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Complex-type N-glycan recognition by potent broadly neutralizing HIV antibodies

Mouquet, Hugo and Scharf, Louise and Euler, Zelda and Liu, Yan and Eden, Caroline and Scheid, Johannes F. and Halper-Stromberg, Ariel and Gnanapragasam, Priyanthi N. P. and Spencer, Daniel I. R. and Seaman, Michael S. and Schuitemaker, Hanneke and Feizi, Ten and Nussenzweig, Michel C. and Bjorkman, Pamela J. (2012) Complex-type N-glycan recognition by potent broadly neutralizing HIV antibodies. Proceedings of the National Academy of Sciences of the United States of America, 109 (47). E3268-E3277. ISSN 0027-8424. PMCID PMC3511153. doi:10.1073/pnas.1217207109.

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Broadly neutralizing HIV antibodies (bNAbs) can recognize carbohydrate-dependent epitopes on gp120. In contrast to previously characterized glycan-dependent bNAbs that recognize high-mannose N-glycans, PGT121 binds complex-type N-glycans in glycan microarrays. We isolated the B-cell clone encoding PGT121, which segregates into PGT121-like and 10-1074–like groups distinguished by sequence, binding affinity, carbohydrate recognition, and neutralizing activity. Group 10-1074 exhibits remarkable potency and breadth but no detectable binding to protein-free glycans. Crystal structures of unliganded PGT121, 10-1074, and their likely germ-line precursor reveal that differential carbohydrate recognition maps to a cleft between complementarity determining region (CDR)H2 and CDRH3. This cleft was occupied by a complex-type N-glycan in a “liganded” PGT121 structure. Swapping glycan contact residues between PGT121 and 10-1074 confirmed their importance for neutralization. Although PGT121 binds complex-type N-glycans, PGT121 recognized high-mannose-only HIV envelopes in isolation and on virions. As HIV envelopes exhibit varying proportions of high-mannose- and complex-type N-glycans, these results suggest promiscuous carbohydrate interactions, an advantageous adaptation ensuring neutralization of all viruses within a given strain.

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URLURL TypeDescription DOIArticle CentralArticle
Liu, Yan0000-0002-5837-4908
Nussenzweig, Michel C.0000-0003-0592-8564
Bjorkman, Pamela J.0000-0002-2277-3990
Additional Information:© 2012 National Academy of Sciences. Freely available online through the PNAS open access option. Contributed by Pamela J. Bjorkman, October 4, 2012 (sent for review September 15, 2012). Published online before print October 30, 2012. Author contributions: H.M and M.C.N conceived the project; H.M., L.S., Z.E., Y.L., H.S., T.F., M.C.N., and P.J.B. designed research; H.M., L.S., Z.E., Y.L., H.S., T.F., M.C.N., and P.J.B. performed research; H.M. produced the antibodies and the HIV Env proteins; H.M. performed and analyzed antibody-binding experiments; L.S. determined and interpreted crystal structures; C.E., J.F.S., and A.H.-S. contributed new reagents/analytic tools; Z.E. and H.S. performed and analyzed PBMC-based neutralization assays; Y.L. performed carbohydrate microarray analyses; P.N.P.G. performed and analyzed neutralization assays using viral strains produced in GnTI −/− cells; D.I.R.S. isolated and characterized the NA2 glycan; M.S.S. performed and analyzed TZM-bl neutralization assays; and H.M., L.S., Y.L., T.F., M.C.N., and P.J.B. wrote the paper. Conflict of interest statement: M.C.N., H.M., P.J.B. and L.S. have a pending patent application for the new PGT121 antibody variants described in the present study with the United States Patent and Trademark Office. Data deposition: The atomic coordinates and structure factors have been deposited in the Protein Data Bank, [PDB ID codes 4FQ1 (unliganded PGT121 Fab), 4FQC (“liganded” PGT121 Fab), 4FQ2 (10-1074 Fab), and 4FQQ (GL Fab)]. We thank Tim Feliciano and the Caltech Protein Expression Center for expression of proteins, Terri Lee for producing pseudoviruses in HEK 293S GnTI −/− cells, Anthony West for germ-line gene analyses, and the T.F. laboratory for establishing the neoglycolipid-based microarray system. This research was supported by The Rockefeller University, National Institutes of Health Grant 1 P01 AI081677 (to M.C.N.), the International AIDS Vaccine Initiative and the Bill and Melinda Gates Foundation [Comprehensive Antibody-Vaccine Immune Monitoring Consortium Grant 1032144 (to M.S.S.); Collaboration for AIDS Vaccine Discovery Grants 38660 (to P.J.B.) and 38619s (to M.C.N.)], UK Research Councils’ Basic Technology Initiative “Glycoarrays” Grant GRS/79268, Engineering and Physical Sciences Research Council Translational Grant EP/G037604/1, Wellcome Trust Grant WT093378MA, National Cancer Institute Alliance of Glycobiologists for Detection of Cancer and Cancer Risk Grant U01 CA128416, and the Molecular Observatory at Caltech supported by the Gordon and Betty Moore Foundation. Operations at the Stanford Synchrotron Radiation Lightsource are supported by the US Department of Energy and the National Institutes of Health. M.C.N. and P.J.B. are Howard Hughes Medical Institute investigators.
Funding AgencyGrant Number
Rockefeller UniversityUNSPECIFIED
NIH1 P01 AI081677
International AIDS Vaccine InitiativeUNSPECIFIED
Bill and Melinda Gates Foundation Comprehensive Antibody-Vaccine Immune Monitoring Consortium Grant1032144
Collaboration for AIDS Vaccine Discovery Grants38660
Collaboration for AIDS Vaccine Discovery Grants38619s
UK Research Council Basic Technology InitiativeGRS/79268
Engineering and Physical Sciences Research Council (EPSRC)EP/G037604/1
Wellcome TrustWT093378MA
National Cancer InstituteU01 CA128416
Gordon and Betty Moore FoundationUNSPECIFIED
Issue or Number:47
PubMed Central ID:PMC3511153
Record Number:CaltechAUTHORS:20130103-133115442
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Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:36148
Deposited By: Jason Perez
Deposited On:04 Jan 2013 22:39
Last Modified:09 Nov 2021 23:20

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