Quantifying Crowding Effects on Transient Encounter Complex Formation during Protein Binding

Abstract

Formation of transient encounter complexes during the early steps of protein binding is known to play an important role in the specific-complex formation by enhancing the association rate. The cellular medium is crowded with an ensemble of macromolecules, e.g., proteins, nucleic acids, sugars, lipids, etc. These macromolecules occupy the cell as high as 40% of its volume, thereby affecting the stability and speed of protein-protein interactions. We investigate the effects of macromolecular crowding on the formation of protein complexes, especially, encounter complexes, using a residue-based coarse-grained model for proteins and spherical macromolecular crowders. Crowders with solely repulsive interactions with protein(s) stabilize the formation of the native complex, while destabilizing most of the encounter complexes. However, certain encounter complexes, whose shapes are similar to that of the native complex, are shown to be stabilized by these repulsive crowders. On the other hand, attractive crowders exhibit the opposite trend, destabilizing the native complex and stabilizing the encounter complexes. The principal component analysis on the protein complexes shows that the free-energy landscape on the leading principal coordinates is affected by crowders, in which the energy barrier between the native complex and the dominant encounter complex is increased. We develop a theoretical model based on the scaled particle theory to quantify the crowding effects on the formation of encounter complexes. The newly developed theory can predict the effect of crowding accurately over a wide range of crowder sizes and interaction strengths between crowders and proteins. Our study provides the first (to our knowledge) theoretical description of crowding effects on the encounter complexes. We are currently extending its scope to provide microscopic understanding of the protein-protein interactions inside a cell.