Probing antibody internal dynamics with fluorescence anisotropy and molecular dynamics simulations

Area of Science:

• Biophysics
• Structural Biology
• Immunology

Background:

• Antibody function is intrinsically linked to their dynamic behavior in solution.
• Understanding these internal dynamics is key to elucidating antibody mechanisms.

Purpose of the Study:

• To investigate the complex internal solution dynamics of antibody molecules.
• To correlate molecular dynamics simulations with experimental data for a comprehensive analysis.

Main Methods:

• Utilized time-resolved fluorescence anisotropy experiments on IgG1 antibodies.
• Performed extensive all-atom molecular dynamics (MD) simulations in explicit water (over 2 microseconds).
• Analyzed correlated motions using mutual information entropy and Markov-state models.

Main Results:

• Identified extensive correlated motions within antibody molecules.
• Revealed high flexibility with constant formation and breakage of polar and non-polar contacts between F(ab) and F(c) domains.
• Observed dynamic salt bridge rearrangements, with partners changing over time.
• MD simulations provided accurate timescales but showed motions approximately 3-fold faster than experimental observations.

Conclusions:

• Antibodies do not possess a single stable state of atomic contacts.
• Antibody flexibility allows for diverse atomic interactions during different dynamic motions.
• The study provides a coarse-grained description of antibody motions, highlighting their dynamic nature.