Protein molecular dynamics with electrostatic force entirely determined by a single Poisson-Boltzmann calculation.
The electrostatic force including the intramolecular Coulombic interactions and the electrostatic contribution of solvation effect were entirely calculated by using the finite difference Poisson-Boltzmann method (FDPB), which was incorporated into the GROMOS96 force field to complete a new finite difference stochastic dynamics procedure (FDSD). Simulations were performed on an insulin dimer. Different relative dielectric constants were successively assigned to the protein interior; a value of 17 was selected as optimal for our system. The simulation data were analyzed and compared with those obtained from 500-ps molecular dynamics (MD) simulation with explicit water and a 500-ps conventional stochastic dynamics (SD) simulation without the mean solvent force. The results indicate that the FDSD method with GROMOS96 force field is suitable to study the dynamics and structure of proteins in solution if used with the optimal protein dielectric constant.
Department of Astronomy and Applied Physics, University of Science and Technology of China, Hefei, China.
Ben Zhuo
BZ
Lu
Wei Zu
WZ
Chen
Cun Xin
CX
Wang
Xiao-jie
XJ
Xu
D019295:Computational Biology; D003198:Computer Simulation; D006860:Hydrogen Bonding; D007328:Insulin / Q000737:chemistry; D007700:Kinetics; D008958:Models, Molecular; D008962:Models, Theoretical; D016012:Poisson Distribution; D011506:Proteins / Q000737:chemistry*; D012997:Solvents / Q000737:chemistry; D055672:Static Electricity; D013269:Stochastic Processes
D007328:Insulin; D011506:Proteins; D012997:Solvents; C034329:insulin dimers