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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
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Antibody Actions01:26

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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
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Antibody Structure and Classes01:25

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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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Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins
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Modeling Antibody-Antigen Complexes by Information-Driven Docking.

Francesco Ambrosetti1, Brian Jiménez-García2, Jorge Roel-Touris2

  • 1Department of Physics, Sapienza University, Piazzale Aldo Moro 5, 00184 Rome, Italy; Faculty of Science - Chemistry, Computational Structural Biology Group, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.

Structure (London, England : 1993)
|November 16, 2019
PubMed
Summary

Computational docking of antibody-antigen complexes is crucial for drug design. HADDOCK software best models these interactions, outperforming others by using epitope information for improved accuracy.

Keywords:
ClusProH3 modelingHADDOCKLightDockZDOCKantibodybinding sitesconformational changesdocking

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Area of Science:

  • Immunology
  • Structural Biology
  • Computational Chemistry

Background:

  • Antibodies are key proteins in the immune response, crucial for targeted therapies due to their specific antigen recognition.
  • Understanding antibody-antigen interactions is vital for developing effective biological drugs.
  • Computational methods, like molecular docking, offer a rapid alternative to experimental techniques for structural analysis of these complexes.

Purpose of the Study:

  • To evaluate how complementarity-determining region and epitope information can guide antibody-antigen complex modeling.
  • To compare the performance of four antibody-antigen docking software suites: ClusPro, LightDock, ZDOCK, and HADDOCK.
  • To assess the utility of these tools for designing therapeutic antibodies.

Main Methods:

  • A dataset of 16 antibody-antigen complexes was used for evaluation.
  • Four docking software suites (ClusPro, LightDock, ZDOCK, HADDOCK) with antibody-specific options were compared.
  • The study investigated the impact of incorporating epitope information into the docking process.

Main Results:

  • HADDOCK demonstrated superior performance compared to other tested software.
  • HADDOCK achieved higher success rates and generated higher-quality models.
  • The benefits of HADDOCK were observed both with and without prior knowledge of the antigen's epitope.

Conclusions:

  • HADDOCK is the most effective computational tool for modeling antibody-antigen complexes.
  • Utilizing epitope information significantly enhances the accuracy of molecular docking for antibody-antigen interactions.
  • These findings will aid in the rational design of antibody-based therapeutics.