Protein secondary structure preferencs

Abstract

This paper addresses the question to what extent steric properties of sequence neighbors effect the preferences of an amino acid residue to assume theα-helical or some other secondary structure conformation. We find that an amino acid has increased tendency to be inα-helical conformation when its sequence neighbors are bulky. This result is an outcome of our automated method for finding conformational preferences as functions of physical parameters important for protein folding. The steric environment for a given residue in a protein is defined as an average of water-accessible surface areas of its primary structure neighbors in extended conformation for model tripeptides. For all amino acids, including non-helix formers like glycine and arginine, the preference for the helical structure increases if their primary structure neighbors form a larger steric environment.