The predicted role of steric specificity in crowding-mediated effects on reversible biomolecular association

Abstract

A fundamental question in biology is whether the presence of non-reacting macromolecules in the cytoplasm affects the rates and extents of reversible association reactions, a phenomenon often referred to as ‘macromolecular crowding.’ Under certain conditions, crowding has been proposed to dramatically alter the kinetics and thermodynamics of chemical reactions, making it difficult to quantitatively relate rates and extents of reactions measured in vitro to those occurring in vivo. In this work, we use Brownian dynamics simulation and Monte Carlo methods to (1) quantify the overall thermodynamic and kinetic effects of crowding by independently investigating each step of reversible bimolecular association (i.e. translational diffusion, steric specific binding, and dissociation), and (2) provide an explicit, quantitative investigation of how the degree of steric specificity of protein dimerization influences crowding-mediated effects on association and dissociation. We find that kon decreases by ∼2-fold for non-steric specific reactions, and increases by ∼3-fold for highly steric specific reactions. In addition, koff decreases by only ∼30%–60% in the presence of crowders, depending on the strength of the bond between the reactant pair, so that the equilibrium constant is increased by ∼4-fold, at most. These results suggest that crowding-mediated effects on globular protein dimerization reactions in the cytoplasm are modulated by the steric specificity of the reactants, and that reversible protein–protein association is relatively insensitive to the physical presence of crowders (i.e. steric repulsion effects in the cytoplasm) for crowders of similar size and shape to reactants over a range of volume fractions (0–0.3).