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Unraveling Entropic Rate Acceleration Induced by Solvent Dynamics in Membrane Enzymes
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Diffusional correlations among multiple active sites in a single enzyme.

Carlos Echeverria1, Raymond Kapral

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

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Summary
This summary is machine-generated.

Enzymes with multiple active sites show reduced reactivity due to substrate competition. This simulation reveals diffusional correlations impacting enzymatic chemical reactions.

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Area of Science:

  • Biochemistry
  • Computational Chemistry
  • Chemical Physics

Background:

  • Enzymes with multiple active sites are crucial in biological processes.
  • Understanding substrate binding and reactivity in such systems is complex.
  • Diffusional effects can influence enzyme kinetics.

Purpose of the Study:

  • To investigate diffusional correlations in the chemical reactivity of multiple active sites within a model enzyme.
  • To elucidate the impact of substrate competition on enzymatic activity.

Main Methods:

  • Developed a coarse-grain, particle-based, mesoscopic model.
  • Employed a hybrid simulation scheme combining molecular dynamics and multiparticle collision dynamics.
  • Simulated enzyme, substrate, product, and solvent dynamics.

Main Results:

  • Identified significant reduction in the reactivity of individual active sites.
  • Observed diffusional correlations in chemical reactivity.
  • Attributed reduced reactivity to diffusive competition for substrates among active sites.

Conclusions:

  • Diffusive competition among multiple active sites substantially reduces individual site reactivity.
  • This finding highlights the importance of considering diffusional dynamics in multi-site enzyme systems.