Molecular dynamics simulations of highly crowded amino acid solutions: comparisons of eight different force field combinations with experiment and with each other.

ABSTRACT: Although it is now commonly accepted that the highly crowded conditions encountered inside biological cells have the potential to significantly alter the thermodynamic properties of biomolecules, it is not known to what extent the thermodynamics of fundamental types of interactions such as salt bridges and hydrophobic interactions are strengthened or weakened by high biomolecular concentrations. As one way of addressing this question we have performed a series of all-atom explicit solvent molecular dynamics (MD) simulations to investigate the effect of increasing solute concentration on the behavior of four types of zwitterionic amino acids in aqueous solution. We have simulated systems containing glycine, valine, phenylalanine or asparagine at concentrations of 50, 100, 200 and 300 mg/ml.

SUBMITTER: Andrews CT 

PROVIDER: S-EPMC3881310 | biostudies-literature | 2013 Oct

REPOSITORIES: biostudies-literature