title: Structure of the ordered hydration of amino acids in proteins: analysis of crystal structures.
abstract: 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 has 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.
authors.affiliation: Laboratory of Biomolecular Recognition, Institute of Biotechnology CAS, Videnska 1083, 142 20 Prague, Czech Republic.
authors.forename: Lada
authors.initials: L
authors.lastname: Biedermannová
authors.affiliation: Laboratory of Biomolecular Recognition, Institute of Biotechnology CAS, Videnska 1083, 142 20 Prague, Czech Republic.
authors.forename: Bohdan
authors.initials: B
authors.lastname: Schneider
mesh_terms: D000596:Amino Acids / Q000032:analysis*; D000818:Animals; D018360:Crystallography, X-Ray; D030562:Databases, Protein; D006801:Humans; D006860:Hydrogen Bonding; D008958:Models, Molecular; D008968:Molecular Conformation; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry*; D014867:Water / Q000032:analysis*
chemical_list: D000596:Amino Acids; D011506:Proteins; D014867:Water
keywords: X-ray crystallography; protein hydration; structural biology