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Calculation of higher protonation states and of a new resting state for vanadium chloroperoxidase using QM/MM, with an Atom-in-Molecules analysis.
Journal of Molecular Graphics and Modelling ( IF 2.7 ) Pub Date : 2020-04-30 , DOI: 10.1016/j.jmgm.2020.107624
Gregory A Anderson 1 , Raghu Nath Behera 2 , Ravi Gomatam 3
Affiliation  

Earlier QM/MM studies of the resting state of vanadium chloroperoxidase (VCPO) focused on the diprotonated states of the vanadate cofactor. Herein, we report a new extensive QM/MM study that includes the tri- and quadprotonated states of VCPO at neutral pH. We identify certain di- and triprotonated states as being candidates for the resting state based on a comparison of relative energies. The quadprotonated states as well as some of the triprotonated states are ruled out as the resting state. An Atoms-in-Molecules (AIM) analysis of the complex hydrogen bonding around the vanadate cofactor helps to explain the relative energies of the protonation states considered herein, and it also indicates new hydrogen bonding which has not been recognized previously. A Natural Bond Orbital (NBO) study is presented to give a better understanding of the electronic structure of the vanadate co-factor.



中文翻译:

使用QM / MM和原子分子分析法计算钒氯过氧化物酶的更高质子化态和新的静止态。

钒氯过氧化物酶(VCPO)静止状态的早期QM / MM研究着眼于钒酸盐辅因子的双质子化状态。在此,我们报告了一项新的广泛的QM / MM研究,其中包括在中性pH下VCPO的三和四质子化状态。基于相对能量的比较,我们确定某些二元化和三价质子化态为静止态的候选者。排除了质子化的四价态以及某些三价质子化态作为静止态。钒酸盐辅因子周围复杂氢键的分子内原子(AIM)分析有助于解释本文所考虑的质子化态的相对能量,并且还表明了以前尚未认识到的新氢键。

更新日期:2020-04-30
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