A REDUCED MODEL OF SHORT-RANGE INTERACTIONS IN POLYPEPTIDE-CHAINS

A simple model of short range interactions is proposed for a reduced l attice representation of polypeptide conformation. The potential is de rived on the basis of statistical regularities seen in the known cryst al structures of globular proteins. This potential accounts for the ge neric stiffness of polypeptides, the correlation between peptide bond plates, and the sequence dependent correlations between consecutive se gments of the C alpha-trace. This model is used for simulation of the equilibrium and dynamic properties of polypeptides in the denatured st ate. It is shown that the proposed factorization of the local conforma tional propensities reproduces secondary structure tendencies encoded in the protein sequence. Possible applications for modeling of protein folding are briefly discussed. (C) 1995 American Institute of Physics .