Pathways to folding, nucleation events, and native geometry

J Chem Phys. 2007 Oct 14;127(14):145106. doi: 10.1063/1.2777150.

Abstract

We perform extensive Monte Carlo simulations of a lattice model and the Gō potential [N. Gō and H. Taketomi, Proc. Natl. Acad. Sci. U.S.A. 75, 559563 (1978)] to investigate the existence of folding pathways at the level of contact cluster formation for two native structures with markedly different geometries. Our analysis of folding pathways revealed a common underlying folding mechanism, based on nucleation phenomena, for both protein models. However, folding to the more complex geometry (i.e., that with more nonlocal contacts) is driven by a folding nucleus whose geometric traits more closely resemble those of the native fold. For this geometry folding is clearly a more cooperative process.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Computer Simulation*
  • Monte Carlo Method*
  • Protein Conformation
  • Protein Folding*
  • Proteins / chemistry*
  • Time Factors

Substances

  • Proteins