Structural Basis of Antibody Conformation and Stability Modulation by Framework Somatic Hypermutation

Area of Science:

• Structural bioinformatics
• Immunology
• Computational biology

Background:

• Somatic hypermutation (SHM) is crucial for increasing antibody binding affinity to antigens in vivo.
• The structural underpinnings of how many SHMs influence antibody function remain poorly understood.

Purpose of the Study:

• To develop a high-throughput pipeline integrating molecular dynamics (MD) simulations and data mining to analyze SHM effects.
• To investigate the impact of individual and combined SHMs on antibody conformation, flexibility, stability, and affinity.

Main Methods:

• Utilized atomistic molecular dynamics (MD) simulations and data mining.
• Developed a high-throughput structural bioinformatics pipeline.
• Analyzed effects of SHMs at specific framework positions (39_H, 91_H, 38_L, 87_L) and light chain framework 4 (FWR4_L) insertions.

Main Results:

• Identified a common mechanism where SHMs disrupt a conserved hydrogen-bond network, modulating heavy-light chain pairing orientation.
• Observed that Q39L_H, alone or with FWR4_L insertions, altered the inter-domain elbow angle, enhancing binding affinity in anti-HIV-1 antibodies.
• Demonstrated that Q39L_H mitigated aggregation induced by FWR4_L insertion, indicating remote epistasis.

Conclusions:

• The developed pipeline provides tools for understanding antibody affinity maturation.
• Insights gained can guide the engineering of functionally improved antibodies with enhanced binding and stability.