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Ströbaek J, Tang D, Gueto-Tettay C, Gomez Toledo A, Olofsson B, Hartman E, Heusel M, Malmström J, Malmström L
Int J Mol Sci 26 (4) - [2025-02-11; online 2025-02-11]
Antibodies are critical to the host's immune defense against bacterial pathogens. Understanding the mechanisms of antibody-antigen interactions is essential for developing new targeted immunotherapies. Building computational workflows that can identify where an antibody binds its cognate antigen and deconvoluting the interaction interface in a high-throughput manner are critical for advancing this field. Cross-linking mass spectrometry (XL-MS) integrated with structural modeling offers a flexible and high-resolution strategy to map protein-protein interactions from low sample amounts. However, cross-linking and in silico modeling have limitations that require robust analytical workflows to make accurate inferences. In this study, we introduce Sidewinder, a modular high-throughput pipeline combining state-of-the-art computational structural prediction and molecular docking with rapid XL-MS analysis, enabling comprehensive interrogation of antibody-antigen systems. We validated this pipeline on antibodies targeting two Streptococcus pyogenes virulence factors. Using recently published data, we identified a well-defined monoclonal antibody epitope on Streptolysin O by generating and querying a large ensemble of interaction models probabilistically. We also showcased the utility of the Sidewinder pipeline by analyzing a more complex system, involving monoclonal antibodies that target the cell wall-anchored M1 protein. The flexibility and robustness of the Sidewinder pipeline provide a powerful framework for future studies of complex antibody-antigen systems, potentially leading to new therapeutic strategies.
Structural Proteomics [Service]
PubMed 40003954
DOI 10.3390/ijms26041488
Crossref 10.3390/ijms26041488
pmc: PMC11855800
pii: ijms26041488