Pathways to folding, nucleation events, and native geometry

摘要

We perform extensive Monte Carlo simulations of a lattice model and the G5 potential N. Ge 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.