Journal
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
Volume 3, Issue 1, Pages 156-169Publisher
AMER CHEMICAL SOC
DOI: 10.1021/ct600085e
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Funding
- NATIONAL CENTER FOR RESEARCH RESOURCES [C06RR017588] Funding Source: NIH RePORTER
- NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES [R01GM057513, R01GM076121] Funding Source: NIH RePORTER
- NCRR NIH HHS [C06 RR017588] Funding Source: Medline
- NIGMS NIH HHS [R01 GM076121, R01 GM057513, R01 GM076121-01A1] Funding Source: Medline
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Generalized Born (GB) models provide a computationally efficient means of representing the electrostatic effects of solvent and are widely used, especially in molecular dynamics (MD). A class of particularly fast GB models is based on integration over an interior volume approximated as a pairwise union of atom sphereseffectively, the interior is defined by a van der Waals rather than Lee-Richards molecular surface. The approximation is computationally efficient but, if uncorrected, allows for high dielectric (water) regions smaller than a water molecule between atoms, leading to decreased accuracy. Here, an earlier pairwise GB model is extended by a simple analytic correction term that largely alleviates the problem by correctly describing the solvent-excluded volume of each pair of atoms. The correction term introduces a free energy barrier to the separation of nonbonded atoms. This free energy barrier is seen in explicit solvent and Lee-Richards molecular surface implicit solvent calculations but has been absent from earlier pairwise GB models. When used in MD, the correction term yields protein hydrogen bond length distributions and polypeptide conformational ensembles that are in better agreement with explicit solvent results than earlier pairwise models. The robustness and simplicity of the correction preserves the efficiency of the pairwise GB models while making them a better approximation to reality.
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