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Cited by 1Mosquito-borne diseases and controlEnzyme Structure and FunctionProtein Structure and Dynamics

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Secreted dengue virus NS1 from infection is predominantly dimeric and in complex with high-density lipoprotein

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Chew, Bing Liang Alvin, Ngoh, AN Qi, Phoo, Wint Wint, Chan, Kitti Wing Ki, Ser, Zheng, Tulsian, Nikhil K, Lim, Shiao See, Weng, Mei Jie Grace, Watanabe, Satoru, Choy, Milly M, Low, Jenny, Ooi, Eng Eong, Ruedl, Christiane, Sobota, Radoslaw M, Vasudevan, Subhash G, Luo, Dahai·2024·eLife
DOI 10.7554/elife.90762.3

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Abstract

Severe dengue infections are characterized by endothelial dysfunction shown to be associated with the secreted nonstructural protein 1 (sNS1), making it an attractive vaccine antigen and biotherapeutic target. To uncover the biologically relevant structure of sNS1, we obtained infection-derived sNS1 (isNS1) from dengue virus (DENV)-infected Vero cells through immunoaffinity purification instead of recombinant sNS1 (rsNS1) overexpressed in insect or mammalian cell lines. We found that isNS1 appeared as an approximately 250 kDa complex of NS1 and ApoA1 and further determined the cryoEM structures of isNS1 and its complex with a monoclonal antibody/Fab. Indeed, we found that the major species of isNS1 is a complex of the NS1 dimer partially embedded in a high-density lipoprotein (HDL) particle. Crosslinking mass spectrometry studies confirmed that the isNS1 interacts with the major HDL component ApoA1 through interactions that map to the NS1 wing and hydrophobic domains. Furthermore, our studies demonstrated that the sNS1 in sera from DENV-infected mice and a human patient form a similar complex as isNS1. Our results report the molecular architecture of a biological form of sNS1, which may have implications for the molecular pathogenesis of dengue.

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Research works printed but not linked: 72

  1. Acton, 1996, Identification of scavenger receptor SR-BI as a high density lipoprotein receptor, Science, 271, 518, 10.1126/science.271.5248.518 · DOI · Paper page
  2. Akey, 2014, Flavivirus NS1 structures reveal surfaces for associations with membranes and the immune system, Science, 343, 881, 10.1126/science.1247749 · DOI
  3. Alcalá, 2017, The dengue virus non-structural protein 1 (NS1) is secreted from infected mosquito cells via a non-classical caveolin-1-dependent pathway, The Journal of General Virology, 98, 2088, 10.1099/jgv.0.000881 · DOI
  4. Alcalá, 2022, Dengue virus ns1 uses scavenger receptor b1 as a cell receptor in cultured cells, Journal of Virology, 96, 10.1128/JVI.01664-21 · DOI
  5. Alcon, 2002, Enzyme-linked immunosorbent assay specific to Dengue virus type 1 nonstructural protein NS1 reveals circulation of the antigen in the blood during the acute phase of disease in patients experiencing primary or secondary infections, Journal of Clinical Microbiology, 40, 376, 10.1128/JCM.40.02.376-381.2002 · DOI
  6. Alcon-LePoder, 2005, The secreted form of dengue virus nonstructural protein NS1 is endocytosed by hepatocytes and accumulates in late endosomes: implications for viral infectivity, Journal of Virology, 79, 11403, 10.1128/JVI.79.17.11403-11411.2005 · DOI
  7. Avirutnan, 2007, Secreted NS1 of dengue virus attaches to the surface of cells via interactions with heparan sulfate and chondroitin sulfate E, PLOS Pathogens, 3, 10.1371/journal.ppat.0030183 · DOI
  8. Beatty, 2015, Dengue virus NS1 triggers endothelial permeability and vascular leak that is prevented by NS1 vaccination, Science Translational Medicine, 7, 10.1126/scitranslmed.aaa3787 · DOI
  9. Benfrid, 2022, Dengue virus NS1 protein conveys pro-inflammatory signals by docking onto high-density lipoproteins, EMBO Reports, 23, 10.15252/embr.202153600 · DOI
  10. Bepler, 2019, Positive-unlabeled convolutional neural networks for particle picking in cryo-electron micrographs, Nature Methods, 16, 1153, 10.1038/s41592-019-0575-8 · DOI
  11. Bhatt, 2013, The global distribution and burden of dengue, Nature, 496, 504, 10.1038/nature12060 · DOI · Paper page
  12. Biering, 2021, Structural basis for antibody inhibition of flavivirus NS1-triggered endothelial dysfunction, Science, 371, 194, 10.1126/science.abc0476 · DOI
  13. Bloch, 2020, Structure and mechanism of the ER-based glucosyltransferase ALG6, Nature, 579, 443, 10.1038/s41586-020-2044-z · DOI
  14. Brown, 2016, Extended surface for membrane association in Zika virus NS1 structure, Nature Structural & Molecular Biology, 23, 865, 10.1038/nsmb.3268 · DOI
  15. Bullock, 2018, Jwalk and MNXL web server: model validation using restraints from crosslinking mass spectrometry, Bioinformatics, 34, 3584, 10.1093/bioinformatics/bty366 · DOI
  16. Chan, 2019, A T164S mutation in the dengue virus NS1 protein is associated with greater disease severity in mice, Science Translational Medicine, 11, 10.1126/scitranslmed.aat7726 · DOI
  17. Coelho, 2021, Apoa1 neutralizes proinflammatory effects of dengue virus ns1 protein and modulates viral immune evasion, Journal of Virology, 95, 10.1128/JVI.01974-20 · DOI
  18. de la Rosa-Trevín, 2013, Xmipp 3.0: an improved software suite for image processing in electron microscopy, Journal of Structural Biology, 184, 321, 10.1016/j.jsb.2013.09.015 · DOI
  19. de la Rosa-Trevín, 2016, Scipion: A software framework toward integration, reproducibility and validation in 3D electron microscopy, Journal of Structural Biology, 195, 93, 10.1016/j.jsb.2016.04.010 · DOI
  20. Diamond, 2015, Molecular insight into dengue virus pathogenesis and its implications for disease control, Cell, 162, 488, 10.1016/j.cell.2015.07.005 · DOI
  21. Edeling, 2014, Structural basis of Flavivirus NS1 assembly and antibody recognition, PNAS, 111, 4285, 10.1073/pnas.1322036111 · DOI
  22. Flamand, 1999, Dengue virus type 1 nonstructural glycoprotein NS1 is secreted from mammalian cells as a soluble hexamer in a glycosylation-dependent fashion, Journal of Virology, 73, 6104, 10.1128/JVI.73.7.6104-6110.1999 · DOI
  23. Glasner, 2018, The good, the bad, and the shocking: the multiple roles of dengue virus nonstructural protein 1 in protection and pathogenesis, Annual Review of Virology, 5, 227, 10.1146/annurev-virology-101416-041848 · DOI
  24. Graham, 2019, xiView: A Common Platform for the Downstream Analysis of Crosslinking Mass Spectrometry Data, 10.1101/561829 · DOI
  25. Gutsche, 2011, Secreted dengue virus nonstructural protein NS1 is an atypical barrel-shaped high-density lipoprotein, PNAS, 108, 8003, 10.1073/pnas.1017338108 · DOI
  26. Han, 2020, High-yield monolayer graphene grids for near-atomic resolution cryoelectron microscopy, PNAS, 117, 1009, 10.1073/pnas.1919114117 · DOI
  27. Harsløf, 2023, Lower levels of small HDL particles associated with increased infectious disease morbidity and mortality: a population-based cohort study of 30 195 individuals, Cardiovascular Research, 119, 957, 10.1093/cvr/cvac194 · DOI
  28. He, 2019, Apolipoprotein a1 forms 5/5 and 5/4 antiparallel dimers in human high-density lipoprotein, Molecular & Cellular Proteomics, 18, 854, 10.1074/mcp.RA118.000878 · DOI · Paper page
  29. Kao, 2011, Development of a novel cross-linking strategy for fast and accurate identification of cross-linked peptides of protein complexes, Molecular & Cellular Proteomics, 10, 10.1074/mcp.M110.002212 · DOI
  30. Kitti, 2019, The role of genetic variants of non-structural protein 1 in dengue pathogenesis
  31. Lagerwaard, 2022, Xlink Mapping and AnalySis (XMAS) - Smooth Integrative Modeling in ChimeraX, 10.1101/2022.04.21.489026 · DOI
  32. Lau, 2021, Deuteros 2.0: peptide-level significance testing of data from hydrogen deuterium exchange mass spectrometry, Bioinformatics, 37, 270, 10.1093/bioinformatics/btaa677 · DOI
  33. Lee, 2020, Relative contribution of nonstructural protein 1 in dengue pathogenesis, The Journal of Experimental Medicine, 217, 10.1084/jem.20191548 · DOI
  34. Libraty, 2002, High circulating levels of the dengue virus nonstructural protein NS1 early in dengue illness correlate with the development of dengue hemorrhagic fever, The Journal of Infectious Diseases, 186, 1165, 10.1086/343813 · DOI
  35. Low, 2014, Efficacy and safety of celgosivir in patients with dengue fever (CELADEN): a phase 1b, randomised, double-blind, placebo-controlled, proof-of-concept trial, The Lancet. Infectious Diseases, 14, 706, 10.1016/S1473-3099(14)70730-3 · DOI
  36. Lu, 2018, Identification of MS-cleavable and noncleavable chemically cross-linked peptides with metamorpheus, Journal of Proteome Research, 17, 2370, 10.1021/acs.jproteome.8b00141 · DOI
  37. Malajczuk, 2021, Structure and intermolecular interactions in spheroidal high-density lipoprotein subpopulations, Journal of Structural Biology, 5, 10.1016/j.yjsbx.2020.100042 · DOI
  38. Mastronarde, 2005, Automated electron microscope tomography using robust prediction of specimen movements, Journal of Structural Biology, 152, 36, 10.1016/j.jsb.2005.07.007 · DOI
  39. Mirdita, 2022, ColabFold: making protein folding accessible to all, Nature Methods, 19, 679, 10.1038/s41592-022-01488-1 · DOI · Paper page
  40. Modhiran, 2015, Dengue virus NS1 protein activates cells via Toll-like receptor 4 and disrupts endothelial cell monolayer integrity, Science Translational Medicine, 7, 10.1126/scitranslmed.aaa3863 · DOI
  41. Modhiran, 2021, A broadly protective antibody that targets the flavivirus NS1 protein, Science, 371, 190, 10.1126/science.abb9425 · DOI
  42. Moreland, 2010, High affinity human antibody fragments to dengue virus non-structural protein 3, PLOS Neglected Tropical Diseases, 4, 10.1371/journal.pntd.0000881 · DOI
  43. Muller, 2012, Structure of the dengue virus glycoprotein non-structural protein 1 by electron microscopy and single-particle analysis, The Journal of General Virology, 93, 771, 10.1099/vir.0.039321-0 · DOI
  44. Paranavitane, 2014, Dengue NS1 antigen as a marker of severe clinical disease, BMC Infectious Diseases, 14, 10.1186/s12879-014-0570-8 · DOI
  45. Perez-Riverol, 2022, The PRIDE database resources in 2022: a hub for mass spectrometry-based proteomics evidences, Nucleic Acids Research, 50, D543, 10.1093/nar/gkab1038 · DOI · Paper page
  46. Pettersen, 2021, UCSF ChimeraX: Structure visualization for researchers, educators, and developers, Protein Science, 30, 70, 10.1002/pro.3943 · DOI
  47. Płaszczyca, 2019, A novel interaction between dengue virus nonstructural protein 1 and the NS4A-2K-4B precursor is required for viral RNA replication but not for formation of the membranous replication organelle, PLOS Pathogens, 15, 10.1371/journal.ppat.1007736 · DOI
  48. Poonsiri, 2018, Structural study of the c-terminal domain of nonstructural protein 1 from japanese encephalitis virus, Journal of Virology, 92, 10.1128/JVI.01868-17 · DOI
  49. Puerta-Guardo, 2016, Dengue virus NS1 disrupts the endothelial glycocalyx, leading to hyperpermeability, PLOS Pathogens, 12, 10.1371/journal.ppat.1005738 · DOI
  50. Puerta-Guardo, 2019, Flavivirus NS1 triggers tissue-specific vascular endothelial dysfunction reflecting disease tropism, Cell Reports, 26, 1598, 10.1016/j.celrep.2019.01.036 · DOI
  51. Punjani, 2017, cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination, Nature Methods, 14, 290, 10.1038/nmeth.4169 · DOI · Paper page
  52. Punjani, 2020, Non-uniform refinement: adaptive regularization improves single-particle cryo-EM reconstruction, Nature Methods, 17, 1214, 10.1038/s41592-020-00990-8 · DOI
  53. Rodriguez-Roche, 2005, Virus evolution during a severe dengue epidemic in Cuba, 1997, Virology, 334, 154, 10.1016/j.virol.2005.01.037 · DOI
  54. Rozen-Gagnon, 2012, Expression and immunoaffinity purification of recombinant dengue virus 2 NS1 protein as a cleavable SUMOstar fusion, Protein Expression and Purification, 82, 20, 10.1016/j.pep.2011.11.003 · DOI
  55. Scaturro, 2015, Dengue virus non-structural protein 1 modulates infectious particle production via interaction with the structural proteins, PLOS Pathogens, 11, 10.1371/journal.ppat.1005277 · DOI
  56. Shu, 2022, CryoEM structures of the multimeric secreted NS1, a major factor for dengue hemorrhagic fever, Nature Communications, 13, 10.1038/s41467-022-34415-1 · DOI
  57. Silva, 2008, Structure of apolipoprotein A-I in spherical high density lipoproteins of different sizes, PNAS, 105, 12176, 10.1073/pnas.0803626105 · DOI
  58. Tall, 2021, HDL in morbidity and mortality: a 40+ year perspective, Clinical Chemistry, 67, 19, 10.1093/clinchem/hvaa148 · DOI
  59. Tan, 2017, Addressing preferred specimen orientation in single-particle cryo-EM through tilting, Nature Methods, 14, 793, 10.1038/nmeth.4347 · DOI
  60. Trinder, 2020, Causal inference for genetically determined levels of high-density lipoprotein cholesterol and risk of infectious disease, Arteriosclerosis, Thrombosis, and Vascular Biology, 40, 267, 10.1161/ATVBAHA.119.313381 · DOI
  61. Wagner, 2019, SPHIRE-crYOLO is a fast and accurate fully automated particle picker for cryo-EM, Communications Biology, 2, 10.1038/s42003-019-0437-z · DOI
  62. Wales, 2008, High-speed and high-resolution UPLC separation at zero degrees Celsius, Analytical Chemistry, 80, 6815, 10.1021/ac8008862 · DOI
  63. Wang, 2017, A mutation identified in neonatal microcephaly destabilizes zika virus ns1 assembly in vitro, Scientific Reports, 7, 10.1038/srep42580 · DOI
  64. Wang, 2019, Endocytosis of flavivirus NS1 is required for NS1-mediated endothelial hyperpermeability and is abolished by a single N-glycosylation site mutation, PLOS Pathogens, 15, 10.1371/journal.ppat.1007938 · DOI
  65. Watterson, 2016, The many faces of the flavivirus NS1 protein offer a multitude of options for inhibitor design, Antiviral Research, 130, 7, 10.1016/j.antiviral.2016.02.014 · DOI
  66. Wu, 2012, Fabs enable single particle cryoEM studies of small proteins, Structure, 20, 582, 10.1016/j.str.2012.02.017 · DOI
  67. Xu, 2016, Contribution of intertwined loop to membrane association revealed by Zika virus full-length NS1 structure, The EMBO Journal, 35, 2170, 10.15252/embj.201695290 · DOI
  68. Young, 2000, An antigen capture enzyme-linked immunosorbent assay reveals high levels of the dengue virus protein NS1 in the sera of infected patients, Journal of Clinical Microbiology, 38, 1053, 10.1128/JCM.38.3.1053-1057.2000 · DOI
  69. Zivanov, 2018, New tools for automated high-resolution cryo-EM structure determination in RELION-3, eLife, 7, 10.7554/eLife.42166 · DOI
  70. Chew BLA, Luo D. 2023. CryoEM structure of isNS1 in complex with Fab56.2. EMDataResource. https://www.emdataresource.org/EMD-36483. EMD-36483.
  71. Chew BLA, Luo D. 2023. CryoEM structure of isNS1 in complex with Fab56.2 and HDL. EMDataResource. https://www.emdataresource.org/EMD-36480. EMD-36480.
  72. Sobota R, Zheng S, Phoo WW, Luo D. 2023. Secreted dengue virus NS1 is predominantly dimeric and in complex with high-density lipoprotein. Jpost repository. https://repository.jpostdb.org/entry/JPST001925. JPST001925.

Metadata

Authors
Chew, B. L. A., Ngoh, A. Q., Phoo, W. W., Chan, K. W. K., Ser, Z., Tulsian, N. K., Lim, S. S., Weng, M. J. G., Watanabe, S., Choy, M. M., Low, J., Ooi, E. E., Ruedl, C., Sobota, R. M., Vasudevan, S. G., & Luo, D.
Affiliations
  • Nanyang Technological University (SG)
  • Duke-NUS Medical School (SG)
  • Agency for Science, Technology and Research (SG)
  • National University of Singapore (SG)
  • Singapore General Hospital (SG)
  • Griffith University (AU)
ORCID
Venue
eLife
Publisher
eLife Sciences Publications, Ltd
Published
2024-05-24
Volume
12
ISSN
2050-084X (ISSN-L)
DOI
10.7554/elife.90762.3
OpenAlex
W4398777229
Cited by
1
References
1
Citations by year
2026: 1
FWCI
0.42
Type
journal article
Language
en
Open access
Licence
Locations
eLife (publishedVersion, cc-by)
Funders
  • Ministry of Education - Singapore (T2EP30220-0020)
  • National Medical Research Council (MOH-OFIRG20nov-0002, MOHOFIRG18may-0006)
  • Agency for Science, Technology and Research (Career Development Fund 2021)
  • Lee Kong Chian School of Medicine, Nanyang Technological University (LKCMedicine Dean's Postdoctoral Fellowship)
Topics
  • Health Sciences › Medicine › Public Health, Environmental and Occupational Health › Mosquito-borne diseases and control
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › Enzyme Structure and Function
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
Keywords
dengue virus NS1, high-density lipoprotein, apolipoprotein A-I, protein-lipid complex, cryo-EM structure, endothelial dysfunction, severe dengue, molecular pathogenesis, cross-linking mass spectrometry

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