Computational spectroscopy of ubiquitin: Comparison between theory and experiments

Journal of Chemical Physics

Volumn 126, Issue 4, 2007, Pages

  Choi, Jun Ho ^b   Lee, Hochan ^b   Lee, Kyung Koo ^b   Hahn, Seungsoo ^b   Cho, Minhaeng ^a  

^a Korea University   (South Korea)

^b NONE

Author keywords

[No Author keywords available]

Indexed keywords

DICHROISM; HAMILTONIANS; INFRARED ABSORPTION; MOLECULAR DYNAMICS; QUANTUM CHEMISTRY; SPECTROSCOPIC ANALYSIS;

HESSIAN MATRIX RECONSTRUCTION; QUANTUM CHEMISTRY CALCULATION; VCD SPECTRUM; VIBRATIONAL CIRCULAR DICHROISM;

PROTEINS;

UBIQUITIN;

ARTICLE; CHEMICAL MODEL; CHEMICAL STRUCTURE; CHEMISTRY; CIRCULAR DICHROISM; COMPARATIVE STUDY; COMPUTER SIMULATION; EVALUATION; INFRARED SPECTROPHOTOMETRY; PROTEIN CONFORMATION; ULTRASTRUCTURE; VALIDATION STUDY;

CIRCULAR DICHROISM; COMPUTER SIMULATION; MODELS, CHEMICAL; MODELS, MOLECULAR; PROTEIN CONFORMATION; SPECTROPHOTOMETRY, INFRARED; UBIQUITIN;

EID: 33847691555     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.2424711     Document Type: Article

References (81)

1. J. Kubelka, J. Kim, P. Bour, and T. A. Keiderling, Vib. Spectrosc. 42, 63 (2006).
2. R. Schweitzer-Stenner, Vib. Spectrosc. 42, 98 (2006).
3. P. Hamm, M. Lim, and R. M. Hochstrasser, J. Phys. Chem. B 102, 6123 (1998).
4. S. M. Decatur, Acc. Chem. Res. 39, 169 (2006).
5. V. Baumruk and T. A. Keiderling, J. Am. Chem. Soc. 115, 6939 (1993).
6. S. Krimm and J. Bandekar, Adv. Protein Chem. 38, 181 (1986).
7. J. Wang, J. Chen, and R. M. Hochstrasser, J. Phys. Chem. B 110, 7545 (2006).
8. H. Maekawa, C. Toniolo, A. Moretto, Q. B. Broxterman, and N.-H. Ge, J. Phys. Chem. B 110, 5834 (2006).
9. R. Schweitzer-Stenner, T. Measey, A. Hagarman, F. Eker, and K. Griebenow, Biochemistry 45, 2810 (2006).
10. A. V. Mikhonin, S. V. Bykov, N. S. Myshakina, and S. A. Asher, J. Phys. Chem. B 110, 1928 (2006).
11. A. W. Smith, H. S. Chung, Z. Ganim, and A. Tokmakoff, J. Phys. Chem. B 109, 17025 (2005).
12. A. V. Mikhonin, N. S. Myshakina, S. V. Bykov, and S. A. Asher, J. Am. Chem. Soc. 127, 7712 (2005).
13. V. Setnička, R. Huang, C. L. Thomas, M. A. Etienne, J. Kubelka, R. P. Hammer, and T. A. Keiderling, J. Am. Chem. Soc. 127, 4992 (2005).
14. H. S. Chung, M. Khalil, A. W. Smith, Z. Ganim, and A. Tokmakoff, Proc. Natl. Acad. Sci. U.S.A. 102, 612 (2005).
15. R. Schweitzer-Stenner, J. Phys. Chem. B 108, 16965 (2004).
16. C. Fang, J. Wang, Y. S. Kim, A. K. Charnley, W. Barber-Armstrong, A. B. Smith III, S. M. Decatur, and R. M. Hochstrasser, J. Phys. Chem. B 108, 10415 (2004).
17. N. Demirdöven, C. M. Cheatum, H. S. Chung, M. Khalil, J. Knoester, and A. Tokmakoff, J. Am. Chem. Soc. 126, 7981 (2004).
18. F. Eker, K. Griebenow, and R. Schweitzer-Stenner, Biochemistry 43, 6893 (2004).
19. R. Huang, J. Kubelka, W. Barber-Armstrong, R. A. G. D. Silva, S. M. Decatur, and T. A. Keiderling, J. Am. Chem. Soc. 126, 2346 (2004).
20. W. Barber-Armstrong, T. Donaldson, H. Wijesooriya, R. A. G. D. Silva, and S. M. Decatur, J. Am. Chem. Soc. 126, 2339 (2004).
21. R. A. G. D. Silva, W. Barber-Armstrong, and S. M. Decatur, J. Am. Chem. Soc. 125, 13674 (2003).
22. A. Barth and C. Zscherp, Q. Rev. Biophys. 35, 369 (2002).
23. F. Eker, X. Cao, L. Nafie, and R. Schweitzer-Stenner, J. Am. Chem. Soc. 124, 14330 (2002).
24. T. A. Keiderling, Curr. Opin. Chem. Biol. 6, 682 (2002).
25. J. Kubelka and T. A. Keiderling, J. Am. Chem. Soc. 123, 12048 (2001).
26. S. A. Asher, A. Ianoul, G. Mix, M. N. Boyden, A. Karnoup, M. Diem, and R. Schweitzer-Stenner, J. Am. Chem. Soc. 123, 11775 (2001).
27. C. Zhao, P. L. Polavarapu, C. Das, and P. Balaram, J. Am. Chem. Soc. 122, 8228 (2000).
28. S. M. Decatur, Biopolymers 54, 180 (2000).
29. Circular Dichroism: Principles and Applications, edited by, N. Berova, K. Nakanishi, and, R. W. Woody, (Wiley-VCH, New York, 2000).
30. W. K. Surewicz, H. H. Mantsch, and D. Chapman, Biochemistry 32, 389 (1993).
31. H. Susi and D. M. Byler, Methods Enzymol. 130, 290 (1986).
32. J. W. Brauner, C. R. Flach, and R. Mendelsohn, J. Am. Chem. Soc. 127, 100 (2005).
33. S. Woutersen and P. Hamm, J. Chem. Phys. 115, 7737 (2001).
34. A. T. Krummel, P. Mukherjee, and M. T. Zanni, J. Phys. Chem. B 107, 9165 (2003).
35. A. T. Krummel and M. T. Zanni, J. Phys. Chem. B 110, 13991 (2006).
36. J. Zheng, K. Kwak, J. B. Asbury, X. Chen, I. Piletic, and M. D. Fayer, Science 309, 1338 (2005).
37. J. Zheng, K. Kwak, X. Chen, J. B. Asbury, and M. D. Fayer, J. Am. Chem. Soc. 128, 2977 (2006).
38. P. Bour, J. Sopkova, L. Bednarova, P. Malon, and T. A. Keiderling, J. Comput. Chem. 18, 646 (1997).
39. M. Cho, J. Chem. Phys. 118, 3480 (2003).
40. G. Holzwarth and I. Chabay, J. Chem. Phys. 57, 1632 (1972).
41. S. Krimm, J. Mol. Biol. 4, 528 (1962).
42. T. Miyazawa, J. Chem. Phys. 32, 1647 (1960).
43. A. M. Moran, S.-M. Park, J. Dreyer, and S. Mukamel, J. Chem. Phys. 118, 3651 (2003).
44. J. Wang and R. M. Hochstrasser, Chem. Phys. 297, 195 (2004).
45. S. Krimm and Y. Abe, Proc. Natl. Acad. Sci. U.S.A. 69, 2788 (1972).
46. H. Torii and M. Tasumi, J. Chem. Phys. 96, 3379 (1992).
47. J.-H. Choi, S. Ham, and M. Cho, J. Chem. Phys. 117, 6821 (2002).
48. J. Kubelka and T. A. Keiderling, J. Am. Chem. Soc. 123, 6142 (2001).
49. J.-H. Choi, S. Hahn, and M. Cho, Int. J. Quantum Chem. 104, 616 (2005).
50. S. Ham, S. Hahn, C. Lee, T.-K. Kim, K. Kwak, and M. Cho, J. Phys. Chem. B 108, 9333 (2004).
51. C. Lee and M. Cho, J. Phys. Chem. B 108, 20397 (2004).
52. S. Hahn, S.-S. Kim, C. Lee, and M. Cho, J. Chem. Phys. 123, 084905 (2005).
53. S. Hahn, S. Ham, and M. Cho, J. Phys. Chem. B 109, 11789 (2005).
54. M. Rechsteiner, Ubiquitin (Plenum, New York, 1984).
55. C. S. Colley, I. P. Clark, S. R. Griffiths-Jones, M. W. George, and M. S. Searle, Chem. Commun. (Cambridge) 16, 1493 (2000).
56. S. T. Thomas and G. I. Makhatadze, Biochemistry 39, 10275 (2000).
57. M. W. Schmidt, K. K. Baldridge, J. A. Boatz, J. Comput. Chem. 14, 1347 (1993).
58. S. Ham, S. Cha, J.-H. Choi, and M. Cho, J. Chem. Phys. 119, 1451 (2003).
59. J.-H. Choi, S. Ham, and M. Cho, J. Phys. Chem. B 107, 9132 (2003).
60. D. A. Case, D. A. Pearlman, and J. W. Caldwell, AMBER 7, University of California, San Francisco, 2002.
61. T. Darden, D. York, and L. Pedersen, J. Chem. Phys. 98, 10089 (1993).
62. H. J. C. Berendsen, J. P. M. Postma, W. F. van Gunsteren, A. DiNola, and J. R. Haak, J. Chem. Phys. 81, 3684 (1984).
63. S. Ham and M. Cho, J. Chem. Phys. 118, 6915 (2003).
64. J.-H. Choi, S. Hahn, and M. Cho, Biopolymers 83, 519 (2006).
65. J.-H. Choi and M. Cho, J. Chem. Phys. 120, 4383 (2004).
66. J.-H. Choi, J.-S. Kim, and M. Cho, J. Chem. Phys. 122, 174903 (2005).
67. L. Z. Rosenfeld, Z. Phys. 52, 161 (1928).
68. P. M. Bayley, E. B. Nielsen, and J. A. Schellman, J. Phys. Chem. 73, 228 (1969).
69. R. W. Woody, J. Chem. Phys. 49, 4797 (1968).
70. I. Tinoco, Adv. Chem. Phys. 4, 113 (1962).
71. G. Kurapkat, P. Krüger, A. Wollmer, J. Fleischhauer, B. Kramer, E. Zobel, A. Koslowski, H. Botterweck, and R. W. Woody, Biopolymers 41, 267 (1997).
72. J. D. Hirst, D. M. Hirst, and C. L. Brooks III, J. Phys. Chem. A 101, 4821 (1997).
73. R. W. Woody and N. Sreerama, J. Chem. Phys. 111, 2844 (1999).
74. N. A. Besley and J. D. Hirst, J. Am. Chem. Soc. 121, 9636 (1999).
75. R. W. Woody, Monatsch. Chem. 136, 347 (2005).
76. M. Schreiber and Y. Toyozawa, J. Phys. Soc. Jpn. 51, 1537 (1982).
77. D. J. Thouless, Phys. Rep. 13, 93 (1974).
78. G. Shanmugam and P. L. Polavarapu, J. Am. Chem. Soc. 126, 10292 (2004).
79. J. Hilario, J. Kubelka, and T. A. Keiderling, J. Am. Chem. Soc. 125, 7562 (2003).
80. M. T. Zanni, N.-H. Ge, Y. S. Kim, and R. M. Hochstrasser, Proc. Natl. Acad. Sci. U.S.A. 98, 11265 (2001).
81. C. M. Cheatum, A. Tokmakoff, and J. Knoester, J. Chem. Phys. 120, 8201 (2004).