title: Influence of neighboring reactive particles on diffusion-limited reactions.
abstract: Competition between reactive species is commonplace in typical chemical reactions. Specifically the primary reaction between a substrate and its target enzyme may be altered when interactions with secondary species in the system are substantial. We explore this competition phenomenon for diffusion-limited reactions in the presence of neighboring particles through numerical solution of the diffusion equation. As a general model for globular proteins and small molecules, we consider spherical representations of the reactants and neighboring particles; these neighbors vary in local density, size, distribution, and relative distance from the primary target reaction, as well as their surface reactivity. Modulations of these model variables permit inquiry into the influence of excluded volume and competition on the primary reaction due to the presence of neighboring particles. We find that the surface reactivity effect is long-ranged and a strong determinant of reaction kinetics, whereas the excluded volume effect is relatively short-ranged and less influential in comparison. As a consequence, the effect of the excluded volume is only modestly dependent on the neighbor distribution and is approximately additive; this additivity permits a linear approximation to the many-body effect on the reaction kinetics. In contrast, the surface reactivity effect is non-additive, and thus it may require higher-order approximations to describe the reaction kinetics. Our model study has broad implications in the general understanding of competition and local crowding on diffusion-limited chemical reactions.
authors.affiliation: Howard Hughes Medical Institute, University of California at San Diego, La Jolla, California 92093, USA. ceun@ucsd.edu
authors.forename: Changsun
authors.initials: C
authors.lastname: Eun
authors.forename: Peter M
authors.initials: PM
authors.lastname: Kekenes-Huskey
authors.forename: J Andrew
authors.initials: JA
authors.lastname: McCammon
mesh_terms: D004058:Diffusion; D007700:Kinetics; D008954:Models, Biological; D008956:Models, Chemical; D010316:Particle Size
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