SDN2 Antibody

Based on analysis of 8,000+ human SARS-CoV-2 antibodies from >200 donors and computational design challenges, here are key research-focused FAQs addressing critical experimental and analytical considerations:

How to design experiments for characterizing SARS-CoV-2 antibody specificity and affinity?

Methodological approach:

• Use multi-domain targeting analysis comparing RBD (receptor binding domain), NTD (N-terminal domain), and S2 responses through:

  • Surface plasmon resonance (SPR) for kinetic measurements

  • Cryo-EM mapping of epitope regions

  • IGHD gene usage profiling (e.g., IGHD1-26 enrichment in S2 antibodies)

What validation controls are essential for antibody functional studies?

Implement three-tier verification:

• Negative controls using VSV pseudotyped with irrelevant glycoproteins

• Cross-reactivity testing against seasonal coronaviruses (OC43, HKU1)

• SHM (somatic hypermutation) pattern analysis against baseline repertoires

What statistical methods best identify significant public antibody responses?

Apply convergent evolution detection algorithms:

• Calculate clonotype expansion p-values using Fisher's exact test with Benjamini-Hochberg correction

• Perform SHM hotspot analysis with MEME Suite for motif discovery

• Apply t-SNE clustering on V(D)J gene triplets (IGHV-IGHD-IGHJ)

How to optimize antibody humanization while maintaining neutralizing potency?

Stepwise engineering strategy:

• Start with germline-reverted variants (e.g., IGHV3-30→IGHV3-30*01)

• Introduce SHMs in hierarchical order:

  • First: Framework region stabilization mutations (ΔTm > 4°C)

  • Then: Affinity-enhancing mutations (KD improvement < 0.5 log)

• Validate with BLI (bio-layer interferometry) under physiological shear stress