Understanding the structural role of the distinctive CDR-H2 amino acid substitutions in HV1-69-sBnAbs.

<p>A) VDW contact analysis (black lines) shows that Ser52 of F10 and CR9114 (orange), and Ile52 of CR6261(gray) make only intramolecular contacts; i.e., do not form contacts with their respective H5VN04s. Antibodies are shown in color; HA is in light gray. At far right, steric consequences of the germline Ile52 and the Ile52Ser substitutions are shown when the Abs are overlaid on their framework residues (RMSD ∼0.5 Å). Comparing structures of the HV1-69-sBnAbs, centered on Ile52 of CR6261 (green), with F10 (yellow) and CR9114 (cyan), the Ile52Ser mutation in F10 and CR9114 enables the 2 strands to come closer together, as indicated by the yellow and cyan arrows. Distances in red indicate hypothetical steric clashes (<3 Å) that would be created if Ile52 were present in CR9114 and F10. B) Comparison between the unbound (PDB 4FQH, left) and H5VN04-bound structures (PDB 4FQI, right) of CR9114, colored according to the magnitude of structural change after superposition on the main-chain of the VH domain (from blue = 0 Å, through white = 1 Å, to red = 1.8 Å). CDRs and side-chains of the major contact residues are shown, as depicted in <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1004103#ppat-1004103-g001" target="_blank">Figure 1A</a>. Distances between the Cα and Cβ atoms of Phe54 and the Cα atom of CDR-H3 Tyr98 (shown as dashed lines) are indicated. Large rotations of the side chains of CDR-H3 Tyr98, CDR-H2 Phe54 and CDR-H2 Ile53 are also evident, as previously noted <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1004103#ppat.1004103-Dreyfus1" target="_blank">[7]</a>.