The Gō model revisited: Native structure and the geometric coupling between local and long-range contacts.
Monte Carlo simulations show that long-range interactions play a major role in determining the folding rates of 48-mer three-dimensional lattice polymers modeled by the Gō potential. For three target structures with different native geometries we found a sharp increase in the folding time when the relative contribution of the long-range interactions to the native state's energy is decreased from approximately 50% towards zero. However, the dispersion of the simulated folding times is strongly dependent on native geometry and Gō polymers folding to one of the target structures exhibits folding times spanning three orders of magnitude. We have also found that, depending on the target geometry, a strong geometric coupling may exist between local and long-range contacts, which means that, when this coupling exists, the formation of long-range contacts is forced by the previous formation of local contacts. The absence of a strong geometric coupling results in a kinetics that is more sensitive to the interaction energy parameters; in this case, the formation of local contacts is not capable of promoting the establishment of long-range ones when the latter are strongly penalized energetically and this results in longer folding times.
Faísca
Patrícia F N
PF
Centro de Física Teórica e Computacional da Universidade de Lisboa, Lisboa Codex, Portugal. patnev@alf1.cii.fc.ul.pt
Telo da Gama
Margarida M
MM
Nunes
Ana
A
D001665:Binding Sites; D003198:Computer Simulation; D008958:Models, Molecular; D009010:Monte Carlo Method; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism*
D011506:Proteins