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VH -VL interdomain dynamics observed by computer simulations and NMR.

Monica L Fernández-Quintero1, Valentin J Hoerschinger1, Leonida M Lamp1

  • 1Institute of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain, Austria.

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Summary

Antibody binding sites show flexibility due to variable domain orientation. This flexibility, confirmed by simulations and NMR, is crucial for antibody design and therapeutic applications.

Keywords:
NMRVH and VL domain orientationantibodiesmolecular dynamics simulations

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Area of Science:

  • Structural Biology
  • Immunology
  • Computational Biology

Background:

  • Antibody specificity is determined by the antigen-binding site (paratope), shaped by the relative orientation of variable heavy (VH) and variable light (VL) domains.
  • Understanding this orientation is critical for antibody design, particularly for therapeutic applications.

Purpose of the Study:

  • To characterize the VH-VL domain orientation and its dynamics in antibody fragments.
  • To investigate the implications of this domain flexibility on antibody binding and specificity.

Main Methods:

  • Utilized ABangle software to quantify VH-VL orientation using angles and distance.
  • Performed molecular dynamics simulations on antibody variable fragments (Fvs).
  • Validated simulation findings with Nuclear Magnetic Resonance (NMR) experiments on antibody fragments (scFv, Fab).

Main Results:

  • Molecular dynamics simulations revealed significant fluctuations in VH-VL domain orientation.
  • NMR experiments confirmed these dynamics, showing similar interdomain variations across different antibody fragments (Fab, scFv, Fv).
  • Analysis indicated timescales of 0.1-10 GHz for the fastest collective interdomain movements, highlighting considerable binding interface flexibility.

Conclusions:

  • The inherent flexibility of the VH-VL domain orientation is a key structural feature of antibodies, expanding the antibody repertoire and potential binding partners.
  • This flexibility, occurring on the nanosecond timescale, is essential for understanding antibody binding and specificity.
  • Consideration of this binding site flexibility is recommended for the design and optimization of therapeutic antibodies.