Electrostatic and hydrodynamic orientational steering effects in enzyme-substrate association.
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.
Antosiewicz
J
J
Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla 92093-0365, USA.
McCammon
J A
JA
D000465:Algorithms; D001665:Binding Sites; D003198:Computer Simulation; D004058:Diffusion; D004563:Electrochemistry; D004798:Enzymes / Q000737:chemistry* / Q000378:metabolism*; D007700:Kinetics; D008433:Mathematics; D008962:Models, Theoretical; D011485:Protein Binding; D012984:Software
D004798:Enzymes