Conformational Plasticity in the HIV-1 Fusion Peptide Facilitates Recognition by Broadly Neutralizing Antibodies
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Adams, 2010, PHENIX: a comprehensive Python-based system for macromolecular structure solution, Acta Crystallogr. D Biol. Crystallogr., 66, 213, 10.1107/S0907444909052925
Agirre, 2015, Privateer: software for the conformational validation of carbohydrate structures, Nat. Struct. Mol. Biol., 22, 833, 10.1038/nsmb.3115
Aricescu, 2006, A time- and cost-efficient system for high-level protein production in mammalian cells, Acta Crystallogr. D Biol. Crystallogr., 62, 1243, 10.1107/S0907444906029799
Arnold, 2006, The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling, Bioinformatics, 22, 195, 10.1093/bioinformatics/bti770
Barad, 2015, EMRinger: side chain-directed model and map validation for 3D cryo-electron microscopy, Nat. Methods, 12, 943, 10.1038/nmeth.3541
Blattner, 2014, Structural delineation of a quaternary, cleavage-dependent epitope at the gp41-gp120 interface on intact HIV-1 Env trimers, Immunity, 40, 669, 10.1016/j.immuni.2014.04.008
Blumenthal, 2012, HIV entry and envelope glycoprotein-mediated fusion, J. Biol. Chem., 287, 40841, 10.1074/jbc.R112.406272
Chen, 2010, MolProbity: all-atom structure validation for macromolecular crystallography, Acta Crystallogr. D Biol. Crystallogr., 66, 12, 10.1107/S0907444909042073
Chuang, 2019, Structural survey of broadly neutralizing antibodies targeting the HIV-1 Env trimer delineates epitope categories and characteristics of recognition, Structure, 27, 196, 10.1016/j.str.2018.10.007
Crooks, 2004, WebLogo: a sequence logo generator, Genome Res., 14, 1188, 10.1101/gr.849004
de Taeye, 2015, Immunogenicity of stabilized HIV-1 envelope trimers with reduced exposure of non-neutralizing epitopes, Cell, 163, 1702, 10.1016/j.cell.2015.11.056
Derking, 2015, Comprehensive antigenic map of a cleaved soluble HIV-1 envelope trimer, PLoS Pathog., 11, e1004767, 10.1371/journal.ppat.1004767
DiMaio, 2009, Refinement of protein structures into low-resolution density maps using Rosetta, J. Mol. Biol., 392, 181, 10.1016/j.jmb.2009.07.008
Dingens, 2018, Complete functional mapping of infection- and vaccine-elicited antibodies against the fusion peptide of HIV, PLoS Pathog., 14, e1007159, 10.1371/journal.ppat.1007159
Dingens, 2019, An antigenic atlas of HIV-1 escape from broadly neutralizing antibodies distinguishes functional and structural epitopes, Immunity, 50, 520, 10.1016/j.immuni.2018.12.017
Dougherty, 2013, The cation-π interaction, Acc. Chem. Res., 46, 885, 10.1021/ar300265y
Emsley, 2004, Coot: model-building tools for molecular graphics, Acta Crystallogr. D Biol. Crystallogr., 60, 2126, 10.1107/S0907444904019158
Eswar, 2006, Comparative protein structure modeling using Modeller, Curr. Protoc. Bioinformatics, 15, 6.1, 10.1002/0471250953.bi0506s15
Falkowska, 2014, Broadly neutralizing HIV antibodies define a glycan-dependent epitope on the prefusion conformation of gp41 on cleaved envelope trimers, Immunity, 40, 657, 10.1016/j.immuni.2014.04.009
Frenz, 2019, Automatically fixing errors in glycoprotein structures with Rosetta, Structure, 27, 134, 10.1016/j.str.2018.09.006
Gabrys, 2013, Solid-state nuclear magnetic resonance measurements of HIV fusion peptide 13CO to lipid 31P proximities support similar partially inserted membrane locations of the α helical and β sheet peptide structures, J. Phys. Chem. A, 117, 9848, 10.1021/jp312845w
Gilman, 2015, Characterization of a prefusion-specific antibody that recognizes a quaternary, cleavage-dependent epitope on the RSV fusion glycoprotein, PLoS Pathog., 11, e1005035, 10.1371/journal.ppat.1005035
Guttman, 2014, CD4-induced activation in a soluble HIV-1 Env trimer, Structure, 22, 974, 10.1016/j.str.2014.05.001
Huang, 2014, Broad and potent HIV-1 neutralization by a human antibody that binds the gp41-gp120 interface, Nature, 515, 138, 10.1038/nature13601
Johnson, 1998, Preferred CDRH3 lengths for antibodies with defined specificities, Int. Immunol., 10, 1801, 10.1093/intimm/10.12.1801
Julien, 2013, Crystal structure of a soluble cleaved HIV-1 envelope trimer, Science, 342, 1477, 10.1126/science.1245625
Julien, 2015, Design and structure of two HIV-1 clade C SOSIP.664 trimers that increase the arsenal of native-like Env immunogens, Proc. Natl. Acad. Sci. USA, 112, 11947, 10.1073/pnas.1507793112
Kimanius, 2016, Accelerated cryo-EM structure determination with parallelisation using GPUs in RELION-2, eLife, 5, e18722, 10.7554/eLife.18722
Kong, 2016, Fusion peptide of HIV-1 as a site of vulnerability to neutralizing antibody, Science, 352, 828, 10.1126/science.aae0474
Krissinel, 2007, Inference of macromolecular assemblies from crystalline state, J. Mol. Biol., 372, 774, 10.1016/j.jmb.2007.05.022
Kumar, 2019, Capturing the inherent structural dynamics of the HIV-1 envelope glycoprotein fusion peptide, Nat. Commun., 10, 763, 10.1038/s41467-019-08738-5
Kunert, 1998, Molecular characterization of five neutralizing anti-HIV type 1 antibodies: identification of nonconventional D segments in the human monoclonal antibodies 2G12 and 2F5, AIDS Res. Hum. Retroviruses, 14, 1115, 10.1089/aid.1998.14.1115
Lee, 2016, Cryo-EM structure of a native, fully glycosylated, cleaved HIV-1 envelope trimer, Science, 351, 1043, 10.1126/science.aad2450
Lütteke, 2005, Carbohydrate Structure Suite (CSS): analysis of carbohydrate 3D structures derived from the PDB, Nucleic Acids Res., 33, D242, 10.1093/nar/gki013
Lyumkis, 2013, Cryo-EM structure of a fully glycosylated soluble cleaved HIV-1 envelope trimer, Science, 342, 1484, 10.1126/science.1245627
McCoy, 2007, Phaser crystallographic software, J. Appl. Crystallogr., 40, 658, 10.1107/S0021889807021206
McCoy, 2018, The expanding array of HIV broadly neutralizing antibodies, Retrovirology, 15, 70, 10.1186/s12977-018-0453-y
McCoy, 2016, Holes in the glycan shield of the native HIV envelope are a target of trimer-elicited neutralizing antibodies, Cell Rep., 16, 2327, 10.1016/j.celrep.2016.07.074
Pettersen, 2004, UCSF Chimera—a visualization system for exploratory research and analysis, J. Comput. Chem., 25, 1605, 10.1002/jcc.20084
Pugach, 2015, A native-like SOSIP.664 trimer based on an HIV-1 subtype B env gene, J. Virol., 89, 3380, 10.1128/JVI.03473-14
Punjani, 2017, cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination, Nat. Methods, 14, 290, 10.1038/nmeth.4169
Rantalainen, 2018, Co-evolution of HIV envelope and apex-targeting neutralizing antibody lineage provides benchmarks for vaccine design, Cell Rep., 23, 3249, 10.1016/j.celrep.2018.05.046
Sackett, 2014, Solid-state NMR spectroscopy of the HIV gp41 membrane fusion protein supports intermolecular antiparallel β sheet fusion peptide structure in the final six-helix bundle state, J. Mol. Biol., 426, 1077, 10.1016/j.jmb.2013.11.010
Sanders, 2013, A next-generation cleaved, soluble HIV-1 Env trimer, BG505 SOSIP.664 gp140, expresses multiple epitopes for broadly neutralizing but not non-neutralizing antibodies, PLoS Pathog., 9, e1003618, 10.1371/journal.ppat.1003618
Sanders, 2015, HIV-1 VACCINES. HIV-1 neutralizing antibodies induced by native-like envelope trimers, Science, 349, aac4223, 10.1126/science.aac4223
Sarkar, 2018, Structure of a cleavage-independent HIV Env recapitulates the glycoprotein architecture of the native cleaved trimer, Nat. Commun., 9, 1956, 10.1038/s41467-018-04272-y
Scharf, 2014, Antibody 8ANC195 reveals a site of broad vulnerability on the HIV-1 envelope spike, Cell Rep., 7, 785, 10.1016/j.celrep.2014.04.001
Scheid, 2011, Sequence and structural convergence of broad and potent HIV antibodies that mimic CD4 binding, Science, 333, 1633, 10.1126/science.1207227
Sharma, 2015, Cleavage-independent HIV-1 Env trimers engineered as soluble native spike mimetics for vaccine design, Cell Rep., 11, 539, 10.1016/j.celrep.2015.03.047
Sok, 2018, Recent progress in broadly neutralizing antibodies to HIV, Nat. Immunol., 19, 1179, 10.1038/s41590-018-0235-7
Sok, 2013, The effects of somatic hypermutation on neutralization and binding in the PGT121 family of broadly neutralizing HIV antibodies, PLoS Pathog., 9, e1003754, 10.1371/journal.ppat.1003754
Stewart-Jones, 2016, Trimeric HIV-1-Env structures define glycan shields from clades A, B, and G, Cell, 165, 813, 10.1016/j.cell.2016.04.010
Suloway, 2005, Automated molecular microscopy: the new Leginon system, J. Struct. Biol., 151, 41, 10.1016/j.jsb.2005.03.010
van den Kerkhof, 2014, Early development of broadly reactive HIV-1 neutralizing activity in elite neutralizers, AIDS, 28, 1237, 10.1097/QAD.0000000000000228
van Gils, 2016, An HIV-1 antibody from an elite neutralizer implicates the fusion peptide as a site of vulnerability, Nat. Microbiol., 2, 16199, 10.1038/nmicrobiol.2016.199
Voss, 2009, DoG Picker and TiltPicker: software tools to facilitate particle selection in single particle electron microscopy, J. Struct. Biol., 166, 205, 10.1016/j.jsb.2009.01.004
Walker, 2011, Broad neutralization coverage of HIV by multiple highly potent antibodies, Nature, 477, 466, 10.1038/nature10373
Ward, 2017, The HIV-1 envelope glycoprotein structure: nailing down a moving target, Immunol. Rev., 275, 21, 10.1111/imr.12507
Wibmer, 2017, Structure and recognition of a novel HIV-1 gp120-gp41 interface antibody that caused MPER exposure through viral escape, PLoS Pathog., 13, e1006074, 10.1371/journal.ppat.1006074
Wilson, 1981, Structure of the haemagglutinin membrane glycoprotein of influenza virus at 3 Å resolution, Nature, 289, 366, 10.1038/289366a0
Winter, 2010, xia2: an expert system for macromolecular crystallography data reduction, J. Appl. Crystallogr., 43, 186, 10.1107/S0021889809045701
Wu, 1970, An analysis of the sequences of the variable regions of Bence Jones proteins and myeloma light chains and their implications for antibody complementarity, J. Exp. Med., 132, 211, 10.1084/jem.132.2.211
Wu, 2010, Rational design of envelope identifies broadly neutralizing human monoclonal antibodies to HIV-1, Science, 329, 856, 10.1126/science.1187659
Xu, 2018, Epitope-based vaccine design yields fusion peptide-directed antibodies that neutralize diverse strains of HIV-1, Nat. Med., 24, 857, 10.1038/s41591-018-0042-6
Yang, 2018, Structure-guided redesign improves NFL HIV Env trimer integrity and identifies an inter-protomer disulfide permitting post-expression cleavage, Front. Immunol., 9, 1631, 10.3389/fimmu.2018.01631
Ye, 2013, IgBLAST: an immunoglobulin variable domain sequence analysis tool, Nucleic Acids Res., 41, W34, 10.1093/nar/gkt382
Yu, 2014, Immunologic basis for long HCDR3s in broadly neutralizing antibodies against HIV-1, Front. Immunol., 5, 250, 10.3389/fimmu.2014.00250
Zhang, 2016, Gctf: real-time CTF determination and correction, J. Struct. Biol., 193, 1, 10.1016/j.jsb.2015.11.003
Zheng, 2017, MotionCor2: anisotropic correction of beam-induced motion for improved cryo-electron microscopy, Nat. Methods, 14, 331, 10.1038/nmeth.4193