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Structural basis for ligand binding to an enzyme by a conformational selection pathway.

Michael Kovermann1,2, Christin Grundström3, A Elisabeth Sauer-Eriksson3

  • 1Department of Chemistry, Umeå University, SE-901 87 Umeå, Sweden; magnus.wolf-watz@umu.se michael.kovermann@uni-konstanz.de.

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|June 1, 2017
PubMed
Summary

Researchers describe a high-energy enzyme state crucial for catalysis using a disulfide bond to trap adenylate kinase. This arrested state reveals aligned catalytic machinery and enhanced ligand binding, clarifying enzyme mechanisms.

Keywords:
adenylate kinaseenzymatic catalysisligand bindingstructural biology

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Area of Science:

  • Biochemistry and Molecular Biology
  • Enzymology
  • Structural Biology

Background:

  • Proteins bind targets via induced fit or conformational selection, with high-energy states critical for enzymatic catalysis.
  • Dynamic interconversion between enzyme ground and high-energy states can be rate-limiting, but transient states hinder direct observation.

Purpose of the Study:

  • To provide a molecular description of a high-energy enzyme state within the conformational selection pathway.
  • To investigate the properties and catalytic relevance of transient, high-energy enzyme conformations.

Main Methods:

  • Utilized a combination of NMR spectroscopy, protein engineering, and X-ray crystallography.
  • Introduced a disulfide bond to arrest adenylate kinase in a high-energy conformation.
  • Determined a 1.9-Å X-ray structure of the arrested enzyme with a transition state analog.

Main Results:

  • Successfully trapped adenylate kinase in a closed, high-energy, catalytically relevant conformation.
  • The arrested state exhibits properly aligned catalytic sidechains and enhanced ligand binding affinity compared to wild-type.
  • Substrate binding to the high-energy state is not sterically hindered; ligand binding quenches motions dominated by enzyme-substrate interactions.

Conclusions:

  • The study provides direct molecular insight into a transient, high-energy enzyme state essential for catalysis.
  • Arresting this state validates its role in the conformational selection mechanism and catalytic efficiency.
  • Ligand binding dynamics are primarily driven by enzyme-substrate interactions rather than intramolecular conformational changes.