Conformational sampling of a 40-residue protein consisting of α and β secondary-structure elements in explicit solvent

Abstract Multicanonical molecular dynamics (McMD) simulations were performed for a 40-residue protein, the C-terminal domain of H-NS, having α and β 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 α and β structures provided native-topology structures with the smallest backbone rmsd, 3.27 A, 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.

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