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Biomolecular electrostatics and solvation: a computational perspective

Published online by Cambridge University Press:  07 December 2012

Pengyu Ren ,
Jaehun Chun ,
Dennis G. Thomas ,
Michael J. Schnieders ,
Marcelo Marucho ,
Jiajing Zhang  and
Nathan A. Baker
Pengyu Ren
Affiliation:
Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX 78712, USA
Jaehun Chun
Affiliation:
Pacific Northwest National Laboratory, Richland, WA 99352, USA
Dennis G. Thomas
Affiliation:
Pacific Northwest National Laboratory, Richland, WA 99352, USA
Michael J. Schnieders
Affiliation:
Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX 78712, USA
Marcelo Marucho
Affiliation:
Department of Physics and Astronomy, The University of Texas at San Antonio, San Antonio, TX 78249, USA
Jiajing Zhang
Affiliation:
Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX 78712, USA
Nathan A. Baker*
Affiliation:
Pacific Northwest National Laboratory, Richland, WA 99352, USA
*
*Author for correspondence: Nathan A. Baker, Pacific Northwest National Laboratory, PO Box 999, MSID K7-29, Richland, WA 99352, USA. Tel.: +1-509-375-3997; Email: nathan.baker@pnnl.gov
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Abstract

An understanding of molecular interactions is essential for insight into biological systems at the molecular scale. Among the various components of molecular interactions, electrostatics are of special importance because of their long-range nature and their influence on polar or charged molecules, including water, aqueous ions, proteins, nucleic acids, carbohydrates, and membrane lipids. In particular, robust models of electrostatic interactions are essential for understanding the solvation properties of biomolecules and the effects of solvation upon biomolecular folding, binding, enzyme catalysis, and dynamics. Electrostatics, therefore, are of central importance to understanding biomolecular structure and modeling interactions within and among biological molecules. This review discusses the solvation of biomolecules with a computational biophysics view toward describing the phenomenon. While our main focus lies on the computational aspect of the models, we provide an overview of the basic elements of biomolecular solvation (e.g. solvent structure, polarization, ion binding, and non-polar behavior) in order to provide a background to understand the different types of solvation models.

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Type
Review Article
Information
Quarterly Reviews of Biophysics , Volume 45 , Issue 4 , November 2012 , pp. 427 - 491
Copyright
Copyright © Cambridge University Press 2012

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