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Detecting Allosteric Networks Using Molecular Dynamics Simulation.

S Bowerman1, J Wereszczynski1

  • 1Center for Molecular Study of Condensed Soft Matter, Illinois Institute of Technology, Chicago, IL, United States.

Methods in Enzymology
|August 7, 2016
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Summary
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Molecular dynamics simulations reveal enzyme allosteric networks by analyzing correlated motions. For thrombin, hirugen binding alters these networks, reducing enzyme accessibility and activity.

Keywords:
Allosteric networksCommunity analysisCorrelated motionMolecular dynamics

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Area of Science:

  • Biochemistry
  • Computational Biology
  • Enzymology

Background:

  • Allosteric networks enable enzymes to transmit signals and regulate catalytic activity over long distances.
  • Molecular dynamics (MD) simulations offer a way to study these mechanisms, but extracting allosteric signals can be challenging.

Purpose of the Study:

  • To describe methods for analyzing MD simulations to reveal allosteric networks.
  • To demonstrate these methods using the coagulation enzyme thrombin.

Main Methods:

  • Calculating residue-pair correlations from atomic fluctuations and mutual information.
  • Combining correlation data with contact information to identify allosteric networks.
  • Dynamically clustering systems into highly correlated communities.

Main Results:

  • MD simulations successfully identified allosteric networks in thrombin.
  • Binding of the antagonist hirugen significantly altered thrombin's correlation landscape.
  • Hirugen binding created pathways between Exosite I and the catalytic core, curtailing dynamic diversity.

Conclusions:

  • The described methods effectively reveal enzyme allosteric networks from MD simulations.
  • Hirugen binding to thrombin enforces stricter regulatory control, reducing enzyme accessibility.