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

0457403 - BTÚ 2016 RIV GB eng J - Journal Article
Biedermannová, Lada - Schneider, Bohdan
Structure of the ordered hydration of amino acids in proteins: analysis of crystal structures.
Acta Crystallographica Section D-Biological Crystallography. Roč. 71, č. 11 (2015), s. 2178-2202. ISSN 1399-0047. E-ISSN 2059-7983
Institutional support: RVO:86652036
Keywords : protein hydration * structural biology * X-ray crystallography
OECD category: Biochemistry and molecular biology
Impact factor: 2.512, year: 2015
Method of publishing: Open access
http://journals.iucr.org/d/issues/2015/11/00/dw5143/index.html

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 angstrom, 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-pi 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.
Permanent Link: http://hdl.handle.net/11104/0257805