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Antibody Structure

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

Antibody Structure

Antibody Structure and Classes

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.

Molecular Models

Molecular Models

Physical models representing molecular architectures of chemical compounds play essential roles in understanding chemistry. The use of molecular models makes it easier to visualize the structures and shapes of atoms and molecules.

Protein Organization

Protein Organization

Proteins are polymers of amino acid residues. They are versatile and responsible for different cellular functions, including DNA replication, molecular transport, catalysis, and structural support. Proteins have a hierarchical structure comprising at least three levels of organization: primary, secondary, and tertiary structure. Some large proteins have a quaternary structure where individual protein subunits are linked together.
The primary structure of a protein is its amino acid sequence....

Antibody Actions

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...

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Antibody modeling assessment II. Structures and models.

Alexey Teplyakov¹, Jinquan Luo, Galina Obmolova

¹Janssen Research & Development, LLC, 1400 McKean Road, Spring House, Pennsylvania, 19477.

|March 18, 2014

Summary

This summary is machine-generated.

Antibody structure modeling shows promise, but challenges remain in predicting variable domains (Fv) and CDR-H3 regions. Errors in template selection and existing databases hinder accurate antibody modeling.

Keywords:

CDR VL/VH packing canonical structure crystal structure structure prediction

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Area of Science:

Structural biology
Immunoinformatics
Computational chemistry

Background:

Accurate antibody structure modeling is crucial for therapeutic development.
Existing methods face challenges in predicting the complex structures of antibody variable regions.

Purpose of the Study:

To evaluate the current state-of-the-art in antibody structure prediction methodologies.
To identify key sources of error in modeling antibody variable domains (Fv) and complementarity-determining regions (CDRs).

Main Methods:

A blinded study comparing seven Fv modeling methods against eleven unpublished Fab crystal structures.
Two rounds of modeling: initial Fv models and subsequent CDR-H3 modeling in a corrected environment.

Main Results:

Template selection (CDR canonical structures and VL/VH packing) was a significant source of prediction errors.
Errors from existing Protein Data Bank structures were propagated into new models.
Modeling non-canonical structures, particularly CDR-H3, proved to be the most difficult task.

Conclusions:

Current antibody structure prediction methods require refinement, especially for CDR-H3.
The quality of template structures and curated databases is critical for improving prediction accuracy.
Further development is needed to address non-canonical antibody structures.