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Computational modeling of human paraoxonase 1: preparation of protein models, binding studies, and mechanistic insights
Author(s) -
Sanan Toby T.,
Muthukrishnan Sivaramakrishnan,
Beck Jeremy M.,
Tao Peng,
Hayes Carrigan J.,
Otto Tamara C.,
Cerasoli Douglas M.,
Lenz David E.,
Hadad Christopher M.
Publication year - 2010
Publication title -
journal of physical organic chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.325
H-Index - 66
eISSN - 1099-1395
pISSN - 0894-3230
DOI - 10.1002/poc.1678
Subject(s) - chemistry , homology modeling , protein data bank (rcsb pdb) , paraoxonase , enzyme , gene isoform , protein design , biochemistry , docking (animal) , stereochemistry , nerve agent , protein structure , aryldialkylphosphatase , computational biology , pon1 , acetylcholinesterase , gene , biology , medicine , nursing , genotype
The enzyme human paraoxonase 1 (huPON1) has demonstrated significant potential for use as a bioscavenger for treatment of exposure to organophosphorus (OP) nerve agents. Herein we report the development of protein models for the human isoform derived from a crystal structure of a chimeric version of the protein (pdb ID: 1V04) and a homology model derived from the related enzyme diisopropylfluorophosphatase (pdb ID: 1XHR). From these structural models, binding modes for OP substrates are predicted, and these poses are found to orient substrates in proximity to residues known to modulate specificity of the enzyme. Predictions are made with regard to the role that residues play in altering substrate binding and turnover, in particular with regard to the stereoselectivity of the enzyme, and the known differences in activity related to a natural polymorphism in the enzyme. Potential mechanisms of action of the protein for catalytic hydrolysis of OP substrates are also evaluated in light of the proposed binding modes. Copyright © 2010 John Wiley & Sons, Ltd.