Model of protein folding: inclusion of short-, medium-, and long-range interactions.

Abstract

A hypothesis for protein folding is proposed, in which the native structure is formed by a three-step mechanism: (A) formation of ordered backbone structures by short-range interactions, (B) formation of small contact regions by medium-range interactions, and (C) association of the small contact regions into the native structure by long-range interactions. Empirical interaction parameters (free energy of formation of a contact) between amino-acid residues were evaluated from the frequency of contacts in the x-ray structures of native proteins. On the basis of this mechanism, a Monte Carlo simulation of protein folding (with an accompanying decrease in the total contact free energy) was carried out for bovine pancreatic trypsin inhibitor. The predicted three-dimensional structure is in fairly good agreement with the experimental one.