Conformational analysis of proteins and peptides

Current Organic Chemistry

Volumn 7, Issue 18, 2003, Pages 1841-1854

  Cai, Xianmei ^a   Dass, Chhabil ^a  

^a University of Memphis   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CIRCULAR DICHROISM SPECTROSCOPY; CONFORMATIONS; DICHROISM; FLUORESCENCE; NUCLEAR MAGNETIC RESONANCE; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PEPTIDES; SELF ASSEMBLY; X RAY CRYSTALLOGRAPHY;

'CURRENT; BIOCHEMICAL FUNCTIONS; BIOLOGICAL FUNCTIONS; CONFORMATIONAL ANALYSIS; FOLDINGS; HIGHLY ORDERED STRUCTURE; INFRARED AND RAMAN SPECTROSCOPY; PROTEIN FUNCTIONS; SPECTROMETRY TECHNIQUE; UNFOLDINGS;

MASS SPECTROMETRY;

PEPTIDE; PROTEIN;

AROMA; BIOCHEMISTRY; CIRCULAR DICHROISM; FLUORESCENCE SPECTROSCOPY; HUMAN; INFRARED SPECTROSCOPY; INTERMETHOD COMPARISON; MASS SPECTROMETRY; MODULATION; NONHUMAN; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PROTEIN ANALYSIS; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEIN FUNCTION; PROTEIN STRUCTURE; RAMAN SPECTROMETRY; REVIEW; SPECTROMETRY; STRUCTURE ANALYSIS; TECHNIQUE; ULTRAVIOLET SPECTROSCOPY; X RAY CRYSTALLOGRAPHY;

EID: 0344899932     PISSN: 13852728     EISSN: None     Source Type: Journal    
DOI: 10.2174/1385272033486161     Document Type: Review

References (155)

1. Brooks, C.L.; Karplus, M.; Pettitt, B.M. Proteins: A Theoretical Perspective of Dynamics Structure, and Thermodynamics, Wiley: New York, 1998.
2. Crighton, T.E. Proteins Structure and Molecular Principles, Freeman: New York, 1984.
3. Creighton, T.E. Biochemistry J. 1990, 270, 1.
4. Fasman, G.D. Circular Dichroism and the Conformational Analysis of Biomolecules, Plenum Press: New York, 1996.
5. Berova, N.; Nakanishi, K.; Woody, R.W. Circular Dichroism: Principles and Applications, Wiley: New York, 2000.
6. Bai, Y.; Sosmick, T.R.; Mayne, L.; Englander, S.W. Science, 1995, 269, 192.
7. Osbome, H.B.; Nabedryk-Viala, E. Methods Enzymol., 1982, 88, 676.
8. Vogel, R.; Freidrich, S. Biochemistry, 2002, 41, 3536.
9. Pelton, J.T.; McLean, L.R. Anal. Biochem., 2000, 277, 167.
10. Ozdemir, A.; Lednev, L.K.; Asher, S.A. Biochemistry, 2002, 41, 1893.
11. Thomson, J.A.; Shirley, B.A.; Grimsley, G.R.; Pace, C.N. J. Biol. Chem., 1998, 264, 11614.
12. Juneja, J.; Udgaonkar, J.B. Biochemistry, 2002, 41, 2641.
13. Eftink, M. Biophys. J. 1994, 66, 481.
14. Nettleton, E.J.; Robinson, C.V. Methods Enzymol., 1999, 309, 633.
15. Dass, C. Principle and Practice of Biological Mass Spectrometry, John Wiley & Sons, Inc.: New York, 2000.
16. Xu, D.; Xu, Y.; Uberbacher, E.C. Current Prot. Pept. Sci., 2000, 1, 1.
17. Skolnick, J.; Kolinski, A. Comput. Sci. Eng., 2001, 3, 40.
18. Ke, H, In Macromolecular Crystallography, Part A. Carter, C.W.; Sweet, R.M. Ed., Academic Press: San Diego, 1997, Vol. 276, pp. 448-461.
19. Keith, M.; Zhong, R. Curr. Opin. Struct. Biol., 1997, 7, 689.
20. Wetlaufer, D. Adv. Protein Chem., 1962, 17, 303.
21. Lowry, O.H.; Rosenbrough, N.J.; Farr, A.L.; Randall, R.J. J. Biol. Chem., 1995, 193, 265.
22. Bradford, M.M. Anal. Biochem., 1976, 72, 248.
23. Mach, H.; Volkin, D.B.; Bruke, C.J.; Middaugh, C.R. In Methods in Molecular Biology, Shirley, B.A., Ed., Humana Press: Totowa, N.J., 1995, Vol 40, PP: 91-113.
24. Fell, A.F. Trends Anal. Chem., 1983, 2, 63.
25. Royer, C.A. In Methods in Molecular Biology, 1995, Vol. 40, PP: 65-88.
26. Perez, G.M.; Howard, P.; Weill, A.; Beechem, J.M. Biophys, J., 1992, 61, 2805.
27. Seethaler, N.; Beechem, J.M. Biophys, J., 1992, 61, A179.
28. Royer, C.A.; Mann, C.J.; Matthews, C.R. Protein. Sci., 1993, 2, 1844.
29. Fernanndo, T.; Royer, C.A. Biochemistry, 1992, 31, 6683.
30. Bierzynski, A. Acta Biochim. Plonica, 2001, 48, 1091.
31. Förster, T. In Modern Quantum Chemistry; Sinanoglu, O., Ed., Academic Press: New York, 1965, Vol. 3.
32. Amir, D.; Hass, E. Biochemistry, 1998, 27, 8889.
33. James, E.; Wu, P.G.; Stites, W.; Brand, L. Biochemistry, 1992, 31, 10217.
34. Yamamoto, T.; Ikemoto, N. Biochemistry, 2002, 41, 1492.
35. Lankiewicz, L.; Malicka, J.; Wiczk, W. Acta Biochim Polan., 1997, 44, 477.
36. Brand, L.; Goulke, J.R. Annu. Rev. Biochem., 1972, 41, 808.
37. Middaugh, C.R.; Mach, H.; Ryan, J.A.; Sanyal, G.; Volkin, D.A. In Methods in Molecular Biology, Shirley, B.A., Ed., Humana Pres: Totowa, NJ, 1995, Vol 40, PP: 137-156.
38. Harris, P.I.; Chapman, D. Trends Biochem. Sci. 1992, 17, 328.
39. Sarver, R.W. Jr.; Krueger, W.C. Anal. Biochem., 1991, 194, 89.
40. Doussea, F.; Pezolet, M. Biochemistry, 1990, 29, 8771.
41. Bandeka, J. Biochim. Biophys. Acta, 1992, 1120, 123.
42. Hashimoto, S.; Sasaki, M.; Takeuchi, H.; Needleman, R., ; Lanyi, J.K. Biochemistry, 2002, 41, 6495.
43. Johnson, W.C. Annu. Rev. Biophys. Chem., 1988, 17, 145.
44. Kuwajima, K. In Methods in Molecular Biology, Shirley, B.A., Ed., Humana Press: Totowa, NJ, 1995, Vol 40, PP: 115-135.
45. Sreerama, N.; Woody, R.W. In Circular Dichroism: Principles and Applications, Berova, N.; Nakanishi, K.; Woody, R.W. Eds., Wiley: New York, 2000, PP: 601-620.
46. Keiderling, T.A. In Circular Dichroism: Principles and Applications, Berova, N.; Nakanishi, K.; Woody, R.W. Eds., Wiley: New York, 2000, PP: 621-666.
47. Greenfield, N.J. Anal. Biochem., 1996, 235, 1.
48. Sreerama, N.; Woody, R.W. Anal. Biochem., 1993, 209, 32.
49. Adler, A.J.; Greenfield, N.J.; Fasman, G.D. Methods. Enzymol., 1972, 27, 675.
50. Yang, J.T.; Wu, C-S. C.; Martinez, H.M. Methods Enzymol., 1986, 130, 208.
51. Greenfield, N.J.; Davidson, B.; Fasman, G.D. Biochemistry, 1966, 35, 699.
52. Harrington, W.F.; Josephs, R.; Segal, D.M. Annu. Rev. Biochem., 1966, 35, 599.
53. Greenfield, N.J.; Fasman, G.D. Biochemistry, 1969, 8, 4108.
54. Toumadje, A.; Alcorn, S.W.; Johnson, W.C. Jr. Anal. Biochem., 1992, 200, 321.
55. Brahms, S.; Brahms, J. J. Mol. Biol., 1980, 138, 149.
56. Chang, C.T.; Wu, C-S.C.; Yang, J.T. Anal. Biochem., 1978, 91, 13.
57. Hennessey, J.P.; Johnson, W.C. Biochemistry, 1981, 20, 1085.
58. Manavalan, P.; Johnson, W.C. Jr. Anal. Biochem., 1987, 167, 76.
59. Van Stokkum, I. H.M.; Spoelder, H.J.W.; Bloemendal, M.L.; Van Grondelle, R.; Groen, F.C.A. Anal. Biochem., 1990, 191, 110.
60. Provencher, S.W.; Glöckner, J. Biochemistry, 1981, 20, 33.
61. Sreerama, N.; Woody, R.W. Biochemistry, 1994, 33, 10022.
62. Sreerama, N.; Venyaminov, Y.S.; Woody, R.W. Anal. Biochem., 2000, 287, 243.
63. Perczel, A.; Park, K.; Fasman, G.D. Anal. Biochem., 1992, 203, 83.
64. Bohm, G.; Muher, R.; Jaenicke, R. Protein. Eng., 1992, 5, 191.
65. Andrade, M.A.; Chacon, P.; Merolo, J.J.; Moran, PE, 1993, 6, 383.
66. Sreerama, N.; Woody, R.W. Mol. Biol., 1994, 242, 497.
67. Johnson, W.C. Proteins: Struct. Funct. Genet., 1999, 35, 313.
68. Venyaminov, S.Y.; Yang, J.T. Circular Dichroism and the Conformational Analysis of Bimolecules, Fasman, G.D., Ed.; Plenum Press: New York, 1996, pp: 69-107.
69. Yenyaminov, S.Y.; Vassilenko, K.S. Anal. Biochem., 1994, 222, 176.
70. Gronenborn, A.M.; Clore, G.M. Anal. Chem., 1990, 62, 2.
71. Kaptein, A.M.; Boelens, R.; Scheek, R.M.; Van Gunsteren, W.F. Biochemistry, 1988, 27, 5389.
72. Wüthrich, K. J. Biol. Chem., 1990, 265, 22059.
73. Wüthrich, K. Science, 1989, 243, 45.
74. Wüthrich, K. NMR of the Proteins and Nucleic Acids, Wiley: New York, 1986.
75. Neuhaus, D.; Williamson, M.P. The Nuclear Overhauser Effect in Structural and Conformational Analysis, John Wiley & Sons, Inc; New York, 2000.
76. Braunschweiler, L.; Ernst, R.R. J. Magn. Reson., 1983, 53, 521.
77. Bax, A.; Kay, L.E.; Sparks, S.W.; Torchia, D.L. J. Am. Chem. Soc., 1989, 111, 408.
78. Kaptein, R.; Zuiderweg, E.R.P.; Scheek, R.M.; Boelens, R.; Van Gunsteren, W.F. J. Mol. Biol., 1985, 182, 179.
79. Zuiderweg, E.R.P.; Billeter, M.; Boelens, R.; Scheek, R. M.; Wüthrich, K.; Kaptein, R. FEBS Lett., 1984, 174, 243.
80. Havel, T.F.; Wüthrich, K. J. Mol. Biol., 1985, 182, 281.
81. Williamson, M.P.; Havel, T.F.; Wüthrich, K. J. Mol. Biol., 1985, 182, 295.
82. Braun, W.; Gö, N. J. Mol. Biol., 1985, 186, 611.
83. Nilges, M.; Clore, G.M.; Gronenborn, A.M. FEBS Lett., 1988, 239, 129.
84. Clore, G.M.; Brünger, A.T.; Karplus, M.; Gronenborn, A.M. J. Mol. Biol., 1988, 191-523.
85. Clore, G.M.; Gronenborn, A.M. CRC Crit. Rev. Biochem., 1989, 24, 479.
86. Braun, W. Q. Rev. Biophys., 1987, 19, 115.
87. Wüthrich, K. Acc. Chem. Res., 1989, 22, 36.
88. Bax, A. Annu. Rev. Biochem., 1989, 58, 223.
89. Oppenheimer, N.J.; James, T.L. (Eds) Methods Enzymol., 1989, Vol. 176 and 177.
90. Otting, G.; Wüthrich, K. Q. Rev. Biophys., 1990, 23, 39.
91. Zuiderweg, E.R.P.; Kaptein, R.; Wüthrich, K. Proc. Natl, Acad. Sci. U.S.A. 1983, 80, 5837.
92. Pardi, A.; Billeter, M.; Wüthrich, K. J. Mol. Biol., 1984, 180, 741.
93. Smith, D. L.; Deng, Y.; Zhang, Z. J. Mass Spectrom. 1997, 32, 135.
94. Smith, D. L.; Zhang, Z. Mass Spectrom. Rev. 1994, 13, 411.
95. Fenn, J. B.; Mann, M.; Meng, C. K.; Wong, S. F.; Whitehouse, C. M. Science, 1989, 246, 64.
96. Karas, M.; Hellenkamp, F. Anal. Chem., 1988, 60, 2299.
97. Engen, J.R.; Smith, D.L. Anal. Chem., 2001, 73, 256 A.
98. Guevremont, R.; Siu, K. W. M.; Le Blanck, J. C. Y.; Berman, S. S. J. Am. Soc. Mass Spectrom. 1992, 3, 216.
99. Smith, R. D.; Loo, J. A.; Edmonds, C. G.; Barinaga, C.J.; Udseth, H. R. Anal. Chem. 1990, 62, 882.
100. Robinson, C. V. Methods in Molecular Biology, 1996, 61, 129.
101. Chowdhury, S.K.; Katta, V.; Chait, B.T. J. Am. Chem. Soc., 1990, 112, 9012.
102. Konermann, L.; Douglas, D.J. Biochemistry, 1997, 36, 12296.
103. Hamdan, M.; Curcuruto, O. Rapid Commun, Mass Spectrom., 1994, 8, 144.
104. Fang, F.; Tang, X. Biochemistry, 1996, 35, 4069.
105. Maier, C.S.; Shirmerlik, M.I.; Denizer, M.L. Biochemistry, 1999, 38, 1136.
106. Lin, H.; Dass, C. Rapid Commun, Mass Spectrom., 2001, 15, 2341.
107. Lin, H.; Dass, C. Eur. J. Mass Spectrom., 2002, 8, 381.
108. Yang, H. H.; Li, X. C.; Amft, M.; Grotemeyer, J. Anal. Biochem., 1998, 258, 118.
109. Kriwacki, R.; Wu, J.; Siuzdak, G.; Wright, P. E. J. Am. Chem. Soc., 1996, 118, 5320.
110. Kriwacki, R.; Wu, J.; Tennant, L.; Wright, P. E.; Siuzdak, G. J. Chromtogr., 1996, A 777, 23.
111. Nelson, R. W. Mass Spectrom. Rev., 1997, 16, 353.
112. Konermann, L.; Collings, B.A.; Douglas, D.J. Biochemistry, 1997, 36, 5554.
113. Lee, V.W.S.; Chen, Y-L.; Konermann, L. Anal. Chem., 1999, 71, 4154.
114. Simmons, D.A.; Konermann, L. Biochemistry, 2002, 41, 1906.
115. Sogbein, O.O.; Simmons, D.A.; Konermann, L. J. Am. Soc. Mass Spectrom., 2000, 11, 312.
116. Clemmer, D. E.; Jarrold, M. F. J. Mass Spectrom., 1997, 32, 577.
117. Shelimov, K.; Jarrold, M.F. J. Am. Chem. Soc., 1996, 118, 10313.
118. Purves, R.W.; Barnett, D.A.; Ells, B.; Guevremont, R. J. Am. Soc. Mass Spectrom., 2000, 11, 338.
119. Purves, R.W.; Barnett, D.A.; Ells, B.; Guevremont, R. J. Am Soc. Mass Spectrom., 2001,12, 894.
120. Rappsiber, J.; Sinossoglou, S.; Hurt, E.C.; Mann, M. Anal. Chem., 2000, 72, 267.
121. Houliston, R.S.; Liu, C.; Singh, L.M.R.; Meiering, E.M. Biochemistry, 2002, 41, 1182.
122. Li, R.; Woodward, C. Prortein Sci., 1999, 8, 1571.
123. Bai, Y.; Englander, S.W. Proteins: Struct. Funct. Genet., 1996, 26, 145.
124. Englander, S.W. Annu. Rev. Biophys. Biomol. Struct., 2000, 29, 213.
125. Katta, V.; Chait, B.T. J. Am. Chem. Soc., 1993, 115, 6317.
126. Wagner, D.S.; Anderegg, R.J. Anal. Chem., 1994, 66, 706.
127. Wagner, D.S.; Melton, L.G.; Yan, Y.; Erickson, B.W.; Anderergg, R.J. Protein Sci. 1994, 3, 1305.
128. Le Cotre, J.; Turk, E.; Kaback, H.R.; Wright, E.M. Biochemistry, 2002, 41, 8082.
129. Belva, H.; Lange, C.; Rapid Commun, Mass Spectrom., 2000, 14, 1433.
130. Eyles, S.J.; Dresch, T.; Gierasch, L.M.; Kaltashov, I.A. J. Mass Spectrom., 1999, 34, 1289.
131. Kraus, M.; Janek, K.; Beinert, M.; Krause, E. Rapid Commun, Mass Spectrom., 2000, 14, 1094.
132. Faull, K.F.; Higinson, J. et al. J. Mass Spectrom., 2000, 35, 392.
133. Deng, Y.; Zhang, Z.; Smith, D.L. J. Am. Soc. Mass Spectrom., 1999, 10, 675.
134. Miranker, A.; Robinson, C.V.; Radford, S.E.; Aplin, R.T.; Dobson, C.M. Science, 1993, 262, 896.
135. Deng, Y.; Smith, D.L. Biochemistry, 1998, 37, 6256.
136. Figueroa, I. D.; Russell, D. H. J. Am Soc. Mas Spectrom, 1999, 10, 719.
137. Powell, K. D.; Fitzgerald, M.C. Anal. Chem., 2001, 73, 3300.
138. Mendell, J.G.; Falick, A.M.; Komives, E.A. Proc. Natl. Acad. Sci., 1998, 25, 14705.
139. Mao, D.; Douglas, D.J. J. Am. Soc. Mass Spectrom., 2003, 14, 85.
140. Freitas, M.A.; Hendrickson, C.L.; Emmett, M.R.; Marshall, A.G. Int. J. Mass Spectrom., 1999, 185, 565.
141. Bihan, T. L.; Blichet, J.-E.; Desormeaux, A.; Marion, D.; Pezolet, M. Biochemistry, 1996, 35, 12712.
142. Chatani, E.; Nonomura, K.; Kayashi, R.; Balny, C.; Lange, R. Biochemistry, 2002, 41, 4567.
143. Li, T.; Yamane, H.; Arakawa, T.; Narhi, L.O. Protein Eng., 2002, 15, 59.
144. Lasagna, M.; Gratton, E.; Jameson, D. M.; Brunet, J. E. Biophys. J, 1999, 76, 443.
145. Sathish, H.A.; Cusan, M.; Aisenbrey, C.; Bechinger, B. Biochemistry, 2002, 41, 5340.
146. Xiao, B.; Shi, G.; Gao, J.; Blaszczyk, J.; Liu, Q.; Ji, X.; Yan, H. J. Biol. Chem., 2001, 276, 40274.
147. Swaminathan, G.J.; Holloway, D.E.; Veluraja, K.; Acharya, K.R. Biochemistry, 2002, 41, 3341.
148. Shelimov, K.; Clemmer, D. E.; Hudgins, R. R.; Jarrold, M. F. J. Am. Chem. Soc., 1997, 119, 2240.
149. Shelimov, K.; Jarrold, M.F. J. Am. Chem. Soc., 1997, 119, 2987.
150. Valentine, S. J.; Clemmer, D. E. J. Am. Chem. Soc., 1997, 119, 3558.
151. Valentine, S. J.; Anderson, J.; Ellington, A. E.; Clemmer, D. E. J. Phys. Chem., 1997, 101, 3891.
152. Valentine, S. J.; Counterman, A. E.; Clemmer D. E. J. Am. Soc. Mass Spectrom., 1997, 8, 954.
153. Purves, R. W.; Barnett, D.A.; Guevremont, R. J. Am. Soc. Mass Spectrom., 2000, 11, 738.
154. Leite, J.F.; Cascio, M. Biochemistry, 2002, 41, 6140.
155. Bader, R.; Rytz, G.; Lerch, M.; Beck-Sickinger, A.G.; Zerbe, O. Biochemistry, 2002, 41, 8031.