FIG 6.

Structural basis for interaction of cluster A MAbs with gp120 antigen. (A) Mapping of the N60-i3 and JR4 contact residues on the primary sequence of the gp120 inner domain of the 93TH057 isolate. The topology diagram depicting a distribution of secondary structure elements is shown above the gp120 sequences. Buried residues are highlighted in green and blue. Main chain (o), side chain (+), and both side and main chain (*) interactions are shown immediately above the residues as defined by a 5-Å distance criterion cutoff and colored based on contact type: hydrophobic, blue; hydrophilic, green; or both, black. Residues forming the N5-i5 and 2.2c epitopes as described in reference 53 are indicated by blue and gray lines below the gp120 sequence, respectively. (B) Epitope footprints of MAb N60-i3, JR4, N5-i5, and 2.2c. The Cα atoms of the gp120 residues involved in Fab binding are shown as spheres and displayed over the gp120 ribbon diagram. The selected residues of layer 2 and of the seven-stranded β-sandwich contribution to Fab binding and all the residues in the α1-helix involved in N60-i3, JR4, and N5-i5 binding are labeled. (C) Comparison of binding of MAb N60-i3, JR4, N5-i5, and 2.2c to CD4-triggered gp120 antigen. The N60-i3 Fab-gp120_93TH057 core_e-M48, JR4 Fab-gp120_93TH057 core_e-M48U1, and 2.2c Fab-gp120_YU2 core_e-M48U1 complexes were superimposed based on the gp120 outer domain onto the N5-i5 Fab-gp120_93TH057 core_e-d1d2CD4 complex and oriented relative to the target cell membrane. In the 180° view only the gp120_93TH057 core_e and d1d2CD4 from N5-i5 Fab-gp120_93TH057 core_e-d1d2CD4 complex (53) are shown, with variable heavy and light (V_H and V_L) domains of Fabs displayed as balls. Insets show rotation angles calculated using gp120's center of mass as an origin and the average α-carbon position for the heavy chain framework region 2 (residues 36 to 49) as a reference point for each antibody (top) and a 90°rotation of the 180°view (bottom).