Pathways to folding, nucleation events, and native geometry.
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.
Travasso
Rui D M
RD
Centro de Física Teórica e Computacional, Faculdade de Ciências, Universidade de Lisboa, Avenida Professor Gama Pinto 2, 1649-003 Lisbon, Portugal. rui@cii.fc.ul.pt
Telo da Gama
Margarida M
MM
Faísca
Patrícia F N
PF
D003198:Computer Simulation; D009010:Monte Carlo Method; D011487:Protein Conformation; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry*; D013997:Time Factors
D011506:Proteins