Electrostatic screening in molecular dynamics simulations.
The screened Coulombic potential has been shown to describe satisfactorily equilibrium properties like pK shifts, the effects of charged groups on redox potentials and binding constants of metal ions. To test how well the screening of the electrostatic potential describes the dynamical trajectory of a macromolecular system, a series of comparative simulations have been carried out on a protein system which explicitly included water molecules and a system in vacuo. For the system without solvent the results of using (i) the standard potential form were compared with results of (ii) the potential where the Coulomb term was modified by the inclusion of a distance dependent dielectric, epsilon (r), to model the screening effect of bulk water, and (iii) standard potential modified by reducing the charge on ionized residue side chains. All molecular dynamics simulations have been carried out on bovine pancreatic trypsin inhibitor. Comparisons between the resulting trajectories, averaged structures, hydrogen bonding patterns and properties such as solvent accessible surface area and radius of gyration are described. The results show that the dynamical behaviour of the protein calculated with a screened electrostatic term compares more favourably with the time-dependent structural changes of the full system with explicitly included water than the standard vacuum simulation.
Solmajer
T
T
Department of Structural Biology, University of Basel, Switzerland.
Mehler
E L
EL
D000818:Animals; D002417:Cattle; D003198:Computer Simulation; D003461:Crystallography; D006860:Hydrogen Bonding; D046911:Macromolecular Substances; D008432:Mathematical Computing; D008956:Models, Chemical; D011522:Protons; D012984:Software; D014361:Trypsin Inhibitors / Q000737:chemistry*; D014867:Water / Q000737:chemistry
D046911:Macromolecular Substances; D011522:Protons; D014361:Trypsin Inhibitors; D014867:Water