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Protein Networks02:26

Protein Networks

An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
Immunoprecipitation01:20

Immunoprecipitation

Immunoprecipitation, or IP, is a widely used technique that employs protein-antibody interactions to isolate proteins or protein complexes in their native state for studying protein-protein interactions, quaternary structures, or supramolecular complexes. Various modifications of the technique, including chromatin IP, cross-linking IP, and fluorescence IP, are commonly used.
Chromatin Immunoprecipitation
Chromatin immunoprecipitation, also known as ChIP, is used to study protein-DNA or...
Protein-protein Interfaces02:04

Protein-protein Interfaces

Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a polypeptide...
Protein Families02:47

Protein Families

Protein families are groups of homologous proteins; that is, they have similarities in amino acid sequences and three-dimensional structures. Protein families usually occur because of gene duplication, where an additional copy of a gene is inserted into the genome of an organism.   Mutations that change the amino acids but still allow the protein to be properly synthesized, will lead to new protein family members.   If these new proteins contain similar amino acids in key locations, protein...
Conservation of Protein Domains Over Different Proteins02:26

Conservation of Protein Domains Over Different Proteins

Protein domains are small structurally independent units that are part of a single amino acid chain.  Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...
Cross-reactivity00:42

Cross-reactivity

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Related Experiment Video

Updated: May 9, 2026

Electronic Tongue Generating Continuous Recognition Patterns for Protein Analysis
08:46

Electronic Tongue Generating Continuous Recognition Patterns for Protein Analysis

Published on: September 16, 2014

Recognition of higher order patterns in proteins: immunologic kernels.

Robert D Bremel1, E Jane Homan

  • 1ioGenetics LLC, Madison, Wisconsin, United States of America. robert_bremel@iogenetics.com

Plos One
|August 8, 2013
PubMed
Summary

Researchers identified repeating patterns of short peptides, termed "immunologic kernels," that contain signals for adaptive immunity. These kernels are bounded by cathepsin cleavage sites and include B-cell epitopes and MHC-binding peptides, suggesting a coordinated immune system logic.

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Area of Science:

  • Immunology
  • Computational Biology
  • Proteomics

Background:

  • The adaptive immune system relies on complex signaling pathways for recognition, response, and memory.
  • Understanding the fundamental units of immunologic signaling is crucial for vaccine development and immunotherapy.

Purpose of the Study:

  • To identify repeating structural and functional units within proteins that mediate adaptive immune responses.
  • To investigate the relationship between amino acid physical properties, protein processing, and immunologic signaling.

Main Methods:

  • Analysis of principal components of amino acid physical properties.
  • Prediction of cathepsin cleavage sites, MHC binding affinity, and B-cell epitope binding probability.
  • Cross-correlation analysis of these metrics across various protein sequences.

Main Results:

  • Identification of a recurring pattern of ~30 amino acid peptides, termed "immunologic kernels."
  • These kernels are flanked by cathepsin cleavage sites and contain B-cell linear epitopes and MHC-I/MHC-II binding peptides.
  • The findings suggest a higher-order spatial integration and symbolic logic coordinating the adaptive immune system.

Conclusions:

  • "Immunologic kernel" peptides represent fundamental units of adaptive immunologic cognition, response, and recall.
  • These patterns reveal a potential symbolic logic governing the adaptive immune system's coordination.
  • The study provides insights into the structural basis of immune signaling and memory.