Visualization of the HIV-1 Env glycan shield across scales
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Abstract
Significance: The HIV-1 Env “glycan shield” masks the surface of the protein from immune recognition, yet intrinsic heterogeneity defies a typical structure–function description. Using an integrated approach of cryo-EM, computational modeling, and mass spectrometry, we visualized the glycan shield structure in a new light. Our approach facilitated development of cryo-EM analysis methods and allowed for validation of models against experiment. Comparison of Env expressed in different cell lines revealed how subtle differences in composition impact glycan shield structure and affect the accessibility of epitopes on the surface, providing insights for vaccine design. Finally, time-resolved cryo-EM experiments uncovered how highly connected glycan clusters help stabilize the prefusion trimer, suggesting the glycan shield may function beyond immune evasion.
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Each pathogen poses a unique set of challenges, including high lethality, rapid mutations, immune evasion, new strains and variants.
“Each pathogen poses a unique set of challenges, including high lethality, rapid mutations, immune evasion, new strains and variants252–258.”
From mRNA vaccines for infectious diseases: principles, delivery and clinical translation (2021) · cites this paper as [257]
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Cites
UCSF Chimera—A visualization system for exploratory research and analysis
Pettersen, E. F., Goddard, T. D., Huang, C. C., Couch, G. S., Greenblatt, D. M., Meng, E. C., & Ferrin, T. E. (2004) · Journal of Computational Chemistry · doi:10.1002/jcc.20084 · Cited by 45,260 · see citing works
<i>Coot</i> : model-building tools for molecular graphics
Emsley, P., & Cowtan, K. (2004) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444904019158 · Cited by 30,571 · see citing works
cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination
Punjani, A., Rubinstein, J. L., Fleet, D. J., & Brubaker, M. A. (2017) · Nature Methods · doi:10.1038/nmeth.4169 · Cited by 9,168 · see citing works
Comparative Protein Structure Modeling Using Modeller
Eswar, N., Webb, B., Martı́-Renom, M. A., Madhusudhan, M. S., Eramian, D., Shen, M., Pieper, U., & Šali, A. (2006) · Current Protocols in Bioinformatics · doi:10.1002/0471250953.bi0506s15 · Cited by 4,564 · see citing works
New tools for automated high-resolution cryo-EM structure determination in RELION-3
Zivanov, J., Nakane, T., Forsberg, B., Kimanius, D., Hagen, W., Lindahl, E., & Scheres, S. (2018) · eLife · doi:10.7554/elife.42166 · Cited by 4,377 · see citing works
Kwong, P. D., Wyatt, R. T., Robinson, J. E., Sweet, R. W., Sodroski, J., & Hendrickson, W. A. (1998) · Nature · doi:10.1038/31405 · Cited by 2,963 · see citing works
Comparative Protein Structure Modeling Using MODELLER
Eswar, N., Webb, B., Martı́-Renom, M. A., Madhusudhan, M. S., Eramian, D., Shen, M., Pieper, U., & Šali, A. (2007) · Current Protocols in Protein Science · doi:10.1002/0471140864.ps0209s50 · Cited by 2,862 · see citing works
Antibody neutralization and escape by HIV-1
Wei, X., Decker, J. M., Wang, S., Hui, H., Kappes, J. C., Wu, X., Salazar-Gonzalez, J. F., Salazar, M. G., Kilby, J. M., Saag, M. S., et al. (2003) · Nature · doi:10.1038/nature01470 · Cited by 2,421 · see citing works
Intracellular Functions of N-Linked Glycans
Helenius, A., & Aebi, A. M. (2001) · Science · doi:10.1126/science.291.5512.2364 · Cited by 2,405 · see citing works
Symbol Nomenclature for Graphical Representations of Glycans
Varki, A. P., Cummings, R. D., Aebi, M., Packer, N. H., Seeberger, P. H., Esko, J. D., Stanley, P., Hart, G. W., Darvill, A. G., Kinoshita, T., et al. (2015) · Glycobiology · doi:10.1093/glycob/cwv091 · Cited by 1,060 · see citing works
Self-citationLeonard, C. K., Spellman, M. W., Riddle, L. M., Harris, R. J., Thomas, J. N., & Gregory, T. (1990) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(18)86956-3 · Cited by 986 · see citing works
Sanders, R. W., Derking, R., Cupo, A., Julien, J., Yasmeen, A., de Val, N., Kim, H. J., Blattner, C., de la Peña, A. T., Korzun, J., et al. (2013) · PLoS Pathogens · doi:10.1371/journal.ppat.1003618 · Cited by 937 · see citing works
Self-citationAccelerated cryo-EM structure determination with parallelisation using GPUs in RELION-2
Kimanius, D., Forsberg, B. O., Scheres, S. H. W., & Lindahl, E. R. (2016) · eLife · doi:10.7554/elife.18722 · Cited by 903 · see citing works
Comparative protein modeling by satisfaction of spatial restraints
⩽ali, A. (1995) · Molecular Medicine Today · doi:10.1016/s1357-4310(95)91170-7 · Cited by 785 · see citing works
Mechanisms and principles of N-linked protein glycosylation
Schwarz, F., & Aebi, M. (2011) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2011.08.005 · Cited by 695 · see citing works
Cryo-EM Structure of a Fully Glycosylated Soluble Cleaved HIV-1 Envelope Trimer
Lyumkis, D., Julien, J., de Val, N., Cupo, A., Potter, C. S., Klasse, P.-J., Burton, D. R., Sanders, R. W., Moore, J. P., Carragher, B. O., et al. (2013) · Science · doi:10.1126/science.1245627 · Cited by 669 · see citing works
Self-citationEffect of glycosylation on protein folding: A close look at thermodynamic stabilization
Shental-Bechor, D., & Levy, Y. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0801340105 · Cited by 619 · see citing works
A Primer to Single-Particle Cryo-Electron Microscopy
Cheng, Y., Grigorieff, N., Penczek, P. A., & Walz, T. (2015) · Cell · doi:10.1016/j.cell.2015.03.050 · Cited by 570 · see citing works
Evolutionary and immunological implications of contemporary HIV-1 variation
Korber, B., Gaschen, B. K., Yusim, K., Thakallapally, R., Keşmir, C., & Detours, V. (2001) · British Medical Bulletin · doi:10.1093/bmb/58.1.19 · Cited by 534 · see citing works
Automated structure refinement of macromolecular assemblies from cryo-EM maps using Rosetta
Wang, R. Y.-R., Song, Y., Barad, B. A., Cheng, Y., Fraser, J. S., & DiMaio, F. (2016) · eLife · doi:10.7554/elife.17219 · Cited by 457 · see citing works
Cryo-EM structure of a native, fully glycosylated, cleaved HIV-1 envelope trimer
Lee, J. H., Ozorowski, G., & Ward, A. B. (2016) · Science · doi:10.1126/science.aad2450 · Cited by 422 · see citing works
Self-citationTrimeric HIV-1-Env Structures Define Glycan Shields from Clades A, B, and G
Stewart-Jones, G. B. E., Soto, C. S., Lemmin, T., Chuang, G., Druz, A., Kong, R., Thomas, P. V., Wagh, K., Zhou, T., Behrens, A., et al. (2016) · Cell · doi:10.1016/j.cell.2016.04.010 · Cited by 406 · see citing works
Effect of N-linked glycosylation on glycopeptide and glycoprotein structure
Imperiali, B., & O'Connor, S. E. (1999) · Current Opinion in Chemical Biology · doi:10.1016/s1367-5931(99)00021-6 · Cited by 387 · see citing works
SPARX, a new environment for Cryo-EM image processing
Hohn, M. H., Tang, G., Goodyear, G., Baldwin, P. R., Huang, Z. X., Penczek, P. A., Yang, C., Glaeser, R. M., Adams, P. D., & Ludtke, S. J. (2006) · Journal of Structural Biology · doi:10.1016/j.jsb.2006.07.003 · Cited by 364 · see citing works
Neutralization of the AIDS Retrovirus by Antibodies to a Recombinant Envelope Glycoprotein
Lasky, L. A., Groopman, J. E., Fennie, C., et al. (1986) · Science · doi:10.1126/science.3014647 · Cited by 353 · see citing works
Envelope glycans of immunodeficiency virions are almost entirely oligomannose antigens
Doores, K. J., Bonomelli, C., Harvey, D. J., Vasiljević, S., Dwek, R. A., Burton, D. R., Crispin, M., & Scanlan, C. N. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1006498107 · Cited by 329 · see citing works
Lee, H. S., Qi, Y., & Im, W. (2015) · Scientific Reports · doi:10.1038/srep08926 · Cited by 290 · see citing works
Crystal structure of the human sterol transporter ABCG5/ABCG8
Lee, J., Kinch, L. N., Borek, D., Wang, J., Wang, J., Urbatsch, I. L., Xie, X., Grishin, N. V., Cohen, J. C., Otwinowski, Z., et al. (2016) · Nature · doi:10.1038/nature17666 · Cited by 271 · see citing works
A generalized HIV vaccine design strategy for priming of broadly neutralizing antibody responses
Steichen, J. M., Lin, Y., Havenar‐Daughton, C., Pecetta, S., Ozorowski, G., Willis, J. R., Toy, L., Sok, D., Liguori, A., Kratochvil, S., et al. (2019) · Science · doi:10.1126/science.aax4380 · Cited by 265 · see citing works
Self-citationFolding of glycoproteins: toward understanding the biophysics of the glycosylation code
Shental-Bechor, D., & Levy, Y. (2009) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2009.07.002 · Cited by 251 · see citing works
Behrens, A., Vasiljević, S., Pritchard, L. K., Harvey, D. J., Andev, R. S., Krumm, S. A., Struwe, W. B., Cupo, A., Kumar, A., Zitzmann, N., et al. (2016) · Cell Reports · doi:10.1016/j.celrep.2016.02.058 · Cited by 251 · see citing works
Self-citationThe HIV ‐1 envelope glycoprotein structure: nailing down a moving target
Ward, A. B., & Wilson, I. A. (2017) · Immunological Reviews · doi:10.1111/imr.12507 · Cited by 245 · see citing works
Self-citationOpen and closed structures reveal allostery and pliability in the HIV-1 envelope spike
Ozorowski, G., Pallesen, J., de Val, N., Lyumkis, D., Cottrell, C. A., Torres, J. L., Copps, J., Stanfield, R. L., Cupo, A., Pugach, P., et al. (2017) · Nature · doi:10.1038/nature23010 · Cited by 237 · see citing works
Self-citationHanson, S. R., Culyba, E. K., Hsu, T.-L., Wong, C., Kelly, J. W., & Powers, E. T. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0810318105 · Cited by 236 · see citing works
Native‐like Env trimers as a platform for HIV ‐1 vaccine design
Sanders, R. W., & Moore, J. P. (2017) · Immunological Reviews · doi:10.1111/imr.12481 · Cited by 227 · see citing works
Global site-specific N-glycosylation analysis of HIV envelope glycoprotein
Cao, L., Diedrich, J. K., Kulp, D. W., Pauthner, M. G., He, L., Park, S.-K. R., Sok, D., Su, C.-Y., Delahunty, C. M., Menis, S., et al. (2017) · Nature Communications · doi:10.1038/ncomms14954 · Cited by 208 · see citing works
Self-citationBianchi, M., Turner, H. L., Nogal, B., Cottrell, C. A., Oyen, D., Pauthner, M. G., Bastidas, R. B., Nedellec, R., McCoy, L. E., Wilson, I. A., et al. (2018) · Immunity · doi:10.1016/j.immuni.2018.07.009 · Cited by 205 · see citing works
Self-citationQuantification of the Impact of the HIV-1-Glycan Shield on Antibody Elicitation
Zhou, T., Doria‐Rose, N. A., Cheng, C., Stewart-Jones, G. B. E., Chuang, G., Chambers, M. J., Druz, A., Geng, H., McKee, K., Kwon, Y. D., et al. (2017) · Cell Reports · doi:10.1016/j.celrep.2017.04.013 · Cited by 176 · see citing works
Structure-based model of allostery predicts coupling between distant sites
Weinkam, P., Pons, J., & Šali, A. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1116274109 · Cited by 157 · see citing works
Gerken, T. A., Butenhof, K. J., & Shogren, R. L. (1989) · Biochemistry · doi:10.1021/bi00439a030 · Cited by 148 · see citing works
Dubrovskaya, V., Tran, K., Ozorowski, G., et al. (2019) · Immunity · doi:10.1016/j.immuni.2019.10.008 · Cited by 129 · see citing works
Pritchard, L. K., Spencer, D. I. R., Royle, L., Bonomelli, C., Seabright, G. E., Behrens, A., Kulp, D. W., Menis, S., Krumm, S. A., Dunlop, D. C., et al. (2015) · Nature Communications · doi:10.1038/ncomms8479 · Cited by 125 · see citing works
Self-citationDifferential processing of HIV envelope glycans on the virus and soluble recombinant trimer
Cao, L., Pauthner, M. G., Andrabi, R., Rantalainen, K. I., Berndsen, Z. T., Diedrich, J. K., Menis, S., Sok, D., Bastidas, R. B., Park, S. K. R., et al. (2018) · Nature Communications · doi:10.1038/s41467-018-06121-4 · Cited by 125 · see citing works
Self-citationMer, G., Hietter, H., & Lefèvre, J. (1996) · Nature Structural Biology · doi:10.1038/nsb0196-45 · Cited by 121 · see citing works
Solá, R. J., Rodríguez‐Martínez, J. A., & Griebenow, K. H. (2007) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-007-6551-y · Cited by 120 · see citing works
Structural analysis of glycoproteins: building N-linked glycans withCoot
Emsley, P., & Crispin, M. (2018) · Acta Crystallographica Section D Structural Biology · doi:10.1107/s2059798318005119 · Cited by 117 · see citing works
Wang, W., Nie, J., Prochnow, C., Truong, C., Jia, Z., Wang, S., Chen, X. S., & Wang, Y. (2013) · Retrovirology · doi:10.1186/1742-4690-10-14 · Cited by 114 · see citing works
João, H. C., & Dwek, R. A. (1993) · European Journal of Biochemistry · doi:10.1111/j.1432-1033.1993.tb18370.x · Cited by 99 · see citing works
Simultaneous Determination of Protein Structure and Dynamics Using Cryo-Electron Microscopy
Bonomi, M., Pellarin, R., & Vendruscolo, M. (2018) · Biophysical Journal · doi:10.1016/j.bpj.2018.02.028 · Cited by 99 · see citing works
Lee, J. H., de Val, N., Lyumkis, D., & Ward, A. C. (2015) · Structure · doi:10.1016/j.str.2015.07.020 · Cited by 89 · see citing works
Self-citationFunctions of HIV envelope glycans
Fenouillet, E., Gluckman, J. C., & Jones, I. M. (1994) · Trends in Biochemical Sciences · doi:10.1016/0968-0004(94)90034-5 · Cited by 89 · see citing works
Nogal, B., Bianchi, M., Cottrell, C. A., Kirchdoerfer, R. N., Sewall, L. M., Turner, H. L., Zhao, F., Sok, D., Burton, D. R., Hangartner, L., et al. (2020) · Cell Reports · doi:10.1016/j.celrep.2020.02.061 · Cited by 89 · see citing works
Self-citationDetermination of protein structural ensembles using cryo-electron microscopy
Bonomi, M., & Vendruscolo, M. (2018) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2018.10.006 · Cited by 88 · see citing works
All-Atom Ensemble Modeling to Analyze Small-Angle X-Ray Scattering of Glycosylated Proteins
Guttman, M., Weinkam, P., Šali, A., et al. (2013) · Structure · doi:10.1016/j.str.2013.02.004 · Cited by 81 · see citing works
Mapping the immunogenic landscape of near-native HIV-1 envelope trimers in non-human primates
Cottrell, C. A., van Schooten, J., Bowman, C. A., et al. (2020) · PLoS Pathogens · doi:10.1371/journal.ppat.1008753 · Cited by 81 · see citing works
Self-citationDey, A., Cupo, A., Ozorowski, G., Sharma, V. K., Behrens, A., Go, E. P., Ketas, T. J., Yasmeen, A., Klasse, P. J., Sayeed, E., et al. (2017) · Biotechnology and Bioengineering · doi:10.1002/bit.26498 · Cited by 75 · see citing works
Self-citationDacheux, L., Moreau, A., Ataman‐Önal, Y., et al. (2004) · Journal of Virology · doi:10.1128/jvi.78.22.12625-12637.2004 · Cited by 74 · see citing works
Analysis of site-specific<i>N</i>-glycan remodeling in the endoplasmic reticulum and the Golgi
Hang, I., Lin, C.-W., Grant, O. C., Fleurkens, S., Villiger, T. K., Soos, M., Morbidelli, M., Woods, R. J., Gauss, R., & Aebi, M. (2015) · Glycobiology · doi:10.1093/glycob/cwv058 · Cited by 67 · see citing works
Factors limiting the immunogenicity of HIV-1 gp120 envelope glycoproteins
Grundner, C., Pancera, M., Kang, J.-M., et al. (2004) · Virology · doi:10.1016/j.virol.2004.08.037 · Cited by 60 · see citing works
Bayesian Weighing of Electron Cryo-Microscopy Data for Integrative Structural Modeling
Bonomi, M., Hanot, S., Greenberg, C. H., Šali, A., Nilges, M., Vendruscolo, M., & Pellarin, R. (2018) · Structure · doi:10.1016/j.str.2018.09.011 · Cited by 57 · see citing works
Lu, D., Yang, C. L., & Liu, Z. (2011) · The Journal of Physical Chemistry B · doi:10.1021/jp203926r · Cited by 53 · see citing works
Depetris, R. S., Julien, J., Khayat, R., Lee, J. H., Pejchal, R., Katpally, U., Cocco, N., Kachare, M. D., Massi, E., David, K. B., et al. (2012) · Journal of Biological Chemistry · doi:10.1074/jbc.m112.371898 · Cited by 51 · see citing works
Self-citationOhgimoto, S., Shioda, T., Mori, K., et al. (1998) · Journal of Virology · doi:10.1128/jvi.72.10.8365-8370.1998 · Cited by 48 · see citing works
Dubrovskaya, V., Guenaga, J., de Val, N., Wilson, R., Feng, Y., Movsesyan, A., Hedestam, G. B. K., Ward, A. B., & Wyatt, R. T. (2017) · PLoS Pathogens · doi:10.1371/journal.ppat.1006614 · Cited by 45 · see citing works
Self-citationLemmin, T., Soto, C. S., Stuckey, J., & Kwong, P. D. (2017) · Structure · doi:10.1016/j.str.2017.07.018 · Cited by 44 · see citing works
Conformational Heterogeneity of the HIV Envelope Glycan Shield
Yang, M., Huang, J., Simon, R., Wang, L., & MacKerell, A. D. (2017) · Scientific Reports · doi:10.1038/s41598-017-04532-9 · Cited by 43 · see citing works
The Influence of N-Linked Glycans on the Molecular Dynamics of the HIV-1 gp120 V3 Loop
Wood, N. T., Fadda, E., Davis, R., Grant, O. C., Martin, J. C., Woods, R. J., & Travers, S. A. A. (2013) · PLoS ONE · doi:10.1371/journal.pone.0080301 · Cited by 40 · see citing works
Rathore, U., Saha, P., Kesavardhana, S., Kumar, A. A., Datta, R., Sankar, D. S., Das, R., Mascola, J. R., & Varadarajan, R. (2017) · Journal of Biological Chemistry · doi:10.1074/jbc.m117.788919 · Cited by 31 · see citing works
Liang, Y., Guttman, M., Williams, J. A., Verkerke, H., Alvarado, D., Hu, S.-L., & Lee, K. K. (2016) · Journal of Virology · doi:10.1128/jvi.01116-16 · Cited by 27 · see citing works
Behrens, A., Kumar, A., Medina-Ramírez, M., Cupo, A., Marshall, K., Portillo, V. M. C., Harvey, D. J., Ozorowski, G., Zitzmann, N., Wilson, I. A., et al. (2018) · Journal of Proteome Research · doi:10.1021/acs.jproteome.7b00639 · Cited by 22 · see citing works
Self-citationQuantification of the Resilience and Vulnerability of HIV-1 Native Glycan Shield at Atomistic Detail
Chakraborty, S., Berndsen, Z. T., Hengartner, N., Korber, B., Ward, A. B., & Gnanakaran, S. (2020) · iScience · doi:10.1016/j.isci.2020.101836 · Cited by 22 · see citing works
Self-citationJianhui, T., López, C. A., Derdeyn, C. A., Jones, M. S., Pinter, A., Korber, B., & Gnanakaran, S. (2016) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1005094 · Cited by 17 · see citing works
Self-citationFerreira, R.-C., Grant, O. C., Moyo-Gwete, T., Dorfman, J. R., Woods, R. J., Travers, S. A. A., & Wood, N. T. (2018) · Scientific Reports · doi:10.1038/s41598-018-33390-2 · Cited by 17 · see citing works
Role of N-glycosylation in activation of proMMP-9. A molecular dynamics simulations study
Kumar, S., & Cieplak, P. (2018) · PLoS ONE · doi:10.1371/journal.pone.0191157 · Cited by 12 · see citing works
Dong, C., Lee, J., Kim, S., Lai, W., Webb, E. B., Öztekin, A., Zhang, X. H., & Im, W. (2018) · Scientific Reports · doi:10.1038/s41598-018-34374-y · Cited by 8 · see citing works
Quantification of the Resilience and Vulnerability of HIV-1 Native Glycan Shield at Atomistic DetailPreprint
Chakraborty, S., Berndsen, Z. T., Hengartner, N., et al. (2020) · SSRN Electronic Journal · doi:10.2139/ssrn.3606299 · Cited by 4 · see citing works
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Chaudhary, N., Weissman, D., & Whitehead, K. A. (2021) · Nature Reviews Drug Discovery · doi:10.1038/s41573-021-00283-5 · Cited by 1,555 · see citing works
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Mansbach, R. A., Chakraborty, S., Nguyen, K., Montefiori, D. C., Korber, B., & Gnanakaran, S. (2021) · Science Advances · doi:10.1126/sciadv.abf3671 · Cited by 206 · see citing works
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- Authors
- Berndsen, Z. T., Chakraborty, S., Wang, X., Cottrell, C. A., Torres, J. L., Diedrich, J. K., López, C. A., Yates, J. R., van Gils, M. J., Paulson, J. C., Gnanakaran, S., & Ward, A. B.
- Affiliations
- Scripps Research Institute (US)
- Los Alamos National Laboratory (US)
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87545;
- Department of Medical Microbiology, Amsterdam University Medical Center, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands;
- Corresponding author
- Gnanakaran, Sandrasegaram
- Ward, Andrew B.
- ORCID
- Venue
- Proceedings of the National Academy of Sciences
- Publisher
- National Academy of Sciences
- Published
- 2020-10-22
- Volume
- 117
- Issue
- 45
- Pages
- 28014-28025
- ISSN
- 0027-8424 (ISSN-L)
- 1091-6490
- PMC
- PMC7668054
- OpenAlex
- W3094127650
- Cited by
- 86
- References
- 76
- Citations by year
- 2026: 14 · 2025: 16 · 2024: 8 · 2023: 8 · 2022: 15 · 2021: 21 · 2020: 4
- FWCI
- 3.89
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Proceedings of the National Academy of Sciences (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Pure Amsterdam UMC (publishedVersion, other-oa)
- OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information) (submittedVersion)
- Data Archiving and Networked Services (DANS) (submittedVersion, other-oa)
- Funders
- Bill and Melinda Gates Foundation (OPP1100639, OPP1115782, OPP1196345)
- Division of Intramural Research, National Institute of Allergy and Infectious Diseases (UM1 AI100663, UM1 AI144462, AI113867, P41GM103533, UM1 AI100645, UM1 AI144371)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Glycosylation and Glycoproteins Research
- Life Sciences › Immunology and Microbiology › Virology › HIV Research and Treatment
- Physical Sciences › Chemistry › Organic Chemistry › Carbohydrate Chemistry and Synthesis
- Keywords
- HIV-1 envelope glycoprotein, glycan shield, N-glycans, epitope accessibility, immunogenicity, deglycosylation, vaccine production
- MeSH terms
- Antibody Formation, Epitopes, Computer Simulation, Glycosylation, HIV Seropositivity, Humans, Models, Molecular, Polysaccharides, Mass Spectrometry, HIV Antibodies, HIV-1, HIV Envelope Protein gp120, Cryoelectron Microscopy, env Gene Products, Human Immunodeficiency Virus, Immune Evasion, Antibodies, Neutralizing
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