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Title: Structure of the ordered hydration of amino acids in proteins: analysis of crystal structures

The hydration of protein crystal structures was studied at the level of individual amino acids. The dependence of the number of water molecules and their preferred spatial localization on various parameters, such as solvent accessibility, secondary structure and side-chain conformation, was determined. Crystallography provides unique information about the arrangement of water molecules near protein surfaces. Using a nonredundant set of 2818 protein crystal structures with a resolution of better than 1.8 Å, the extent and structure of the hydration shell of all 20 standard amino-acid residues were analyzed as function of the residue conformation, secondary structure and solvent accessibility. The results show how hydration depends on the amino-acid conformation and the environment in which it occurs. After conformational clustering of individual residues, the density distribution of water molecules was compiled and the preferred hydration sites were determined as maxima in the pseudo-electron-density representation of water distributions. Many hydration sites interact with both main-chain and side-chain amino-acid atoms, and several occurrences of hydration sites with less canonical contacts, such as carbon–donor hydrogen bonds, OH–π interactions and off-plane interactions with aromatic heteroatoms, are also reported. Information about the location and relative importance of the empirically determined preferred hydration sites in proteins hasmore » applications in improving the current methods of hydration-site prediction in molecular replacement, ab initio protein structure prediction and the set-up of molecular-dynamics simulations.« less
Authors:
;  [1]
  1. Institute of Biotechnology CAS, Videnska 1083, 142 20 Prague (Czech Republic)
Publication Date:
OSTI Identifier:
22515192
Resource Type:
Journal Article
Resource Relation:
Journal Name: Acta Crystallographica. Section D: Biological Crystallography; Journal Volume: 71; Journal Issue: Pt 11; Other Information: PMCID: PMC4631476; PMID: 26527137; PUBLISHER-ID: dw5143; OAI: oai:pubmedcentral.nih.gov:4631476; Copyright (c) Biedermannová & Schneider 2015; This is an open-access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are cited.; Country of input: International Atomic Energy Agency (IAEA)
Country of Publication:
Denmark
Language:
English
Subject:
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND SUPERFLUIDITY; AMINO ACIDS; CRYSTAL STRUCTURE; CRYSTALLIZATION; ELECTRON DENSITY; HYDRATION; INTERACTIONS; MOLECULAR DYNAMICS METHOD; MOLECULES; PROTEIN STRUCTURE; X RADIATION