期刊
BIOCHIMIE
卷 88, 期 11, 页码 1631-1638出版社
ELSEVIER FRANCE-EDITIONS SCIENTIFIQUES MEDICALES ELSEVIER
DOI: 10.1016/j.biochi.2006.05.015
关键词
actinide; hard Lewis acid; structural analysis; metal binding site; screening; amber; uranium
Documenting the modes of interaction of uranyl (UO22+) with large biomolecules, and particularly with proteins, is instrumental for the interpretation of its behavior in vitro and in vivo. The gathering of three-dimensional information concerning uranyl-first shell atoms from two structural databases, the Cambridge Structural Databank and the Protein Data Bank (PDB) allowed a screening of corresponding topologies in proteins of known structure. In the cornputer-aided procedure, all potentially bound residues from the template structure were granted full flexibility using a rotamer library. The Amber force-field was used to loosen constraints and score each predicted site. Our algorithm was validated as a first stage through the recognition of existing experimental data in the PDB. The coherent localization of missing atoms in the density map of an ambiguous uranium/uranyl-protein complex exemplified the efficiency of our approach, which is currently suggesting the experimental investigation of uranyl-protein binding site. (c) 2006 Elsevier Masson SAS. All rights reserved.
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