Kinetic principles of chemical cross-link formation for protein–protein interactions

Proteins play a central role in most biological processes within the cell, and deciphering how they interact is key to understand their function. Cross-linking coupled with mass spectrometry is an essential tool for elucidating protein–protein interactions (PPIs). Despite its importance, we still know surprisingly little about the principles that underlie the process of chemical cross-link formation itself and how it is influenced by different physicochemical factors. To understand the molecular details of cross-link formation, we have set up a comprehensive kinetic model and carried out simulations of protein cross-linking on large protein complexes. We dissect the contribution on the cross-link yield of parameters such as amino acid reactivity, cross-linker concentration, and hydrolysis rate. Our model can compute cross-link formation based solely on the structure of a protein complex, thereby enabling realistic predictions for a diverse set of systems. We quantitatively show how cross-links and mono-links are in direct competition and how the hydrolysis rate and abundance of cross-linker and proteins directly influence their relative formation. We show how cross-links and mono-links exist in an “all-against-all” competition due to their simultaneous formation, resulting in a nonintuitive network of interdependence. We show that this interdependence is locally confined and mainly limited to direct neighbors or residues in direct vicinity. These results enable us to identify the optimal cross-linker concentration at which the maximal number of cross-links is formed. Taken together, our study establishes a comprehensive kinetic model to quantitatively describe cross-link formation for PPIs.