Figure 3. The negatively charged amino acids contributed by the V_H replacement “footprints” in CD4i antibodies are located at the interaction interface for binding gp120.

A. Amino acid sequence analysis of the CDR3 region of CD4i antibodies encoded by V_H replacement products. The amino acids contributed by the V_H replacement “footprints” are underlined. Negatively charged residues are highlighted in red. B. Frequencies of none charged, positively charged, and negatively charged amino acids encoded by the identified V_H replacement products from control IgH gene sequences or IgH genes encoding CD4i antibodies. The differences of negatively charged residues in these two groups of V_H replacement footprints encoded amino acids were determined by two tailed Chi-square test with Yates' correction (p = 0.0011). C. Structural analysis of the IgH CDR3 of CD4i antibodies. The complex structure (PDB ID: 2B4C) shows the relative positions of each peptide chain, gp120 (orange), CD4 (yellow), X5 heavy chain (blue), and X5 light chain (gray). Solved or predicted structures of the IgH CDR3 regions in CD4i antibodies X5, 17b, 47e, and E51 are shown. The yellow arrows represent β-strand conformation, which are located at the ends of the CDR3 regions. Amino acids encoded by the V_H replacement “footprints” (highlighted in red) within X5, 17b, 47e, and E51 antibodies are located at or near the tips of the CDR3 loops, which are the predicted interaction interface for binding gp120.