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Related Concept Videos

Antibody Structure01:10

Antibody Structure

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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...
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Antibody Structure and Classes01:25

Antibody Structure and Classes

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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.
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Cooperative Allosteric Transitions01:58

Cooperative Allosteric Transitions

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Cooperative allosteric transitions can occur in multimeric proteins, where each subunit of the protein has its own ligand-binding site. When a ligand binds to any of these subunits, it triggers a conformational change that affects the binding sites in the other subunits; this can change the affinity of the other sites for their respective ligands. The ability of the protein to change the shape of its binding site is attributed to the presence of a mix of flexible and stable segments in the...
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Antibody Actions01:26

Antibody Actions

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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...
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Diversity of Antigen Receptors01:28

Diversity of Antigen Receptors

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Antigen receptors are essential components of the immune system crucial in defending the body against foreign invaders. These receptors are present on the surface of B and T cells, enabling them to recognize antigens and mount an appropriate immune response.
Before encountering any antigen, lymphocytes express these receptors. On B cells, the antigen receptor is a membrane-bound antibody molecule called BCR; on T cells, it is a T cell receptor or TCR. B and T cell receptors are composed of two...
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Conserved Binding Sites01:49

Conserved Binding Sites

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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...
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Using X-ray Crystallography, Biophysics, and Functional Assays to Determine the Mechanisms Governing T-cell Receptor Recognition of Cancer Antigens
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Do antibody CDR loops change conformation upon binding?

Chu'nan Liu1, Lilian M Denzler1, Oliver E C Hood1

  • 1Structural and Molecular Biology, Division of Biosciences, University College London, London, UK.

Mabs
|March 13, 2024
PubMed
Summary
This summary is machine-generated.

Antibody drug development requires understanding antigen binding. This study analyzed antibody structures, finding complementarity-determining regions (CDRs) show minimal conformational change upon binding, except for CDR-H3.

Keywords:
CDR flexibilityCDRsantibodiesantibody bindingantibody structurecomplementarity determining regions

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Area of Science:

  • Structural biology
  • Immunology
  • Computational chemistry

Background:

  • Antibodies are crucial therapeutics, with over 100 licensed drugs.
  • Modifying antibody affinity necessitates understanding antibody-antigen interactions.
  • The conformational changes of complementarity-determining regions (CDRs) upon antigen binding remain an open question.

Purpose of the Study:

  • To conduct a large-scale survey of CDR conformational changes during antibody-antigen binding.
  • To analyze the impact of antigen binding on antibody CDR structures.
  • To provide data for improving antibody modeling and drug design.

Main Methods:

  • Compiled a dataset (AbAgDb) of 177 antibodies with both bound and unbound structures from the Protein Data Bank.
  • Analyzed Cα backbone conformational changes in CDRs using RMSD analysis.
  • Compared bound CDR conformations with the conformational space of unbound CDRs.

Main Results:

  • Most CDRs, excluding CDR-H3, exhibit minimal conformational changes upon antigen binding.
  • 70.6% and 87% of CDR-H3s showed global Cα RMSD ≤ 1.0Å and ≤ 2.0Å, respectively.
  • The majority of bound CDR conformations were found within the conformational space of unbound CDRs.

Conclusions:

  • Antibody CDRs, particularly CDR-H3, undergo limited conformational adjustments when binding antigens.
  • Existing unbound CDR conformational data adequately represents bound states for most CDRs.
  • Findings will inform antibody modeling, docking strategies, and drug development.