Macromolecular Crowding Effects On Multiprotein Binding Equilibria: Molecular Simulation and Theory

We present a coarse-grained model for studying the effects of macromolecular crowding on the thermodynamic and structural properties of multiprotein complexes. Residue-level interactions between proteins and crowding agents are incorporated in a recently developed transferable coarse-grained model of multiprotein complexes. The model is used to study the binding equilibrium between two protein complexes, ubiquitin/UIM and cytochrome c/cytochrome c peroxidase using replica exchange Monte Carlo simulations. We find that the change in binding free energy due to purely repulsive crowding can be quantitatively described by a scaled particle theory (SPT) model without any fitting parameters. The same SPT model can also be used to predict the effects of mixed crowding - a mixture of crowding particles with different sizes, using an additivity ansatz. We find that attractions between proteins and crowding molecules can give rise to a nonmonotonic change in the binding free energy with increasing attraction strength and the formation of higher order (ternary, etc.) complexes. A modified SPT model which includes the effect of protein-crowder attractions in a mean-field manner can describe the change in binding free energy due to crowding semi-quantitatively. Our structural analysis suggests that crowding may significantly change the fraction of specific versus non-specific transient encounter complexes in a crowded environment.