Conformational variability of organophosphorus hydrolase upon soman and paraoxon binding.
Conformational variability of organophosphorus hydrolase upon soman and paraoxon binding.
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DOI：
10.1021/jp208787g
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发表时间：
2011-12-29
影响因子：
3.3
通讯作者：
Soares, Thereza A.
中科院分区：
文献类型：
--
作者：
Gomes, Diego E. B.;Lins, Roberto D.;Pascutti, Pedro G.;Lei, Chenghong;Soares, Thereza A.
细菌有机磷水解酶（OPH）具有催化和底物混杂性。它水解各种磷酸三酯（P-O）、硫代膦酸酯（P-S）、磷氟酯（P-F）和磷腈（F-CN）化合物中的键。然而，OPH对不同底物的催化效率差异很大，限制了其在农药和化学战剂生物修复中的广泛应用。在本研究中，pKa计算和多个显式溶剂分子动力学（MD）模拟进行表征和对比的结构动力学OPH绑定到两个底物水解具有非常不同的催化效率：神经毒剂梭曼（O-频哪醇-甲基-膦酰氟）和农药对氧磷（二乙基对硝基苯基磷酸酯）。底物结合和未结合酶的pKa计算显示，残基254 His和275 Arg的pKa相对于标准值（ΔpKa=±3单位）发生显著偏移。分子动力学模拟的双质子化的254组氨酸揭示了一个动态的氢键网络连接的催化残基301天冬氨酸通过254组氨酸的232天冬氨酸，233天冬氨酸，275精氨酸和235天冬氨酸，并与先前假设的质子中继机制，渡轮质子远离活性位点的基板，不需要激活的离去基团。301 Asp和254 His之间的氢键在OPH-对氧磷复合物中是持久的，但在OPH-梭曼复合物中不是，这表明这种相互作用在OPH更有效地水解对氧磷中的潜在作用。这些结果与先前对残基254 His的突变研究一致，该研究导致OPH对梭曼的催化效率增加，但对对氧磷的催化效率降低。此外，OPH结合梭曼和对氧磷的分子轨迹的比较分析表明，后者的结合有利于OPH从开放到封闭的亚状态的构象转变，促进对氧磷更紧密的结合。
The bacterial enzyme organophosphorous 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, pKa 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). pKa calculations for the substrate-bound and unbound enzyme showed a significant pKa shift from standard values (ΔpKa=±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.
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DOI：
10.1126/science.1198542
发表时间：
2011-04-08
期刊：
Science (New York, N.Y.)
影响因子：
--
作者：
Bhabha G;Lee J;Ekiert DC;Gam J;Wilson IA;Dyson HJ;Benkovic SJ;Wright PE
通讯作者：
Wright PE
DOI：
10.1021/jp9083635
发表时间：
2010-01-14
期刊：
The journal of physical chemistry. B
影响因子：
--
作者：
Gomes DE;Lins RD;Pascutti PG;Lei C;Soares TA
通讯作者：
Soares TA
影响因子：
2.9
作者：
Bas, Delphine C.;Rogers, David M.;Jensen, Jan H.
通讯作者：
Jensen, Jan H.
影响因子：
56.9
作者：
Boehr, David D.;McElheny, Dan;Wright, Peter E.
通讯作者：
Wright, Peter E.
影响因子：
64.8
作者：
Eisenmesser, EZ;Millet, O;Kern, D
通讯作者：
Kern, D