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Biophys J. Jul 1995; 69(1): 57–65.
PMCID: PMC1236224

Electrostatic and hydrodynamic orientational steering effects in enzyme-substrate association.

Abstract

Diffusional encounters between a dumbbell model of a cleft enzyme and a dumbbell model of an elongated ligand are simulated by Brownian dynamics. The simulations take into account electrostatic and hydrodynamic interactions between the molecules. It is shown that the primary effect of inclusion of hydrodynamic interactions into the simulation is an overall decrease in the rate constant. Hydrodynamic orientational effects are of modest size for the systems considered here. They are manifested when changes in the rate constants for diffusional encounters favored by hydrodynamic interactions are compared with those favored by electrostatic interactions as functions of the overall strength of electrostatic interactions. The electrostatic interactions modify the hydrodynamic torques by modifying the drift velocity of the substrate toward the enzyme. We conclude that simulations referring only to electrostatic interactions between an enzyme and its ligand may yield rate constants that are somewhat (e.g., 20%) too high, but provide realistic descriptions of the orientational steering effects in the enzyme-ligand encounters.

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Selected References

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  • Antosiewicz J, Gilson MK, Lee IH, McCammon JA. Acetylcholinesterase: diffusional encounter rate constants for dumbbell models of ligand. Biophys J. 1995 Jan;68(1):62–68. [PMC free article] [PubMed]
  • Brune D, Kim S. Hydrodynamic steering effects in protein association. Proc Natl Acad Sci U S A. 1994 Apr 12;91(8):2930–2934. [PMC free article] [PubMed]
  • Garcia de la Torre JG, Bloomfield VA. Hydrodynamic properties of complex, rigid, biological macromolecules: theory and applications. Q Rev Biophys. 1981 Feb;14(1):81–139. [PubMed]
  • Teller DC, Swanson E, de Haën C. The translational friction coefficient of proteins. Methods Enzymol. 1979;61:103–124. [PubMed]
  • Wade RC, Luty BA, Demchuk E, Madura JD, Davis ME, Briggs JM, McCammon JA. Simulation of enzyme-substrate encounter with gated active sites. Nat Struct Biol. 1994 Jan;1(1):65–69. [PubMed]
  • Zwanzig R, Kiefer J, Weiss GH. On the validity of the kirkwood-riseman theory. Proc Natl Acad Sci U S A. 1968 Jun;60(2):381–386. [PMC free article] [PubMed]

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