Figure 1.
Structure of the llama heavy chain antibody fragment VHH D7.
(A) Ribbon representation of D7; the complementarity determining regions (CDR) are highlighted in yellow (CDR1), orange (CDR2) and salmon (CDR3). The first and last residue of each CDR is shown together with the side chain of Trp96 critical for gp120 interaction and neutralization. The dotted line indicates CDR3 residues lacking continuous main chain density for residues Arg100 to Ser100B. (B) A close-up of the CDR interaction network reveals multiple polar interactions between CDR1 and CDR3 as well as CDR2 and CDR3.
Figure 2.
Structure based sequence alignment of D7 with VHH A12 and C8 as well as with the VH domains from the neutralizing antibodies b12, b13, F105 and m18.
The residue numbering is according to Chothia [38] and the CDRs are indicated by coloured bars.
Table 1.
X-ray data collection and refinement statistics.
Figure 3.
Comparison of CDR2 and CDR3 from D7, b12, b13, F105 and m18 indicates different modes of gp120 interaction.
The Cα atoms of the heavy chain variable domains (b12 pdb code 2NY7; F105 pdb code 3HI1; b13 pdb code 3IDX; m18 pdb code 2AJ3) were superimposed and the CDR H2 and H3 are represented in the same orientation. Amino acids are labelled using the one letter code for clarity. (A) All CDR3 loops expose aromatic residues at their apex. (B) The CDR2 of D7 varies from CDR H2 of b12 indicating a different mode of gp120 interaction. Residues implicated in gp120 interaction are highlighted in orange.
Table 2.
Solvent accessible areas of CDR3 D7 residues.
Table 3.
Binding affinities of D7 wild type and D7 mutants to gp120 (IIIB).
Figure 4.
Surface representation of the CDRs.
(A) Surface representation of D7 revealing the gp120 docking interface based on gp120 binding and HIV-1 neutralization results. The CDRs are coloured as in figure 1. CDR3 residues affecting gp120 interaction and HIV-1 IIIB neutralization are indicated in white and residue differences between D7 and A12 are labelled in black. (B) Electrostatic potential map of the surface generated by the CDRs.
Table 4.
IC50 values of VHH D7 against HIV-1 IIIB in TZM-bl cells.