Modeling the absorption spectrum of tryptophan in proteins

Journal of Physical Chemistry B

Volumn 109, Issue 48, 2005, Pages 23061-23069

  Rogers, David M ^a   Besley, Nicholas A ^a   O'Shea, Paul ^a   Hirst, Jonathan D ^a  

^a UNIVERSITY OF NOTTINGHAM   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ABSORPTION; CHROMOPHORES; SPECTRUM ANALYSIS; TORSIONAL STRESS;

AB INITIO METHODS; HUMAN SERUM ALBUMIN; TIME-DEPENDENT DENSITY FUNCTIONAL THEORY (TDDFT); TRYPTOPHAN CHROMOPHORE; VERTICAL TRANSITION ENERGIES;

PROTEINS;

EID: 29544448844     PISSN: 15206106     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp053309j     Document Type: Article

References (48)

1. Platt, J. R. J. Chem. Phys. 1949, 17, 484-495.
2. Song, A.-I.; Li, L.-Z.; Yu, T.; Chen, S.-M.; Huang, Z.-X. Protein Eng. 2003, 16, 435-441.
3. Curry, S.; Mandelkow, H.; Brick, P.; Franks, N. Nat. Struct. Biol. 1998, 5, 827-835.
4. Chadborn, N.; Bryant, J.; Bain, A. J.; O'Shea, P. Biophys. J. 1999, 76, 2198-2207.
5. Serrano-Andrés, L.; Roos, B. O.J. Am. Chem. Soc. 1996, 118, 185-195.
6. Catalan, J.; Diaz, C. Chem. Phys. Lett. 2003, 368, 717-723.
7. Korter, T. M.; Pratt, D. W.; Küpper, J. J. Phys. Chem. A 1998, 102, 7211-7216.
8. Carney, J. R.; Zwier, T. S. J. Phys. Chem. A 1999, 103, 9943-9957.
9. Zwier, T. S. Annu. Rev. Phys. Chem. 1996, 47, 205-241.
10. Muiño, P. L.; Callis, P. R J. Chem. Phys. 1994, 100, 4093-4109.
11. Ilich, P.; Haydock, C.; Prendergast, F. G. Chem. Phys. Lett. 1989, '158, 129-134.
12. Chabalowski, C. F.; Garmer, D. R.; Jensen, J. O.; Krauss, M. J. Phys. Chem. 1993, 97, 4608-4613.
13. Fang, W.-H. J. Chem. Phys. 1999, 111, 5361-5367.
14. Sobolewski, A. L.; Domcke, W. Chem. Phys. Lett. 2000, 329, 130-137.
15. Rogers, D. M.; Hirst, J. D. J. Phys. Chem. A 2003, 107, 11191-11200.
16. Somers, K. R. F.; Ceulemans, A. J. Phys. Chem. A 2004, 108, 7577-7583.
17. Dedonder-Lardeux, C.; Jouvet, C.; Perun, S.; Sobolewski, A. L. Phys. Chem. Chem. Phys. 2003, 5, 5118-5126.
18. Somers, K. R. F.; Krüger, P.; Bucikiewicz, S.; De Mayer, M.; Engelborghs, Y.; Ceulemans, A. Protein Sci. 2004, 13, 1823-1831.
19. Roos, B. O. The Complete Active Space Self-Consistent Field Method and Its Applications in Electronic Structure Calculations. In Ab Initio Methods in Quantum Chemistry Part II; Prigogine, I., Rice, S. A., Eds.; Wiley: New York, 1987; Vol. 69, pp 399-446.
20. Roos, B. O.; Fülscher, M. P.; Malmqvist, P.-Å.; Merchán, M.; Serrano-Andrés, L. Theoretical Studies of Electronic Spectra of Organic Molecules. In Quantum Mechanical Electronic Structure Calculations with Chemical Accuracy; Langhoff, S. R., Ed.; Kluwer Academic Publishers: Dordrecht, The Netherlands, 1995; pp 357-438.
21. Case, D. A.; Pearlman, D. A.; Caldwell, J. W.; Cheatham.T. E., III; Ross, W. S.; Simmerling, C. L.; Darden, T. A.; Merz, K. M.; Stanton, R. V.; Cheng, A. L.; et al. AMBER, version 5; University of California: San Francisco, 1997.
22. Brooks, B. R.; Bruccoleri, R. E.; Olafson, B. D.; States, D. J.; Swaminathan, S.; Karplus, M. J. Comput. Chem. 1983, 4, 187-217.
23. Vivian, J. T.; Callis, P. R. Biophys. J. 2001, 80, 2093-2109.
24. Callis, P. R.; Burgess, B. K. J. Phys. Chem. B 1997, 101, 9429-9432.
25. Callis, P. R.; Vivian, J. T. Chem. Phys. Lett. 2003, 369, 409-414.
26. Callis, P. R.; Liu, T. J. Phys. Chem. B 2004, 108, 4248-4259.
27. Car, R.; Parinello, M. Phys. Rev. Lett. 1985, 55, 2471-2474.
28. Svensson, M.; Humbel, S.; Froese, R. D. J.; Matsubara, T.; Sieber, S.; Morokuma, K. J. Phys. Chem. 1996, 100, 19357-19363.
29. Besley, N. A. Chem. Phys. Lett. 2004, 390, 124-129.
30. Besley, N. A.; Oakley, M. T.; Cowan, A. J.; Hirst, J. D. J. Am. Chem. Soc. 2004, 126, 13502-13511.
31. Hirata, S.; Head-Gordon, M. Chem. Phys. Lett. 1999, 17, 291-299.
32. Stephens, P. J.; Devlin, F. J.; Chabalowski, C. F.; Frisch, M. J. J. Phys. Chem. 1994, 98, 11623-11627.
33. Hehre, W. J.; Ditchfield R.; Pople, J. A. J. Chem. Phys. 1972, 56, 2257-2261.
34. Clark, T.; Chandrasekhar, J.; Schleyer, P. v. R. J. Comp. Chem. 1983 4, 294-301.
35. Hariharan, P. C.; Pople, J. A. Theor. Chim. Acta 1973, 28, 213-222.
36. Kong, J.; White, C. A.; Krylov, A. I.; Sherrill, C. D.; Adamson, R. D.; Furlani, T. R.; Lee, M. S.; Lee, A. M.; Gwaltney, S. R.; Adams, T. R.; Ochsenfeld, C.; Gübert, A. T. B.; Kedziora, G. S.; Rassolov, V. A.; Maurice, D. R.; Nair, N.; Shao, Y.; Besley, N. A.; Maslen, P. E.; Dombroski, J. P.; Dachsel, H.; Zhang, W. M.; Korambath, P. P.; Baker, J.; Byrd, E. F. C.; Van Voorhis, T.; Oumi, M.; Hirata, S.; Hsu, C. P.; Ishikawa, N.; Florian, J.; Warshel, A.; Johnson, B. G.; Gill, P. M. W.; Head-Gordon, M.; Pople, J. A. J. Comput. Chem. 2000, 21, 1532-1548.
37. Mulliken, R. S. J. Chem. Phys. 1955, 23, 1833-1840.
38. 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., III; 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.
39. Brooks, C. L., III; Karplus, M. J. Chem. Phys. 1983, 79, 6312-6325.
40. Brooks, C. L., III; Karplus, M.; Pettitt, B. M. Proteins: A theoretical, perspective of dynamics, structure and thermodynamics. Wiley: New York, 1988.
41. Brooks, C. L., III; Karplus, M. J. Mol. Biol. 1989, 208, 159-181.
42. Berman, H. M.; Westbrook, J.; Feng, Z.; Gilliland, G.; Bhat, T. N.; Weissig, H.; Shindyalov, I. N.; Bourne, P. E. Nucleic Acids Res. 2000, 28, 235-242.
43. Jorgensen, W. L.; Chandraseklar, J.; Madura, J. D.; Impey, R. W.; Klein, M. L. J. Chem. Phys. 1983, 79, 926-935.
44. Ryckaert, J.-P.; Ciccotti, G.; Berendsen, H. J. C. J. Comput. Phys. 1977, 23, 327-341.
45. Merrer, D. C.; Ozcetinkaya, S.; Shinnar, A. E. Tetrahedron Lett. 2004, 45, 4899-4902.
46. Somers, K. R. F.; Kryachko, E. S.; Ceulemans, A. Chem. Phys. 2004, 301, 61-79.
47. De Beuckeleer, K.; Volckaert, G.; Engelborghs, Y. Proteins 1999, 36, 42-53.
48. Willaert, K.; Loewenthal, R.; Sancho, J.; Froeyen, M.; Fersht, A.; Engelborghs, Y. Biochemistry 1992, 31, 711-716.