Volume Determination of Globular Proteins by Molecular Dynamics
Soft Condensed Matter
2014-04-08 v1 Biological Physics
Biomolecules
Abstract
Molecular dynamics simulations of myoglobin and aspartate aminotransferase, with explicit solvent, are shown to accurately reproduce the experimentally measured molar volumes. Single amino-acid substitution at VAL39 of aspartate aminotransferase is known to produce large volumetric changes in the enzyme, and this effect is demonstrated in simulation as well. This molecular dynamics approach, while more computationally expensive that extant computational methods of determining the apparent volume of biological systems, is quite feasible with modern computer hardware and is shown to yield accurate volumetric data with as little as several nanoseconds of dynamics.
Keywords
Cite
@article{arxiv.1404.1616,
title = {Volume Determination of Globular Proteins by Molecular Dynamics},
author = {Jonathan L. Belof and Edward W. Lowe and Randy W. Larsen and Brian Space},
journal= {arXiv preprint arXiv:1404.1616},
year = {2014}
}