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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.

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Antibodies as a model system for comparative model refinement.

Benjamin D Sellers1, Jerome P Nilmeier, Matthew P Jacobson

  • 1Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158-2517, USA.

Proteins
|July 6, 2010
PubMed
Summary
This summary is machine-generated.

This study enhances protein loop prediction for homology modeling, improving accuracy for antibody complementarity determining regions (CDRs) and other proteins. The refined method better predicts near-native conformations, even with surrounding model errors.

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Area of Science:

  • Structural biology
  • Computational biology
  • Protein modeling

Background:

  • Predicting protein loop conformations is crucial for homology modeling.
  • Existing algorithms face challenges, especially with errors in surrounding protein structures.
  • Antibodies serve as a model system to address these prediction difficulties.

Purpose of the Study:

  • To investigate strategies for robustly predicting loop conformations in homology models with existing errors.
  • To improve the accuracy of complementarity determining region (CDR) loop predictions in antibodies.
  • To develop a more effective loop prediction method applicable to various proteins.

Main Methods:

  • Utilized antibodies as a model system, predicting CDR loops using knowledge-based and ab initio methods.
  • Compared a previously published loop prediction method with a modified approach.
  • Tested the modified method on shorter (5-7 residues) and longer (8-9 residues) H3 loops, and subsequently on loops in complete models of non-antibody proteins.

Main Results:

  • The original method predicted H3 loops with an average backbone RMSD of 2.7 Å (shorter) and 5.1 Å (longer).
  • The modified method significantly improved accuracy to 1.3 Å RMSD (shorter) and 3.1 Å RMSD (longer) by reducing sensitivity to surrounding structures.
  • The enhanced method showed promising results for predicting loops in complete models of non-antibody proteins.

Conclusions:

  • The modified loop prediction method enhances the ability to sample near-native conformations, even with errors in the surrounding protein model.
  • This approach offers a potentially valuable tool for improving antibody structure prediction and general homology modeling.
  • Further development is needed, but the method represents a promising step toward more accurate loop prediction in complex protein models.