Effects of acids, bases, and heteroatoms on proximal radial distribution functions for proteins

Bao Linh Nguyen, Bernard Pettitt

Research output: Contribution to journalArticle

6 Citations (Scopus)

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 additional information from charged amino acid side-chain atom types from both small models and protein averages reveals the effects of surface charge distribution on solvent density and improves the reconstruction errors relative to simulation. Solvent density reconstructions from the small-molecule models are as effective and less computationally demanding than reconstructions from full macromolecular models in reproducing preferred hydration sites and solvent density fluctuations.

Original languageEnglish (US)
Pages (from-to)1399-1409
Number of pages11
JournalJournal of Chemical Theory and Computation
Volume11
Issue number4
DOIs
StatePublished - Apr 14 2015

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radial distribution
Distribution functions
distribution functions
proteins
Proteins
acids
Acids
Atoms
Molecules
amino acids
atoms
Water
Amino acids
molecules
water
Amino Acids
Charge distribution
Solvation
Surface charge
Sulfur

ASJC Scopus subject areas

  • Physical and Theoretical Chemistry
  • Computer Science Applications

Cite this

Effects of acids, bases, and heteroatoms on proximal radial distribution functions for proteins. / Nguyen, Bao Linh; Pettitt, Bernard.

In: Journal of Chemical Theory and Computation, Vol. 11, No. 4, 14.04.2015, p. 1399-1409.

Research output: Contribution to journalArticle

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