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: 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.
Levitt
M
M
Department of Chemical Physics, Weizmann Institute of Science, Rehovot, Israel.
Sharon
R
R
D000818:Animals; D007611:Aprotinin / Q000378:metabolism*; D003198:Computer Simulation; D008956:Models, Chemical; D011506:Proteins / Q000378:metabolism*; D012996:Solutions; D014867:Water / Q000378:metabolism
D011506:Proteins; D012996:Solutions; D014867:Water; D007611:Aprotinin