Borowski Tomasz, Quesne Matthew, Szaleniec Maciej
Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Kraków, Poland.
Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Kraków, Poland; Manchester Institute of Biotechnology and Faculty of Life Sciences, The University of Manchester, Manchester, United Kingdom.
Adv Protein Chem Struct Biol. 2015;100:187-224. doi: 10.1016/bs.apcsb.2015.06.005. Epub 2015 Jul 3.
The review focus is a comparison of QM and QM/MM modeling techniques applied to study of metalloenzymes. The chapter aim is to highlight many of the advantages and potential pitfalls of the exciting and revolutionary QM/MM techniques using both large QM/MM systems and QM-only modeling as references. The review is illustrated by case studies for isopenicillin N synthase, ethylbenzene dehydrogenase, cytochrome P450 enzyme, AlkB DNA repair enzyme as well as 4-hydroxyphenylpyruvate dioxygenase. We find many advantages in various QM/MM techniques, over the more traditional QM cluster approaches, while at the same time offering some advice about how to avoid potential complications arising from some of these approaches' most notable drawbacks. We conclude that while there will always be an important role for QM cluster models, in computational studies, the revolutionary developments in QM/MM techniques open a bright and exciting future of new research.
本综述的重点是比较应用于金属酶研究的量子力学（QM）和量子力学/分子力学（QM/MM）建模技术。本章的目的是通过使用大型QM/MM系统和仅QM建模作为参考，突出令人兴奋且具有革命性的QM/MM技术的诸多优点和潜在陷阱。通过对异青霉素N合酶、乙苯脱氢酶、细胞色素P450酶、AlkB DNA修复酶以及4-羟基苯丙酮酸双加氧酶的案例研究对本综述进行说明。我们发现，与更传统的QM簇方法相比，各种QM/MM技术具有许多优点，同时就如何避免这些方法一些最显著缺点所引发的潜在复杂性提供了一些建议。我们得出结论，虽然在计算研究中QM簇模型始终将发挥重要作用，但QM/MM技术的革命性发展开启了新研究的光明且令人兴奋的未来。
