COMPARISON OF STRUCTURAL AND DYNAMIC PROPERTIES OF DIFFERENT SIMULATION METHODS APPLIED TO SH3

The dynamic and static properties of molecular dynamics simulations us ing various methods for treating solvent were compared. The SH3 protei n domain was chosen as a test case because of its small size and high surface-to-volume ratio. The simulations were analyzed in structural t erms by examining crystal packing, distribution of polar residues, and conservation of secondary structure. In addition, the ''essential dyn amics'' method was applied to compare each of the molecular dynamics t rajectories with a full solvent simulation. This method proved to be a powerful tool for the comparison of large concerted atomic motions in SH3. It identified methods of simulation that yielded significantly d ifferent dynamic properties compared to the full solvent simulation. S imulating SH3 using the stochastic dynamics algorithm with a vacuum (r educed charge) force field produced properties close to those of the f ull solvent simulation. The application of a recently described solvat ion term did not improve the dynamic properties. The large concerted a tomic motions in the full solvent simulation as revealed by the essent ial dynamics method were analyzed for possible biological implications . Two loops, which have been shown to be involved in ligand binding, w ere seen to move in concert to open and close the ligand-binding site.