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Related Experiment Videos

Electrostatic and hydrodynamic orientational steering effects in enzyme-substrate association

J Antosiewicz1, J A McCammon

  • 1Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla 92093-0365, USA.

Biophysical Journal
|July 1, 1995
PubMed
Summary

Simulations show that including hydrodynamic interactions in enzyme-ligand binding models decreases the rate constant. Electrostatic interactions also influence binding, but hydrodynamic effects are modest for these systems.

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Area of Science:

  • Biophysics
  • Computational Chemistry
  • Biochemistry

Background:

  • Enzyme-ligand interactions are crucial for biological processes.
  • Accurate modeling of these interactions requires considering multiple physical forces.
  • Previous models often focused primarily on electrostatic interactions.

Purpose of the Study:

  • To investigate the impact of hydrodynamic interactions on enzyme-ligand binding rates.
  • To compare the effects of hydrodynamic and electrostatic interactions on binding dynamics.
  • To assess the accuracy of simulations that exclude hydrodynamic effects.

Main Methods:

  • Brownian dynamics simulations were used.
  • Dumbbell models for cleft enzymes and elongated ligands were employed.

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  • Both electrostatic and hydrodynamic interactions were incorporated.

    • Main Results:

    • Hydrodynamic interactions generally decrease the binding rate constant.
    • Hydrodynamic orientational effects were found to be modest.
    • Electrostatic interactions modify hydrodynamic torques, influencing substrate drift.

    Conclusions:

    • Simulations neglecting hydrodynamic interactions may overestimate binding rate constants by approximately 20%.
    • However, these simplified simulations can still realistically describe orientational steering effects.
    • Including hydrodynamic interactions provides a more comprehensive understanding of enzyme-ligand encounters.