The Early Events of the Protein Folding Process

J.   P.   Dal Molin; Antonio      Caliri

Abstract

One remarkable aspect of small globular proteins folding process is the fastness. However, different proteins of similar sizes may paradoxically present folding rates that differ by several orders of magnitude. In the present work we show how reliably a specific minimalist lattice model can reproduce such large range of folding characteristic times during the search stage of the protein folding process. We select nine representative protein-like (compact) structures, which illustrate distinct combinations of cooperative and non-cooperative structural patterns. The respective sequences of residues are designed by a general rule, and then submitted to extensive Monte Carlo simulations to determine the characteristic folding time of each target structure. Our results reproduce the experimentally observed exponential-like folding kinetics --of small, two-state globular proteins, and strongly support the idea that the search mechanism for the native structure is fully governed by the hydrophobic effect and steric constraints. The present results are achieved through the application of nonextensive statistical mechanics.

Keywords: Protein folding, Stereochemical model, Monte Carlo, Nonextensive, Superstatistics, hydrophobic, minimalist lattice, thermodynamic, natural residues.