Peptide secondary structure determination by three-pulse coherent vibrational spectroscopies: A simulation study

Journal of Physical Chemistry B

Volumn 108, Issue 46, 2004, Pages 18034-18045

  Abramavicius, Darius ^a   Zhuang, Wei ^a   Mukamel, Shaul ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ENERGY MIGRATION; GLOBULAR PROTEINS; ISOTOPE SUBSTITUTIONS;

BAND STRUCTURE; CHEMICAL BONDS; COMPUTER SIMULATION; POLARIZATION; RAMAN SPECTROSCOPY; X RAY CRYSTALLOGRAPHY;

POLYPEPTIDES;

EID: 9944253859     PISSN: 15206106     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp047711u     Document Type: Article

References (69)

1. Stryer, L. Biochemistry, 2nd ed.; W. H. Freeman Company: New York, 1995
2. Segel, D. J.; Bachmann, A.; Hofrichter, J.; Hodgson, K. O.; Doniach, S.; Kiefhaber, T. J. Mol. Biol. 1999, 288, 489.
3. Arai, S.; Hirai, M. Biophys. J. 1999, 76, 2192.
4. Baibach, J. J. Am. Chem. Soc. 2000, 122, 5887.
5. Pfuhl, M.; Driscoll, P. C. Philos. Trans. R. Soc. London, Ser. A 2000, 358, 513.
6. Wuthrich, K. NMR of Proteins and Nucleic Acids; Wiley-Interscience: New York, 1986.
7. Domche, W., Hochstrasser, R. M., Trommsdorff, H., Eds. Chem. Phys. 2004, Special issue - Ultrafast Science with X-rays and Electrons.
8. Fasman, G. Circular Dichroism and the Conformational Analysis of Biomolecules; Plenum: New York, 1996.
9. Parker, F. Applications of Infrared, Raman, and Resonance Raman Spectroscopy; Plenum: New York, 1983.
10. Mantsch, H. H.; Chapman, D. Infrared Spectroscope of Biomolecules; Wiley-Liss: Chichester, U.K., 1996.
11. Havel, H. Spectroscopic Methods for Determining Protein Structure in Solution; VCH Publishers: NewYork, 1996.
12. Creighton, T. E. Proteins: Structures and Molecular Properties; W. H. Freeman and Company: New York, 1997.
13. Torii, H.; Tatsumi, T.; Kanazawa, T.; Tasumi, M. J. Phys. Chem. B 1998, 102, 309.
14. Surewicz., W. K.; Mantsch, H. H.; Chapman, D. Biochemistry 1993, 32, 389.
15. Jackson, M.; Mantsch, H. H. Crit. Rev. Biochem. Mol. Biol. 1995, 30, 95.
16. Bredenbeck, J.; Helbing, J.; Behrendt, R.; Renner, C.; Moroder, L.; Wachtveitl, J.; Hamm, P. J. Phys. Chem. B 2003, 107, 8654.
17. Woutersen, S.; Hamm, P. J. Chem. Phys. 2001, 115, 7737.
18. Woutersen, S.; Pfister, R.; Hamm, P.; Mu, Y.; Kosov, D. S.; Stock, G. J. Chem. Phys. 2002, 117, 6833.
19. Bredenbeck, J.; Helbing, J.; Sieg, A.; Schrader, T.; Zinth, W.; Renner, C.; Behrendt, R.; Moroder, L.; Wachtveitl, J.; Hamm, P. Proc. Natl. Acad. Sci. U.S.A. 2003, 100, 6452.
20. Chi, Z.; Chen, X. G.; Holtz, J. S. W.; Asher, S. A. Biochemistry 1998, 37, 2854.
21. Baumruk, V.; Pancoska, P.; Keiderling, T. A. J. Mol. Biol. 1996, 259, 774.
22. Stephens, P. J.; Lowe, M. A. Annu. Rev. Phys. Chem. 1985, 36, 231.
23. Mukamel, S. Annu. Rev. Phys. Chem. 2000, 51, 691.
24. Mukamel, S.; Hochstrasser, R. M. Chem. Phys. 2001, 266, special issue on Multidimensional Spectroscopies.
25. Nibbering, E. T. J.; Elsasser, T. Chem. Rev. 2004, 104, 1887.
26. Hamm, P.; Hochstrasser, R. M. Structure and Dynamics of Proteins and Peptides: femtosecond two-dimensional spectroscopy. Ultrafast Infrared and Raman Spectroscopy; Marcel Dekker, Inc.: New York, 2001.
27. Fang, C.; Wang, J.; Charnley, A. K.; Barber-Armstrong, W.; Smith, A. B.; Decatur, S. M.; Hochstrasser, R. M. Chem. Phys. Lett. 2003, 382, 586.
28. Khalil, M.: Tokmakoff, A. Chem. Phys. 2001, 266, 213.
29. Golonzka, O.; Khalil, M.; Demirdoven, N.; Tokmakoff, A. Phys. Rev. Lett. 2001, 86, 2154.
30. Zhang, W. M.; Chernyak, V.; Mukamel, S. J. Chem. Phys. 1999, 110, 5011.
31. Zanni, M. T.; Ge, N. H.; Kim, Y. S.; Hochstrasser, R. M. Proc. Natl. Acad. Sci. U.S.A. 2001, 98, 11265.
32. Ge, N. H.; Zanni, M. T.; Hochstrasser, R. M. J. Phys. Chem. A 2002, 106, 962.
33. Hamm, P.; Lim, M. H.; Hochstrasser, R. M. J. Phys. Chem. B 1998, 102, 6123.
34. Hamm, P. Chem. Phys. 1995, 200, 415.
35. Joo, T. H.; Jia, Y. W.; Yu, J. Y.; Jonas, D. M.; Fleming, G. R. J. Phys. Chem. 1996, 100, 2399.
36. Jimenez, R.; vanMourik, F.; Yu, J. Y.; Fleming, G. R. J. Phys. Chem. B 1997, 101, 7350.
37. Bruccoleri, R.; Karplus, M. Biopolymers 1987, 26, 137.
38. Brunger, A.; Karplus, M. Science 1987, 255, 458.
39. Weiner, S.; Kollman, P.; Case, D.; Singh, U.; Ghio, C.; Alagona, G.; Profeta, S.; Weiner, P. J. Am. Chem. Soc. 1984, 106, 765.
40. Kirkpatrick, S.; Gelatt, C.; Vecchi, M. Science 1983, 220, 671.
41. VanGunsteren, W. F. Prog. Biophys. Mol. Biol. 1996, 65, SA301.
42. Brooks, C.; Onuchic, J.; Wales, D. Science 2001, 293, 612.
43. Moran, A. M.; Park, S. M.; Mukamel, S. J. Chem. Phys. 2003, 118, 9971.
44. Davydov, A. Theory of Molecular Excitons; McGraw-Hill: New York, 1962.
45. Kuhn, T.; Schwalbe, H. J. Am. Chem. Soc. 2000, 122, 6169.
46. Piryatinski, A.; Chernyak, V.; Mukamel, S. Chem. Phys. 2000, 266, 285.
47. MacroModel 8.5 User Manual; Schrodinger Company: New York, 2003.
48. Leach, A. Molecular Modelling: Principles and Applications; Addison Wesley Longman, Limited: Reading, MA, 1998.
49. Luzar, A.; Chandler, D. Nature 1996, 379, 55.
50. Moran, A.; Mukamel, S. Proc. Natl. Acad. Sci. U.S.A. 2004, 101, 506.
51. Krimm, S.; Abe, Y. Proc. Natl. Acad. Sci. U.S.A. 1972, 69, 2792.
52. Moore, W. H.; Krimm, S. Proc. Natl. Acad. Sci. U.S.A. 1975, 72, 4933.
53. Krimm, S.; Bandekar, J. Adv. Protein Chem. 1986, 38, 181.
54. Torii, H.; Tasumi, M. J. Raman Spectrosc. 1998, 29, 81.
55. Mukamel, S. Principles of Nonlinear Optical Spectroscopy; Oxford University Press: New York, 1995.
56. Mukamel, S.; Abramavicius, D. Chem. Rev. 2004, 104, 2073.
57. Soreghan, B.; Pike, C.; Kayed, R.; Tian, W. Q.; Milton, S.; Cotman, C.; Glabe, C. G. NeuroMol. Med. 2002, 1, 81.
58. Soreghan, B.; Kosmoski, J.; Glabe, C. J. Biol Chem. 1994, 269, 28551.
59. Cribbs, D. H.; Velazquez, P.; Soreghan, B.; Glabe, C. G.; Tenner, A. J. Neuroreport 1997, 8, 3457.
60. Yong, W.; Lomakin, A.; Kirkitadze, M. D.; Teplow, D. B.; Chen, S. H.; Benedek, G. B. Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 150.
61. Walsh, D. M.; Lomakin, A.; Benedek, G. B.; Condron, M. M.; Teplow, D. B. J. Biol. Chem. 1997, 272, 22364.
62. Chirgadze, Y. N.; Shestopalov, B. V.; Venyaminov, S. Y. Biopolymers 1973, 12, 1337.
63. Jackson, M.; Haris, P. I.; Chapman, D. J. Mol. Struct. 1989, 214, 329.
64. Byler, D. M.; Susi, H. Biopolymers 1986, 25, 469.
65. Surewicz, W. K.; Mantsch, H. H. Biochim. Biophys. Acta 1988, 952, 115.
66. Demirdoven, N.; Cheatum, C.; Chung, H.; Khalil, M.; Knoester, J.; Tokmakoff, A. J. Am. Chem. Soc. 2004, 126, 7981.
67. Abramavicius, D.; van Grondelle, R.; Valkunas, L. Phys. Chem. Chem. Phys. 2004, 6, 3097.
68. Andrews, D. L.; Thirumachandran, T. J. Chem. Phys. 1977, 67, 5026. Hochstrasser, R. M. Chem. Phys. 2001, 266, 273.
69. Andrews, D. L.; Thirumachandran, T. J. Chem. Phys. 1977, 67, 5026. Hochstrasser, R. M. Chem. Phys. 2001, 266, 273.