title: Robustness of atomistic Gō models in predicting native-like folding intermediates.
abstract: Gō models are exceedingly popular tools in computer simulations of protein folding. These models are native-centric, i.e., they are directly constructed from the protein's native structure. Therefore, it is important to understand up to which extent the atomistic details of the native structure dictate the folding behavior exhibited by Gō models. Here we address this challenge by performing exhaustive discrete molecular dynamics simulations of a Gō potential combined with a full atomistic protein representation. In particular, we investigate the robustness of this particular type of Gō models in predicting the existence of intermediate states in protein folding. We focus on the N47G mutational form of the Spc-SH3 folding domain (x-ray structure) and compare its folding pathway with that of alternative native structures produced in silico. Our methodological strategy comprises equilibrium folding simulations, structural clustering, and principal component analysis.
authors.affiliation: Centro de Física da Matéria Condensada and Departamento de Física, Universidade de Lisboa, Av. Prof. Gama Pinto 2, 1649-003 Lisboa, Portugal.
authors.forename: S G
authors.initials: SG
authors.lastname: Estácio
authors.forename: C S
authors.initials: CS
authors.lastname: Fernandes
authors.forename: H
authors.initials: H
authors.lastname: Krobath
authors.forename: P F N
authors.initials: PF
authors.lastname: Faísca
authors.forename: E I
authors.initials: EI
authors.lastname: Shakhnovich
mesh_terms: D018360:Crystallography, X-Ray; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D009154:Mutation; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry* / Q000235:genetics; D013816:Thermodynamics; D018909:src Homology Domains / Q000235:genetics
chemical_list: D011506:Proteins