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Eigenvector centrality for characterization of protein allosteric pathways.

Christian F A Negre1,2,3, Uriel N Morzan4,3, Heidi P Hendrickson2,3,5

  • 1Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545; uriel.morzan@yale.edu cnegre@lanl.gov ivan.rivalta@ens-lyon.fr victor.batista@yale.edu.

Proceedings of the National Academy of Sciences of the United States of America
|December 12, 2018
PubMed
Summary
This summary is machine-generated.

This study introduces eigenvector centrality to map allosteric pathways in enzymes, revealing key residues and interactions. This method provides a cost-effective way to understand molecular mechanisms and guide drug discovery.

Keywords:
IGPSallosteryeigenvector centralitygraph theoryinformation theory

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Area of Science:

  • Biochemistry
  • Molecular Biology
  • Computational Biology

Background:

  • Allosteric regulation is crucial for enzyme function but challenging to study.
  • Current methods lack the resolution to fully characterize energy transfer pathways.

Purpose of the Study:

  • To develop and validate a novel computational method for elucidating allosteric mechanisms.
  • To identify key residues and pathways involved in enzyme regulation.

Main Methods:

  • Developed eigenvector centrality metric based on mutual information.
  • Applied the method to imidazole glycerol phosphate synthase (IGPS).
  • Validated findings using solution Nuclear Magnetic Resonance (NMR) spectroscopy.

Main Results:

  • Identified specific amino acid residues in IGPS highly sensitive to effector binding.
  • Provided experimental evidence for interdomain motion and the role of helix h[Formula: see text].
  • Characterized the short-range correlations governing the allosteric mechanism.

Conclusions:

  • Eigenvector centrality analysis is a powerful, generalizable tool for understanding allosteric regulation.
  • The findings offer insights into IGPS function and potential therapeutic targets.
  • This methodology facilitates fundamental understanding of molecular mechanisms.