Accurate simulation of protein dynamics in solution.

Simulation of the molecular dynamics of a small protein, bovine pancreatic trypsin inhibitor, was found to be more realistic when water molecules were included than when in vacuo, using atom-centered forces and classical mechanics.

Abstract

Simulation of the molecular dynamics of a small protein, bovine pancreatic trypsin inhibitor, was found to be more realistic when water molecules were included than when in vacuo: the time-averaged structure was much more like that observed in high-resolution x-ray studies, the amplitudes of atomic vibration in solution were smaller, and fewer incorrect hydrogen bonds were formed. Our approach, which provides a sound basis for reliable simulation of diverse properties of biological macromolecules in solution, uses atom-centered forces and classical mechanics.