Modeling of Electrostatic Effects in Macromolecules

Part of the Springer Series in Bio-/Neuroinformatics book series (SSBN, volume 1)

Abstract

Electrostatic energy and forces are primary important factors defining macromolecular interactions and its self-organization in an aqueous solution. The unique property of electrostatic forces is its long-range character. Therefore, an accurate modeling of the long-range electrostatic interactions and related energy of macromolecule in an aqueous solvent at given temperature, salt, and hydrogen ion concentration is the long-standing problem. One of the most advanced solutions of macromolecular electrostatics is a single-molecule approach with an implicit solvent electrostatic model for macromolecular simulations in water proton bath is considered here. The fundamental quantity that implicit electrostatic models approximate is the solute potential of mean force, which is obtained by averaging over solvent degrees of freedom. The implicit solvent models suggest practical ways to calculate free energies of macromolecular conformations taking into account equilibrium interactions with water solvent and proton bath, while the explicit solvent approach is unable to do that due to the need to account for a large number of solvent degrees of freedom and long-range nature of the electrostatic interactions. The most advanced realizations of the implicit continuum electrostatic models by different research groups are discussed, their accuracy is examined and some applications of the implicit solvent electrostatic models to macromolecular modeling, such as protein free energy calculations, protein folding, ionization equilibria, and pKa’s of ionizable groups and constant pH molecular dynamics are highlighted.

Keywords

Free Energy Boundary Element Method Solvation Free Energy Electrostatic Effect Hydration Free Energy 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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© Springer-Verlag Berlin Heidelberg 2014

Authors and Affiliations

  1. 1.Institute of Chemical Biology and Fundamental Medicine of the Siberian Branch of the Russian Academy of ScienceNovosibirskRussia

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