酶催化过程的全程模拟

摘要

Enzymatic catalytic processes generally involve substrate delivery,selective catalytic reaction,and product release.Owing to the complex protein environment effect,any nonchemical or chemical step may determine the enzyme activity.Herein,to comprehensively understand enzymatic activity,extensive combined quantum mechanics/molecular mechanics (QM/MM) and molecular mechanics (MM) molecular dynamics (MD) simulations were carried out on several kinds of enzymes.Possible reaction mechanisms,roles of the conserved residues,and effects of the protein environment on the whole enzymatic process are discussed in detail,which will enrich the knowledge of reactivity in proteins.With the improvement and development of multiscale models and computational methods,it is expected that global simulations of extremely large and complicated enzymes will enable and lend support to enzyme engineering.%酶催化包括底物到活性区的输运、选择催化化学反应及产物释放等复杂过程,由于复杂的蛋白质环境效应,任一化学和非化学过程都有可能是决定酶活性的关键步骤.为了全面认识酶催化活性,我们对几类酶催化过程进行了广泛的组合量子/分子力学(QM/MM)和经典分子力学(MM)动力学模拟(MD)研究,详细地讨论了整个酶催化过程的分子机制、关键残基的作用和蛋白质环境效应,丰富了对酶催化活性的认识.随着多尺度模型和计算模拟方法的进一步完善与发展,有望实现超大复杂生物酶催化过程的全程模拟研究,为酶工程领域的相关研究提供支持.