Quantifying Protein-Protein Interactions in Molecular Simulations

We present simple, accurate, and efficient methods to estimate the dissociation constant K_d and the second osmotic virial coefficient B₂ from molecular simulations. We show that for simulations of two proteins in a box, K_d is determined by B₂ and the fraction of bound protein. We present two different methods to calculate B₂ from Monte Carlo and molecular dynamics simulations using implicit or explicit solvent. We derive a surprisingly simple expression for B₂, adding significantly to the understanding of this important quantity. Non-binding interactions of proteins and other macromolecules shape the physicochemical properties of the crowded environments inside cells and of biomolecular condensates. We show how to extract the contributions of non-binding conformations to B₂ and discuss how these can be determined in analytical ultracentrifugation and SAXS experiments. We expect that our methods will prove to be instrumental in force parameterization efforts and high-throughput studies of large interactomes.