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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...

Antigens Involved in Adaptive Immunity

Antigens Involved in Adaptive Immunity

An antigen is any substance the immune system identifies as foreign and potentially harmful to the body, prompting an immune response. Antigens have two functional properties: immunogenicity and reactivity. Immunogenicity is the ability of an antigen to stimulate a specific immune response. At the same time, reactivity describes the antigen's ability to react with the cells and antibodies produced in response to it.
Complete Antigens
Complete antigens possess both immunogenicity and...

Mitochondrial Precursor Proteins

Mitochondrial Precursor Proteins

Mitochondrial precursors are partially unfolded or loosely folded polypeptide chains. Newly synthesized precursors are inhibited from spontaneously folding into their native conformation by the cytosolic chaperones, heat shock proteins 70 (Hsp70), and mitochondrial import stimulation factors (MSFs). Precursors bound to MSFs are guided to the TOM70-TOM37 receptors, while precursors bound to Hsp70 chaperones are targetted to TOM20-TOM22 receptor complexes.
Most of the mitochondrial...

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...

Cells of the Innate Immune Response

Cells of the Innate Immune Response

The innate immune response is an immediate and non-specific response against pathogens, acting swiftly to prevent the spread of infections. The primary cells involved in this response are phagocytes and natural killer (NK) cells.
Phagocytes
Phagocytes police the peripheral tissues by removing cellular debris and responding to the invasion of foreign substances or pathogens. Many phagocytes attack and remove microorganisms even before lymphocytes detect them. The human body has two general...

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Related Experiment Video

Updated: Nov 1, 2025

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

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

Published on: March 25, 2014

NetCleave: an open-source algorithm for predicting C-terminal antigen processing for MHC-I and MHC-II.

Pep Amengual-Rigo¹, Victor Guallar^2,3

¹Barcelona Supercomputing Center (BSC), 08034, Barcelona, Spain.

Scientific Reports

|June 24, 2021

Summary

NetCleave predicts C-terminal antigen processing, a key step in peptide presentation. This algorithm shows high accuracy for MHC-I pathways and aids in discovering immunogenic peptides.

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Stability and Structure of Bat Major Histocompatibility Complex Class I with Heterologous β2-Microglobulin

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Immunopeptidomics: Isolation of Mouse and Human MHC Class I- and II-Associated Peptides for Mass Spectrometry Analysis

Immunopeptidomics: Isolation of Mouse and Human MHC Class I- and II-Associated Peptides for Mass Spectrometry Analysis

Published on: October 15, 2021

Area of Science:

Immunology
Bioinformatics

Background:

Cell surface antigen presentation is crucial for immune response.
C-terminal antigen processing is a critical bottleneck in peptide presentation pathways, defining the downstream peptidome.

Purpose of the Study:

To introduce NetCleave, an open-source algorithm for predicting C-terminal antigen processing in both MHC-I and MHC-II pathways.
To evaluate NetCleave's performance against existing tools using immunogenicity datasets.

Main Methods:

Developed NetCleave, a neural network-based algorithm.
Trained the network on 46 physicochemical descriptors of cleavage site amino acids.
Assessed prediction accuracy using AUC and evaluated performance on four independent immunogenicity datasets.

Main Results:

NetCleave achieved high prediction accuracy for MHC-I (AUC=0.91).
Prediction for MHC-II remains challenging (AUC=0.66).
NetCleave demonstrated superior performance compared to other prediction tools on immunogenicity datasets.

Conclusions:

NetCleave is a highly accurate tool for predicting C-terminal antigen processing, particularly for MHC-I.
C-terminal processing prediction holds promise for identifying immunogenic peptides, potentially aiding vaccine and immunotherapy development.