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

Joel Ströbaek1, Di Tang1, Carlos Gueto-Tettay1

  • 1Department of Clinical Sciences Lund, Infection Medicine, Faculty of Medicine, Lund University, 221 84 Lund, Sweden.

International Journal of Molecular Sciences
|February 26, 2025
PubMed
Summary
This summary is machine-generated.

This study introduces Sidewinder, a computational pipeline for mapping antibody-antigen interactions. It enables high-throughput analysis of immune responses and aids in developing targeted immunotherapies.

Keywords:
Group A StreptococcusStreptococcus pyogenesantibody–antigen interactionsbacterial infectioncross-linking mass spectrometryepitope mappingimmunotherapy developmentstructural biologytandem mass spectrometry

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Area of Science:

  • Immunology
  • Structural Biology
  • Computational Biology

Background:

  • Antibodies are crucial for immune defense against bacterial pathogens.
  • Understanding antibody-antigen interactions is vital for developing targeted immunotherapies.
  • High-throughput computational methods are needed to map these interactions.

Purpose of the Study:

  • To introduce Sidewinder, a novel computational pipeline for analyzing antibody-antigen interactions.
  • To enable high-throughput mapping of antibody-antigen interfaces.
  • To advance the development of targeted immunotherapies.

Main Methods:

  • Integrated cross-linking mass spectrometry (XL-MS) with computational structural prediction and molecular docking.
  • Developed a modular, high-throughput pipeline named Sidewinder.
  • Validated the pipeline on antibodies targeting *Streptococcus pyogenes* virulence factors.

Main Results:

  • Successfully identified a monoclonal antibody epitope on Streptolysin O using Sidewinder.
  • Demonstrated the pipeline's utility in analyzing complex antibody-antigen systems, including antibodies against the M1 protein.
  • Validated the accuracy and efficiency of the Sidewinder pipeline.

Conclusions:

  • Sidewinder provides a robust and flexible framework for interrogating antibody-antigen systems.
  • This pipeline can accelerate the study of complex immune interactions.
  • The findings have potential implications for developing novel therapeutic strategies.