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FT方法对含铜亚硝酸盐还原酶远程三质子耦合电子转移(PCET)的计算性能评估

omputational performance evaluation of the remote three-proton-coupled electron transfer (PCET) of copper-containing nitrite reductase by the DFT method

中文摘要英文摘要

含铜亚硝酸盐还原酶将NO2- 还原成NO和水分子需要一个电子和两个质子,已经有一些研究表明含铜亚硝酸还原酶(CuNiRs)催化反应中存在一个远程三质子耦合触发电子转移(PCET)的过程。但是目前还没有比较合适的方法来计算这种复杂的蛋白质反应。基于前期CuNiRs催化反应机理中从K128到H260的远程三质子协同耦合电子转移过程,本文使用15种不同的密度泛函理论方法对上述PCET反应进行研究,通过比较反应能垒、K128到H260的质子转移与双铜位点的单电子分布情况之间的关系来评估不同DFT方法对K128到H260的PCET反应的计算精度。结果表明,加了色散校正的杂化泛函或100%长程校正的纯密度泛函或两者都加校正的泛函计算精度好,与M06计算方法相比,LC-BLYP、ωB97X-D、LC-BPW91、B3LYP-D3这几种泛函都得到较一致的自旋密度分布结果,但从能垒上分析最优的泛函还是M06。这一结果为计算含有金属铜参与的PCET反应的生物大分子提供了方法选择。

he reduction of NO2- to NO and water by copper-containing nitrite reductase requires one electron and two protons. There have been some studies showed a remote three-proton coupled triggered electron transfer (PCET) process in the copper-containing nitrite reductase (CuNiRs) catalytic reaction. However, there is no suitable method to calculate this complex protein reaction. Based on the long-range three-proton cooperative coupled electron transfer process from K128 to H260 in the prophase catalytic reaction mechanism of CuNiRs. In this paper, we used 15 different density functional theory (DFT) methods to research the PCET reactions, evaluating the accuracy of the PCET reactions from K128 to H260 by comparing the relationship between the reaction barrier, the proton transfer of K128 to H260 and the single-electron distribution of the two copper site. This results show that the hybrid functional with dispersion correction or the 100% long-range-corrected pure density functional or both add corrected functional works well, compared with M06, LC-BLYP, ωB97X-D, LC-BPW91, and B3LYP-D3 have get consistent results on the spin density distribution, but the functional optimal from the energy barrier and electron density is still M06. This result also provides a method choice for calculating biological macromolecules of the PCET reaction with metallic copper participation.

陈效华、阳钰宁、刘思君

生物科学研究方法、生物科学研究技术生物化学生物物理学

化学含铜亚硝酸盐还原酶质子耦合电子转移密度泛函理论

hemistrycopper-containing nitrite reductaseproton-coupled electron transferdensity functional theory

陈效华,阳钰宁,刘思君.FT方法对含铜亚硝酸盐还原酶远程三质子耦合电子转移(PCET)的计算性能评估[EB/OL].(2023-04-06)[2025-08-26].http://www.paper.edu.cn/releasepaper/content/202304-81.点此复制

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