화학공학소재연구정보센터
Chemical Physics Letters, Vol.443, No.4-6, 364-368, 2007
Conformational sampling of a 40-residue protein consisting of alpha and beta secondary-structure elements in explicit solvent
Multicanonical molecular dynamics (McMD) simulations were performed for a 40-residue protein, the C-terminal domain of H-NS, having alpha and beta secondary-structure elements, starting the simulation from a disordered structure, and free-energy landscapes were obtained from 280 K to 700 K. Cooperative formation of alpha and beta structures provided native-topology structures with the smallest backbone rmsd, 3.27 angstrom, to the NMR structure, although such structures were minority even when a knowledge-based force field was applied to the backbone dihedral potentials. Current study suggests that our McMD simulation could sample many different structures including the native-topology ones, and that the force field issue should be critical. (c) 2007 Published by Elsevier B.V.