Dichroic statistical model for prediction and analysis of peptide helicity

Proteins: Structure, Function and Genetics

Volumn 28, Issue 4, 1997, Pages 467-480

  Shalongo, William ^a   Stellwagen, Earle ^a  

^a UNIVERSITY OF IOWA   (United States)

Author keywords

Circular dichroism; Peptide bond ellipticity; Peptide helix prediction; Residue statistical weights; Statistical model

Indexed keywords

ARTICLE; CIRCULAR DICHROISM; MATHEMATICAL MODEL; PRIORITY JOURNAL; PROTEIN STRUCTURE; STATISTICAL ANALYSIS;

ALGORITHMS; CIRCULAR DICHROISM; MODELS, MOLECULAR; MODELS, STATISTICAL; PEPTIDES; PROTEIN CONFORMATION;

EID: 0030752270     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1097-0134(199708)28:4<467::AID-PROT2>3.0.CO;2-7     Document Type: Article

References (21)

1. Chen, Y.-H., Yang, J.T., Chau, K.H. Determination of the helix and β form of proteins in aqueous solution using circular dichroism. Biochemistry 13:3350-3359, 1974.
2. Scholtz, J.M., Qian, H., York, E.J., Stewart, J.M., Baldwin, R.L. Parameters of helix-coil transition theory for alanine based peptides of varying chain lengths in water. Biopolymers 31:1463-1470, 1991.
3. Gans, P.J., Lyu, P.C., Manning, M.C., Woody, R.W., Kallenbach, N.R. The helix-coil transitions in heterogeneous peptides with specific side chain interactions: Theory and comparison with circular dichroism spectral data Biopolymers 31:1605-1614, 1991.
4. 10-helix. J. Chem Phys. 46:4927-4945, 1967.
5. Madison, V., Schellman, J. Optical activity of polypeptides and proteins. Biopolymers 11:1041-1076, 1972.
6. Manning, M.C., Woody, R.W. Theoretical CD studies of polypeptide helices: Examination of important electronic and geometric factors. Biopolymers 31:569-586, 1991.
7. Schellman, J.A. Circular dichroism and optical rotation. Chem. Rev. 75:323-331, 1975.
8. Hansen, A.E., Bouman, T.D. Natural chiroptical spectroscopy: Theory and computations. Adv. Chem. Phys 44:545-644, 1980.
9. Sears, D.W., Beychok, S. Circular dichroism In: "Physical Principles and Techniques of Protein Chemistry, Part C." Leach, S.J. (ed.). New York: Academic Press, 1973:445-593.
10. Zimm, B.H., Bragg, B.K. Theory of phase transition between helix and random coil in polypeptide chains. J. Chem. Phys. 31:526-535, 1959.
11. Lifson, S., Roig, A. On the theory of helix-coil transition in polypeptides. J. Chem. Phys. 34:1963-1974, 1961.
12. Doig, A.M., Chakrabartty, A., Klingler, T.M., Baldwin, R.L. Determination of free energies of N-capping in α-helices by modification of the Lifson-Roig helix-coil theory to include N-and C-capping. Biochemistry 33:3396-3403, 1994.
13. Chakrabartty, A., Kortemme, T., Baldwin, R.L. Helix propensities of the amino acids measured in alanine-based peptides without helix-stabilizing side-chain interactions. Protein Sci. 3:843-852, 1994.
14. Zhou, H.X., Lyu, P., Wemmer, D.E., Kallenbach, N.R. Alpha helix capping in synthetic model peptides by reciprocal side main-main chain interactions: Evidence for an N terminal "capping box." Proteins 18:1-7, 1994.
15. Munoz, V., Blanco, F.J., Serrano, L. The hydrophobic-staple motif and a role for loop-residues in α-helix stability and protein folding. Nature Struct. Biol. 2:380-385, 1995.
16. Richardson, J.S., Richardson, D.C. Amino acid preferences for specific locations at the ends of α helices. Science 240:1648-1652, 1988.
17. O'Neil, K.T., DeGrado, W.F. A thermodynamic scale for the helix-forming tendencies of the commonly occurring amino acids. Science 250:646-651, 1990.
18. Lyu, P.C., Liff, M.I., Marky, L.Z., Kallenbach, N.R. Side-chain contributions to the stability of alpha-helical structure in peptides. Science 250:669-673, 1990.
19. Merutka, G., Lipton, W., Shalongo, W., Park, S.H., Stellwagen, E. Effect of central-residue replacements on the helical stability of a monomeric peptide. Biochemistry 29:7511-7515, 1990.
20. Doig, A.J., Baldwin, R.L. N-and C-capping preferences for all 20 amino acids in α-helical peptides. Protein Sci. 4:1325-1336, 1995.
21. Renold, P., Tsang, K.Y., Shimizu, L.S., Kemp, D.S. Helical propensities of lysine residues within short helical alanine-lysine peptides exhibit large temperature dependencies. J. Am. Chem. Soc., 118:12234-12235, 1996.