ArticleJournal of chemical theory and computation2015
Effects of Acids, Bases, and Heteroatoms on Proximal Radial Distribution Functions for Proteins.
Article in Journal of chemical theory and computation, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed.
- Article
- Contributions of higher-order proximal distribution functions to solvent structure around proteins.The Journal of chemical physics · 2021Article
- Generation of the configurational ensemble of an intrinsically disordered protein from unbiased molecular dynamics simulation.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- Conformation and Domain Movement Analysis of Human Matrix Metalloproteinase-2: Role of Associated ZnInternational journal of molecular sciences · 2019Article
- Free Energy Calculations Based on Coupling Proximal Distribution Functions and Thermodynamic Cycles.Journal of chemical theory and computation · 2019Article
- Effects of Selective Substitution of Cysteine Residues on the Conformational Properties of Chlorotoxin Explored by Molecular Dynamics Simulations.International journal of molecular sciences · 2019Article
- Nonpolar Solvation Free Energy from Proximal Distribution Functions.The journal of physical chemistry. B · 2017Article
- Solute-Solvent Energetics Based on Proximal Distribution Functions.The journal of physical chemistry. B · 2016Article
- Solvation and cavity occupation in biomolecules.Biochimica et biophysica acta · 2015Article
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Authors and funding
2 authors.
Funding
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.
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