Continuum description of ionic and dielectric shielding for molecular-dynamics simulations of proteins in solution.
We extend our continuum description of solvent dielectrics in molecular-dynamics (MD) simulations, which has provided an efficient and accurate solution of the Poisson equation, to ionic solvents as described by the linearized Poisson-Boltzmann (LPB) equation. We start with the formulation of a general theory for the electrostatics of an arbitrarily shaped molecular system, which consists of partially charged atoms and is embedded in a LPB continuum. This theory represents the reaction field induced by the continuum in terms of charge and dipole densities localized within the molecular system. Because these densities cannot be calculated analytically for systems of arbitrary shape, we introduce an atom-based discretization and a set of carefully designed approximations. This allows us to represent the densities by charges and dipoles located at the atoms. Coupled systems of linear equations determine these multipoles and can be rapidly solved by iteration during a MD simulation. The multipoles yield the reaction field forces and energies. Finally, we scrutinize the quality of our approach by comparisons with an analytical solution restricted to perfectly spherical systems and with results of a finite difference method.
Egwolf
Bernhard
B
Theoretische Biophysik, Lehrstuhl fur BioMolekulare Optik, Ludwig-Maximilians-Universitat Munchen, Oettingenstr. 67, D-80538 Munchen, Germany.
Tavan
Paul
P
D001665:Binding Sites; D003198:Computer Simulation; D004563:Electrochemistry / Q000379:methods; D004573:Electrolytes / Q000737:chemistry*; D007477:Ions / Q000737:chemistry; D007700:Kinetics; D008956:Models, Chemical; D008958:Models, Molecular; D011485:Protein Binding; D011506:Proteins / Q000737:chemistry*; D012996:Solutions; D012997:Solvents / Q000737:chemistry*; D055672:Static Electricity
D004573:Electrolytes; D007477:Ions; D011506:Proteins; D012996:Solutions; D012997:Solvents