A SIMPLIFIED AMINO-ACID POTENTIAL FOR USE IN STRUCTURE PREDICTIONS OFPROTEINS

A simplified description and a corresponding force field for polypepti des is introduced. Each amino acid residue is reduced to one interacti on site, representing the backbone, and one or two side chain sites de pending on its size and complexity. Site-site interactions are paramet erized after a hydrophobicity criterium. The treatment of backbone sit es is in addition designed to reproduce typical polypeptide hydrogen b onding patterns, as well as yielding conformations in accord with the allowed phi and psi angles through an effective angle potential. There are no explicit charges in the model. The derived energy functions, w hich are based on thermodynamic data and sterical consideration of all owed backbone conformations, correspond to the introduction of an effe ctive potential. The model is tested on two small proteins, avian panc reatic polypeptide and a parathyroid hormone-related protein, by simul ating folding from an initially extended state using Monte Carlo metho ds. The reduced amino acid description is able to satisfactorily repro duce the experimentally determined native structures. (C) 1994 Wiley-L iss, Inc.