Chemical Reaction Mechanisms

Formation of a μ-oxo nucleophile enables efficient hydrolysis by a trinuclear metal center in Family II inorganic pyrophosphatase

The paper elucidates the hydrolysis mechanism of Family II inorganic pyrophosphatase using structural and computational methods, identifying a μ-oxo nucleophile as the rate-limiting step.

Unravelling the Enantioselective Mechanism of Benzylsuccinate Synthase: Insights into Anaerobic Hydrocarbon Degradation Through Multiscale Modelling and Kinetics

The ability of enzymes to preserve reactive conformations with well-positioned residues during enzyme-catalyzed reactions can be an important factor for efficient catalysis: a case study of CARNMT1

This study uses computational simulations to show that preserving reactive conformations with well-positioned residues is critical for catalytic efficiency in CARNMT1, as demonstrated by comparing wild-type and mutant enzymes.

Influence of Wobbling Tryptophan and Mutations on PET Degradation Explored by QM/MM Free Energy Calculations

This study uses QM/MM simulations to analyze PET degradation mechanisms in PET hydrolases, revealing conformational changes and the impact of QM methods on reaction pathways.

Mechanistic insights into the phosphoryl transfer reaction in cyclin-dependent kinase 2: a QM/MM study

This study uses QM/MM calculations to analyze the phosphoryl transfer reaction in CDK2, finding the base-assisted mechanism is preferred with a potential energy barrier close to experimental values.