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Epitope Mapping with Sidewinder : An XL-MS and Structural Modeling Approach

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Τίτλος: Epitope Mapping with Sidewinder : An XL-MS and Structural Modeling Approach
Συγγραφείς: Ströbaek, Joel, Tang, Di, Gueto-Tettay, Carlos, Gomez Toledo, Alejandro, Olofsson, Berit, Hartman, Erik, Heusel, Moritz, Malmström, Johan, Malmström, Lars
Πηγή: International Journal of Molecular Sciences; 26(4), pp 1-17 (2025) ; ISSN: 1422-0067
Στοιχεία εκδότη: MDPI AG
Έτος έκδοσης: 2025
Συλλογή: Lund University Publications (LUP)
Θεματικοί όροι: Bioinformatics (Computational Biology), Epitope Mapping/methods, Streptococcus pyogenes/immunology, Bacterial Proteins/chemistry, Molecular Docking Simulation, Antibodies, Monoclonal/chemistry, Mass Spectrometry/methods, Epitopes/immunology, Streptolysins/chemistry, Bacterial/immunology
Περιγραφή: 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.
Τύπος εγγράφου: article in journal/newspaper
Γλώσσα: English
Relation: http://dx.doi.org/10.3390/ijms26041488; pmid:40003954; scopus:85218901966
DOI: 10.3390/ijms26041488
Διαθεσιμότητα: https://lup.lub.lu.se/record/18960a88-0ea4-4ce7-a6c1-34132a89496d
https://doi.org/10.3390/ijms26041488
Αριθμός Καταχώρησης: edsbas.BE47FE4B
Βάση Δεδομένων: BASE
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  Data: Epitope Mapping with Sidewinder : An XL-MS and Structural Modeling Approach
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  Data: International Journal of Molecular Sciences; 26(4), pp 1-17 (2025) ; ISSN: 1422-0067
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  Data: 2025
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  Data: 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.
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      – SubjectFull: Bioinformatics (Computational Biology)
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      – SubjectFull: Epitope Mapping/methods
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