Functional understanding of solvent structure in GroEL cavity through dipole field analysis.

ABSTRACT: Solvent plays a ubiquitous role in all biophysical phenomena. Yet, just how the molecular nature of water impacts processes in biology remains an important question. While one can simulate the behavior of water near biomolecules such as proteins, it is challenging to gauge the potential structural role solvent plays in mediating both kinetic and equilibrium processes. Here, we propose an analysis scheme for understanding the nature of solvent structure at a local level. We first calculate coarse-grained dipole vector fields for an explicitly solvated system simulated through molecular dynamics. We then analyze correlations between these vector fields to characterize water structure under biologically relevant conditions. In applying our method to the interior of the wild type chaperonin co

SUBMITTER: Weber JK 

PROVIDER: S-EPMC3651261 | biostudies-literature | 2013 Apr

REPOSITORIES: biostudies-literature