Flavivirus Zika NS4A protein forms large oligomers in liposomes and in mild detergent.
Analytical ultracentrifugation
Dengue virus
Flavivirus
Non-structural protein 4A
Oligomerization
Zika virus
Journal
Scientific reports
ISSN: 2045-2322
Titre abrégé: Sci Rep
Pays: England
ID NLM: 101563288
Informations de publication
Date de publication:
31 May 2024
31 May 2024
Historique:
received:
11
04
2023
accepted:
28
05
2024
medline:
1
6
2024
pubmed:
1
6
2024
entrez:
31
5
2024
Statut:
epublish
Résumé
In flaviviruses such as Dengue or Zika, non-structural (NS) NS4A protein forms homo-oligomers, participates in membrane remodelling and is critical for virulence. In both viruses, mature NS4A has the same length and three predicted hydrophobic domains. The oligomers formed by Dengue NS4A are reported to be small (n = 2, 3), based on denaturing SDS gels, but no high-resolution structure of a flavivirus NS4A protein is available, and the size of the oligomer in lipid membranes is not known. Herein we show that crosslinking Zika NS4A protein in lipid membranes results in oligomers at least up to hexamers. Further, sedimentation velocity shows that NS4A in mild detergent C14-betaine appears to be in fast equilibrium between at least two species, where one is smaller, and the other larger, than a trimer or a tetramer. Consistently, sedimentation equilibrium data was best fitted to a model involving an equilibrium between dimers (n = 2) and hexamers (n = 6). Overall, the large, at least hexameric, oligomers obtained herein in liposomes and in mild detergent are more likely to represent the forms of NS4A present in cell membranes.
Identifiants
pubmed: 38822066
doi: 10.1038/s41598-024-63407-y
pii: 10.1038/s41598-024-63407-y
doi:
Substances chimiques
Liposomes
0
Viral Nonstructural Proteins
0
Detergents
0
NS4A protein, flavivirus
0
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
12533Informations de copyright
© 2024. The Author(s).
Références
Dick, G. W. A. Zika virus (I). Isolations and serological specificity. Trans. R. Soc. Trop. Med. Hyg. 46, 509–520. https://doi.org/10.1016/0035-9203(52)90042-4 (1952).
doi: 10.1016/0035-9203(52)90042-4
pubmed: 12995440
Zanluca, C. et al. First report of autochthonous transmission of Zika virus in Brazil. Mem. Inst. Oswaldo Cruz 110, 569–572. https://doi.org/10.1590/0074-02760150192 (2015).
doi: 10.1590/0074-02760150192
pubmed: 26061233
pmcid: 4501423
WHO. Countries and Territories with Current or Previous Zika Virus Transmission. https://cdn.who.int/media/docs/default-source/documents/emergencies/zika/countries-with-zika-and-vectors-table_february-2022.pdf?sfvrsn=4dc1f8ab_9 (2022).
Gould, E. & Solomon, T. Pathogenic flaviviruses. The Lancet 371, 500–509. https://doi.org/10.1016/S0140-6736(08)60238-X (2008).
doi: 10.1016/S0140-6736(08)60238-X
Diagne, C. T. et al. Potential of selected Senegalese Aedes spp. mosquitoes (Diptera: Culicidae) to transmit Zika virus. BMC Infect. Dis. 15, 2. https://doi.org/10.1186/s12879-015-1231-2 (2015).
doi: 10.1186/s12879-015-1231-2
Li, M. I., Wong, P. S. J., Ng, L. C. & Tan, C. H. Oral susceptibility of Singapore Aedes (Stegomyia) aegypti (Linnaeus) to Zika virus. PLoS Negl. Trop. Dis. 6, 1792. https://doi.org/10.1371/journal.pntd.0001792 (2012).
doi: 10.1371/journal.pntd.0001792
Hamel, R. et al. Biology of Zika virus infection in human skin cells. J. Virol. 89, 8880–8896. https://doi.org/10.1128/JVI.00354-15 (2015).
doi: 10.1128/JVI.00354-15
pubmed: 26085147
pmcid: 4524089
Besnard, M., Lastère, S., Teissier, A., Cao-Lormeau, V. M. & Musso, D. Evidence of perinatal transmission of zika virus, French Polynesia, December 2013 and February 2014. Eurosurveillance 19, 1 (2014).
doi: 10.2807/1560-7917.ES2014.19.13.20751
Foy, B. D. et al. Probable non-vector-borne transmission of Zika virus, Colorado, USA. Emerg. Infect. Dis. 17, 880–882. https://doi.org/10.3201/eid1705.101939 (2011).
doi: 10.3201/eid1705.101939
pubmed: 21529401
pmcid: 3321795
Musso, D. et al. Potential for Zika virus transmission through blood transfusion demonstrated during an outbreak in French Polynesia, November 2013 to February 2014. Eurosurveillance 19, 1 (2014).
doi: 10.2807/1560-7917.ES2014.19.14.20761
Duffy, M. R. et al. Zika virus outbreak on Yap Island, Federated States of Micronesia. N. Engl. J. Med. 360, 2536–2543. https://doi.org/10.1056/NEJMoa0805715 (2009).
doi: 10.1056/NEJMoa0805715
pubmed: 19516034
Higgs, S. Zika virus: Emergence and emergency. Vector-Borne Zoonotic Dis. 16, 75–76. https://doi.org/10.1089/vbz.2016.29001.hig (2016).
doi: 10.1089/vbz.2016.29001.hig
pubmed: 26824625
Martines, R. B. et al. Evidence of Zika virus infection in brain and placental tissues from two congenitally infected newborns and two fetal losses—Brazil, 2015. Morb. Mortal. Wkly. Rep. 65, 159–160 (2016).
doi: 10.15585/mmwr.mm6506e1
Mlakar, J. et al. Zika virus associated with microcephaly. New Engl. J. Med. 374, 951–958. https://doi.org/10.1056/NEJMoa1600651 (2016).
doi: 10.1056/NEJMoa1600651
pubmed: 26862926
Schuler-Faccini, L. et al. Possible association between Zika virus infection and microcephaly—Brazil, 2015. Morb. Mortal. Wkly. Rep. 65, 59–62 (2016).
doi: 10.15585/mmwr.mm6503e2
Rubin, E. J., Greene, M. F. & Baden, L. R. Zika virus and microcephaly. New Engl. J. Med. 374, 984–985. https://doi.org/10.1056/NEJMe1601379 (2016).
doi: 10.1056/NEJMe1601379
pubmed: 26862812
Vhp, L. et al. Congenital zika virus infection: A review with emphasis on the spectrum of brain abnormalities. Curr. Neurol. Neurosci. Rep. 20, 1–11. https://doi.org/10.1007/s11910-020-01072-0 (2020).
doi: 10.1007/s11910-020-01072-0
Garcez, P. P. et al. Zika virus: Zika virus impairs growth in human neurospheres and brain organoids. Science 352, 816–818. https://doi.org/10.1126/science.aaf6116 (2016).
doi: 10.1126/science.aaf6116
pubmed: 27064148
Beattie, J. et al. Zika virus-associated Guillain–Barre syndrome in a returning US traveler. Infect. Dis. Clin. Pract. 26, e80–e84. https://doi.org/10.1097/IPC.0000000000000654 (2018).
doi: 10.1097/IPC.0000000000000654
Oehler, E. et al. Zika virus infection complicated by Guillain–Barré syndrome case report, French Polynesia, December 2013. Eurosurveillance 19, 1 (2014).
doi: 10.2807/1560-7917.ES2014.19.9.20720
Cao-Lormeau, V. M. et al. Guillain-Barré Syndrome outbreak associated with Zika virus infection in French Polynesia: A case-control study. The Lancet 387, 1531–1539. https://doi.org/10.1016/S0140-6736(16)00562-6 (2016).
doi: 10.1016/S0140-6736(16)00562-6
Pielnaa, P. et al. Zika virus-spread, epidemiology, genome, transmission cycle, clinical manifestation, associated challenges, vaccine and antiviral drug development. Virology 543, 34–42. https://doi.org/10.1016/j.virol.2020.01.015 (2020).
doi: 10.1016/j.virol.2020.01.015
pubmed: 32056845
Ribeiro, G. S. & Kitron, U. Zika virus pandemic: A human and public health crisis. Rev. Soc. Bras. Med. Trop. 49, 1–3. https://doi.org/10.1590/0037-8682-0036-2016 (2016).
doi: 10.1590/0037-8682-0036-2016
pubmed: 27163559
Kuno, G. & Chang, G. J. J. Full-length sequencing and genomic characterization of Bagaza, Kedougou, and Zika viruses. Arch. Virol. 152, 687–696. https://doi.org/10.1007/s00705-006-0903-z (2007).
doi: 10.1007/s00705-006-0903-z
pubmed: 17195954
Martin-Acebes, M. A. & Saiz, J. C. West Nile virus: A re-emerging pathogen revisited. World J. Virol. 1, 51–70 (2012).
doi: 10.5501/wjv.v1.i2.51
pubmed: 24175211
pmcid: 3782267
Acosta, E. G., Kumar, A. & Bartenschlager, R. Revisiting dengue virus–host cell interaction: New insights into molecular and cellular virology. Adv. Virus Res. 88, 1–109 (2014).
doi: 10.1016/B978-0-12-800098-4.00001-5
pubmed: 24373310
Ye, Q. et al. Genomic characterization and phylogenetic analysis of Zika virus circulating in the Americas. Infect. Genet. Evol. 43, 43–49. https://doi.org/10.1016/j.meegid.2016.05.004 (2016).
doi: 10.1016/j.meegid.2016.05.004
pubmed: 27156653
Welsch, S. et al. Composition and three-dimensional architecture of the dengue virus replication and assembly sites. Cell Host Microbe 5, 365–375. https://doi.org/10.1016/j.chom.2009.03.007 (2009).
doi: 10.1016/j.chom.2009.03.007
pubmed: 19380115
pmcid: 7103389
Miorin, L. et al. Three-dimensional architecture of tick-borne encephalitis virus replication sites and trafficking of the replicated RNA. J. Virol. 87, 6469–6481. https://doi.org/10.1128/JVI.03456-12 (2013).
doi: 10.1128/JVI.03456-12
pubmed: 23552408
pmcid: 3648123
Romero-Brey, I. & Bartenschlager, R. Endoplasmic reticulum: The favorite intracellular niche for viral replication and assembly. Viruses 8, 160. https://doi.org/10.3390/v8060160 (2016).
doi: 10.3390/v8060160
pubmed: 27338443
pmcid: 4926180
Miller, S. & Krijnse-Locker, J. Modification of intracellular membrane structures for virus replication. Nat. Rev. Microbiol. 6, 363–374. https://doi.org/10.1038/nrmicro1890 (2008).
doi: 10.1038/nrmicro1890
pubmed: 18414501
pmcid: 7096853
Miller, S., Kastner, S., Krijnse-Locker, J., Bühler, S. & Bartenschlager, R. The non-structural protein 4A of dengue virus is an integral membrane protein inducing membrane alterations in a 2K-regulated manner. J. Biol. Chem. 282, 8873–8882. https://doi.org/10.1074/jbc.M609919200 (2007).
doi: 10.1074/jbc.M609919200
pubmed: 17276984
Roby, J. A., Setoh, Y. X., Hall, R. A. & Khromykh, A. A. Post-translational regulation and modifications of flavivirus structural proteins. J. Gen. Virol. 96, 1551–1569. https://doi.org/10.1099/vir.0.000097 (2015).
doi: 10.1099/vir.0.000097
pubmed: 25711963
Mukhopadhyay, S., Kuhn, R. J. & Rossmann, M. G. A structural perspective of the Flavivirus life cycle. Nat. Rev. Microbiol. 3, 13–22. https://doi.org/10.1038/nrmicro1067 (2005).
doi: 10.1038/nrmicro1067
pubmed: 15608696
Sonnhammer, E. L., von Heijne, G. & Krogh, A. A hidden Markov model for predicting transmembrane helices in protein sequences. Proc. Int. Conf. Intell. Syst. Mol. Biol. 6, 175–182 (1998).
pubmed: 9783223
Stern, O. et al. An N-terminal amphipathic helix in dengue virus nonstructural protein 4A mediates oligomerization and is essential for replication. J. Virol. 87, 4080–4085. https://doi.org/10.1128/JVI.01900-12 (2013).
doi: 10.1128/JVI.01900-12
pubmed: 23325687
pmcid: 3624192
Kumar, A., Kumar, P. & Giri, R. Zika virus NS4A cytosolic region (residues 1–48) is an intrinsically disordered domain and folds upon binding to lipids. Virology 550, 27–36. https://doi.org/10.1016/j.virol.2020.07.017 (2020).
doi: 10.1016/j.virol.2020.07.017
pubmed: 32871423
Hung, Y. F. et al. Amino terminal region of dengue virus NS4A cytosolic domain binds to highly curved liposomes. Viruses 7, 4119–4130. https://doi.org/10.3390/v7072812 (2015).
doi: 10.3390/v7072812
pubmed: 26197333
pmcid: 4517141
Hung, Y. F. et al. Dengue virus NS4A cytoplasmic domain binding to liposomes is sensitive to membrane curvature. Biochem. Biophys. Acta 1119–1126, 2015. https://doi.org/10.1016/j.bbamem.2015.01.015 (1848).
doi: 10.1016/j.bbamem.2015.01.015
Tian, J. N., Wu, R. H., Chen, S. L., Chen, C. T. & Yueh, A. Mutagenesis of the dengue virus NS4A protein reveals a novel cytosolic N-terminal domain responsible for virus-induced cytopathic effects and intramolecular interactions within the N-terminus of NS4A. J. Gen. Virol. 100, 457–470. https://doi.org/10.1099/jgv.0.001227 (2019).
doi: 10.1099/jgv.0.001227
pubmed: 30707666
Zmurko, J., Neyts, J. & Dallmeier, K. Flaviviral NS4b, chameleon and jack-in-the-box roles in viral replication and pathogenesis, and a molecular target for antiviral intervention. Rev. Med. Virol. 25, 205–223. https://doi.org/10.1002/rmv.1835 (2015).
doi: 10.1002/rmv.1835
pubmed: 25828437
pmcid: 4864441
Zou, J. et al. Characterization of dengue virus NS4A and NS4B protein interaction. J. Virol. 89, 3455–3470. https://doi.org/10.1128/JVI.03453-14 (2015).
doi: 10.1128/JVI.03453-14
pubmed: 25568208
pmcid: 4403404
Klaitong, P. & Smith, D. R. Roles of non-structural protein 4A in flavivirus infection. Viruses 13, 77. https://doi.org/10.3390/v13102077 (2021).
doi: 10.3390/v13102077
Roosendaal, J., Westaway, E. G., Khromykh, A. & Mackenzie, J. M. Regulated cleavages at the West Nile virus NS4A-2K-NS4B junctions play a major role in rearranging cytoplasmic membranes and golgi trafficking of the NS4A protein. J. Virol. 80, 4623–4632. https://doi.org/10.1128/JVI.80.9.4623-4632.2006 (2006).
doi: 10.1128/JVI.80.9.4623-4632.2006
pubmed: 16611922
pmcid: 1472005
Li, Y., Lee, M. Y., Loh, Y. R. & Kang, C. Secondary structure and membrane topology of dengue virus NS4A protein in micelles. Biochem. Biophys. Acta 442–450, 2018. https://doi.org/10.1016/j.bbamem.2017.10.016 (1860).
doi: 10.1016/j.bbamem.2017.10.016
MacKenzie, J. M., Khromykh, A. A., Jones, M. K. & Westaway, E. G. Subcellular localization and some biochemical properties of the flavivirus Kunjin nonstructural proteins NS2A and NS4A. Virology 245, 203–215. https://doi.org/10.1006/viro.1998.9156 (1998).
doi: 10.1006/viro.1998.9156
pubmed: 9636360
Khromykh, A. A., Harvey, T. J., Abedinia, M. & Westaway, E. G. Expression and purification of the seven nonstructural proteins of the flavivirus Kunjin in the E. coli and the baculovirus expression systems. J. Virol. Methods 61, 47–58. https://doi.org/10.1016/0166-0934(96)02068-x (1996).
doi: 10.1016/0166-0934(96)02068-x
pubmed: 8882936
Lee, C. M. et al. Determinants of dengue virus NS4A protein oligomerization. J. Virol. 89, 6171–6183. https://doi.org/10.1128/JVI.00546-15 (2015).
doi: 10.1128/JVI.00546-15
pubmed: 25833044
pmcid: 4474302
Cortese, M. et al. Determinants in nonstructural protein 4A of dengue virus required for RNA replication and replication organelle biogenesis. J. Virol. 95, e0131021. https://doi.org/10.1128/JVI.01310-21 (2021).
doi: 10.1128/JVI.01310-21
pubmed: 34379504
Wicker, J. A. et al. Mutational analysis of the West Nile virus NS4B protein. Virology 426, 22–33. https://doi.org/10.1016/j.virol.2011.11.022 (2012).
doi: 10.1016/j.virol.2011.11.022
pubmed: 22314017
Umareddy, I., Chao, A., Sampath, A., Gu, F. & Vasudevan, S. G. Dengue virus NS4B interacts with NS3 and dissociates it from single-stranded RNA. J. Gen. Virol. 87, 2605–2614. https://doi.org/10.1099/vir.0.81844-0 (2006).
doi: 10.1099/vir.0.81844-0
pubmed: 16894199
Xie, X., Zou, J., Wang, Q. Y. & Shi, P. Y. Targeting dengue virus NS4B protein for drug discovery. Antiviral Res. 118, 39–45. https://doi.org/10.1016/j.antiviral.2015.03.007 (2015).
doi: 10.1016/j.antiviral.2015.03.007
pubmed: 25796970
Surya, W., Chooduang, S., Choong, Y. K., Torres, J. & Boonserm, P. Binary toxin subunits of Lysinibacillus sphaericus are monomeric and form heterodimers after in vitro activation. PLoS ONE 11, e0158356. https://doi.org/10.1371/journal.pone.0158356 (2016).
doi: 10.1371/journal.pone.0158356
pubmed: 27341696
pmcid: 4920411
Li, Y., Surya, W., Claudine, S. & Torres, J. Structure of a conserved golgi complex-targeting signal in coronavirus envelope proteins. J. Biol. Chem. 289, 12535–12549. https://doi.org/10.1074/jbc.M114.560094 (2014).
doi: 10.1074/jbc.M114.560094
pubmed: 24668816
pmcid: 4007446
Gan, S. W. et al. The small hydrophobic protein of the human respiratory syncytial virus forms pentameric ion channels. J. Biol. Chem. 287, 24671–24689. https://doi.org/10.1074/jbc.M111.332791 (2012).
doi: 10.1074/jbc.M111.332791
pubmed: 22621926
pmcid: 3397895
Tatko, C. D., Nanda, V., Lear, J. D. & DeGrado, W. F. Polar networks control oligomeric assembly in membranes. J. Am. Chem. Soc. 128, 4170–4171. https://doi.org/10.1021/ja055561a (2006).
doi: 10.1021/ja055561a
pubmed: 16568959
Fleming, K. G. et al. Thermodynamics of glycophorin A transmembrane helix dimerization in C14 betaine micelles. Biophys. Chem. 108, 43–49. https://doi.org/10.1016/j.bpc.2003.10.008 (2004).
doi: 10.1016/j.bpc.2003.10.008
pubmed: 15043920
Lear, J. D., Stouffer, A. L., Gratkowski, H., Nanda, V. & Degrado, W. F. Association of a model transmembrane peptide containing gly in a heptad sequence motif. Biophys. J. 87, 3421–3429. https://doi.org/10.1529/biophysj.103.032839 (2004).
doi: 10.1529/biophysj.103.032839
pubmed: 15315956
pmcid: 1304808
To, J. & Torres, J. Trimerisation of the N-terminal tail of Zika virus NS4A protein: A potential in vitro antiviral screening assay. Membranes 11, 335. https://doi.org/10.3390/membranes11050335 (2021).
doi: 10.3390/membranes11050335
pubmed: 33946585
pmcid: 8147241
Slusky, J. S., Yin, H. & DeGrado, W. F. Polypeptides that Bind Membrane Proteins US Patent US8349791B2 (2007).
Gan, S. W. Structural and Functional Characterization of the Human Respiratory Syncytial Virus Small Hydrophobic Protein. PhD thesis, Nanyang Technological University, Singapore (2010).
Surya, W. & Torres, J. Sedimentation equilibrium of a small oligomer-forming membrane protein: Effect of histidine protonation on pentameric stability. J. Vis. Exp. 1, e52404. https://doi.org/10.3791/52404 (2015).
doi: 10.3791/52404
Gratkowski, H., Lear, J. D. & DeGrado, W. F. Polar side chains drive the association of model transmembrane peptides. Proc. Natl. Acad. Sci. U.S.A. 98, 880–885. https://doi.org/10.1073/pnas.98.3.880 (2001).
doi: 10.1073/pnas.98.3.880
pubmed: 11158564
pmcid: 14678
Choma, C., Gratkowski, H., Lear, J. D. & DeGrado, W. F. Asparagine-mediated self-association of a model transmembrane helix. Nat. Struct. Biol. 7, 161–166. https://doi.org/10.1038/72440 (2000).
doi: 10.1038/72440
pubmed: 10655620
Burgess, N. K., Stanley, A. M. & Fleming, K. G. Determination of membrane protein molecular weights and association equilibrium constants using sedimentation equilibrium and sedimentation velocity. Method. Cell Biol. 84, 181–211. https://doi.org/10.1016/s0091-679x(07)84007-6 (2008).
doi: 10.1016/s0091-679x(07)84007-6
Fleming, K. G. Determination of membrane protein molecular weight using sedimentation equilibrium analytical ultracentrifugation. Curr. Protoc. Protein Sci. 7, 53. https://doi.org/10.1002/0471140864.ps0712s53 (2008).
doi: 10.1002/0471140864.ps0712s53
Brown, P. H. & Schuck, P. Macromolecular size-and-shape distributions by sedimentation velocity analytical ultracentrifugation. Biophys. J. 90, 4651–4661. https://doi.org/10.1529/biophysj.106.081372 (2006).
doi: 10.1529/biophysj.106.081372
pubmed: 16565040
pmcid: 1471869
Laue, T. M., Shah, B., Ridgeway, T. M. & Pelletier, S. L. In Analytical Ultracentrifugation in Biochemistry and Polymer Science (eds Harding, S. E. et al.) 90–125 (Royal Society of Chemistry, 1992).
Surya, W., Queralt-Martin, M., Mu, Y., Aguilella, V. M. & Torres, J. SARS-CoV-2 accessory protein 7b forms homotetramers in detergent. Virol. J. 19, 193. https://doi.org/10.1186/s12985-022-01920-0 (2022).
doi: 10.1186/s12985-022-01920-0
pubmed: 36414943
pmcid: 9680129
Fleming, K. G. In Analytical Ultracentrifugation: Instrumentation, Software, and Applications (eds Uchiyama, S. et al.) 311–327 (Springer, 2016).
doi: 10.1007/978-4-431-55985-6_15
le Maire, M., Champeil, P. & Møller, J. V. Interaction of membrane proteins and lipids with solubilizing detergents. Biochim. Biophys. Acta 1508, 86–111. https://doi.org/10.1016/S0304-4157(00)00010-1 (2000).
doi: 10.1016/S0304-4157(00)00010-1
pubmed: 11090820
Cole, J. L. Analysis of heterogeneous interactions. Methods Enzymol. 384, 212–232. https://doi.org/10.1016/s0076-6879(04)84013-8 (2004).
doi: 10.1016/s0076-6879(04)84013-8
pubmed: 15081689
pmcid: 2924680
Schuck, P. Size-distribution analysis of macromolecules by sedimentation velocity ultracentrifugation and lamm equation modeling. Biophys. J. 78, 1606–1619. https://doi.org/10.1016/S0006-3495(00)76713-0 (2000).
doi: 10.1016/S0006-3495(00)76713-0
pubmed: 10692345
pmcid: 1300758
Brautigam, C. A. In Methods in Enzymology Vol. 562 (ed. Cole, J. L.) 109–133 (Academic Press, 2015).
Mirdita, M. et al. ColabFold: Making protein folding accessible to all. Nat. Methods 19, 679–682. https://doi.org/10.1038/s41592-022-01488-1 (2022).
doi: 10.1038/s41592-022-01488-1
pubmed: 35637307
pmcid: 9184281
Pettersen, E. F. et al. UCSF Chimera—A visualization system for exploratory research and analysis. J. Comput. Chem. 25, 1605–1612. https://doi.org/10.1002/jcc.20084 (2004).
doi: 10.1002/jcc.20084
pubmed: 15264254
Pettersen, E. F. et al. UCSF ChimeraX: Structure visualization for researchers, educators, and developers. Protein Sci. 30, 70–82. https://doi.org/10.1002/pro.3943 (2021).
doi: 10.1002/pro.3943
pubmed: 32881101
Mariani, V., Biasini, M., Barbato, A. & Schwede, T. lDDT: A local superposition-free score for comparing protein structures and models using distance difference tests. Bioinformatics 29, 2722–2728. https://doi.org/10.1093/bioinformatics/btt473 (2013).
doi: 10.1093/bioinformatics/btt473
pubmed: 23986568
pmcid: 3799472
Tunyasuvunakool, K. et al. Highly accurate protein structure prediction for the human proteome. Nature 596, 590–596. https://doi.org/10.1038/s41586-021-03828-1 (2021).
doi: 10.1038/s41586-021-03828-1
pubmed: 34293799
pmcid: 8387240
Zhao, H. Sedimentation Velocity Analytical Ultracentrifugation 27–64 (CRC Press, 2017).
Jumper, J. et al. Highly accurate protein structure prediction with AlphaFold. Nature 596, 583–589. https://doi.org/10.1038/s41586-021-03819-2 (2021).
doi: 10.1038/s41586-021-03819-2
pubmed: 34265844
pmcid: 8371605
Varadi, M. et al. AlphaFold protein structure database: Massively expanding the structural coverage of protein-sequence space with high-accuracy models. Nucleic Acids Res. 50, D439–D444. https://doi.org/10.1093/nar/gkab1061 (2022).
doi: 10.1093/nar/gkab1061
pubmed: 34791371
van den Elsen, K., Chew, B. L. A., Ho, J. S. & Luo, D. Flavivirus nonstructural proteins and replication complexes as antiviral drug targets. Curr. Opin. Virol. 59, 101305. https://doi.org/10.1016/j.coviro.2023.101305 (2023).
doi: 10.1016/j.coviro.2023.101305
pubmed: 36870091
pmcid: 10023477
Speight, G. & Westaway, E. G. Positive identification of NS4A, the last of the hypothetical nonstructural proteins of flaviviruses. Virology 170, 299–301. https://doi.org/10.1016/0042-6822(89)90383-8 (1989).
doi: 10.1016/0042-6822(89)90383-8
pubmed: 2541547
Surya, W., Liu, Y. & Torres, J. The cytoplasmic N-terminal tail of Zika virus NS4A protein forms oligomers in the absence of detergent or lipids. Sci. Rep. 13, 7360. https://doi.org/10.1038/s41598-023-34621-x (2023).
doi: 10.1038/s41598-023-34621-x
pubmed: 37147499
pmcid: 10163220
Li, Q. & Kang, C. Dengue virus NS4B protein as a target for developing antivirals. Front. Cell. Infect. Microbiol. 12, 959727. https://doi.org/10.3389/fcimb.2022.959727 (2022).
doi: 10.3389/fcimb.2022.959727
pubmed: 36017362
pmcid: 9398000