Electrostatics of proteins in dielectric solvent continua. II. First applications in molecular dynamics simulations.
In the preceding paper by Stork and Tavan, [J. Chem. Phys. 126, 165105 (2007)], the authors have reformulated an electrostatic theory which treats proteins surrounded by dielectric solvent continua and approximately solves the associated Poisson equation [B. Egwolf and P. Tavan, J. Chem. Phys. 118, 2039 (2003)]. The resulting solution comprises analytical expressions for the electrostatic reaction field (RF) and potential, which are generated within the protein by the polarization of the surrounding continuum. Here the field and potential are represented in terms of Gaussian RF dipole densities localized at the protein atoms. Quite like in a polarizable force field, also the RF dipole at a given protein atom is induced by the partial charges and RF dipoles at the other atoms. Based on the reformulated theory, the authors have suggested expressions for the RF forces, which obey Newton's third law. Previous continuum approaches, which were also built on solutions of the Poisson equation, used to violate the reactio principle required by this law, and thus were inapplicable to molecular dynamics (MD) simulations. In this paper, the authors suggest a set of techniques by which one can surmount the few remaining hurdles still hampering the application of the theory to MD simulations of soluble proteins and peptides. These techniques comprise the treatment of the RF dipoles within an extended Lagrangian approach and the optimization of the atomic RF polarizabilities. Using the well-studied conformational dynamics of alanine dipeptide as the simplest example, the authors demonstrate the remarkable accuracy and efficiency of the resulting RF-MD approach.
Stork
Martina
M
Theoretische Biophysik, Lehrstuhl für BioMolekulare Optik, Ludwig-Maximilians-Universität München, Oettingenstrasse 67, D-80538 München, Germany.
Tavan
Paul
P
D000409:Alanine / Q000737:chemistry*; D001696:Biomechanical Phenomena; D003198:Computer Simulation; D004151:Dipeptides / Q000737:chemistry*; D004574:Electromagnetic Fields; D008962:Models, Theoretical; D011487:Protein Conformation; D012997:Solvents / Q000737:chemistry*; D055672:Static Electricity
D004151:Dipeptides; D012997:Solvents; D000409:Alanine