Structure of a High-affinity “Mimotope” Peptide Bound to HIV-1-neutralizing Antibody b12 Explains its Inability to Elicit gp120 Cross-reactive Antibodies

Department of Immunology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.
Journal of Molecular Biology (Impact Factor: 4.33). 07/2007; 369(3):696-709. DOI: 10.1016/j.jmb.2007.01.060
Source: PubMed


The human antibody b12 recognizes a discontinuous epitope on gp120 and is one of the rare monoclonal antibodies that neutralize a broad range of primary human immunodeficiency virus type 1 (HIV-1) isolates. We previously reported the isolation of B2.1, a dimeric peptide that binds with high specificity to b12 and competes with gp120 for b12 antibody binding. Here, we show that the affinity of B2.1 was improved 60-fold over its synthetic-peptide counterpart by fusing it to the N terminus of a soluble protein. This affinity, which is within an order of magnitude of that of gp120, probably more closely reflects the affinity of the phage-borne peptide. The crystal structure of a complex between Fab of b12 and B2.1 was determined at 1.8 A resolution. The structural data allowed the differentiation of residues that form critical contacts with b12 from those required for maintenance of the antigenic structure of the peptide, and revealed that three contiguous residues mediate B2.1's critical contacts with b12. This single region of critical contact between the B2.1 peptide and the b12 paratope is unlikely to mimic the discontinuous key binding residues involved in the full b12 epitope for gp120, as previously identified by alanine scanning substitutions on the gp120 surface. These structural observations are supported by experiments that demonstrate that B2.1 is an ineffective immunogenic mimic of the b12 epitope on gp120. Indeed, an extensive series of immunizations with B2.1 in various forms failed to produce gp120 cross-reactive sera. The functional and structural data presented here, however, suggest that the mechanism by which b12 recognizes the two antigens is very different. Here, we present the first crystal structure of peptide bound to an antibody that was originally raised against a discontinuous protein epitope. Our results highlight the challenge of producing immunogens that mimic discontinuous protein epitopes, and the necessity of combining complementary experimental approaches in analyzing the antigenic and immunogenic properties of putative molecular mimics.

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    • "When the divergence from the peptides used for priming group 3 was compared among groups (Figure 6B) we found that it was higher in groups 1 and 3 compared to control although this difference did not reach statistical significance. The divergence from the CD4 binding site mimotope was not calculated because this peptide was shown not to be immunogenic [46]. On the other hand, we observed that the divergence from the consensus sequence of the inoculum was greater in controls than in vaccinees (t-test p<0.01) (Figure 6B, right panel). "
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