Decomposing Dynamical Couplings in Mutated scFv Antibody Fragments into Stabilizing and Destabilizing Effects.

Area of Science:

• Biophysics
• Structural Biology
• Immunology

Background:

• Single-chain variable fragment (scFv) antibodies are crucial in therapeutics.
• Understanding their conformational dynamics is key to antibody engineering.

Purpose of the Study:

• To characterize conformational fluctuations in scFv antibodies.
• To investigate the dynamic allostery and functional implications within antibodies.

Main Methods:

• Employed a novel perturbation-response decomposition of molecular dynamics (MD) trajectories.
• Analyzed stabilizing and destabilizing conditions on antibody structures.
• Utilized normal mode analysis to describe dynamic shifts.

Main Results:

• The linker between VH and VL domains showed dominant dynamical response, coupled to the entire protein.
• Perturbations in complementarity-determining regions (CDRs) induced significant dynamic responses.
• Stabilizing a CDR in one domain triggered destabilizing effects in the other, and vice versa.
• Specific residue destabilizations in VL domain could stabilize CDR loops in both VH and VL domains.

Conclusions:

• scFv antibody dynamics exhibit complex inter-domain communication.
• Findings suggest a propensity for dynamic allostery with potential applications in bispecific antibody design.