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Most chemical reactions in cells require enzymes—biological catalysts that speed up the reaction without being consumed or permanently changed. They reduce the activation energy needed to convert the reactants into products. Enzymes are proteins, that usually work by binding to a substrate—a reactant molecule that they act upon.
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Enzyme kinetics studies the rates of biochemical reactions. Scientists monitor the reaction rates for a particular enzymatic reaction at various substrate concentrations. Additional trials with inhibitors or other molecules that affect the reaction rate may also be performed.
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Interplay between conformational dynamics and substrate binding regulates enzymatic activity: a single-molecule FRET

David Scheerer1, Dorit Levy1, Remi Casier1

  • 1Department of Chemical and Biological Physics, Weizmann Institute of Science Rehovot 761001 Israel david.scheerer@weizmann.ac.il gilad.haran@weizmann.ac.il.

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|January 29, 2025
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Summary
This summary is machine-generated.

Urea activates adenylate kinase by promoting its open conformation, which aids substrate positioning. This surprising finding reveals how protein dynamics and chemical steps interplay to regulate enzyme function.

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Area of Science:

  • Biochemistry
  • Enzymology
  • Molecular Biophysics

Background:

  • Proteins utilize domain and subunit motions for function.
  • Adenylate kinase (AK) uses large-scale domain motions for catalysis, enclosing substrates ATP and AMP.
  • AK is surprisingly activated by urea, a common denaturant.

Purpose of the Study:

  • To investigate the role of conformational dynamics in adenylate kinase (AK) mechanism using urea activation.
  • To understand how urea influences AK's conformational states and substrate binding.
  • To elucidate the interplay between protein dynamics and enzymatic activity.

Main Methods:

  • Single-molecule Förster Resonance Energy Transfer (smFRET) spectroscopy.
  • Enzymatic activity assays.
  • Kinetic analysis.

Main Results:

  • Urea promotes the open conformation of adenylate kinase.
  • Urea aids in the proper positioning of ATP and AMP substrates.
  • Urea decreases AMP affinity, paradoxically enhancing catalytic progression.
  • A complete kinetic scheme including open/close transitions was defined.

Conclusions:

  • Conformational dynamics are crucial for regulating enzyme activity.
  • The interplay between protein dynamics and chemical steps is a general enzymatic property.
  • Single-molecule techniques provide novel insights into enzyme conformational regulation.