The Role of Molecular Dynamics Potential of Mean Force Calculations in the Investigation of Enzyme Catalysis

Y. Yang, L. Pan, Felice C Lightstone, K. M. Merz

Research output: Contribution to journalArticle

2 Citations (Scopus)

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.

Original languageEnglish (US)
JournalMethods in Enzymology
DOIs
StateAccepted/In press - 2016
Externally publishedYes

Fingerprint

Molecular Dynamics Simulation
Catalysis
Molecular dynamics
Biological Phenomena
Enzymes
Free energy
Sampling
Computer simulation
Research

Keywords

  • Molecular dynamics
  • Potential of mean force
  • Quantum mechanics/molecular mechanics
  • Steered MD
  • Umbrella sampling

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology

Cite this

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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.",
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AU - Lightstone, Felice C

AU - Merz, K. M.

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AB - 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.

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