Effects of Acids, Bases, and Heteroatoms on Proximal Radial Distribution Functions for Proteins.

ABSTRACT: The proximal distribution of water around proteins is a convenient method of quantifying solvation. We consider the effect of charged and sulfur-containing amino acid side-chain atoms on the proximal radial distribution function (pRDF) of water molecules around proteins using side-chain analogs. The pRDF represents the relative probability of finding any solvent molecule at a distance from the closest or surface perpendicular protein atom. We consider the near-neighbor distribution. Previously, pRDFs were shown to be universal descriptors of the water molecules around C, N, and O atom types across hundreds of globular proteins. Using averaged pRDFs, a solvent density around any globular protein can be reconstructed with controllable relative error. Solvent reconstruction using the addition

SUBMITTER: Nguyen BL 

PROVIDER: S-EPMC4570738 | biostudies-literature | 2015 Apr

REPOSITORIES: biostudies-literature