An Integrated Approach for Determining a Protein-Protein Binding Interface in Solution and an Evaluation of HDX Kinetics for Adjudicating Candidate Docking Models

We describe an integrated approach of using hydrogen deuterium exchange mass spectrometry (HDX-MS), chemical crosslinking mass spectrometry (XL-MS), and molecular docking to characterize the binding interface and to predict the three-dimensional quaternary structure of a protein-protein complex in solution. Interleukin 7 (IL-7) and its -receptor, IL-7R, serving as essential mediators in the immune system, are the model system. HDX kinetics report widespread protection on IL-7R but show no differential evidence of binding-induced protection or remote conformational change. Crosslinking with reagents that differ in spacer lengths and targeting residues increases the spatial resolution. Using five cross-links as distance restraints for protein-protein docking, we generated a high-confidence model of the IL-7/IL-7Rα complex. Both the predicted binding interface and regions with direct contacts agree well with those in the solid-state structure, as confirmed by previous X-ray crystallography. An additional ...