Solution structure and dynamics of biomolecules from Ramam optical activity

Progress in Biophysics and Molecular Biology

Volumn 73, Issue 1, 2000, Pages 1-49

  Barron, L D ^a   Hecht, L ^a   Blanch, E W ^a   Bell, A F ^a  

^a UNIVERSITY OF GLASGOW   (United Kingdom)

Author keywords

Biomolecular structure and dynamics; Carbohydrates; Nucleic acids; Proteins; Raman optical activity; Vibrational optical activity; Viruses

Indexed keywords

CARBOHYDRATE; M PROTEIN; NUCLEIC ACID; PEPTIDE; POLYPEPTIDE; PROTEIN;

ANIMAL; AQUEOUS SOLUTION; CARBOHYDRATE ANALYSIS; CHEMICAL STRUCTURE; CHEMISTRY; CHIRALITY; CONFORMATION; HUMAN; METHODOLOGY; MOLECULAR DYNAMICS; PROTEIN ANALYSIS; PROTEIN FOLDING; RAMAN SPECTROMETRY; REVIEW; SPECTRAL SENSITIVITY; VIRUS;

ANIMALS; CARBOHYDRATES; HUMANS; NUCLEIC ACIDS; PEPTIDES; PROTEINS; SPECTRUM ANALYSIS, RAMAN; VIRUSES;

EID: 0034118337     PISSN: 00796107     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0079-6107(99)00017-6     Document Type: Review

References (144)

1. Adler A.J., Greenfield N.J., Fasman G.D. Methods Enzymol. 27:1973;675-735.
2. Adzhubei A.A., Eisenmenger F., Tumanyan V.G., Zinke M., Brodzinski S., Esipova N.G. J. Biomol. Struct. Dyn. 5:1987;689-704.
3. Andrews D.A. J. Chem. Phys. 72:1980;4141-4144.
4. Athès V., Combes D., Zwick A. J. Raman Spectrosc. 29:1998;373-378.
5. Atkins P.W., Barron L.D. Mol. Phys. 16:1969;453-466.
6. Barlow D.J., Thornton J.M. J. Mol. Biol. 201:1988;601-619.
7. Barron L.D. Molecular Light Scattering and Optical Activity. 1982;Cambridge University Press, Cambridge.
8. Barron L.D., Buckingham A.D. Mol. Phys. 20:1971;1111-1119.
9. Barron L.D., Buckingham A.D. J. Am. Chem. Soc. 96:1974;4769-4773.
10. Barron L.D., Bogaard M.P., Buckingham A.D. J. Am. Chem. Soc. 95:1973;603-605.
11. Barron L.D., Hecht L., Bell A.F., Wilson G. Appl. Spectrosc. 50:1996;619-629.
12. Barron L.D., Hecht L., Gargaro A.R., Hug W. J. Raman Spectrosc. 21:1990;375-379.
13. Barron L.D., Hecht L., Wilson G. Biochemistry. 36:1997;13143-13147.
14. Bell A.F., Barron L.D., Hecht L. Carbohydr. Res. 257:1994;11-24.
15. Bell A.F., Hecht L., Barron L.D. J. Am. Chem. Soc. 116:1994;5155-5161.
16. Bell A.F., Hecht L., Barron L.D. Spectrochim. Acta. 51A:1995;1367-1378.
17. Bell A.F., Hecht L., Barron L.D. J. Raman Spectrosc. 26:1995;1071-1074.
18. Bell A.F., Hecht L., Barron L.D. Chem. Eur. J. 3:1997;1292-1298.
19. Bell A.F., Hecht L., Barron L.D. J. Chem. Soc. Faraday Trans. 93:1997;553-562.
20. Bell A.F., Hecht L., Barron L.D. J. Am. Chem. Soc. 119:1997;6006-6013.
21. Bell A.F., Hecht L., Barron L.D. Biospectroscopy. 4:1998;107-111.
22. Bell A.F., Hecht L., Barron L.D. J. Am. Chem. Soc. 120:1998;5820-5821.
23. Bell A.F., Hecht L., Barron L.D. J. Raman Spectrosc. 30:1999;651-656.
24. Bergethon P.R. The Physical Basis of Biochemistry. 1998;Springer-Verlag, New York.
25. Bertoluzza A., Bonora S., Fini G., Morelli M.A. Can. J. Appl. Spectrosc. 37:1992;58-61.
26. Blanch E.W., Bell A.F., Hecht L., Day L.A., Barron L.D. J. Mol. Biol. 290:1999;1-7.
27. Blanch E.W., Hecht L., Barron L.D. Protein Sci. 8:1999;1362-1367.
28. Blanch, E.W., Morozova-Roche, L.A., Hecht, L., Noppe, W., Barron, L.D., Submitted for publication.
29. Blundell T.L., Barlow D.J., Borkakoti N., Thornton J.M. Nature. 306:1983;281-283.
30. Branden C., Tooze J. Introduction to Protein Structure, 2. 1999;Garland Publishing, New York.
31. Buckingham A.D. Adv. Chem. Phys. 12:1967;107-142.
32. Bychkova V.E., Ptitsyn O.B. FEBS Lett. 359:1995;6-8.
33. Bychkova V.E., Pain R.H., Ptitsyn O.B. FEBS Lett. 238:1988;231-234.
34. Carey P.R. Biochemical Applications of Raman and Resonance Raman Spectroscopies. 1982;Academic Press, New York.
35. Carrell R.W., Lomas D.A. Lancet. 350:1997;134-138.
36. Chen X.G., Schweitzer-Stenner R., Krimm S., Mirkin N.G., Asher S.A. J. Am. Chem. Soc. 116:1994;11141-11142.
37. Chi Z., Chen X.G., Holtz J.S.W., Asher S.A. Biochemistry. 37:1998;2854-2864.
38. Chi Z., Chen X.G., Holtz J.S.W., Asher S.A. Biochemistry. 37:1998;2865-2872.
39. Chou K.C., Zhang C.T., Maggiora G.M. Proteins: Struct. Func. Genet. 28:1997;99-108.
40. Creighton T.E. Protein Folding. 1992;W.H. Freeman and Co, New York.
41. Crick F.H.C. What Mad Pursuit. 1990;Penguin Books, London.
42. Dalal S., Balasubramanian S., Regan L. Fold. Des. 2:1997;R71-R79.
43. De Rijk P., De Wachter R. Nucleic Acids Res. 25:1997;4679-4684.
44. DiCapua F.M., Swaminathan S., Beveridge D.L. J. Am. Chem. Soc. 113:1991;6145-6155.
45. Denisov V.P., Jonsson B.-H., Halle B. Nature Struct. Biol. 6:1999;253-260.
46. Diem M. Modern Vibrational Spectroscopy. 1993;Wiley, New York.
47. Dill K.A. Nature. 400:1999;309-310.
48. Dill K.A. Protein Sci. 8:1999;1166-1180.
49. Dobson C.M. Curr. Biol. 4:1994;636-640.
50. Donate L.E., Rufino S.D., Canard L.H.J., Blundell T.L. Protein Sci. 5:1996;2600-2616.
51. Efimov A.V. Curr. Opin. Struct. Biol. 3:1993;379-384.
52. Efimov A.V. Prog. Biophys. Mol. Biol. 60:1993;201-239.
53. Eisenberg D., Schwarz E., Komaromy M., Wall R. J. Mol. Biol. 179:1984;125-142.
54. Fasman G.D. Biopolymers. 26:1987;S59-S79.
55. Fasman G.D. Circular Dichroism and the Conformational Analysis of Biomolecules. 1996;Plenum Press, New York.
56. Fiebig K.M., Schwalbe H., Buck M., Smith L.J., Dobson C.M. J. Phys. Chem. 100:1996;2661-2666.
57. Ford S.J., Cooper A., Hecht L., Wilson G., Barron L.D. J. Chem. Soc. Faraday Trans. 91:1995;2087-2093.
58. Ford S.J., Wen Z.Q., Hecht L., Barron L.D. Biopolymers. 34:1994;303-313.
59. Forge V., Wijesinha R.T., Balbach J., Brew K., Robinson C.V., Redfield C., Dobson C.M. J. Mol. Biol. 288:1999;673-688.
60. Frauenfelder H., Pesko G.A., Tsernoglou D. Nature. 280:1979;558-563.
61. Gargaro A.R., Barron L.D., Hecht L. J. Raman Spectrosc. 24:1993;91-96.
62. Geetha V., Munson P.J. Protein Sci. 6:1997;2538-2547.
63. Gratias R., Konat R., Kessler H., Crisma M., Valle G., Polese A., Formaggio F., Toniolo C., Broxterman Q.B., Kamphuis J. J. Am. Chem. Soc. 120:1998;4763-4770.
64. Griko Y.V., Freire E., Privalov P.L. Biochemistry. 33:1994;1889-1899.
65. Hammonds K.D., Deng H., Heine V., Dove M.T. Phys. Rev. Lett. 78:1997;3701-3704.
66. Han W.-G., Jalkanen K.J., Elster M., Suhai S. J. Phys. Chem. B. 102:1998;2587-2602.
67. Haris P.I., Chapman D. Biopolymers. 37:1995;251-263.
68. Hecht L., Barron L.D., Hug W. Chem. Phys. Lett. 158:1989;341-344.
69. Hecht L., Barron L.D. Appl. Spectrosc. 44:1990;483-491.
70. Hecht L., Barron L.D. Faraday Discuss. 99:1994;35-47.
71. Hecht L., Barron L.D. Modern Techniques in Raman Spectroscopy. 1996;265-304 Wiley, Chichester, UK.
72. Hecht L., Barron L.D., Blanch E.W., Bell A.F., Day L.A. J. Raman Spectrosc. 30:1999;815-825.
73. Helgaker T., Ruud K., Bak K.L., Jørgensen P., Olsen J. Faraday Discuss. 99:1994;165-180.
74. Hoffmann G.G. Infrared and Raman Spectroscopy. 1995;543-572 VCH Publishers, Weinheim, Germany.
75. Higgs P.W. Proc. R. Soc. A. 220:1953;472-485.
76. Homans S.W. Structural Glycobiology. 1994;230-257 Oxford University Press, Oxford.
77. Hug W. Chimia. 48:1994;386-390.
78. Hug W., Hangartner G. J. Raman Spectrosc. 30:1999;841-852.
79. Karplus M., Shakhnovich E. Protein Folding. 1992;127-195 W.H. Freeman, New York.
80. Keiderling T.A. Circular Dichroism and the Conformational Analysis of Biomolecules. 1996;555-598 Plenum Press, New York.
81. Lord Kelvin. Baltimore Lectures. 1904;C.J. Clay and Sons, London.
82. Kraulis P.J. J. Appl. Crystallogr. 24:1991;946-950.
83. Krimm S., Bandekar J. Adv. Prot. Chem. 38:1986;181-364.
84. Lednev I.K., Karnoup A.S., Sparrow M.C., Asher S.A. J. Am. Chem. Soc. 121:1999;8074-8086.
85. Lee S.H., Krimm S. J. Raman Spectrosc. 29:1998;73-80.
86. Lee S.H., Krimm S. Biopolymers. 46:1998;283-317.
87. Mathlouthi M., Koenig J.L. Adv. Carbohydr. Chem. Biochem. 44:1986;7-89.
88. Miura T., Thomas G.J. Jr. Subcellular Biochemistry. vol. 24: Proteins: Structure, Function and Engineering:1995;55-99 Plenum Press, New York.
89. Morozova-Roche L.A., Arico-Muendel C.C., Haynie D.T., Emelyanenko V.I., Van Dael H., Dobson C.M. J. Mol. Biol. 268:1997;903-921.
90. Nafie L.A. Appl. Spectrosc. 50:1996;14A-26A.
91. Nafie L.A. Ann. Rev. Phys Chem. 48:1997;357-386.
92. Nafie L.A., Che D. Adv. Chem. Phys. 85:1994;105-222.
93. Nafie L.A., Yu G.S., Qu X., Freedman T.B. Faraday Discuss. 99:1994;13-24.
94. Nakanishi K., Berova N., Woody R.W. Circular Dichroism: Principles and Applications for Biologists. 2 :2000;Wiley, New York.
95. Nesloney C.L., Kelly J.W. Bioorg. Med. Chem. 4:1996;739-766.
96. Orengo C.A., Jones D.T., Thornton J.M. Nature. 372:1994;631-634.
97. Otting G. Prog. NMR Spectrosc. 31:1997;259-285.
98. Overman S.A., Thomas G.J. Jr. J. Raman Spectrosc. 29:1998;23-29.
99. Overman S.A., Thomas G.J. Jr. Biochemistry. 37:1998;5654-5665.
100. Overman S.A., Thomas G.J. Jr. Biochemistry. 38:1999;4018-4027.
101. Pain R.H. Mechanisms of Protein Folding. 1994;IRL Press, Oxford.
102. Parthasarathy R., Chaturvedi S., Go K. Prog. Biophys. Molec. Biol. 64:1995;1-54.
103. Perutz M.F. Is Science Necessary? 1989;Oxford University Press, Oxford.
104. Perutz M.F. Nature. 385:1997;773-775.
105. Philp D., Stoddart J.F. Angew. Chem. Int. Ed. Engl. 35:1996;1154-1196.
106. Polavarapu P.L. J. Phys. Chem. 94:1990;8106-8112.
107. Polavarapu P.L. Vibrational Spectra: Principles and Applications with Emphasis on Optical Activity. 1998;Elsevier, Amsterdam.
108. Polavarapu P.L., Deng Z. Faraday Discuss. 99:1994;151-163.
109. Ptitsyn O.B. Adv. Prot. Chem. 47:1995;83-229.
110. Qin B.Y., Bewley M.C., Creamer L.K., Baker H.M., Baker E.N., Jameson G.B. Biochemistry. 37:1998;14014-14023.
111. Rader S.D., Agard D.A. Protein Sci. 6:1997;1375-1386.
112. Reisdorf W.C. Jr, Krimm S. Biochemistry. 35:1996;1383-1386.
113. Rodger A., Nordén B. Circular Dichroism and Linear Dichroism. 1997;Oxford University Press, Oxford.
114. Saenger W. Principles of Nucleic Acid Structure. 1984;Springer-Verlag, New York.
115. Salemme F.R. Prog. Biophys. Molec. Biol. 42:1983;95-133.
116. Schülke N., Schmid F.X. J. Biol. Chem. 263:1988;8832-8837.
117. Sekharudu C.Y., Sundaralingam M. Water and Biological Macromolecules. 1993;CRC Press, Boca Raton, FL.
118. Smith L.J., Fiebig K.M., Schwalbe H., Dobson C.M. Fold. Des. 1:1996;R95-R106.
119. Sundaralingam M., Sekharudu Y.C. Science. 244:1989;1333-1337.
120. Sundaralingam M., Sekharudu Y.C. Structure and Methods. vol. 2: DNA Protein Complexes and Proteins:1990;Adenine Press, Schenectady, NY.
121. Swindells M.B., MacArthur M.W., Thornton J.M. Nature Struct. Biol. 2:1995;596-603.
122. Szejtli J., Osa T. Comprehensive Supramolecular Chemistry. vol. 3:1996;Pergamon Press, Oxford.
123. Tanford C., Bunville L.G., Nozaki Y. J. Am. Chem. Soc. 81:1959;4032-4036.
124. Teraoka J., Bell A.F., Hecht L., Barron L.D. J. Raman Spectrosc. 29:1998;67-71.
125. Terpstra P.A., Otto C., Greve J. Biopolymers. 41:1997;751-763.
126. Thomas G.J. Jr. Raman Spectra and The Conformations of Biological Macromolecules. Biological Applications of Raman Spectroscopy. vol. 1:1987;137-201 Wiley, New York.
127. Thomas G.J. Jr. Annu. Rev. Biophys. Biomol. Struct. 28:1999;1-27.
128. Tiffany M.L., Krimm S. Biopolymers. 6:1968;1379-1382.
129. Tu A.T. Adv. Spectrosc. 13:1986;47-112.
130. Vargek M., Freedman T.B., Lee E., Nafie L.A. Chem. Phys. Lett. 287:1998;359-364.
131. Vargek M., Freedman T.B., Nafie L.A. J. Raman Spectrosc. 28:1997;627-633.
132. Vecchio G., Bossi A., Pasta P., Carrea G. Int. J. Peptide Protein Res. 48:1996;113-117.
133. Wen Z.Q., Barron L.D., Hecht L. J. Am. Chem. Soc. 115:1993;285-292.
134. Wen Z.Q., Hecht L., Barron L.D. Protein Sci. 2:1994;435-439.
135. Wilson G., Hecht L., Barron L.D. J. Chem. Soc. Faraday Trans. 92:1996;1503-1510.
136. Wilson G., Hecht L., Barron L.D. Biochemistry. 35:1996;12518-12525.
137. Wilson G., Hecht L., Barron L.D. J. Mol. Biol. 261:1996;341-347.
138. Wilson G., Hecht L., Barron L.D. J. Phys. Chem. 101:1997;694-698.
139. Woody R.W. Adv. Biophys. Chem. 2:1992;37-79.
140. Wormald M.R., Dwek R.A. Structure. 7:1999;R155-R160.
141. Xu D., Evans K.O., Nordlund T.M. Biochemistry. 33:1994;9592-9599.
142. Yu N.T. Crit. Rev. Biochem. 4:1977;229-280.
143. Yu G.S., Freedman T.B., Nafie L.A., Deng Z., Polavarapu P.L. J. Phys. Chem. 99:1995;835-843.
144. Zhong H., Gilmanshin R., Callender R. J. Phys. Chem. 103:1999;3947-3953.