Molecular Determinants of Xenobiotic Metabolism: QM/MM Simulation of the Conversion of 1-Chloro-2,4-dinitrobenzene Catalyzed by M1-1 Glutathione S-Transferase

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• 作者：Anna L. Bowman ; Lars Ridder ; Ivonne M. C. M. Rietjens ; Jacques Vervoort ; Adrian J. Mulholland
• 刊名：Biochemistry
• 出版年：2007
• 出版时间：May 29, 2007
• 年：2007
• 卷：46
• 期：21
• 页码：6353 - 6363
• 全文大小：143K
• 年卷期：v.46,no.21(May 29, 2007)
• ISSN：1520-4995

文摘

Modeling methods allow the identification and analysis of determinants of reactivity andspecificity in enzymes. The reaction between glutathione and 1-chloro-2,4-dinitrobenzene (CDNB) is widelyused as a standard activity assay for glutathione S-transferases (GSTs). It is important to understand thecauses of differences between catalytic GST isoenzymes and the effects of mutations and geneticpolymorphisms. Quantum mechanical/molecular mechanical (QM/MM) molecular dynamics simulationshave been performed here to investigate the addition of the glutathione anion to CDNB in the wild-typeM1-1 GST isoenzyme from rat and in three single point mutant (Tyr6Phe, Tyr115Phe, and Met108Ala)M1-1 GST enzymes. We have developed a specifically parameterized QM/MM method (AM1-SRP/CHARMM22) to model this reaction by fitting to experimental heats of formation and ionization potentials.Free energy profiles were obtained from molecular dynamics simulations of the reaction using umbrellasampling and weighted histogram analysis techniques. The reaction in solution has also been simulatedand is compared to the enzymatic reaction. The free energies are in excellent agreement with experimentalresults. Overall the results of the present study show that QM/MM reaction pathway analysis providesdetailed insight into the chemistry of GST and can be used to obtain mechanistic insight into the effectsof specific mutations on this catalytic process.