Contribution of transition dipole coupling to amide coupling in IR spectra of peptide secondary structures

Vibrational Spectroscopy

Volumn 42, Issue 1, 2006, Pages 63-73

  Kubelka, Jan ^a,b   Kim, Joohyun ^a   Bour, Petr ^c   Keiderling, Timothy A ^a  

^a UNIVERSITY OF ILLINOIS AT CHICAGO   (United States)

^b UNIVERSITY OF WYOMING   (United States)

^c INSTITUTE OF ORGANIC CHEMISTRY AND BIOCHEMISTRY   (Czech Republic)

Author keywords

Helix; Sheet; Density functional theory; Peptide amide I IR; Transition dipole coupling

Indexed keywords

Α-HELIX; Β-SHEET; TRANSITION DIPOLE COUPLING; VIBRATIONAL PARAMETERS;

AMINO ACIDS; CONFORMATIONS; INFRARED SPECTROSCOPY; PARAMETER ESTIMATION; PROBABILITY DENSITY FUNCTION; PROTEINS;

AMINES;

EID: 33749635854     PISSN: 09242031     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.vibspec.2006.04.003     Document Type: Article

References (67)

1. Barth A., and Zscherp C. Quart. Rev. Biophys. 35 (2002) 369-430
2. Haris P.I. In: Ram Singh B. (Ed). Infrared Analysis of Peptides and Proteins: Principles and Applications. ACS Symposium Series (2000), ACS, Washington, DC pp. 54-95
3. Eker F., Cao X., Nafie L., and Schweitzer-Stenner R. J. Am. Chem. Soc. 124 (2002) 14330-14341
4. Schweitzer-Stenner R., Eker F., Huang Q., and Griebenow K. J. Am. Chem. Soc. 123 (2001) 9628-9633
5. Asher S.A., Ianoul A., Mix G., Boyden M.N., Karnoup A., Diem M., and Schweitzer-Stenner R. J. Am. Chem. Soc. 123 (2001) 11775-11781
6. Zhao X.J., and Spiro T.G. J. Raman Spectrosc. 29 (1998) 49-55
7. Williams R.W. Meth. Enzymol. 130 (1986) 311-331
8. Woutersen S., and Hamm P. J. Phys. Chem. B 104 (2000) 11316-11320
9. Woutersen S., and Hamm P. J. Chem. Phys. 114 (2001) 2727-2737
10. Woutersen S., and Hamm P. J. Phys.: Condens. Matter 14 (2002) R1035-R1062
11. Fang C., Wang J., Charnley A.K., Barber-Armstrong W., Smith III A.B., Decatur S.M., and Hochstrasser R.M. Chem. Phys. Lett. 382 (2003) 586-592
12. Talaga D.S., Lau W.L., Roder H., Tang J.Y., Jia Y.W., DeGrado W.F., and Hochstrasser R.M. Proc. Natl. Acad. Sci. U.S.A. 97 (2000) 13021-13026
13. Cheatum C.M., Tokmakoff A., and Knoester J. J. Chem. Phys. 120 (2004) 8201-8215
14. Barber-Armstrong W., Donaldson T., Wijesooriya H., Silva R.A.G.D., and Decatur S.M. J. Am. Chem. Soc. 126 (2004) 2339-2345
15. Decatur S.M. Biolopymers 54 (2000) 180-185
16. Decatur S.M., and Antonic J. J. Am. Chem. Soc. 121 (1999) 11914-11915
17. Silva R.A.G.D., Barber-Armstrong W., and Decatur S.M. J. Am. Chem. Soc. 125 (2003) 13674-13675
18. Silva R.A.G.D., Kubelka J., Decatur S.M., Bour P., and Keiderling T.A. Proc. Natl. Acad. Sci. U.S.A. 97 (2000) 8318-8323
19. Huang C.Y., Getahun Z., Wang T., DeGrado W.F., and Gai F. J. Am. Chem. Soc. 123 (2001) 12111-12112
20. Huang R., Kubelka J., Barber-Armstrong W., Silva R.A.G.D., Decatur S.M., and Keiderling T.A. J. Am. Chem. Soc. 126 (2004) 2346-2354
21. Setnicka V., Huang R., Thomas C.L., Etienne M.A., Kubelka J., Hammer R.P., and Keiderling T.A. J. Am. Chem. Soc. 127 (2005) 4992-4993
22. Keiderling T.A. In: Berova N., Nakanishi K., and Woody R.W. (Eds). Circular Dichroism: Principles and Applications (2000), Wiley-VCH, New York pp. 621-666
23. Keiderling T.A. Curr. Opin. Chem. Biol. 6 (2002) 682-688
24. Keiderling T.A., Kubelka J., and Hilario J. In: Braiman M., and Gregoriou V. (Eds). Vibrational Spectrroscopy of Polymers and Biological Systems (2005), Marcel-Dekker Publ, New York
25. Keiderling T.A., and Silva R.A.G.D. In: Goodman M., and Herrman G. (Eds). Synthesis of Peptides and Peptidomimetics (2002), Georg Thieme Verlag, Stuttgart pp. 715-738
26. Schweitzer-Stenner R., Sieler G., Mirkin N.G., and Krimm S. J. Phys. Chem. 102 (1998) 118-127
27. Brauner J.W., Flack C.R., and Mendelsohn R. J. Am. Chem. Soc. 127 (2005) 100-109
28. Brauner J.W., Dugan C., and Mendelsohn R. J. Am. Chem. Soc. 122 (2000) 677-683
29. Choi J.H., and Cho M. J. Chem. Phys. 120 (2004) 4383-4392
30. Choi J.H., Kim J.S., and Cho M. J. Chem. Phys. 122 (2005) 174903
31. Bour P., and Keiderling T.A. J. Phys. Chem. B 109 (2005) 5348-5357
32. Kubelka J., Huang R., and Keiderling T.A. J. Phys. Chem. B 109 (2005) 8231-8243
33. Fabian H., Chapman D., and Mantsch H.H. In: Mantsch H.H., and Chapman D. (Eds). Infrared Spectroscopy of Biomolecules (1996), Wiley-Liss, Chichester pp. 341-52
34. Halverson K., Sucholeiki I., Ashburn T.T., and Lansbury P.T. J. Am. Chem. Soc. 113 (1991) 6701-6703
35. In: Krimm S., and Zerbi G. (Eds). Modern Polymer Spectroscopy (1999), Wiley-VCH pp. 239-85
36. Torii H., and Tasumi M. J. Chem. Phys. 96 (1992) 3379-3387
37. Bour P., Sopkova J., Bednarova L., Malon P., and Keiderling T.A. J. Comput. Chem. 18 (1997) 646-659
38. Kubelka J., Silva R.A.G.D., Bour P., Decatur S.M., and Keiderling T.A. In: Hicks J.M. (Ed). Chirality: Physical Chemistry. ACS Symposium Series (2002), American Chemical Society, Washington, DC 50-64
39. Kubelka J., and Keiderling T.A. J. Am. Chem. Soc. 123 (2001) 12048-12058
40. Kubelka J., and Keiderling T.A. J. Am. Chem. Soc. 123 (2001) 6142-6150
41. Torii H., and Tasumi M. J. Raman Spectrosc. 29 (1998) 81-86
42. Moore W.H., and Krimm S. Proc. Natl. Acad. Sci. U.S.A. 72 (1975) 4933-4935
43. Krimm S., and Bandekar J. Adv. Protein Chem. 38 (1986) 181-364
44. Lee S.H., and Krimm S. Chem. Phys. 230 (1998) 277-295
45. P. Bour, Computational study of the vibrational optical activity of amides and peptides, Ph.D. Thesis, Academy of Science of the Czech Republic, Prague, Czech Republic, 1993.
46. Bour P., Kubelka J., and Keiderling T.A. Biopolymers 53 (2000) 380-395
47. Kubelka J., Silva R.A.G.D., and Keiderling T.A. J. Am. Chem. Soc. 124 (2002) 5225-5232
48. Bour P., Kubelka J., and Keiderling T.A. Biopolymers 65 (2002) 45-69
49. J. Kubelka, IR and VCD spectroscopy of model peptides. Theory and experiment, Ph.D. thesis, University of Illinois at Chicago, Chicago, 2002.
50. Fraser R.D.B., and McRae: T.P. Conformation in Fibrous Proteins (1973), Academic Press, New York
51. Frisch M.J., Trucks G.W., Schlegel H.B., Scuseria G.E., Robb M.A., Cheeseman J.R., Zakrzewski V.G., Montgomery J., Stratmann J.A.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., and Pople J.A. Gaussian 98 (1998), Gaussian Inc., Pittsburgh, PA
52. Becke A. Phys. Rev. A 38 (1988) 3098-3100
53. Becke A.D. In: Yarkony D.R. (Ed). Modern Electronic Structure Theory (1995), World Scientific, Singapore 1022-1046
54. Perdew J.P., and Wang Y. Phys. Rev. B 45 (1992) 13244
55. Perdew J.P., and Wang Y. Phys. Rev. B 33 (1988) 8800-8802
56. Kubelka J., and Keiderling T.A. J. Phys. Chem. A 105 (2001) 10922-10928
57. Cheeseman J.R., Frisch M.J., Devlin F.J., and Stephens P.J. Chem. Phys. Lett. 252 (1996) 211-220
58. Stephens P.J., Ashvar C.S., Devlin F.J., Cheeseman J.R., and Frisch M.J. Mol. Phys. 89 (1996) 579-594
59. Stephens P.J., Devlin F.J., Ashvar C.S., Chabalowski C.F., and Frisch M.J. Faraday Discuss. 99 (1994) 103-119
60. Krimm S., and Reisdorf Jr. W.C. Faraday Discuss. 99 (1994) 181-194
61. Bour P., and Keiderling T.A. J. Am. Chem. Soc. 114 (1992) 9100-9105
62. Hilario J., Kubelka J., and Keiderling T.A. J. Am. Chem. Soc. 125 (2003) 7562-7574
63. Stephens P.J. J. Phys. Chem. 91 (1987) 1712-1715
64. Krimm S. In: Singh B.R. (Ed). Infrared Analysis of Peptides and Proteins: Principles and Applications. ACS Symposium Series (2000), ACS, Washington, DC 38-53
65. Chirgadze Y.N., and Nevskaya N.A. Biopolymers 15 (1976) 607-625
66. Miyazawa T. J. Chem. Phys. 32 (1960) 1647-1652
67. Bour P., and Keiderling T.A. J. Phys. Chem. B 109 (2005) 23687-23697