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. 2009 Nov 11;17(11):1538-46.
doi: 10.1016/j.str.2009.09.012.

Structural basis of the cross-reactivity of genetically related human anti-HIV-1 mAbs: implications for design of V3-based immunogens

Valicia Burke  1 , Constance Williams, Madhav Sukumaran, Seung-Sup Kim, Huiguang Li, Xiao-Hong Wang, Miroslaw K Gorny, Susan Zolla-Pazner, Xiang-Peng Kong
Affiliations

Structural basis of the cross-reactivity of genetically related human anti-HIV-1 mAbs: implications for design of V3-based immunogens

Valicia Burke et al. Structure. .

Abstract

Human monoclonal antibodies 447-52D and 537-10D, both coded by the VH3 gene and specific for the third variable region (V3) of the HIV-1 gp120, were found to share antigen-binding structural elements including an elongated CDR H3 forming main-chain interactions with the N terminus of the V3 crown. However, water-mediated hydrogen bonds and a unique cation-pi sandwich stacking allow 447-52D to be broadly reactive with V3 containing both the GPGR and GPGQ crown motifs, while the deeper binding pocket and a buried Glu in the binding site of 537-10D limit its reactivity to only V3 containing the GPGR motif. Our results suggest that the design of immunogens for anti-V3 antibodies should avoid the Arg at the V3 crown, as GPGR-containing epitopes appear to select for B cells making antibodies of narrower specificity than V3 that carry Gln at this position.

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Figures

Figure 1
Figure 1. 447-52D and 537-10D: sequences of the variable fragments and cross-reactivity with V3 peptides
(A) Protein sequence alignments of the variable regions for both heavy and light chains of 447-52D and 537-10D. Boxes indicate the CDR regions (Kabat definition), while asterisks and arrowheads mark the residues making direct or water-mediated interactions in the reported structures with the V3 epitopes, respectively. TrpH47 (arrow) of 537-10D has direct contacts with the epitope, although it is not in any of the CDR loops (see Figures 2B and 4B). Note multiple Tyr residues in CDR H3 of both mAbs. (B) The ELISA reactivities of 447-52D and 537-10D against a panel of V3 peptides (sorted according to their ELISA measurements). Only sequences corresponding to the regions of V3 in the structures that have direct contacts with the antibodies are shown (9 amino acids for 447-52D and 11 for 537-10D), and they are numbered at the bottom in the HXB2 numbering scheme. The colors depict the sequence similarities. Note that 447-52D reacts with both V3GPGR and V3GPGQ peptides, while 537-10D only reacts with V3GPGR.
Figure 2
Figure 2. Structures of Fab 447-52D/V3W2R and Fab 537-10D/V3MN complexes
(A) Stereoview of the 447-52D/V3W2R complex. (B) Stereoview of the 537-10D/V3MN complex. The Fab light chain, heavy chain and the V3 peptide are colored cyan, green and magenta, respectively. Side chains of the residues of the antibodies that have direct contacts with the V3 epitopes are shown. (C) The mAbs 447-52D and (D) 537-10D are shown as surface representations to illustrate the ladle shape of the binding sites. Note that the bowl part of the 447-52D binding site, with an additional spout (arrow), is much shallower than that of 537-10D.
Figure 3
Figure 3. Main-chain interactions
(A) and (B) Main-chain interactions between V3 peptide and CDR H3 in the 447-52D/V3W2R (A), and 537-10D/V3MN (B) complexes. The CDR H3 (green) and V3 (magenta) interactions of the 447-52D and 537-10D Fab/V3 structures are shown as ribbons (top panels) as well as with detailed hydrogen bonds (lower panels).
Figure 4
Figure 4. Structural details of the epitope-binding around the apex of the V3 crown in Fab 447-52D/V3W2R and Fab 537-10D/V3MN complexes
(A) Stereoview of the 447-52D/V3W2R complex. (B) Stereoview of the 537-10D/V3MN complex. Note the two water molecules (water 1 and 2) at the antigen binding site of 447-52D. Also note that TrpH47, a non-CDR residue, has direct contact with the epitope in 537-10D.
Figure 5
Figure 5. Water mediated interactions at the antigen-binding site
(A) Electron densities (the 2Fo-Fc map contoured at 1.2 σ level) around a well-coordinated water (water 1) molecule at the base of the antigen binding site in the 447-52D/V3W2R complex. (B) Water-mediated hydrogenbinding networks in the 447-52D/V3W2R complex. Note that water 1 is coordinated tetrahedrally by the side chains of four surrounding residues. This water molecule is also present in the 447-52D/V3GPGR complexes (see Figure S3). Note also that GlnP315 does not interact directly with AspH95 but mediated by another water molecule (water 2).
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References

    1. Abagyan RA, Totrov M, Kuznetsov D. ICM - A new method for protein modeling and design: Applications to docking and structure prediction from the distorted native conformation. Journal of Computational Chemistry. 1994;15:488–506.
    1. Bell CH, Pantophlet R, Schiefner A, Cavacini LA, Stanfield RL, Burton DR, Wilson IA. Structure of antibody F425-B4e8 in complex with a V3 peptide reveals a new binding mode for HIV-1 neutralization. J Mol Biol. 2008;375:969–978. - PMC - PubMed
    1. Binley JM, Lybarger EA, Crooks ET, Seaman MS, Gray E, Davis KL, Decker JM, Wycuff D, Harris L, Hawkins N, et al. Profiling the specificity of neutralizing antibodies in a large panel of plasmas from patients chronically infected with human immunodeficiency virus type 1 subtypes B and C. J Virol. 2008;82:11651–11668. - PMC - PubMed
    1. Binley JM, Wrin T, Korber B, Zwick MB, Wang M, Chappey C, Stiegler G, Kunert R, Zolla-Pazner S, Katinger H, et al. Comprehensive Cross-Clade Neutralization Analysis of a Panel of Anti-Human Immunodeficiency Virus Type 1 Monoclonal Antibodies. J. Virol. 2004;78:13232–13252. - PMC - PubMed
    1. Brunger AT, Adams PD, Clore GM, DeLano WL, Gros P, Grosse-Kunstleve RW, Jiang JS, Kuszewski J, Nilges M, Pannu NS, et al. Crystallography & NMR system: A new software suite for macromolecular structure determination. Acta Crystallogr D Biol Crystallogr. 1998;54:905–921. - PubMed

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