Ab initio simulation of a 57-residue protein in explicit solvent reproduces the native conformation in the lowest free-energy cluster.

ABSTRACT: An enhanced conformational sampling method, multicanonical molecular dynamics (McMD), was applied to the ab intio folding of the 57-residue first repeat of human glutamyl- prolyl-tRNA synthetase (EPRS-R1) in explicit solvent. The simulation started from a fully extended structure of EPRS-R1 and did not utilize prior structural knowledge. A canonical ensemble, which is a conformational ensemble thermodynamically probable at an arbitrary temperature, was constructed by reweighting the sampled structures. Conformational clusters were obtained from the canonical ensemble at 300 K, and the largest cluster (i.e., the lowest free-energy cluster), which contained 34% of the structures in the ensemble, was characterized by the highest similarity to the NMR structure relative to all alternative clus

SUBMITTER: Ikebe J 

PROVIDER: S-EPMC3047075 | biostudies-literature | 2011 Jan

REPOSITORIES: biostudies-literature