Related Experiment Video
Updated: Mar 16, 2026

Multiscale Sampling of a Heterogeneous Water/Metal Catalyst Interface using Density Functional Theory and Force-Field Molecular Dynamics
Published on: April 12, 2019
The Role of Molecular Dynamics Potential of Mean Force Calculations in the Investigation of Enzyme Catalysis
Y Yang1, L Pan2, F C Lightstone1
1Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, United States.
Abstract:
The potential of mean force simulations, widely applied in Monte Carlo or molecular dynamics simulations, are useful tools to examine the free energy variation as a function of one or more specific reaction coordinate(s) for a given system. Implementation of the potential of mean force in the simulations of biological processes, such as enzyme catalysis, can help overcome the difficulties of sampling specific regions on the energy landscape and provide useful insights to understand the catalytic mechanism. The potential of mean force simulations usually require many, possibly parallelizable, short simulations instead of a few extremely long simulations and, therefore, are fairly manageable for most research facilities. In this chapter, we provide detailed protocols for applying the potential of mean force simulations to investigate enzymatic mechanisms for several different enzyme systems.
More Related Videos
09:42Unraveling Entropic Rate Acceleration Induced by Solvent Dynamics in Membrane Enzymes
Published on: January 16, 2016
07:31Author Spotlight: Advancing Cell Membrane Biophysics - Exploring Interactions and Challenges Through Experimental and Computational Approaches
Published on: September 1, 2023
Related Concept Videos
Introduction to Mechanisms of Enzyme Catalysis
Introduction to Mechanisms of Enzyme Catalysis
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...
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...
Force and Potential Energy in One Dimension