Structural composition of βI- and βII-proteins

Protein Science

Volumn 12, Issue 2, 2003, Pages 384-388

  Sreerama, Narasimha ^a   Woody, Robert W ^a  

^a Department of Environmental and Radiological Health Sciences   (United States)

Author keywords

rich proteins; P2 structure; Protein CD; Protein secondary structure

Indexed keywords

BETA 1 PROTEIN; BETA 2 PROTEIN; GLOBULAR PROTEIN; POLYPEPTIDE; PROTEIN; UNCLASSIFIED DRUG;

ALPHA HELIX; ARTICLE; BETA SHEET; CIRCULAR DICHROISM; MOLECULAR MODEL; NONHUMAN; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN SECONDARY STRUCTURE; CHEMISTRY;

CIRCULAR DICHROISM; PROTEIN STRUCTURE, SECONDARY; PROTEINS;

EID: 0037302324     PISSN: 09618368     EISSN: None     Source Type: Journal    
DOI: 10.1110/ps.0235003     Document Type: Article

References (29)

1. Adzhubei, A.A. and Sternberg, M. 1993. Left-handed polyproline II helices commonly occur in globular proteins. J. Mol. Biol. 229: 472-493.
2. Berman, H.M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T.N., Weissig, H., Shindyalov, I.N., and Bourne, P.E. 2000. The protein data bank. Nucleic Acids Res. 28: 235-242.
3. Brahms, S., Brahms, J., Spach, G., and Brack, A., 1977. Identification of β, β-turns and unordered conformations in polypeptide-chains by vacuum UV circular dichroism. Proc. Natl. Acad. Sci. 74: 3208-3212.
4. Chou, K.C. and Scheraga, H.A. 1982. Origin of the right-handed twist of β-sheets of poly(L-Val) chains. Proc. Natl. Acad. Sci. 79: 7047-7051.
5. Chou, K.C., Pottle, M., Nemethy, G., Ueda, Y., and Scheraga, H.A. 1982. Structure of β-sheets. Origin of the right-handed twist and of the increased stability of antiparallel over parallel sheets. J. Mol. Biol. 162: 89-112.
6. Jenness, G.D., Sprecher, C., and Johnson, Jr., W.C. 1976. Circular dichroism of collagen, gelatin and poly(Proline)II in vacuum ultraviolet. Biopolymers 15: 513-521.
7. Johnson, Jr., W.C. 1988. Secondary structure of proteins through circular dichroism spectroscopy. Annu. Rev. Biophys. Biophys. Chem. 17: 145-166.
8. -. 1999. Analyzing protein circular dichroism spectra for accurate secondary structures. Proteins Struct. Funct. Genet. 35: 307-312.
9. Kabsch, W. and Sander, C. 1983. Dictionary of protein secondary structure: Pattern recognition of hydrogen bonded and geometric features. Biopolymers 22: 2577-2637.
10. Levitt, M. and Chothia, C. 1976. Structural patterns in globular proteins. Nature 261: 552-558.
11. Manavalan, P. and Johnson, Jr., W.C. 1983. Sensitivity of circular dichroism to protein tertiary structure class. Nature 305: 831-832.
12. Manning, M.C., Illangasekare, M., and Woody, R.W. 1988. Circular dichroism studies of distorted α-helices, twisted β-sheets, and β-turns. Biophys. Chem. 31: 77-86.
13. Pancoska, P., Bitto, E., Janota, V., Urbanova, M., Gupta, V.P., and Keiderling, T.A. 1995. Comparison of and limits of accuracy for statistical analyses of vibrational and electronic circular dichroism spectra in terms of correlations to and predictions of protein secondary structure. Protein Sci. 4: 1384-1401.
14. Shi, Z., Woody, R.W., and Kallenbach, N.R. 2002. Is polyproline II a major backbone conformation in unfolded protein? Adv. Protein Chem. 62: 163-240.
15. Sreerama, N. and Woody, R.W. 1994. Poly(Pro)II helices in globular proteins: Identification and circular dichroic analysis. Biochemistry 33: 10022-10025.
16. -. 2000a. Circular dichroism of peptides and proteins. In Circular dichroism: Principles and applications, 2nd ed. (eds. N. Berova, K. Nakanishi, et al.), pp. 601-620. Wiley, New York.
17. -. 2000b. Estimation of protein secondary structure from CD spectra: Comparison of CONTIN. SELCON and CDSSTR methods with an expanded reference set. Anal. Biochem. 282: 252-260.
18. Sreerama, N., Venyaminov, S.Y., and Woody, R.W. 1999. Estimation of the number of α-helical and β-strand segments in proteins using circular dichroism spectroscopy Protein Sci. 8: 370-380.
19. -. 2001. Analysis of protein circular dichroism spectra based on tertiary structure classification. Anal. Biochem. 299: 271-274.
20. Stapley, B.J. and Creamer, T.P. 1999. A survey of left-handed polyproline II helices. Protein Sci. 8: 587-595.
21. Thomas, M.W., Walborg, E.F., and Jirgensons, B. 1977. Circular dichroism and saccharide-induced conformational transitions in wheat germ agglutinin. Arch. Biochem. Biophys. 178: 625-630.
22. Tiffany, M.L. and Krimm, S. 1968. New chain conformations of poly(glutamic acid) and polylysine. Biopolymers 6: 1379-1382.
23. Toniolo, C. and Bonora, G.M. 1975. Structural aspects of small peptides. A circular dichroism study of monodisperse protected homo-oligomers derived from L-alanine. Makromol. Chem. 176: 2547-2558.
24. Toniolo, C., Bonora, G.M., and Fontana, A. 1974. Three-dimensional architecture of monodisperse β-branched linear homo-oligopeptides. Int. J. Peptide Protein Res. 6: 371-380.
25. Toumadje, A., Alcorn, S.W., and Johnson, Jr., W.C. 1992, Extending CD spectra of proteins to 168 nm improves the analysis for secondary structures. Anal. Biochem. 200: 321-331.
26. Woody, R.W. 1969. Optical properties of polypeptides in the β-conformation. Biopolymers 8: 669-683.
27. -. 1992. Circular dichroism of unordered polypeptides. Adv. Biophys. Chem. 2: 37-79.
28. Wu, J., Yang, J.T., and Wu, C-S.C. 1992. β-II conformation of all-β proteins can be distinguished from unordered form by circular dichroism. Anal. Biochem. 200: 359-364.
29. Yang, J.T., Wu, C-S. C., and Martinez, H.M. 1986. Calculation of protein conformation from circular dichroism. Methods Enzymol. 130: 208-269.