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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...

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Characterization of Glycoproteins with the Immunoglobulin Fold by X-Ray Crystallography and Biophysical Techniques

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Published on: July 5, 2018

Rapid structural characterization of human antibody-antigen complexes through experimentally validated computational

Luca Simonelli¹, Martina Beltramello, Zinaida Yudina

¹Institute for Research in Biomedicine, Via Vela 6, 6500 Bellinzona, Switzerland.

Journal of Molecular Biology

|January 8, 2010

Summary

Researchers developed a rapid method combining NMR and computational docking to determine antibody-antigen structures. This approach revealed a dengue virus epitope, explaining limited antibody neutralization effectiveness.

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Area of Science:

Structural biology
Immunology
Virology

Background:

Understanding antibody-antigen interactions is crucial for vaccine design and passive immunization strategies.
Current methods for determining three-dimensional structures of antibody-antigen complexes are often time-consuming.
Biocomputational docking offers speed but may lack accuracy.

Purpose of the Study:

To develop a faster method for determining antibody-antigen complex structures.
To validate computational docking using experimental data.
To investigate the structural basis of antibody recognition for dengue virus.

Main Methods:

Isolation and characterization of a monoclonal antibody from a dengue virus-recovered donor.
Epitope mapping using Nuclear Magnetic Resonance (NMR) chemical shift perturbation.
Three-dimensional structure determination of the antibody-antigen complex via computational docking, guided by NMR data.
Ensemble modeling to represent antibody loop flexibility.

Main Results:

A monoclonal antibody was identified and its epitope on dengue virus E protein domain III was mapped.
The three-dimensional structure of the antibody-dengue virus E protein complex was determined using NMR-guided computational docking.
The antibody binds to a partially accessible region on the viral surface.
The binding site accessibility explains the antibody's limited viral neutralization capacity.

Conclusions:

A hybrid approach of NMR and computational docking provides a rapid and validated method for determining antibody-antigen complex structures.
The identified epitope and binding mode offer insights into dengue virus immune evasion mechanisms.
This methodology can accelerate the development of targeted vaccines and antibody-based therapeutics.