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Title: Conformational Variability of Organophosphorus Hydrolase upon Soman and Paraoxon Binding

Abstract

The bacterial enzyme organophosphorus hydrolase (OPH) exhibits both catalytic and substrate promiscuity. It hydrolyzes bonds in a variety of phosphotriester (P-O), phosphonothioate (P-S), phosphofluoridate (P-F) and phosphonocyanate (F-CN) compounds. However, its catalytic efficiency varies markedly for different substrates, limiting the broad-range application of OPH as catalyst in the bioremediation of pesticides and chemical war agents. In the present study, pK{sub a} calculations and multiple explicit-solvent molecular dynamics (MD) simulations were performed to characterize and contrast the structural dynamics of OPH bound to two substrates hydrolyzed with very distinct catalytic efficiencies: the nerve agent soman (O-pinacolyl-methyl-phosphonofluoridate) and the pesticide paraoxon (diethyl p-nitrophenyl phosphate). pK{sub a} calculations for the substrate-bound and unbound enzyme showed a significant pK{sub a} shift from standard values ({Delta}pK{sub a} = {+-} 3 units) for residues 254His and 275Arg. MD simulations of the doubly protonated 254His revealed a dynamic hydrogen bond network connecting the catalytic residue 301Asp via 254His to 232Asp, 233Asp, 275Arg and 235Asp, and is consistent with a previously postulated proton relay mechanism to ferry protons away from the active site with substrates that do not require activation of the leaving group. Hydrogen bonds between 301Asp and 254His were persistent in the OPH-paraoxon complex but notmore » in the OPH-soman one, suggesting a potential role for such interaction in the more efficient hydrolysis of paraoxon over soman by OPH. These results are in line with previous mutational studies of residue 254His, which led to an increase of the catalytic efficiency of OPH over soman yet decreased its efficiency for paraoxon. In addition, comparative analysis of the molecular trajectories for OPH bound to soman and paraoxon suggests that binding of the latter facilitates the conformational transition of OPH from the open to the closed substate promoting a tighter binding of paraoxon.« less

Authors:
; ; ; ;
Publication Date:
Research Org.:
Pacific Northwest National Laboratory (PNNL), Richland, WA (US), Environmental Molecular Sciences Laboratory (EMSL)
Sponsoring Org.:
USDOE
OSTI Identifier:
1037534
Report Number(s):
PNNL-SA-82894
35413; 400412000; TRN: US201207%%340
DOE Contract Number:  
AC05-76RL01830
Resource Type:
Journal Article
Journal Name:
Journal of Physical Chemistry B
Additional Journal Information:
Journal Volume: 115; Journal Issue: 51
Country of Publication:
United States
Language:
English
Subject:
08 HYDROGEN; BIOREMEDIATION; CATALYSTS; EFFICIENCY; ENZYMES; HYDROGEN; HYDROLASES; HYDROLYSIS; NERVES; PESTICIDES; PROTONS; RESIDUES; SUBSTRATES; TRAJECTORIES; Environmental Molecular Sciences Laboratory

Citation Formats

Gomes, Diego Eb, Lins, Roberto D, Pascutti, Pedro G, Lei, Chenghong, and Soares, Thereza A. Conformational Variability of Organophosphorus Hydrolase upon Soman and Paraoxon Binding. United States: N. p., 2011. Web. doi:10.1021/jp208787g.
Gomes, Diego Eb, Lins, Roberto D, Pascutti, Pedro G, Lei, Chenghong, & Soares, Thereza A. Conformational Variability of Organophosphorus Hydrolase upon Soman and Paraoxon Binding. United States. doi:10.1021/jp208787g.
Gomes, Diego Eb, Lins, Roberto D, Pascutti, Pedro G, Lei, Chenghong, and Soares, Thereza A. Sat . "Conformational Variability of Organophosphorus Hydrolase upon Soman and Paraoxon Binding". United States. doi:10.1021/jp208787g.
@article{osti_1037534,
title = {Conformational Variability of Organophosphorus Hydrolase upon Soman and Paraoxon Binding},
author = {Gomes, Diego Eb and Lins, Roberto D and Pascutti, Pedro G and Lei, Chenghong and Soares, Thereza A},
abstractNote = {The bacterial enzyme organophosphorus hydrolase (OPH) exhibits both catalytic and substrate promiscuity. It hydrolyzes bonds in a variety of phosphotriester (P-O), phosphonothioate (P-S), phosphofluoridate (P-F) and phosphonocyanate (F-CN) compounds. However, its catalytic efficiency varies markedly for different substrates, limiting the broad-range application of OPH as catalyst in the bioremediation of pesticides and chemical war agents. In the present study, pK{sub a} calculations and multiple explicit-solvent molecular dynamics (MD) simulations were performed to characterize and contrast the structural dynamics of OPH bound to two substrates hydrolyzed with very distinct catalytic efficiencies: the nerve agent soman (O-pinacolyl-methyl-phosphonofluoridate) and the pesticide paraoxon (diethyl p-nitrophenyl phosphate). pK{sub a} calculations for the substrate-bound and unbound enzyme showed a significant pK{sub a} shift from standard values ({Delta}pK{sub a} = {+-} 3 units) for residues 254His and 275Arg. MD simulations of the doubly protonated 254His revealed a dynamic hydrogen bond network connecting the catalytic residue 301Asp via 254His to 232Asp, 233Asp, 275Arg and 235Asp, and is consistent with a previously postulated proton relay mechanism to ferry protons away from the active site with substrates that do not require activation of the leaving group. Hydrogen bonds between 301Asp and 254His were persistent in the OPH-paraoxon complex but not in the OPH-soman one, suggesting a potential role for such interaction in the more efficient hydrolysis of paraoxon over soman by OPH. These results are in line with previous mutational studies of residue 254His, which led to an increase of the catalytic efficiency of OPH over soman yet decreased its efficiency for paraoxon. In addition, comparative analysis of the molecular trajectories for OPH bound to soman and paraoxon suggests that binding of the latter facilitates the conformational transition of OPH from the open to the closed substate promoting a tighter binding of paraoxon.},
doi = {10.1021/jp208787g},
journal = {Journal of Physical Chemistry B},
number = 51,
volume = 115,
place = {United States},
year = {2011},
month = {12}
}