Germline V-genes sculpt the binding site of a family of antibodies neutralizing human cytomegalovirus

Abstract

Immunoglobulin genes are generated somatically through specialized mechanisms resulting in a vast repertoire of antigen-binding sites. Despite the stochastic nature of these processes, the V-genes that encode most of the antigen-combining site are under positive evolutionary selection, raising the possibility that V-genes have been selected to encode key structural features of binding sites of protective antibodies against certain pathogens. Human, neutralizing antibodies to human cytomegalovirus that bind the AD-2S1 epitope on its gB envelope protein repeatedly use a pair of well-conserved, germline V-genes IGHV3-30 and IGKV3-11. Here, we present crystallographic, kinetic and thermodynamic analyses of the binding site of such an antibody and that of its primary immunoglobulin ancestor. These show that these germline V-genes encode key side chain contacts with the viral antigen and thereby dictate key structural features of the hypermutated, high-affinity neutralizing antibody. Vgenes may thus encode an innate, protective immunological memory that targets vulnerable, invariant sites on multiple pathogens.

Multiplexed screening of natural humoral immunity identifies antibodies at fine specificity for complex and dynamic viral targets

“…This restriction of both V H and V L germline usage toward AD-2 was also observed in three published studies from different countries 8 and in three different blood donors we identified as well. We concentrated our cloning efforts on one donor found to have a rich natural memory B cell reservoir of in vivo affinity matured anti-AD2 antibodies.…”

“…Co-crystal structures of antigen and antibody have demonstrated a structural basis for this trend. 3,8 This knowledge, however, does not make it any less formidable to clone the optimal mAb from an individual's polyclonal response, particularly in the context of active viral selection toward immune evasion. It is also likely that the history of exposure to disease, vaccines and allergens will provide certain individuals with better antibody reservoirs than others.…”

“…[2][3][4][5][6][7] A fascinating trend is the discovery of specific Ig germline usage among unrelated and geographically disperse individuals against specific viral antigens. 3,8 A parental germline sequence has not generally been anti-viral, but rather provides the best possible scaffold for the development of an affinity-matured, efficacious monoclonal antibody (mAb). Co-crystal structures of antigen and antibody have demonstrated a structural basis for this trend.…”

Characterization of pathogenic human monoclonal autoantibodies against GM-CSF

“…If another unrelated antigen initiates the antibody response and somatic mutations change the antigen-binding site so it binds to an epitope on GM-CSF, it is unlikely that chance somatic mutations would change the antigen-binding sites to bind four nonoverlapping, conformational epitopes on GM-CSF. Two crystallographic studies of affinity maturation of human antibodies (29,30) establish that the increase in affinity is due to stabilization of the original antigen contacts and that the antigen-binding site of the original antibody has the same general conformation as the affinity-matured, high-affinity antibodies. If subsequent affinity maturation is driven by GM-CSF, the epitope on the mutated antibody should still overlap the original epitope on GM-CSF.…”

Structures of Preferred Human IgV Genes–Based Protective Antibodies Identify How Conserved Residues Contact Diverse Antigens and Assign Source of Specificity to CDR3 Loop Variation

“…Using methodology described by Smith et al (17), this authentic human Ab with naturally paired H and L chains was isolated after vaccination with Pneumovax 23 from a donor different from the one providing 023.102. Finally, as a second representative of an anti-HCMV Ab, we show the crystal structure of the AD-2S1 Ag complex of the KE5 Fab, an Ab that also utilizes IGKV3-11 and IGHV3-30 genes but IGHD and IGKJ genes different from those used by a previously crystallized anti-HCMV Fab, 8F9 (24). In the present study, we provide structural evidence that the same germline IgV genes (IGHV3-30 and IGKV3-11) can assume different roles in protective Abs against two very different Ags on two very different pathogens because of their distinct configurations when recombined with diverse CDR3 loops.…”