Because CD4 is the primary receptor for HIV-1, unlike the secondary sites for coreceptor or Fuzeon binding, the initial site of contact on gp120 for CD4 must always be exposed and available to form the initial encounter complex. However, the overall size of the initial site of contact is small and confined mainly to the outer domain of gp120 (ref. 33
). Although this surface is partially recessed on the Env viral spike, antibody b12 nonetheless manages to target this primary contact site and effectively neutralize HIV-1.
Structural analysis has shown that to effect recognition, b12 uses yet another trick, that of heavy chain–only recognition33
(). Most epitopes are bound at the juncture between heavy and light chains of the antibody, which has the advantage of potentially using all six CDRs of the antibody, as well as the natural binding cleft between heavy- and light-chain surfaces. However, if the target epitope is small and fairly recessed, this type of double-headed Fab recognition may encounter steric barriers. Such ideas have been put forward before (for example, the famous ‘canyon hypothesis’34
), but the beauty of the immune system is its ability to find solutions to even the most daunting problem. One potential way to reach into a ‘canyon’ involves the use of extended CDR H3 regions, as has been directly observed in the structure of a rhinovirus-antibody complex35
. Indeed, human antibodies that recognize viral pathogens have CDR H3 regions that are longer than average36
, and b12, for example, has a rigid CDR H3 that protrudes 15 Å above the rest of the antibody paratope37
. However, the criteria for accessing the b12 epitope seem to be strict enough to require a second means of accessing a canyon, that of heavy chain–only recognition.
Crystallographic analysis of the interaction between antibodies and viral envelopes has shown that although heavy-chain recognition often predominates, some level of light-chain recognition is always observed. Heavy chain–only recognition indicates antibody variability is confined to only three CDRs, two of which are germline encoded and together have only about 50 variants in humans. Heavy chain–only recognition thus greatly limits combinatorial diversity but perhaps generates a smaller footprint on the antigen to prevent immune escape. Such variation, however, can be generated by other means—for example, through somatic mutations. Indeed, analysis of the b12 sequence shows more somatic mutations than are obtained with CD4-induced antibodies (45, but for b12, versus 19 ± 5, for the various CD4-induced antibodies)23
, and all of the main residues involved in the b12-gp120 interaction seem to be somatically mutated from the germline sequence33
. Although CDR recognition using a maximum of two to three loops is possible, as has been shown with shark and camelid antibodies, respectively, which naturally have unpaired immunoglobulin heavy chains, such antibodies have additional means of generating diversity38,39
. It will be useful to determine if such exclusive heavy-chain recognition also requires concomitant selection of extended CDR H3 regions in such antibodies. Another case involving influenza virus is discussed below.