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Related Concept Videos

Antibody Structure01:10

Antibody Structure

Overview
Antibodies, also known as immunoglobulins (Ig), are essential players of the adaptive immune system. These antigen-binding proteins are produced by B cells and make up 20 percent of the total blood plasma by weight. In mammals, antibodies fall into five different classes, which each elicits a different biological response upon antigen binding.
The Y-Shaped Structure of Antibodies Consists of Four Polypeptide Chains
Antibodies consist of four polypeptide chains: two identical heavy...
Antibody Structure01:10

Antibody Structure

Overview
Antibodies, also known as immunoglobulins (Ig), are essential players of the adaptive immune system. These antigen-binding proteins are produced by B cells and make up 20 percent of the total blood plasma by weight. In mammals, antibodies fall into five different classes, which each elicits a different biological response upon antigen binding.
The Y-Shaped Structure of Antibodies Consists of Four Polypeptide Chains
Antibodies consist of four polypeptide chains: two identical heavy...
Antibody Structure and Classes01:25

Antibody Structure and Classes

Antibodies, also known as immunoglobulins, are produced by B cells in response to foreign substances, such as bacteria and viruses. These proteins are critical for recognizing and neutralizing these substances, protecting the body from potential harm.
The basic structure of an antibody consists of four protein chains: two identical heavy chains and two identical light chains. These chains are held together by disulfide bonds and other non-covalent interactions, forming a Y-shaped structure.
Antibody Actions01:26

Antibody Actions

Antibodies, or immunoglobulins, are critical players in the immune system's arsenal against invading pathogens. Produced by B cells and plasma cells, their primary role is to detect and bind to specific antigens, molecules found on the surface of pathogens like bacteria or viruses. Beyond antigen recognition, antibodies perform several vital functions that contribute to immune defense.
Neutralization
Antibodies can bind to pathogens, preventing them from infecting host cells. This process...
Conserved Binding Sites01:49

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
Conserved Binding Sites01:49

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...

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Updated: May 24, 2026

Peptide Scanning-assisted Identification of a Monoclonal Antibody-recognized Linear B-cell Epitope
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Peptide Scanning-assisted Identification of a Monoclonal Antibody-recognized Linear B-cell Epitope

Published on: March 24, 2017

Structural consensus among antibodies defines the antigen binding site.

Vered Kunik1, Bjoern Peters, Yanay Ofran

  • 1The Goodman Faculty of Life Sciences, Nanotechnology Building, Bar Ilan University, Ramat Gan, Israel.

Plos Computational Biology
|March 3, 2012
PubMed
Summary

Antibody antigen binding sites extend beyond traditional Complementarity Determining Regions (CDRs). Structural consensus regions, identifiable by sequence, are crucial for antigen binding and antibody engineering.

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Antibody Binding Specificity for Kappa (Vκ) Light Chain-containing Human (IgM) Antibodies: Polysialic Acid (PSA) Attached to NCAM as a Case Study
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Antibody Binding Specificity for Kappa (Vκ) Light Chain-containing Human (IgM) Antibodies: Polysialic Acid (PSA) Attached to NCAM as a Case Study

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Peptide Scanning-assisted Identification of a Monoclonal Antibody-recognized Linear B-cell Epitope
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Published on: March 24, 2017

Antibody Binding Specificity for Kappa (Vκ) Light Chain-containing Human (IgM) Antibodies: Polysialic Acid (PSA) Attached to NCAM as a Case Study
11:10

Antibody Binding Specificity for Kappa (Vκ) Light Chain-containing Human (IgM) Antibodies: Polysialic Acid (PSA) Attached to NCAM as a Case Study

Published on: June 29, 2016

Area of Science:

  • Immunology
  • Structural Biology
  • Computational Biology

Background:

  • Complementarity Determining Regions (CDRs) are traditionally considered the primary sites for antibody antigen binding.
  • Current methods identify CDRs by highlighting sequence or structural differences between antibodies.

Purpose of the Study:

  • To investigate the extent to which antibody residues outside the canonical CDRs contribute to antigen binding.
  • To identify reliable sequence-based methods for pinpointing antigen binding sites.
  • To assess the energetic contribution of different residue groups to antibody-antigen complex stability.

Main Methods:

  • Analysis of antibody structures and sequences to identify antigen-binding residues.
  • Comparison of residue contributions within and outside traditional CDRs.
  • Evaluation of energetic contributions using computational methods.

Main Results:

  • Approximately 20% of antigen-binding residues fall outside the conventionally defined CDRs.
  • Virtually all antigen-binding residues are located within regions of structural consensus across antibodies.
  • These structurally conserved regions, indicative of binding sites, can be identified from antibody sequences.
  • Residues outside traditional CDRs contribute significantly, sometimes more energetically, to antigen binding than those within CDRs.
  • Antigen-binding residues within CDRs but outside structural consensus regions have minimal energetic impact.

Conclusions:

  • Traditional CDR definitions are insufficient for comprehensive identification of antibody antigen binding sites.
  • Structural consensus regions, identifiable via sequence, offer a more accurate map of antigen binding sites.
  • This approach enables systematic and comprehensive antigen binding site identification, aiding antibody engineering and epitope discovery.