Abstract
Hybrid quantum mechanics and molecular mechanics (QM/MM) methods have become a powerful tool to provide an accurate and effective description of complex biological systems. The QM treatment of the electronic structure of an active site region and the rest of the enzyme by molecular mechanics allows enzymatic reaction to being modeled with including the impact of environment. Different reaction pathways of the enzymatic mechanism can be tested--transition states (TS) and intermediates characterized using QM/MM methods, leading to significant advances in understanding enzymatic reactions. This chapter discusses the ideas and the setting up of the structural and computational models for calculations with QM/MM software. The use of QM/MM methodology is also illustrated using the case of the inverting glycosyltransferase GnT-I.
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