Leveraging Cross-Linking Mass Spectrometry for Modeling Antibody–Antigen Complexes

Elucidating antibody–antigen complexes at the atomic level is of utmost interest for understanding immune responses and designing better therapies. Cross-linking mass spectrometry (XL-MS) has emerged as a powerful tool for mapping protein–protein interactions, suggesting valuable structural insights. However, the use of XL-MS studies to enable epitope/paratope mapping of antibody–antigen complexes is still limited up to now. XL-MS data can be used to drive integrative modeling of antibody–antigen complexes, where cross-links information serves as distance restraints for the precise determination of binding interfaces. In this approach, XL-MS data are employed to identify connections between binding interfaces of the antibody and the antigen, thus informing molecular modeling. Current literature provides minimal input about the impact of XL-MS data on the integrative modeling of antibody–antigen complexes. Here, we applied XL-MS to retrieve information about binding interfaces of three antibody–antigen complexes. We leveraged XL-MS data to perform integrative modeling using HADDOCK (active-passive residues and distance restraints strategies) and AlphaLink2. We then compared these three approaches with initial predictions of investigated antibody–antigen complexes by AlphaFold Multimer. This work emphasizes the importance of cross-linking data in resolving conformational dynamics of antibody–antigen complexes, ultimately enhancing the design of better protein therapeutics and vaccines.