Conformational dynamics of individual antibodies using computational docking and AFM

Area of Science:

• Biophysics
• Structural Biology
• Immunology

Background:

• Molecular recognition relies on macromolecular flexibility.
• Monoclonal antibodies (mAbs) are crucial receptors in biological systems.
• Understanding mAb conformational dynamics is essential for drug development.

Purpose of the Study:

• To analyze the conformational variability of individual monoclonal antibodies.
• To develop a method for reconstructing mAb structures from AFM data.
• To investigate the flexibility of antibody subunits.

Main Methods:

• Individual mAbs were imaged using high-resolution atomic force microscopy (AFM).
• Antibodies were chemically immobilized on mica surfaces.
• A surface-constrained computational docking approach was used to assemble mAb subunits.
• Reconstructed structures were compared to X-ray crystallography data.

Main Results:

• Topographical AFM data enabled the reconstruction of antibody structures.
• The separation and relative orientation of antibody subunits were measured.
• Several reconstructed subunit arrangements were comparable to known antibody structures.
• No reconstructed structure perfectly matched X-ray structures due to inherent flexibility.

Conclusions:

• High-resolution AFM imaging is suitable for studying conformational dynamics of individual macromolecules.
• Computational reconstruction tools can effectively analyze AFM data of large molecules.
• Antibody flexibility significantly impacts their conformational states.