Access of Antibody Molecules to the Conserved Coreceptor Binding Site on Glycoprotein gp120 Is Sterically Restricted on Primary Human Immunodeficiency Virus Type 1

Steric restrictions on CD4i antibody neutralization after CD4 attachment. (A) HIV-1 viral spike attached to cell surface CD4. The gp120 trimer (brown) (27) is shown with the threefold axis oriented perpendicular to the target cell surface. Cα worm representations of gp120 and four-domain CD4 are shown in brown and yellow, respectively. N-linked carbohydrate on gp120 is shown in blue. The flexibility between the second and third extracellular CD4 domains allows the observed angle between the membrane-distal (D1D2) and membrane-proximal (D3D4) domains to vary by up to 10° (distinct crystal structure conformations are shown in red and yellow) (58). The distance between the membrane-proximal portion of gp120 and the bottom of the crystallographically ordered CD4 is ∼45 Å. Nine amino acids (shown in gray) occur between the last ordered crystallographic residue (position 363) and the transmembrane domain (starting at position 373), potentially increasing the gp120-target cell membrane distance by 20 Å. There is considerable uncertainty in the degree of flexibility between the second and third extracellular domains of CD4. If the interdomain rotation is increased by 35° (gray), the gp120-target cell membrane distance would increase by an additional 20 Å, resulting in a total gp120-transmembrane distance of up to 85 Å. (B) Dimensions of Fv, Fab, and IgG portions of 17b interacting with gp120. Both gp120 (brown) and antibody fragments (purple) are shown in the Cα worm representation. The gp120 molecule is depicted in precisely the same orientation as the front left protomer in panel A, with the 17b portion oriented by superimposing the X-ray structure (pdb accession number 1G9 M [25]) of the gp120 ternary complex with D1D2 and 17b Fab complex. The length of the 17b Fv along the trimer threefold axis is ∼40 Å, and the length of the Fab is ∼60 Å, with the dimensions measured for the distance between the target membrane-proximal portions of gp120 and 17b. For IgGs, considerable flexibility is found in the hinge region connecting Fab and Fc portions of the IgG. Superimposing the crystal structure of a full-length human antibody (45) onto 17b gives dimensions of 115 Å (shown here) and 140 Å (not shown) for the two alternative Fab superpositions. The figures were generated with GRASP (34).