Related Experiment Video
Updated: Jun 28, 2025

Multiscale Sampling of a Heterogeneous Water/Metal Catalyst Interface using Density Functional Theory and Force-Field Molecular Dynamics
Published on: April 12, 2019
Kinetic View of Enzyme Catalysis from Enhanced Sampling QM/MM Simulations
Dhiman Ray1, Sudip Das1, Umberto Raucci1
1Atomistic Simulations, Italian Institute of Technology, Via Enrico Melen 83, Genova GE 16152, Italy.
Abstract:
The rate constants of enzyme-catalyzed reactions (kcat) are often approximated from the barrier height of the reactive step. We introduce an enhanced sampling QM/MM approach that directly calculates the kinetics of enzymatic reactions, without introducing the transition-state theory assumptions, and takes into account the dynamical equilibrium between the reactive and non-reactive conformations of the enzyme/substrate complex. Our computed kcat values are in order-of-magnitude agreement with the experimental data for two representative enzymatic reactions.
Related Concept Videos
Introduction to Enzyme Kinetics
The experimenter can then plot the initial reaction rate or velocity (Vo) of a given trial against the substrate concentration ([S]) to obtain a graph of the reaction properties. For many enzymatic reactions involving a...
Enzyme Kinetics
Scientists typically study enzyme kinetics with a fixed amount of enzyme in the controlled environment of a test tube. When more reactant, or substrate, is...
Introduction to Mechanisms of Enzyme Catalysis
Catalytically Perfect Enzymes
Most enzymes...
Enzymes
Enzyme deficiencies can often translate into life-threatening diseases. For example, a genetic abnormality resulting in the deficiency of the enzyme G6PD...
Induced-fit Model
Enzymes exhibit substrate specificity, meaning that they can only bind to certain substrates. This is mainly determined by the shape and chemical...

