当前位置: X-MOL 学术Biochemistry › 论文详情
Our official English website, www.x-mol.net, welcomes your feedback! (Note: you will need to create a separate account there.)
Examining the Mechanism of Phosphite Dehydrogenase with Quantum Mechanical/Molecular Mechanical Free Energy Simulations.
Biochemistry ( IF 2.9 ) Pub Date : 2020-02-14 , DOI: 10.1021/acs.biochem.9b01089
David R Stevens 1 , Sharon Hammes-Schiffer 1
Affiliation  

The projected decline of available phosphorus necessitates alternative methods to derive usable phosphate for fertilizer and other applications. Phosphite dehydrogenase oxidizes phosphite to phosphate with the cofactor NAD+ serving as the hydride acceptor. In addition to producing phosphate, this enzyme plays an important role in NADH cofactor regeneration processes. Mixed quantum mechanical/molecular mechanical free energy simulations were performed to elucidate the mechanism of this enzyme and to identify the protonation states of the substrate and product. Specifically, the finite temperature string method with umbrella sampling was used to generate the free energy surfaces and determine the minimum free energy paths for six different initial conditions that varied in the protonation state of the substrate and the position of the nucleophilic water molecule. In contrast to previous studies, the mechanism predicted by all six independent strings is a concerted but asynchronous dissociative mechanism in which hydride transfer from the phosphite substrate to NAD+ occurs prior to attack by the nucleophilic water molecule. His292 is identified as the most likely general base that deprotonates the attacking water molecule. However, Arg237 could also serve as this base if it were deprotonated and His292 were protonated prior to the main chemical transformation, although this scenario is less probable. The simulations indicate that the phosphite substrate is monoanionic in its active form and that the most likely product is dihydrogen phosphate. These mechanistic insights may be helpful for designing mutant enzymes or artificial constructs that convert phosphite to phosphate and NAD+ to NADH more effectively.

中文翻译:

用量子力学/分子机械自由能模拟研究亚磷酸酯脱氢酶的机理。

预计可用磷的减少将需要替代方法来获得可用于肥料和其他应用的磷酸盐。亚磷酸酯脱氢酶以辅因子NAD +作为氢化物受体将亚磷酸酯氧化为磷酸酯。除了产生磷酸盐外,该酶在NADH辅因子再生过程中也起着重要作用。进行了混合量子力学/分子机械自由能模拟,以阐明该酶的机理并鉴定底物和产物的质子化状态。特别,使用带有伞形采样的有限温度串方法生成自由能表面,并确定六个不同初始条件的最小自由能路径,这些条件在底物的质子化状态和亲核水分子的位置发生变化。与以前的研究相比,所有六个独立的字符串预测的机理是一致但异步的解离机理,其中氢化物从亚磷酸酯底物转移到NAD +发生在亲核水分子进攻之前。His292被认为是最有可能使攻击水分子去质子化的一般碱基。但是,如果在主要化学转化之前将Arg237去质子化和His292进行质子化,则Arg237也可以作为该碱,尽管这种情况的可能性较小。模拟表明亚磷酸酯底物以其活性形式为单阴离子,最可能的产物为磷酸二氢。这些机制的见解可能有助于设计突变酶或人工构建体,从而更有效地将亚磷酸酯转化为磷酸酯并将NAD +转化为NADH。
更新日期:2020-02-14
down
wechat
bug