title: 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 complex GroEL+ES, along with nine additional mutant GroEL complexes, we find that dipole field correlations are strongly related to chaperonin function.
authors: Department of Chemistry, Stanford University, Stanford, California 94305-5080, USA.
authors: Jeffrey K
authors: JK
authors: Weber
authors: Vijay S
authors: VS
authors: Pande
mesh_terms: D029968:Escherichia coli Proteins / Q000737:chemistry* / Q000235:genetics; D006360:Heat-Shock Proteins / Q000737:chemistry* / Q000235:genetics; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D015394:Molecular Structure; D012997:Solvents / Q000737:chemistry
chemical_list: D029968:Escherichia coli Proteins; C028715:GroE protein, E coli; D006360:Heat-Shock Proteins; D012997:Solvents
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