QM/MM Analysis of Transition States and Transition State Analogues in Metalloenzymes.

ABSTRACT: Enzymology is approaching an era where many problems can benefit from computational studies. While ample challenges remain in quantitatively predicting behavior for many enzyme systems, the insights that often come from computations are an important asset for the enzymology community. Here we provide a primer for enzymologists on the types of calculations that are most useful for mechanistic problems in enzymology. In particular, we emphasize the integration of models that range from small active-site motifs to fully solvated enzyme systems for cross-validation and dissection of specific contributions from the enzyme environment. We then use a case study of the enzyme alkaline phosphatase to illustrate specific application of the methods. The case study involves examination of the binding

SUBMITTER: Roston D 

PROVIDER: S-EPMC5705176 | biostudies-literature | 2016

REPOSITORIES: biostudies-literature