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Antigen Processing Pathways

Antigen Processing Pathways

MHC molecules are key players in the immune response, enabling T cells to recognize and respond to specific antigens. They are present on the surface of all nucleated cells in the body and are instrumental in presenting antigens to T cells and activating them. T cells recognize the MHC-antigen complex and initiate an immune response. MHC class I and MHC class II are two main types of MHC molecules, each associated with a distinct antigen processing pathway.
MHC Class I: Presenting Endogenous...

T Cell Activation and Clonal Selection

T Cell Activation and Clonal Selection

T cells are integral to our adaptive immune system, recognizing and effectively responding to foreign antigens. T cell activation and clonal selection are pivotal in orchestrating this immune response. This article elucidates these mechanisms, detailing the roles of cluster of differentiation (CD) markers, major histocompatibility complex (MHC) molecules, costimulatory signals, and the process of clonal selection.
Naive T cells that have not yet encountered an antigen express two primary CD...

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Updated: Apr 11, 2026

Using X-ray Crystallography, Biophysics, and Functional Assays to Determine the Mechanisms Governing T-cell Receptor Recognition of Cancer Antigens

Using X-ray Crystallography, Biophysics, and Functional Assays to Determine the Mechanisms Governing T-cell Receptor Recognition of Cancer Antigens

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A structure-informed deep learning framework for modeling TCR-peptide-HLA interactions.

Kai Cao¹, Rui Li^1,2, Martin Stražar¹

¹Broad Institute of MIT and Harvard, Cambridge, MA, United States.

Biorxiv : the Preprint Server for Biology

|April 10, 2026

Summary

This summary is machine-generated.

We developed StriMap, a new framework to predict T cell receptor interactions with peptides and human leukocyte antigens. This tool aids in cancer immunotherapy and identifying autoimmune disease triggers.

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A High Throughput MHC II Binding Assay for Quantitative Analysis of Peptide Epitopes

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Published on: March 25, 2014

Area of Science:

Immunology
Computational Biology
Bioinformatics

Background:

T cell receptor (TCR) interactions with peptides and human leukocyte antigens (HLAs) are crucial for adaptive immunity.
Predicting TCR-peptide-HLA interactions is challenging but vital for applications in cancer immunotherapy and autoimmune disease research.

Purpose of the Study:

To present StriMap, a unified computational framework for predicting TCR-peptide-HLA interactions.
To improve the accuracy and generalizability of TCR-peptide-HLA recognition modeling.

Main Methods:

Integrated physicochemical, sequence-context, and structural features of recognition interfaces.
Developed a novel framework, StriMap, for predicting TCR-peptide-HLA interactions.
Applied StriMap to screen millions of bacterial peptides for molecular mimicry in ankylosing spondylitis.

Main Results:

StriMap achieved state-of-the-art performance in predicting TCR-peptide-HLA interactions.
Identified experimentally validated bacterial peptide mimics that activate T cells in ankylosing spondylitis.
Discovered a peptide enriched in both ankylosing spondylitis and inflammatory bowel disease patients, suggesting shared microbial triggers.

Conclusions:

StriMap offers a generalizable framework for predicting TCR-peptide-HLA interactions.
The framework facilitates rational immunotherapy design and the identification of autoimmune disease drivers.
Findings suggest potential shared microbial origins for ankylosing spondylitis and inflammatory bowel disease.