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QM/MM MD simulations reveal an asynchronous PCET mechanism for nitrite reduction by copper nitrite reductase.
Physical Chemistry Chemical Physics ( IF 2.9 ) Pub Date : 2020-08-22 , DOI: 10.1039/d0cp03053h Ronny Cheng 1 , Chun Wu 2 , Zexing Cao 1 , Binju Wang 1
Physical Chemistry Chemical Physics ( IF 2.9 ) Pub Date : 2020-08-22 , DOI: 10.1039/d0cp03053h Ronny Cheng 1 , Chun Wu 2 , Zexing Cao 1 , Binju Wang 1
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Nitrite reductases are enzymes that aid in the denitrification process by catalyzing the reduction of nitrite to nitric oxide gas. Since this reaction is the first committed step that involves gas formation, it is regarded to be a vital step for denitrification. However, the mechanism of copper-containing nitrite reductase is still under debate due to the discrepancy between the theoretical and experimental data, especially in terms of the roles of secondary shell residues Asp98 and His255 and the electron transfer mechanism between the two copper sites. Herein, we revisited the nitrite reduction mechanism of A. faecalis copper nitrite reductase using QM(B3LYP)/MM-based metadynamics. It is found that the intramolecular electron transfer from T1-Cu to T2-Cu occurs via an asynchronous proton-coupled electron transfer (PCET) mechanism, with electron transfer (ET) preceding proton transfer (PT). In particular, we found that the ET process is driven by the conformation conversion of Asp98 from the gatekeeper to the proximal one, which is much more energy-demanding than the PCET itself. These results highlight that the inclusion of an electron donor is vital to investigate electron-transfer related processes such as PCET.
中文翻译：
QM / MM MD模拟揭示了亚硝酸铜还原酶还原亚硝酸盐的异步PCET机制。
亚硝酸盐还原酶是通过催化将亚硝酸盐还原为一氧化氮气体而有助于反硝化过程的酶。由于该反应是涉及气体形成的第一个重要步骤，因此被认为是反硝化的重要步骤。然而，由于理论和实验数据之间的差异，尤其是在次级壳残基Asp98和His255的作用以及两个铜位点之间的电子转移机理方面，含铜的亚硝酸盐还原酶的机理仍存在争议。在这里，我们基于QM（B3LYP）/ MM的元动力学重新研究了粪屎肠球菌亚硝酸铜还原酶的亚硝酸盐还原机理。发现分子内电子从T1-Cu到T2-Cu的转移是通过异步质子耦合电子转移（PCET）机制，先于质子转移（PT）进行电子转移（ET）。特别是，我们发现ET过程是由Asp98从关守到近端守卫的构象转换驱动的，这比PCET本身要耗能得多。这些结果表明，包含电子供体对于研究与电子转移相关的过程（例如PCET）至关重要。
更新日期：2020-09-23
中文翻译：
QM / MM MD模拟揭示了亚硝酸铜还原酶还原亚硝酸盐的异步PCET机制。
亚硝酸盐还原酶是通过催化将亚硝酸盐还原为一氧化氮气体而有助于反硝化过程的酶。由于该反应是涉及气体形成的第一个重要步骤，因此被认为是反硝化的重要步骤。然而，由于理论和实验数据之间的差异，尤其是在次级壳残基Asp98和His255的作用以及两个铜位点之间的电子转移机理方面，含铜的亚硝酸盐还原酶的机理仍存在争议。在这里，我们基于QM（B3LYP）/ MM的元动力学重新研究了粪屎肠球菌亚硝酸铜还原酶的亚硝酸盐还原机理。发现分子内电子从T1-Cu到T2-Cu的转移是通过异步质子耦合电子转移（PCET）机制，先于质子转移（PT）进行电子转移（ET）。特别是，我们发现ET过程是由Asp98从关守到近端守卫的构象转换驱动的，这比PCET本身要耗能得多。这些结果表明，包含电子供体对于研究与电子转移相关的过程（例如PCET）至关重要。
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