beta-sheet propensity and its correlation with parameters based on conformation.
The dispersion of the main-chain and side-chain conformations in the phi, psi, chi(1) space for all residues have been estimated in terms of three parameters corresponding to the entropy (S) of the distribution, the volume (D(V)) and the area (D(A)) the points are enclosed in. These parameters are inversely correlated with Chou and Fasman beta-sheet propensities, P(beta) (Gly and Pro excluded), suggesting that residues with greater dispersion in the conformational space are weak beta-sheet formers. It was also found that different residues have different relative populations in the bridging region (intervening between the helical and beta-sheet regions) which may lie on the pathway for interconversion between alpha and beta conformations. The energy barrier for this transformation, as obtained from the population of residues in the bridging region relative to the beta region, is directly correlated to P(beta). Residues with high P(beta) have branched side chains, which have greater steric interactions with the main-chain atoms resulting in a shrinking of the available conformational space (first correlation) and a steeper energy gradient beyond the allowed space (second correlation) compared with linear residues. It is proposed that if residues exist in an extended conformation when the polypeptide chain is synthesized, a stretch of residues with high P(beta), because of the high energy barrier for their conversion into the alpha conformation, will continue to remain in the extended conformation and will ultimately constitute a beta-strand in the folded structure.
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Department of Biochemistry, Bose Institute, P-1/12 CIT Scheme VIIM, Calcutta 700 054, India.
Chakrabarti
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D000596:Amino Acids; D019277:Entropy; D008962:Models, Theoretical; D011487:Protein Conformation; D017510:Protein Folding; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry*
D000596:Amino Acids; D011506:Proteins