title: The Role of Molecular Dynamics Potential of Mean Force Calculations in the Investigation of Enzyme Catalysis.
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.
authors: Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, United States.
authors: Y
authors: Y
authors: Yang
authors: Michigan State University, East Lansing, MI, United States.
authors: L
authors: L
authors: Pan
authors: Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, United States.
authors: F C
authors: FC
authors: Lightstone
authors: Michigan State University, East Lansing, MI, United States. Electronic address: kmerz1@gmail.com.
authors: K M
authors: KM
authors: Merz
mesh_terms: D000818:Animals; D055162:Biocatalysis; D004798:Enzymes / Q000737:chemistry / Q000378:metabolism*; D005658:Fungi / Q000201:enzymology; D006801:Humans; D056004:Molecular Dynamics Simulation; D013816:Thermodynamics
chemical_list: D004798:Enzymes
keywords: Molecular dynamics; Potential of mean force; Quantum mechanics/molecular mechanics; Steered MD; Umbrella sampling