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Biochimie. 2006 Nov;88(11):1631-8. Epub 2006 Jun 21.

Structural insights into protein-uranyl interaction: towards an in silico detection method.

Author information

1
CEA VALRHO, DSV-DIEP-SBTN, Service de Biochimie postgénomique et Toxicologie Nucléaire, 30207 Bagnols-sur-Cèze, France. olivier.pible@cea.fr

Abstract

Documenting the modes of interaction of uranyl (UO(2)2+) 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 computer-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.

PMID:
16815621
DOI:
10.1016/j.biochi.2006.05.015
[Indexed for MEDLINE]

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