Side-chain Conformations Cooperatively Restricted in Protein Secondary Structure

II. Side-chain Configurational Entropies of α-helices in the Folding Nuclei

Abstract

Protein side-chain configurational entropies and their correlations were analyzed for α-helices in several proteins. The conformations of several bulky side-chains in helices were found to be cooperatively fixed by the restricted side-chain conformations of the neighboring β-branched amino acids. Such helices correspond well to the experimentally observed nuclei in the folding procedures, so that the folding rates should be significantly accerelated. This phenomenon may be a reasonable answer to the Levinthal paradox.