SEARCH

SEARCH BY CITATION

Keywords:

  • β-sheet propensities;
  • conformational analysis.

The dispersion of the main-chain and side-chain conformations in the ϕ, ψ, χ1 space for all residues have been estimated in terms of three parameters corresponding to the entropy (S) of the distribution, the volume (DV) and the area (DA) the points are enclosed in. These parameters are inversely correlated with Chou and Fasman β-sheet propensities, Pβ (Gly and Pro excluded), suggesting that residues with greater dispersion in the conformational space are weak β-sheet formers. It was also found that different residues have different relative populations in the bridging region (intervening between the helical and β-sheet regions) which may lie on the pathway for interconversion between α and β conformations. The energy barrier for this transformation, as obtained from the population of residues in the bridging region relative to the β region, is directly correlated to Pβ. Residues with high Pβ 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 Pβ, because of the high energy barrier for their conversion into the α conformation, will continue to remain in the extended conformation and will ultimately constitute a β-strand in the folded structure.