QM/MM Molecular Dynamics Studies of Metal Binding Proteins

摘要: Mixed quantum-classical (quantum mechanical/molecular mechanical (QM/MM)) simulations have strongly contributed to providing insights into the understanding of several structural and mechanistic aspects biological molecules. They played a particularly important role in metal binding proteins, where electronic effects transition metals be explicitly taken account for correct representation underlying biochemical process. In this review, after brief description basic concepts QM/MM method, we provide an overview its capabilities using selected examples from our work. Specifically, will focus on heme peroxidases, metallo-β-lactamases, α-synuclein ligase ribozymes show how approach is capable describing catalytic and/or by (Fe, Zn or Cu) main group (Mg) metals. Applications reveal ions influence formation reduction high redox intermediates cycles enhance drug metabolism, amyloidogenic aggregate nucleic acid synthesis. turn, it become manifest that protein frame directs modulates properties reactivity ions.