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Molecular crowding and protein enzymatic dynamics.

Carlos Echeverria1, Raymond Kapral

  • 1Chemical Physics Theory Group, Department of Chemistry, University of Toronto, Toronto, ON M5S 3H6, Canada. rkapral@chem.utoronto.ca.

Physical Chemistry Chemical Physics : PCCP
|April 6, 2012
PubMed
Summary

Molecular crowding significantly alters adenylate kinase dynamics, favoring closed conformations and slowing enzymatic cycles. Transport properties like diffusion also change markedly due to crowding effects.

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Area of Science:

  • Biophysics
  • Computational Biology
  • Protein Dynamics

Background:

  • Adenylate kinase (an enzyme) exhibits large conformational changes during its enzymatic cycle.
  • Understanding how molecular crowding affects protein dynamics is crucial for biological processes.

Purpose of the Study:

  • To investigate the impact of molecular crowding on the conformational dynamics and transport properties of adenylate kinase.
  • To model crowding effects on protein cyclic conformational dynamics using a coarse-grained approach.

Main Methods:

  • Mesoscopic simulations treating protein and solvent in a coarse-grained manner.
  • Representing protein residues as beads and solvent dynamics using multiparticle collision dynamics.
  • Introducing crowding via a stationary array of hard spherical objects with varying volume fractions and sizes.

Main Results:

  • Simulations show adenylate kinase prefers a closed conformation at high volume fractions, more so with smaller obstacles.
  • Enzymatic cycle time and internal motion times deviate significantly under high crowding conditions.
  • Protein transport properties are strongly affected, with diffusive motion becoming subdiffusive and diffusion coefficients changing by over an order of magnitude.

Conclusions:

  • Molecular crowding substantially influences protein conformational preferences and dynamics.
  • Crowding significantly alters protein transport properties, impacting diffusion and orientational relaxation.
  • The study provides insights into how cellular environments affect protein function through physical interactions.