Issue 13, 2014

Diffusional correlations among multiple active sites in a single enzyme

Abstract

Simulations of the enzymatic dynamics of a model enzyme containing multiple substrate binding sites indicate the existence of diffusional correlations in the chemical reactivity of the active sites. A coarse-grain, particle-based, mesoscopic description of the system, comprising the enzyme, the substrate, the product and solvent, is constructed to study these effects. The reactive and non-reactive dynamics is followed using a hybrid scheme that combines molecular dynamics for the enzyme, substrate and product molecules with multiparticle collision dynamics for the solvent. It is found that the reactivity of an individual active site in the multiple-active-site enzyme is reduced substantially, and this effect is analyzed and attributed to diffusive competition for the substrate among the different active sites in the enzyme.

Graphical abstract: Diffusional correlations among multiple active sites in a single enzyme

Article information

Article type
Paper
Submitted
17 Dec 2013
Accepted
06 Feb 2014
First published
24 Feb 2014

Phys. Chem. Chem. Phys., 2014,16, 6211-6216

Diffusional correlations among multiple active sites in a single enzyme

C. Echeverria and R. Kapral, Phys. Chem. Chem. Phys., 2014, 16, 6211 DOI: 10.1039/C3CP55252G

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