Antibody Lineages with Vaccine-Induced Antigen-Binding Hotspots Develop Broad HIV Neutralization

Kong, Rui; Duan, Hongying; Sheng, Zizhang; Xu, Kai; Acharya, Priyamvada; Chen, Xuejun; Cheng, Cheng; Dingens, Adam S.; Gorman, Jason; Sastry, Mallika; Shen, Chen-Hsiang; Zhang, Baoshan; Zhou, Tongqing; Chuang, Gwo-Yu; Chao, Cara W.; Gu, Ying; Jafari, Alexander J.; Louder, Mark K.; O’Dell, Sijy; Rowshan, Ariana P.; Viox, Elise G.; Wang, Yiran; Choi, Chang W.; Corcoran, Martin M.; Corrigan, Angela R.; Dandey, Venkata P.; Eng, Edward T.; Geng, Hui; Foulds, Kathryn E.; Guo, Yicheng; Kwon, Young D.; Lin, Bob; Liu, Kevin; Mason, Rosemarie D.; Nason, Martha C.; Ohr, Tiffany Y.; Ou, Li; Rawi, Reda; Sarfo, Edward K.; Schön, Arne; Todd, John P.; Wang, Shuishu; Wei, Hui; Wu, Winston; Mullikin, James C.; Bailer, Robert T.; Doria-Rose, Nicole A.; Karlsson Hedestam, Gunilla B.; Scorpio, Diana G.; Overbaugh, Julie; Bloom, Jesse D.; Carragher, Bridget; Potter, Clinton S.; Shapiro, Lawrence; Kwong, Peter D.; Mascola, John R.

doi:10.1016/j.cell.2019.06.030

Title: Antibody Lineages with Vaccine-Induced Antigen-Binding Hotspots Develop Broad HIV Neutralization

Journal Article · Thu Jul 25 00:00:00 EDT 2019 · Cell

DOI:https://doi.org/10.1016/j.cell.2019.06.030· OSTI ID:1557322

Kong, Rui ^[1]; Duan, Hongying ^[1]; Sheng, Zizhang ^[2]; Xu, Kai ^[1]; Acharya, Priyamvada ^[3]; Chen, Xuejun ^[1]; Cheng, Cheng ^[1]; Dingens, Adam S. ^[4]; Gorman, Jason ^[5]; Sastry, Mallika ^[1]; Shen, Chen-Hsiang ^[1]; Zhang, Baoshan ^[1]; Zhou, Tongqing ^[1]; Chuang, Gwo-Yu ^[1]; Chao, Cara W. ^[1]; Gu, Ying ^[1]; Jafari, Alexander J. ^[1]; Louder, Mark K. ^[1]; O’Dell, Sijy ^[1]; Rowshan, Ariana P. ^[1] more »

National Institutes of Health (NIH), Bethesda, MD (United States)
Columbia Univ., New York, NY (United States)
National Institutes of Health (NIH), Bethesda, MD (United States); New York Structural Biology Center, New York, NY (United States); Duke Univ. School of Medicine, Durham, NC (United States)
Fred Hutchinson Cancer Research Center, Seattle, WA (United States); Univ. of Washington, Seattle, WA (United States)
National Institutes of Health (NIH), Bethesda, MD (United States); New York Structural Biology Center, New York, NY (United States)
Karolinska Inst., Stockholm (Sweden)
New York Structural Biology Center, New York, NY (United States)
New York Structural Biology Center, New York, NY (United States)
Johns Hopkins Univ., Baltimore, MD (United States)
Univ. of Washington, Seattle, WA (United States)
Fred Hutchinson Cancer Research Center, Seattle, WA (United States); Howard Hughes Medical Inst., Seattle, WA (United States)
National Institutes of Health (NIH), Bethesda, MD (United States); Columbia Univ., New York, NY (United States)

The vaccine-mediated elicitation of antibodies (Abs) capable of neutralizing diverse HIV-1 strains has been a long-standing goal. To understand how broadly neutralizing antibodies (bNAbs) can be elicited, we identified, characterized, and tracked five neutralizing Ab lineages targeting the HIV-1-fusion peptide (FP) in vaccinated macaques over time. Genetic and structural analyses revealed two of these lineages to belong to a reproducible class capable of neutralizing up to 59% of 208 diverse viral strains. B cell analysis indicated each of the five lineages to have been initiated and expanded by FP-carrier priming, with envelope (Env)-trimer boosts inducing cross-reactive neutralization. These Abs had binding-energy hotspots focused on FP, whereas several FP-directed Abs induced by immunization with Env trimer-only were less FP-focused and less broadly neutralizing. Priming with a conserved subregion, such as FP, can thus induce Abs with binding-energy hotspots coincident with the target subregion and capable of broad neutralization.

View Accepted Manuscript (DOE)

Cite

Export

Save

Research Organization:: Argonne National Laboratory (ANL), Argonne, IL (United States). Advanced Photon Source (APS)

Sponsoring Organization:: USDOE Office of Science (SC), Basic Energy Sciences (BES); National Institutes of Health (NIH); Bill and Melinda Gates Foundation; National Science Foundation (NSF); Swedish Research Council (SRC); International AIDS Vaccine Initiative; Simons Foundation; NYSTAR; Agouron Inst.

Contributing Organization:: NISC Comparative Sequencing Program

Grant/Contract Number:: W-31-109-Eng-38; OPP1162123; R21-1R21AI138024-01A1; R01AI140891; DA039543; R01AI120961; DGE-1256082; SF349247; GM103310; F00316; OD019994

OSTI ID:: 1557322

Journal Information:: Cell, Vol. 178, Issue 3; ISSN 0092-8674

Publisher:: ElsevierCopyright Statement

Country of Publication:: United States

Language:: ENGLISH

Citation Metrics:

Cited by: 63 works

Citation information provided by
Web of Science

References (94)

Crystal structure, conformational fixation and entry-related interactions of mature ligand-free HIV-1 Env Do Kwon, Young; Pancera, Marie; Acharya, Priyamvada Nature Structural & Molecular Biology, Vol. 22, Issue 7 https://doi.org/10.1038/nsmb.3051	journal	June 2015
MOLPROBITY: structure validation and all-atom contact analysis for nucleic acids and their complexes Davis, I. W.; Murray, L. W.; Richardson, J. S. Nucleic Acids Research, Vol. 32, Issue Web Server https://doi.org/10.1093/nar/gkh398	journal	July 2004
Immunization for HIV-1 Broadly Neutralizing Antibodies in Human Ig Knockin Mice Dosenovic, Pia; von Boehmer, Lotta; Escolano, Amelia Cell, Vol. 161, Issue 7 https://doi.org/10.1016/j.cell.2015.06.003	journal	June 2015
Comprehensive Mapping of HIV-1 Escape from a Broadly Neutralizing Antibody Dingens, Adam S.; Haddox, Hugh K.; Overbaugh, Julie Cell Host & Microbe, Vol. 21, Issue 6 https://doi.org/10.1016/j.chom.2017.05.003	journal	June 2017
Gene-Specific Substitution Profiles Describe the Types and Frequencies of Amino Acid Changes during Antibody Somatic Hypermutation Sheng, Zizhang; Schramm, Chaim A.; Kong, Rui Frontiers in Immunology, Vol. 8 https://doi.org/10.3389/fimmu.2017.00537	journal	May 2017
Recent progress in broadly neutralizing antibodies to HIV Sok, Devin; Burton, Dennis R. Nature Immunology, Vol. 19, Issue 11 https://doi.org/10.1038/s41590-018-0235-7	journal	October 2018
Principles of Broad and Potent Antiviral Human Antibodies: Insights for Vaccine Design Crowe, James E. Cell Host & Microbe, Vol. 22, Issue 2 https://doi.org/10.1016/j.chom.2017.07.013	journal	August 2017
Mutations in HIV-1 Envelope That Enhance Entry with the Macaque CD4 Receptor Alter Antibody Recognition by Disrupting Quaternary Interactions within the Trimer Boyd, David F.; Peterson, Dylan; Haggarty, Beth S. Journal of Virology, Vol. 89, Issue 2 https://doi.org/10.1128/JVI.02680-14	journal	January 2015
An Antigenic Atlas of HIV-1 Escape from Broadly Neutralizing Antibodies Distinguishes Functional and Structural Epitopes Dingens, Adam S.; Arenz, Dana; Weight, Haidyn Immunity, Vol. 50, Issue 2 https://doi.org/10.1016/j.immuni.2018.12.017	journal	February 2019
Structural Delineation of a Quaternary, Cleavage-Dependent Epitope at the gp41-gp120 Interface on Intact HIV-1 Env Trimers Blattner, Claudia; Lee, Jeong Hyun; Sliepen, Kwinten Immunity, Vol. 40, Issue 5 https://doi.org/10.1016/j.immuni.2014.04.008	journal	May 2014
Elicitation of structure-specific antibodies by epitope scaffolds Ofek, G.; Guenaga, F. J.; Schief, W. R. Proceedings of the National Academy of Sciences, Vol. 107, Issue 42 https://doi.org/10.1073/pnas.1004728107	journal	September 2010
Tailored Immunogens Direct Affinity Maturation toward HIV Neutralizing Antibodies Briney, Bryan; Sok, Devin; Jardine, Joseph G. Cell, Vol. 166, Issue 6 https://doi.org/10.1016/j.cell.2016.08.005	journal	September 2016
Structure of an HIV gp120 envelope glycoprotein in complex with the CD4 receptor and a neutralizing human antibody Kwong, Peter D.; Wyatt, Richard; Robinson, James Nature, Vol. 393, Issue 6686 https://doi.org/10.1038/31405	journal	June 1998
Broadly Neutralizing HIV Antibodies Define a Glycan-Dependent Epitope on the Prefusion Conformation of gp41 on Cleaved Envelope Trimers Falkowska, Emilia; Le, Khoa M.; Ramos, Alejandra Immunity, Vol. 40, Issue 5 https://doi.org/10.1016/j.immuni.2014.04.009	journal	May 2014
Epitope-based vaccine design yields fusion peptide-directed antibodies that neutralize diverse strains of HIV-1 Xu, Kai; Acharya, Priyamvada; Kong, Rui Nature Medicine, Vol. 24, Issue 6 https://doi.org/10.1038/s41591-018-0042-6	journal	June 2018
A Next-Generation Cleaved, Soluble HIV-1 Env Trimer, BG505 SOSIP.664 gp140, Expresses Multiple Epitopes for Broadly Neutralizing but Not Non-Neutralizing Antibodies Sanders, Rogier W.; Derking, Ronald; Cupo, Albert PLoS Pathogens, Vol. 9, Issue 9, Article No. e1003618 https://doi.org/10.1371/journal.ppat.1003618	journal	September 2013
Mapping mutational effects along the evolutionary landscape of HIV envelope Haddox, Hugh K.; Dingens, Adam S.; Hilton, Sarah K. eLife, Vol. 7 https://doi.org/10.7554/eLife.34420	journal	March 2018
Structural Survey of Broadly Neutralizing Antibodies Targeting the HIV-1 Env Trimer Delineates Epitope Categories and Characteristics of Recognition Chuang, Gwo-Yu; Zhou, Jing; Acharya, Priyamvada Structure, Vol. 27, Issue 1 https://doi.org/10.1016/j.str.2018.10.007	journal	January 2019
Optimizing “self-wicking” nanowire grids Wei, Hui; Dandey, Venkata P.; Zhang, Zhening Journal of Structural Biology, Vol. 202, Issue 2 https://doi.org/10.1016/j.jsb.2018.01.001	journal	May 2018
Spotiton: New features and applications Dandey, Venkata P.; Wei, Hui; Zhang, Zhening Journal of Structural Biology, Vol. 202, Issue 2 https://doi.org/10.1016/j.jsb.2018.01.002	journal	May 2018
Frequent microsatellite instability and BAX mutations in T cell acute lymphoblastic leukemia cell lines Inoue, Kaoru; Kohno, Takashi; Takakura, Satoshi Leukemia Research, Vol. 24, Issue 3 https://doi.org/10.1016/S0145-2126(99)00182-4	journal	March 2000
Inference of Macromolecular Assemblies from Crystalline State Krissinel, Evgeny; Henrick, Kim Journal of Molecular Biology, Vol. 372, Issue 3 https://doi.org/10.1016/j.jmb.2007.05.022	journal	September 2007
Human monoclonal antibody 2G12 defines a distinctive neutralization epitope on the gp120 glycoprotein of human immunodeficiency virus type 1. Trkola, A.; Purtscher, M.; Muster, T. Journal of virology, Vol. 70, Issue 2 https://doi.org/10.1128/JVI.70.2.1100-1108.1996	journal	January 1996
UCSF Chimera?A visualization system for exploratory research and analysis Pettersen, Eric F.; Goddard, Thomas D.; Huang, Conrad C. Journal of Computational Chemistry, Vol. 25, Issue 13 https://doi.org/10.1002/jcc.20084	journal	January 2004
Vaccine Induction of Heterologous Tier 2 HIV-1 Neutralizing Antibodies in Animal Models Saunders, Kevin O.; Verkoczy, Laurent K.; Jiang, Chuancang Cell Reports, Vol. 21, Issue 13 https://doi.org/10.1016/j.celrep.2017.12.028	journal	December 2017
An HIV-1 antibody from an elite neutralizer implicates the fusion peptide as a site of vulnerability van Gils, Marit J.; van den Kerkhof, Tom L. G. M.; Ozorowski, Gabriel Nature Microbiology, Vol. 2, Issue 2 https://doi.org/10.1038/nmicrobiol.2016.199	journal	November 2016
Transplanting Supersites of HIV-1 Vulnerability Zhou, Tongqing; Zhu, Jiang; Yang, Yongping PLoS ONE, Vol. 9, Issue 7 https://doi.org/10.1371/journal.pone.0099881	journal	July 2014
Gctf: Real-time CTF determination and correction Zhang, Kai Journal of Structural Biology, Vol. 193, Issue 1 https://doi.org/10.1016/j.jsb.2015.11.003	journal	January 2016
Optimization and validation of the TZM-bl assay for standardized assessments of neutralizing antibodies against HIV-1 Sarzotti-Kelsoe, Marcella; Bailer, Robert T.; Turk, Ellen Journal of Immunological Methods, Vol. 409 https://doi.org/10.1016/j.jim.2013.11.022	journal	July 2014
Error filtering, pair assembly and error correction for next-generation sequencing reads Edgar, Robert C.; Flyvbjerg, Henrik Bioinformatics, Vol. 31, Issue 21 https://doi.org/10.1093/bioinformatics/btv401	journal	July 2015
Induction of HIV Neutralizing Antibody Lineages in Mice with Diverse Precursor Repertoires Tian, Ming; Cheng, Cheng; Chen, Xuejun Cell, Vol. 166, Issue 6 https://doi.org/10.1016/j.cell.2016.07.029	journal	September 2016
Consistent elicitation of cross-clade HIV-neutralizing responses achieved in guinea pigs after fusion peptide priming by repetitive envelope trimer boosting Cheng, Cheng; Xu, Kai; Kong, Rui PLOS ONE, Vol. 14, Issue 4 https://doi.org/10.1371/journal.pone.0215163	journal	April 2019
Experimental Estimation of the Effects of All Amino-Acid Mutations to HIV’s Envelope Protein on Viral Replication in Cell Culture Haddox, Hugh K.; Dingens, Adam S.; Bloom, Jesse D. PLOS Pathogens, Vol. 12, Issue 12 https://doi.org/10.1371/journal.ppat.1006114	journal	December 2016
PHENIX: a comprehensive Python-based system for macromolecular structure solution Adams, Paul D.; Afonine, Pavel V.; Bunkóczi, Gábor Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2, p. 213-221 https://doi.org/10.1107/S0907444909052925	journal	January 2010
Sequential Immunization Elicits Broadly Neutralizing Anti-HIV-1 Antibodies in Ig Knockin Mice Escolano, Amelia; Steichen, Jon M.; Dosenovic, Pia Cell, Vol. 166, Issue 6 https://doi.org/10.1016/j.cell.2016.07.030	journal	September 2016
Targeted Isolation of Antibodies Directed against Major Sites of SIV Env Vulnerability Mason, Rosemarie D.; Welles, Hugh C.; Adams, Cameron PLOS Pathogens, Vol. 12, Issue 4 https://doi.org/10.1371/journal.ppat.1005537	journal	April 2016
B-cell–lineage immunogen design in vaccine development with HIV-1 as a case study Haynes, Barton F.; Kelsoe, Garnett; Harrison, Stephen C. Nature Biotechnology, Vol. 30, Issue 5 https://doi.org/10.1038/nbt.2197	journal	May 2012
Structural Repertoire of HIV-1-Neutralizing Antibodies Targeting the CD4 Supersite in 14 Donors Zhou, Tongqing; Lynch, Rebecca M.; Chen, Lei Cell, Vol. 161, Issue 6 https://doi.org/10.1016/j.cell.2015.05.007	journal	June 2015
Developmental pathway for potent V1V2-directed HIV-neutralizing antibodies Doria-Rose, Nicole A.; Schramm, Chaim A.; Gorman, Jason Nature, Vol. 509, Issue 7498 https://doi.org/10.1038/nature13036	journal	March 2014
Isolation of antibody V(D)J sequences from single cell sorted rhesus macaque B cells Sundling, Christopher; Phad, Ganesh; Douagi, Iyadh Journal of Immunological Methods, Vol. 386, Issue 1-2 https://doi.org/10.1016/j.jim.2012.09.003	journal	December 2012
Complete functional mapping of infection- and vaccine-elicited antibodies against the fusion peptide of HIV Dingens, Adam S.; Acharya, Priyamvada; Haddox, Hugh K. PLOS Pathogens, Vol. 14, Issue 7 https://doi.org/10.1371/journal.ppat.1007159	journal	July 2018
High throughput HIV-1 microneutralization assay Doria-Rose, Nicole; Doria-Rose, Nicole; Bailer, Robert Protocol Exchange https://doi.org/10.1038/protex.2013.069	journal	September 2013
cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination Punjani, Ali; Rubinstein, John L.; Fleet, David J. Nature Methods, Vol. 14, Issue 3 https://doi.org/10.1038/nmeth.4169	journal	February 2017
A new method for vitrifying samples for cryoEM Razinkov, Ivan; Dandey, Venkata P.; Wei, Hui Journal of Structural Biology, Vol. 195, Issue 2 https://doi.org/10.1016/j.jsb.2016.06.001	journal	August 2016
[20] Processing of X-ray diffraction data collected in oscillation mode Otwinowski, Zbyszek; Minor, Wladek Macromolecular Crystallography Part A, 307-326 https://doi.org/10.1016/S0076-6879(97)76066-X	book	January 1997
IgBLAST: an immunoglobulin variable domain sequence analysis tool Ye, Jian; Ma, Ning; Madden, Thomas L. Nucleic Acids Research, Vol. 41, Issue W1 https://doi.org/10.1093/nar/gkt382	journal	May 2013
Neutralization of diverse human immunodeficiency virus type 1 variants by an anti-V3 human monoclonal antibody. Gorny, M. K.; Conley, A. J.; Karwowska, S. Journal of Virology, Vol. 66, Issue 12 https://doi.org/10.1128/JVI.66.12.7538-7542.1992	journal	January 1992
Vaccine-Induced Antibodies that Neutralize Group 1 and Group 2 Influenza A Viruses Joyce, M. Gordon; Wheatley, Adam K.; Thomas, Paul V. Cell, Vol. 166, Issue 3 https://doi.org/10.1016/j.cell.2016.06.043	journal	July 2016
Structure and immune recognition of trimeric pre-fusion HIV-1 Env Pancera, Marie; Zhou, Tongqing; Druz, Aliaksandr Nature, Vol. 514, Issue 7523 https://doi.org/10.1038/nature13808	journal	October 2014
Immunization-Elicited Broadly Protective Antibody Reveals Ebolavirus Fusion Loop as a Site of Vulnerability Zhao, Xuelian; Howell, Katie A.; He, Shihua Cell, Vol. 169, Issue 5 https://doi.org/10.1016/j.cell.2017.04.038	journal	May 2017
Antibodies from a Human Survivor Define Sites of Vulnerability for Broad Protection against Ebolaviruses Wec, Anna Z.; Herbert, Andrew S.; Murin, Charles D. Cell, Vol. 169, Issue 5 https://doi.org/10.1016/j.cell.2017.04.037	journal	May 2017
Broad neutralization coverage of HIV by multiple highly potent antibodies Walker, Laura M.; Huber, Michael; Doores, Katie J. Nature, Vol. 477, Issue 7365 https://doi.org/10.1038/nature10373	journal	September 2011
DoG Picker and TiltPicker: Software tools to facilitate particle selection in single particle electron microscopy Voss, N. R.; Yoshioka, C. K.; Radermacher, M. Journal of Structural Biology, Vol. 166, Issue 2 https://doi.org/10.1016/j.jsb.2009.01.004	journal	May 2009
Computation-Guided Backbone Grafting of a Discontinuous Motif onto a Protein Scaffold Azoitei, M. L.; Correia, B. E.; Ban, Y. -E. A. Science, Vol. 334, Issue 6054 https://doi.org/10.1126/science.1209368	journal	October 2011
HIV-1 neutralizing antibodies: understanding nature's pathways Mascola, John R.; Haynes, Barton F. Immunological Reviews, Vol. 254, Issue 1 https://doi.org/10.1111/imr.12075	journal	June 2013
Vaccine-Induced Protection from Homologous Tier 2 SHIV Challenge in Nonhuman Primates Depends on Serum-Neutralizing Antibody Titers Pauthner, Matthias G.; Nkolola, Joseph P.; Havenar-Daughton, Colin Immunity, Vol. 50, Issue 1 https://doi.org/10.1016/j.immuni.2018.11.011	journal	January 2019
Delineating Antibody Recognition in Polyclonal Sera from Patterns of HIV-1 Isolate Neutralization Georgiev, I. S.; Doria-Rose, N. A.; Zhou, T. Science, Vol. 340, Issue 6133 https://doi.org/10.1126/science.1233989	journal	May 2013
PIGS: automatic prediction of antibody structures Marcatili, P.; Rosi, A.; Tramontano, A. Bioinformatics, Vol. 24, Issue 17 https://doi.org/10.1093/bioinformatics/btn341	journal	July 2008
Use of broadly neutralizing antibodies for HIV-1 prevention Pegu, Amarendra; Hessell, Ann J.; Mascola, John R. Immunological Reviews, Vol. 275, Issue 1 https://doi.org/10.1111/imr.12511	journal	January 2017
Production of individualized V gene databases reveals high levels of immunoglobulin genetic diversity Corcoran, Martin M.; Phad, Ganesh E.; Bernat, Néstor Vázquez Nature Communications, Vol. 7, Issue 1 https://doi.org/10.1038/ncomms13642	journal	December 2016
A hot spot of binding energy in a hormone-receptor interface Clackson, T.; Wells, J. Science, Vol. 267, Issue 5196 https://doi.org/10.1126/science.7529940	journal	January 1995
Appion: An integrated, database-driven pipeline to facilitate EM image processing Lander, Gabriel C.; Stagg, Scott M.; Voss, Neil R. Journal of Structural Biology, Vol. 166, Issue 1 https://doi.org/10.1016/j.jsb.2009.01.002	journal	April 2009
Automated molecular microscopy: The new Leginon system Suloway, Christian; Pulokas, James; Fellmann, Denis Journal of Structural Biology, Vol. 151, Issue 1 https://doi.org/10.1016/j.jsb.2005.03.010	journal	July 2005
Surface-Matrix Screening Identifies Semi-specific Interactions that Improve Potency of a Near Pan-reactive HIV-1-Neutralizing Antibody Kwon, Young D.; Chuang, Gwo-Yu; Zhang, Baoshan Cell Reports, Vol. 22, Issue 7 https://doi.org/10.1016/j.celrep.2018.01.023	journal	February 2018
CTFFIND4: Fast and accurate defocus estimation from electron micrographs Rohou, Alexis; Grigorieff, Nikolaus Journal of Structural Biology, Vol. 192, Issue 2 https://doi.org/10.1016/j.jsb.2015.08.008	journal	November 2015
Rational HIV Immunogen Design to Target Specific Germline B Cell Receptors Jardine, J.; Julien, J. -P.; Menis, S. Science, Vol. 340, Issue 6133 https://doi.org/10.1126/science.1234150	journal	March 2013
SONAR: A High-Throughput Pipeline for Inferring Antibody Ontogenies from Longitudinal Sequencing of B Cell Transcripts Schramm, Chaim A.; Sheng, Zizhang; Zhang, Zhenhai Frontiers in Immunology, Vol. 7 https://doi.org/10.3389/fimmu.2016.00372	journal	September 2016
Proof of principle for epitope-focused vaccine design Correia, Bruno E.; Bates, John T.; Loomis, Rebecca J. Nature, Vol. 507, Issue 7491 https://doi.org/10.1038/nature12966	journal	February 2014
Recent developments in the PHENIX software for automated crystallographic structure determination Adams, Paul D.; Gopal, Kreshna; Grosse-Kunstleve, Ralf W. Journal of Synchrotron Radiation, Vol. 11, Issue 1 https://doi.org/10.1107/S0909049503024130	journal	November 2003
Rational Design of Envelope Identifies Broadly Neutralizing Human Monoclonal Antibodies to HIV-1 Wu, X.; Yang, Z. -Y.; Li, Y. Science, Vol. 329, Issue 5993 https://doi.org/10.1126/science.1187659	journal	July 2010
MotionCor2: anisotropic correction of beam-induced motion for improved cryo-electron microscopy Zheng, Shawn Q.; Palovcak, Eugene; Armache, Jean-Paul Nature Methods, Vol. 14, Issue 4 https://doi.org/10.1038/nmeth.4193	journal	February 2017
Maturation and Diversity of the VRC01-Antibody Lineage over 15 Years of Chronic HIV-1 Infection Wu, Xueling; Zhang, Zhenhai; Schramm, Chaim A. Cell, Vol. 161, Issue 3 https://doi.org/10.1016/j.cell.2015.03.004	journal	April 2015
Epitopes Involved in Antibody-Mediated Protection from Ebola Virus Wilson, J. A. Science, Vol. 287, Issue 5458 https://doi.org/10.1126/science.287.5458.1664	journal	March 2000
WebLogo: A Sequence Logo Generator Crooks, Gavin E.; Hon, Gary; Chandonia, John-Marc Genome Research, Vol. 14, Issue 6, p. 1188-1190 https://doi.org/10.1101/gr.849004	journal	May 2004
Single-Chain Soluble BG505.SOSIP gp140 Trimers as Structural and Antigenic Mimics of Mature Closed HIV-1 Env Georgiev, Ivelin S.; Joyce, M. Gordon; Yang, Yongping Journal of Virology, Vol. 89, Issue 10 https://doi.org/10.1128/JVI.03451-14	journal	March 2015
HIV-1 neutralizing antibodies induced by native-like envelope trimers Sanders, R. W.; van Gils, M. J.; Derking, R. Science, Vol. 349, Issue 6244 https://doi.org/10.1126/science.aac4223	journal	June 2015
The HIV-1 envelope glycoprotein structure: nailing down a moving target Ward, Andrew B.; Wilson, Ian A. Immunological Reviews, Vol. 275, Issue 1 https://doi.org/10.1111/imr.12507	journal	January 2017
HIV-1 broadly neutralizing antibody precursor B cells revealed by germline-targeting immunogen Jardine, J. G.; Kulp, D. W.; Havenar-Daughton, C. Science, Vol. 351, Issue 6280 https://doi.org/10.1126/science.aad9195	journal	March 2016
ggseqlogo: a versatile R package for drawing sequence logos Wagih, Omar Bioinformatics, Vol. 33, Issue 22 https://doi.org/10.1093/bioinformatics/btx469	journal	July 2017
Structure and Diversity of the Rhesus Macaque Immunoglobulin Loci through Multiple De Novo Genome Assemblies Ramesh, Akshaya; Darko, Sam; Hua, Axin Frontiers in Immunology, Vol. 8 https://doi.org/10.3389/fimmu.2017.01407	journal	October 2017
Soluble Prefusion Closed DS-SOSIP.664-Env Trimers of Diverse HIV-1 Strains Joyce, M. Gordon; Georgiev, Ivelin S.; Yang, Yongping Cell Reports, Vol. 21, Issue 10 https://doi.org/10.1016/j.celrep.2017.11.016	journal	December 2017
RELION: Implementation of a Bayesian approach to cryo-EM structure determination Scheres, Sjors H. W. Journal of Structural Biology, Vol. 180, Issue 3, p. 519-530 https://doi.org/10.1016/j.jsb.2012.09.006	journal	December 2012
Dendroscope 3: An Interactive Tool for Rooted Phylogenetic Trees and Networks Huson, Daniel H.; Scornavacca, Celine Systematic Biology, Vol. 61, Issue 6 https://doi.org/10.1093/sysbio/sys062	journal	September 2012
EMRinger: side chain–directed model and map validation for 3D cryo-electron microscopy Barad, Benjamin A.; Echols, Nathaniel; Wang, Ray Yu-Ruei Nature Methods, Vol. 12, Issue 10 https://doi.org/10.1038/nmeth.3541	journal	August 2015
HIV-1 Vaccines Based on Antibody Identification, B Cell Ontogeny, and Epitope Structure Kwong, Peter D.; Mascola, John R. Immunity, Vol. 48, Issue 5 https://doi.org/10.1016/j.immuni.2018.04.029	journal	May 2018
Broadly Neutralizing Antiviral Antibodies Corti, Davide; Lanzavecchia, Antonio Annual Review of Immunology, Vol. 31, Issue 1 https://doi.org/10.1146/annurev-immunol-032712-095916	journal	March 2013
Fusion peptide of HIV-1 as a site of vulnerability to neutralizing antibody Kong, R.; Xu, K.; Zhou, T. Science, Vol. 352, Issue 6287 https://doi.org/10.1126/science.aae0474	journal	May 2016
Fast, scalable generation of high‐quality protein multiple sequence alignments using Clustal Omega Sievers, Fabian; Wilm, Andreas; Dineen, David Molecular Systems Biology, Vol. 7, Issue 1 https://doi.org/10.1038/msb.2011.75	journal	January 2011
Match criteria for human cell line authentication: Where do we draw the line? Capes-Davis, Amanda; Reid, Yvonne A.; Kline, Margaret C. International Journal of Cancer, Vol. 132, Issue 11 https://doi.org/10.1002/ijc.27931	journal	November 2012
Complete mapping of viral escape from neutralizing antibodies Doud, Michael B.; Hensley, Scott E.; Bloom, Jesse D. PLOS Pathogens, Vol. 13, Issue 3 https://doi.org/10.1371/journal.ppat.1006271	journal	March 2017
Influenza vaccine: The challenge of antigenic drift Carrat, F.; Flahault, A. Vaccine, Vol. 25, Issue 39-40 https://doi.org/10.1016/j.vaccine.2007.07.027	journal	September 2007
MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0 Tamura, Koichiro; Stecher, Glen; Peterson, Daniel Molecular Biology and Evolution, Vol. 30, Issue 12 https://doi.org/10.1093/molbev/mst197	journal	October 2013
Mimicry of an HIV broadly neutralizing antibody epitope with a synthetic glycopeptide Alam, S. Munir; Aussedat, Baptiste; Vohra, Yusuf Science Translational Medicine, Vol. 9, Issue 381 https://doi.org/10.1126/scitranslmed.aai7521	journal	March 2017
Software for the analysis and visualization of deep mutational scanning data Bloom, Jesse D. BMC Bioinformatics, Vol. 16, Issue 1 https://doi.org/10.1186/s12859-015-0590-4	journal	May 2015

Cited By (6)

Preclinical Development of a Fusion Peptide Conjugate as an HIV Vaccine Immunogen Ou, Li; Kong, Wing-Pui; Chuang, Gwo-Yu Scientific Reports, Vol. 10, Issue 1 https://doi.org/10.1038/s41598-020-59711-y	journal	February 2020
Development of antibodies with broad neutralization specificities against HIV-1 after long term SHIV infection in macaques Nan, Gao; Yanxin, Gai; Lina, Meng Zenodo https://doi.org/10.5281/zenodo.3608719	text	January 2020
Extensive dissemination and intraclonal maturation of HIV Env vaccine-induced B cell responses Phad, Ganesh E.; Pushparaj, Pradeepa; Tran, Karen Journal of Experimental Medicine, Vol. 217, Issue 2 https://doi.org/10.1084/jem.20191155	journal	November 2019
Development of Antibodies with Broad Neutralization Specificities against HIV-1 after Long Term SHIV Infection in Macaques Gao, Nan; Gai, Yanxin; Meng, Lina Viruses, Vol. 12, Issue 2 https://doi.org/10.3390/v12020163	journal	January 2020
Development of antibodies with broad neutralization specificities against HIV-1 after long term SHIV infection in macaques Nan, Gao; Yanxin, Gai; Lina, Meng Zenodo https://doi.org/10.5281/zenodo.3608718	text	January 2020
Disruption of the HIV-1 Envelope allosteric network blocks CD4-induced rearrangements Henderson, Rory; Lu, Maolin; Zhou, Ye Nature Communications, Vol. 11, Issue 1 https://doi.org/10.1038/s41467-019-14196-w	journal	January 2020

Similar Records

Epitope-based vaccine design yields fusion peptide-directed antibodies that neutralize diverse strains of HIV-1

Journal Article · Mon Jun 04 00:00:00 EDT 2018 · Nature Medicine · OSTI ID:1557322

Xu, Kai; Acharya, Priyamvada; Kong, Rui; +51 more

Boosting of HIV envelope CD4 binding site antibodies with long variable heavy third complementarity determining region in the randomized double blind RV305 HIV-1 vaccine trial

Journal Article · Fri Feb 24 00:00:00 EST 2017 · PLoS Pathogens · OSTI ID:1557322

Easterhoff, David; Moody, M. Anthony; Fera, Daniela; +29 more

Structure and immunogenicity of a stabilized HIV-1 envelope trimer based on a group-M consensus sequence

Journal Article · Wed May 29 00:00:00 EDT 2019 · Nature Communications · OSTI ID:1557322

Sliepen, Kwinten; Han, Byung Woo; Bontjer, Ilja; +32 more

Related Subjects

60 APPLIED LIFE SCIENCES
B cell ontogeny
broadly neutralizing antibody
fusion peptide
HIV-1 vaccine
immune monitoring
interaction hotspot
multidonor antibody class

Title: Antibody Lineages with Vaccine-Induced Antigen-Binding Hotspots Develop Broad HIV Neutralization

Citation Formats

References (94)

Cited By (6)

Similar Records

Related Subjects