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Structural basis for diverse N-glycan recognition by HIV-1–neutralizing V1–V2–directed antibody PG16

Abstract

HIV-1 uses a diverse N-linked-glycan shield to evade recognition by antibody. Select human antibodies, such as the clonally related PG9 and PG16, recognize glycopeptide epitopes in the HIV-1 V1–V2 region and penetrate this shield, but their ability to accommodate diverse glycans is unclear. Here we report the structure of antibody PG16 bound to a scaffolded V1–V2, showing an epitope comprising both high mannose–type and complex-type N-linked glycans. We combined structure, NMR and mutagenesis analyses to characterize glycan recognition by PG9 and PG16. Three PG16-specific residues, arginine, serine and histidine (RSH), were critical for binding sialic acid on complex-type glycans, and introduction of these residues into PG9 produced a chimeric antibody with enhanced HIV-1 neutralization. Although HIV-1–glycan diversity facilitates evasion, antibody somatic diversity can overcome this and can provide clues to guide the design of modified antibodies with enhanced neutralization.

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Figure 1: Cocrystal structure of human antibody PG16 and scaffolded-V1–V2 of HIV-1 gp120 with a high mannose–type N-linked glycan at residue 160gp120 and a hybrid-type N-linked glycan at residue 173gp120.
Figure 2: PG16 and PG9 interactions with V1–V2 domain of HIV-1 gp120.
Figure 3: PG16 interactions with hybrid-type N-linked glycan at residue 156gp120 or 173gp120.
Figure 4: PG16 binds complex-type glycans more tightly than Man5GlcNAc2, whereas PG9 prefers Man5GlcNAc2.
Figure 5: Design and glycan recognition of PG9-16-RSH antibody.
Figure 6: Neutralization activity of PG9, PG16 and PG9-16-RSH.
Figure 7: Effect of sialic acid removal by neuraminidase treatment on PG9, PG16 and PG9-16-RSH antibody-mediated neutralization of HIV-1.
Figure 8: Glycan recognition, binding affinities, and detailed interactions of PG16, PG9 and PG9-16-RSH.

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Acknowledgements

We thank J. Stuckey for assistance with figures and members of the Structural Biology Section and Structural Bioinformatics Core, Vaccine Research Center for discussions or comments on the manuscript; A. Kumar for sharing the ELISA binding protocol with biotinylated lectins; P. Azadi and S. Archer-Hartmann, University of Georgia, for performing glycan analyses and glycopeptide mapping; J. Baalwa (Department of Pathology, University of Alabama at Birmingham, Birmingham, Alabama, USA), D. Ellenberger (International Laboratory Branch, Division of Global HIV/AIDS, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, Georgia, USA), D. Gabuzda (Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute, Boston, Massachusetts, USA), F. Gao (Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, USA), B. Hahn (Department of Pathology, University of Alabama at Birmingham, Birmingham, Alabama, USA), K. Hong (State Key Laboratory for Infectious Disease Control and Prevention, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China), J. Kim (US Military HIV Research Program, Henry M. Jackson Foundation, Bethesda, Maryland, USA), F. McCutchan (US Military HIV Research Program, Henry M. Jackson Foundation, Bethesda, Maryland, USA), D. Montefiori (Department of Surgery, Duke University, Durham, North Carolina, USA), L. Morris, (Centre for HIV and STIs, National Institute for Communicable Diseases, Johannesburg, South Africa), J. Overbaugh (Program for Appropriate Technology in Health, Seattle, Washington, USA), E. Sanders-Buell (US Military HIV Research Program, Henry M. Jackson Foundation, Bethesda, Maryland, USA), G. Shaw (Department of Pathology, University of Alabama at Birmingham, Birmingham, Alabama, USA), R. Swanstrom (University of North Carilina Center for AIDS Research, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA), M. Thomson (University of Birmingham, Birmingham, UK), S. Tovanabutra (Department of Retrovirology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand), C. Williamson (Institute of Infectious Diseases and Molecular Medicine, Division of Medical Virology, University of Cape Town and National Health Laboratory Services, Cape Town, South Africa) and L. Zhang (Department of Public Health, Center for Disease Control and Prevention in Jiangxi Province, Nanchang, China) contributing the HIV-1 Envelope plasmids used in our neutralization panel. Support for this work was provided by the US National Institutes of Health Intramural Research Programs (Vaccine Research Center, National Institute of Allergy and Infectious Diseases, and the National Institute of Diabetes and Digestive and Kidney Diseases), by grants from the International AIDS Vaccine Initiative's Neutralizing Antibody Consortium and by the Center for HIV AIDS Vaccine Immunology Grant AI 5U19 AI 067854-06 from the US National Institutes of Health (J.E., K.E.L., J.B., S.M.A. and B.F.H.), by US National Institutes of Health grant 1R21 AI101035 (M.N.A. and L-X.W.) and by the US National Institutes of Health (NIH/NCRR)-funded grant P41 RR018502-01 to the Complex Carbohydrate Research Center. Use of sector 22 (Southeast Region Collaborative Access team) at the Advanced Photon Source was supported by the US Department of Energy, Basic Energy Sciences, Office of Science under contract number W-31-109-Eng-38.

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M.P., S.S.-u.-H., N.A.D.-R., J.S.M., B.F.H., G.J.N., J.R.M., C.A.B. and P.D.K. designed research and analyzed the data; M.P., S.S.-u.-H., N.A.D.-R., R.T.B., K.D., M.K.L., S.L., R.P.S., Y.Y., B.Z., R.P., J.E., K.E.L., J.B. and S.M.A. performed research; D.R.B. and W.C.K. contributed PG9 and PG16 antibodies; M.N.A. and L.-X.W. contributed N-glycans; M.P., S.S.-u.-H., N.A.D.-R., C.A.B. and P.D.K. wrote the paper, with all principal investigators providing comments or revisions.

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Correspondence to Carole A Bewley or Peter D Kwong.

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Pancera, M., Shahzad-ul-Hussan, S., Doria-Rose, N. et al. Structural basis for diverse N-glycan recognition by HIV-1–neutralizing V1–V2–directed antibody PG16. Nat Struct Mol Biol 20, 804–813 (2013). https://doi.org/10.1038/nsmb.2600

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