phys. 100, 8359-8366.
25. Shiga, M. & Okazaki, S. (1999) J. Chem. Phys. 111, 5390-5401.
26. Mikami, T., Shiga, M. & Okazaki, S. (2001) J. Chem. Phys. 115, 9797-9807.
27. Shi, Q. & Geva, E. (2003) J. Phys. Chem. A 107, 9070-9078.
28. Lawrence, C. P., Nakayama, A., Makri, N. & Skinner, J. L. (2004) J. Chem. Phys. 120, 6621-6624.
29. Maradudin, A. A. & Fein, A. E. (1962) Phys. Rev. 128, 2589-2608.
30. Kenkre, V. M., Tokmakoff, A. & Fayer, M. D. (1994) J. Chem. Phys. 101, 10618-10629.
31. Miller, W. H. (2001) J. Phys. Chem. A 105, 2942-2955.
32. Jungwirth, P. & Gerber, R. B. (1999) Chem. Rev. 99, 1583-1606.
33. Makri, N. (1999) Annu. Rev. Phys. Chem. 50, 167-191.
34. Rabani, E. & Reichman, D. R. (2001) J. Phys. Chem. B 105, 6550-6555.
35. Kim, H. & Rossky, P. J. (2002) J. Phys. Chem. B 106, 8240-8247.
36. Poulsen, J. A., Nyman, G. & Rossky, P. J. (2003) J. Chem. Phys. 119, 12179-12193.
37. Bader, J. S., Berne, B. J., Pollak, E. & Hänggi, P. (1996) J. Chem. Phys. 104, 1111-1119.
38. Henry, E. R., Eaton, W. A. & Hochstrasser, R. M. (1986) Proc. Natl. Acad. Sci. USA 83, 8982-8986.
39. Okazaki, I., Hara, Y. & Nagaoka, M. (2001) Chem. Phys. Lett. 337, 151-157.
40. Sagnella, D. E. & Straub, J. E. (2001) J. Phys. Chem. B 105, 7057-7063.
41. Bu, L. & Straub, J. E. (2003) J. Phys. Chem. B 107, 10634-10639.
42. Bu, L. & Straub, J. E. (2003) J. Phys. Chem. B 107, 12339-12345.
43. Moritsugu, K., Miyashita, O. & Kidera, A. (2003) J. Phys. Chem. B 107, 3309-3317.
44. Hahn, S. & Stock, G. (2000) Chem. Phys. 259, 297-312.
45. Flores, S. C. & Batista, V. S. (2004) J. Phys. Chem. B 108, 6745-6749.
46. Roitberg, A., Gerber, R. B. & Ratner, M. (1997) J. Phys. Chem. B 101, 1700-1706.
47. Hayashi, S., Tajkhorshid, E. & Schulten, K. (2003) Biophys. J. 85, 1440-1449.
48. Wong, C. F., Zheng, C., Shen, J., McCammon, J. A. & Wolynes, P. G. (1993) J. Phys. Chem. 97, 3100-3110.
49. Wang, Q., Wong, C. F. & Rabitz, H. (1998) Biophys. J. 75, 60-69.
50. Garcia, A. E. & Hummer, G. (1999) Proteins 36, 175-191.
51. Humphrey, W., Dalke, A. & Schulten, K. (1996) J. Mol. Graphics 14, 33-38.
52. Bu, L. & Straub, J. E. (2003) Biophys. J. 85, 1429-1439.
53. Brooks, B. R., Bruccoleri, R. E., Olafson, B. D., States, D. J., Swaminathan, S. & Karplus, M. (1983) J. Comp. Chem. 4, 187-217.
54. Stuchebrukhov, A. A. & Marcus, R. A. (1993) J. Chem. Phys. 98, 6044-6061.
55. Madan, B., Keyes, T. & Seeley, G. (1991) J. Chem. Phys. 94, 6762-6769.
56. Cao, J. & Voth, G. A. (1995) J. Chem. Phys. 103, 4211-4220.
57. Ma, J., Huo, S. & Straub, J. E. (1997) J. Am. Chem. Soc. 119, 2541-2551.
58. Ma, J., Huo, S. & Straub, J. E. (1997) J. Am. Chem. Soc. 119, 6454.
59. Meller, J. & Elber, R. (1998) Biophys. J. 74, 789-802.
60. Nguyen, P. H. & Stock, G. (2003) J. Chem. Phys. 119, 11350-11358.
61. Terashima, T., Shiga, M. & Okazaki, S. (2001) J. Chem. Phys. 114, 5663-5673.
62. Woutersen, S. & Hamm, P. (2002) J. Phys. Condens. Matter 14, R1035-R1062.
63. Khalil, K., Demirdöven, N. & Tokmakoff, A. (2003) J. Phys. Chem. A 107, 5258-5279.
64. Kitao, A. & Go, N. (1999) Curr. Opin. Struc. Biol. 9, 164-169.
65. Kamiya, N., Higo, J. & Nakamura, H. (2002) Protein Sci. 11, 2297-2307.
66. Straub, J. E., Rashkin, A. B. & Thirumalai, D. (1994) J. Am. Chem. Soc. 116, 2049-2063.
67. Vitkup, D., Ringe, D., Petsko, G. A. & Karplus, M. (2000) Nat. Struc. Biol. 7, 34-38.
68. Higo, J., Sasai, M., Shirai, H., Nakamura, H. & Kugimiya, T. (2001) Proc. Natl. Acad. Sci. USA 98, 5961-5964.
69. Trek, M. & Tobias, D. J. (2002) Phys. Rev. Lett. 88, 138101-1-4.
70. Fenimore, P. W., Frauenfelder, H., McMahon, B. H. & Parak, F. G. (2002) Proc. Natl. Acad. Sci. USA 99, 16047-16051.
71. Massi, F. & Straub, J. E. (2003) J. Comp. Chem. 24, 143-153.