Solvent effects on IR and VCD spectra of helical peptides: DFT-based static spectral simulations with explicit water

Journal of Physical Chemistry B

Volumn 109, Issue 16, 2005, Pages 8231-8243

  Kubelka, Jan ^a,b   Huang, Rong ^a   Keiderling, Timothy A ^a  

^a UNIVERSITY OF ILLINOIS AT CHICAGO   (United States)

^b NATIONAL INSTITUTE OF DIABETES AND DIGESTIVE AND KIDNEY DISEASES   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EXPLICIT WATER; LIGAND DESIGN; PARALLEL TEMPERING; VCD SIMULATION;

CARBOXYLATION; COMPUTER SIMULATION; FUNCTIONS; HYDROGEN BONDS; INFRARED RADIATION; MOLECULAR STRUCTURE; NATURAL FREQUENCIES; PERMITTIVITY;

POLYPEPTIDES;

PEPTIDE; SOLVENT; WATER;

ARTICLE; CHEMICAL MODEL; CHEMISTRY; CIRCULAR DICHROISM; COMPUTER SIMULATION; INFRARED SPECTROPHOTOMETRY; PROTEIN SECONDARY STRUCTURE; SOLUTION AND SOLUBILITY;

CIRCULAR DICHROISM; COMPUTER SIMULATION; MODELS, CHEMICAL; PEPTIDES; PROTEIN STRUCTURE, SECONDARY; SOLUTIONS; SOLVENTS; SPECTROPHOTOMETRY, INFRARED; WATER;

EID: 18444365588     PISSN: 15206106     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp0506078     Document Type: Article

References (77)

1. Barth, A.; Zscherp, C. Q. Rev. Biophys. 2002, 35, 369.
2. Keiderling, T. A. Curr. Opin. Chem. Biol. 2002, 6, 682.
3. Goormaghtigh, E.; Cabiaux, V.; Ruysschaert, J. M. Determination of soluble and membrane protein structure by Fourier transform infrared spectroscopy. I. Assignments and model compounds. In Subcellular Biochemistry; Hilderson, H. J., Ralston, G. B., Eds.; Plenum: New York, 1994; Vol. 23, p 329.
4. Jackson, M.; Mantsch, H. H. Crit. Rev. Stochem. Mol. Biol. 1995, 30, 95.
5. Haris, P. I. Fourier Transform Infrared Spectroscopic Studies of Peptides: Potentials and Pitfalls. In Infrared Analysis of Peptides and Proteins: Principles and Applications. ACS Symposium Series.; Ram Singh, B., Ed.; American Chemical Society: Washington, DC, 2000; p 54.
6. Eaton, G.; Symons, M. R. C.; Rastogi, P. P. J. Chem. Soc., Faraday Trans. I 1989, 85, 3257.
7. Mayne, L. C.; Hudson, B. J. Phys. Chem. 1991, 95, 2962.
8. Torii, H.; Tatsumi, T.; Kanazawa, T.; Tasumi, M. J. Phys. Chem. B 1998, 102, 309.
9. Kubelka, J.; Keiderling, T. A. J. Phys. Chem. A 2001, 705, 10922.
10. Keiderling, T. A. Peptide and protein conformational studies with vibrational circular dichroism and related spectroscopies. In Circular dichroism: principles and applications, 2nd ed.; Nakanishi, K., Berova, N., Woody, R. A., Eds.; Wiley: New York, 2000; p 621.
11. Bour, P.; Kubelka, J.; Keiderling, T. A. Biopolymers 2000, 53, 380.
12. Silva, R. A. G. D.; Kubelka, J.; Decatur, S. M.; Bour, P.; Keiderling, T. A. Proc. Natl. Acad. Sci. U.S.A. 2000, 97, 8318.
13. Kubelka, J.; Silva, R. A. G. D.; Bour, P.; Decatur, S. M.; Keiderling, T. A. Chirality in peptide vibrations. Ab Initio computational studies of length, solvation, hydrogen bond, dipole coupling and isotope effects on vibrational CD. In Chirality: Physical Chemistry. ACS Symposium Series; Hicks, J. M., Ed.; Oxford University Press: New York, 2002; p 50.
14. Kubelka, J.; Keiderling, T. A. J. Am. Chem. Soc. 2001, 123, 6142.
15. Kubelka, J.; Keiderling, T. A. J. Am. Chem. Soc. 2001, 123, 12048.
16. Kubelka, J.; Silva, R. A. G. D.; Keiderling, T. A. J. Am. Chem. Soc. 2002, 124, 5325.
17. Bour, P.; Kubelka, J.; Keiderling, T. A. Biopolymers 2002, 65, 45.
18. Hilario, J.; Kubelka, J.; Syud, F. A.; Gellman, S. H.; Keiderling, T. A. Biopolymers 2002, 67, 233.
19. Hilario, J.; Kubelka, J.; Keiderling, T. A. J. Am. Chem. Soc. 2003, 125, 7562.
20. Huang, R.; Kubelka, J.; Barber-Armstrong, W.; Silva, R. A. G. D.; Decatur, S. M.; Keiderling, T. A. J. Am. Chem. Soc. 2004, 126, 2346.
21. Bour, P.; Sopkova, J.; Bednarova, L.; Malon, P.; Keiderling, T. A. J. Comput. Chem. 1997, 78, 646.
22. Silva, R. A. G. D.; Yasui, S. C.; Kubelka, J.; Formaggio, F.; Crisma, M.; Toniolo, C.; Keiderling, T. A. Biopolymers 2002, 65, 229.
23. Besley, N. A. J. Phys. Chem. A 2004, 108, 10794.
24. Frimand, K.; Bohr, H.; Jalkanen, K. J.; Suhai, S. Chem. Phys. 2000, 255, 165.
25. Knapp-Mohammady, M.; Jalkanen, K. J.; Nardi, F.; Wade, R. C.; Suhai, S. Chem. Phys. 1999, 240, 63.
26. Tajkhorshid, E.; Jalkanen, K. J.; Suhai, S. J. Phys. Chem. B 1998, 102, 5899.
27. Han, W.-G.; Jalkanen, K. J.; Elstner, M.; Suhai, S. J. Phys. Chem. B 1998, 702, 2587.
28. Creighton, T. E. Proteins: Structures and Molecular Properties, 2nd ed.; W. H. Freeman and Co.: New York, 1993.
29. Guo, H.; Karplus, M. J. Phys. Chem. 1994, 98, 7104.
30. Han, W.-G.; Suhai, S. J. Phys. Chem. 1996, 700, 3942.
31. Markham, L. M.; Hudson, B. S. J. Phys. Chem. 1996, 100, 2731.
32. Kallies, B.; Mitzner, R. J. Chem. Soc., Perkin Trans. 1996, 2, 1403.
33. Torii, H.; Tatsumi, T.; Tasumi, M. J. Roman Spectrosc. 1998, 29, 537.
34. Sundaralingam, M.; Sekharudu, Y. C. Science 1989, 244, 1333.
35. Weiner, S. J.; Kollman, P. A.; Nguyen, D. T.; Case, D. A. J. Comput. Chem. 1986, 7, 230.
36. Insight II; 94.0 ed.; Molecular Simulations Inc.: San Diego, 1997.
37. Frisch, M. J.; Trucks, G. W.; Schiegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Zakrzewski, V. G.; Montgomery, J., J. A.; Stratmann, R. E.; Burant, J. C.; Dapprich, S.; Millam, J. M.; Daniels, A. D.; Kudin, K. N.; Strain, M. C.; Farkas, O.; Tomasi, J.; Barone, V.; Cossi, M.; Cammi, R.; Mennucci, B.; Pomelli, C.; Adamo, C.; Clifford, S.; Ochterski, J.; Petersson, G. A.; Ayala, P. Y.; Cui, Q.; Morokuma, K.; Malick, D. K.; Rabuck, A. D.; Raghavachari, K.; Foresman, J. B.; Cioslowski, J.; Ortiz, J. V.; Stefanov, B. B.; Liu, G.; Liashenko, A.; Piskorz, P.; Komaromi, I.; Gomperts, R.; Martin, R. L.; Fox, D. J.; Keith, T.; Al-Laham, M. A.; Peng, C. Y.; Nanayakkara, A.; Gonzalez, C.; Challacombe, M.; Gill, P. M. W.; Johnson, B.; Chen, W.; Wong, M. W.; Andres, J. L.; Gonzalez, C.; Head-Gordon, M.; Replogle, E. S.; Pople, J. A. Gaussian 98, revision A.6, Gaussian, Inc.: Pittsburgh, PA, 1998.
38. Perdew, J. P.; Wang, Y. Phys. Rev. B 1988, 33, 8800.
39. Perdew, J. P.; Wang, Y. Phys. Rev. B 1992, 45, 13244.
40. Hehre, W. J.; Radom, L.; Schleyer, P. v. R.; Pople, J. A. Ab initio molecular orbital theory; Wiley: New York, 1986.
41. Frisch, A.; Frisch, M. J. Gaussian 98 User's Reference; Gaussian, Inc.: Pittsburgh, PA, 1999.
42. Stephens, P. J. J. Phys. Chem. 1985, 89, 748.
43. Bak, K. L.; Jorgensen, P.; Helgaker. T.; Ruud, K.; Jensen, H. J. J. Chem. Phys. 1993, 98, 8873.
44. Bour, P.; Keiderling, T. A. J. Phys. Chem. B 2005, 109, 5348.
45. Yasui, S. C.; Keiderling, T. A.; Bonora, G. M.; Toniolo. C. Biopolymers 1986, 25, 79.
46. Yasui, S. C.; Keiderling, T. A.; Formaggio, F.; Bonora, G. M.; Toniolo, C. J. Am. Chem. Soc. 1986, 108, 4988.
47. Yoder, G.; Polese, A.; Silva, R. A. G. D.; Formaggio, F.; Crisma, M.; Broxterman, Q. B.; Kamphuis, J.; Toniolo, C.; Keiderling, T. A. J. Am. Chem. Soc. 1997, 119, 10278.
48. Baello, B. I.; Pancoska, P.; Keiderling, T. A. Anal. Biochem. 1997, 250, 212.
49. Malon, P.; Kobrinskaya, R.; Keiderling, T. A. Biopolymers 1988, 27, 733.
50. Dukor, R. K.; Keiderling, T. A. Biopolymers 1991, 31, 1747.
51. Sen, A. C.; Keiderling, T. A. Biopolymers 1984, 23, 1519.
52. Yasui, S. C.; Keiderling, T. A. J. Am. Chem. Soc. 1986, 108, 5576.
53. Baumruk, V.; Huo, D. F.; Dukor, R. K.; Keiderling, T. A.; Lelievre, D.; Brack, A. Biopolymers 1994, 34, 1115.
54. Yoder, G.; Pancoska, P.; Keiderling, T. A. Biochemistry 1997, 36, 15123.
55. Martinez, G.; Millhauser, G. J. Struct. Biol. 1995, 114, 23.
56. Williams, S.; Causgrove, T. P.; Gilmanshin, R.; Fang, K. S.; Callender, R. H.; Woodruff, W. H.; Dyer, R. B. Biochemistry 1996, 55, 691.
57. Decatur, S. M.; Antonic, J. J. Am. Chem. Soc. 1999, 121, 11914.
58. Chen, X. G.; Schweitzer-Stenner, R.; Krimm, S.; Mirkin, N. G.; Asher, S. A. J. Am. Chem. Soc. 1994, 116, 11141.
59. Manas, E. S.; Getahun, Z.; Wright, W. W.; Degrado, W. F.; Vanderkooi, J. M. J. Am. Chem. Soc. 2000, 122, 9883.
60. Bour, P.; Keiderling, T. A. J. Chem. Phys. 2003, 119, 11253.
61. Ham, S.; Hahn, S.; Lee, C.; Kim, T.-K.; Kwac, K.; Cho, M. H. J. Phys. Chem. B 2004, 108, 9333.
62. Kwac, K.; Cho, M. H. J. Chem. Phys. 2003, 119, 2247.
63. Ham, S.; Kim, J. H.; Lee, H.; Cho, M. H. J. Chem. Phys. 2003, 118, 3491.
64. Fiori, W. R.; Miick, S. M.; Millhauser, G. M. Biochemistry 1993, 32, 11957.
65. Tirado-Rives, J.; Maxwell, D. S.; Jorgensen, W. L. J. Am. Chem. Soc. 1993, 115, 11590.
66. Zhang, L.; Hermans, J. J. Am. Chem. Soc. 1994, 116, 11915.
67. Smythe, M. L.; Nakaie, C. R.; Marshall, G. R. J. Am. Chem. Soc. 1995, 117, 10555.
68. Young, W. S.; Brooks, C. L., III J. Mol. Biol. 1996, 259, 560.
69. Ham, S.; Choi, J.-H.; Cho, M. H. J. Chem. Phys. 2003, 119, 1451.
70. Woutersen, S.; Hamm, P. J. Phys. Chem. B 2000, 104, 11316.
71. Woutersen, S.; Hamm, P. J. Chem. Phys. 2001, 115, 7737.
72. Schweitzer-Stenner, R. Biophys. J. 2002, 83, 523.
73. Yasui, S. C.; Keiderling, T. A.; Katachai, R. Biopolymers 1987, 26, 1407.
74. Yasui, S. C.; Keiderling, T. A. Biopolymers 1986, 25, 5.
75. Singh, R. D.; Keiderling, T. A. Biopolymers 1981, 20, 237.
76. Hol, W. G. J. Prog. Biophys. Mol. Biol. 1985, 45, 149.
77. Lockhart, D. J.; Kim, P. S. Science 1992, 257, 947.