Backbone chemical shift assignments for the SARS-CoV-2 non-structural protein Nsp9: intermediate (ms – μs) dynamics in the C-terminal helix at the dimer interface

Garry W. Buchko1, Mowei Zhou2, Jonathan M. Craig1, Wesley C. Van Voorhis1, Peter J. Myler1
1Seattle Structural Genomics Center for Infectious Disease, Seattle, USA
2Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA

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Aden J et al (2011) Extraordinary ms-μs backbone dynamics in Arabidopsis thaliana peroxiredoxin. Q Biochim Biophys Acta 1814:1880–1890. https://doi.org/10.1016/j.bbapap.2011.07.011

Arachchige RJ et al (2018) Solid-state NMR identification of intermolecular interactions in amelogenin bound to hydroxyapatite. Biophys J 115:1666–1672. https://doi.org/10.1016/j.bpj.2018.08.027

Bhattacharjya S, Ping X, Gingras R, Shaykhutdinov R, Wu C, Whiteway M, Ni F (2004) Solution structure of the dimeric SAM domain of MAPKKK Ste11 and its interactions with the adaptor protein STE50 from the budding yeast: implications for Ste11 activitation and signal transmission through the Ste50-Ste11 complex. J Mol Biol 344:1071–1087

Buchko GW et al (1999) Interactions of human nucleotide excision repair protein XPA with DNA and RPA70ΔC327: chemical shift mapping and 15N NMR relaxation studies. Biochemistry 38:15116–15128

Buchko GW, Tarasevich BJ, Bekhazi J, Snead ML, Shaw WJ (2008) A solution NMR investigation into the early events of amelogenin nanosphere self-assembly initiated with sodium chloride or calcium chloride. Biochemistry 47:13215–13222. https://doi.org/10.1021/bi8018288

Buchko GW, Edwards TE, Hewitt SN, Phan IQ, Van Voorhis WC, Miller SI, Myler PJ (2015) Backbone chemical shift assignments for the sensor domain of the Burkholderia pseudomallei histidine kinase RisS: “missing” resonances at the dimer interface. Biomol NMR Assign 9:381–385. doi:https://doi.org/10.1007/s12104-015-9614-2

Campanacci V et al (2003) Structural genomics of the SARS coronavirus: cloning, expression, crystallization and preliminary crystallographic study of the Nsp9 protein. Acta Crystallogr D Biol Crystallogr 59:1628–1631. https://doi.org/10.1107/s0907444903016779

Chen JP et al (2017) Structural analysis of porcine reproductive and respiratory syndrome virus non-structural protein 7α (NSP7α) and identification of its interaction with NSP9. Front Microbiol 8:853. https://doi.org/10.3389/fmicb.2017.00853

Egloff MP et al (2004) The severe acute respiratory syndrome-coronavirus replicative protein nsp9 is a single-stranded RNA-binding subunit unique in the RNA virus world. Proc Natl Acad Sci USA 101:3792–3796. doi:https://doi.org/10.1073/pnas.0307877101

Frieman M et al (2012) Molecular determinants of severe acute respiratory syndrome coronavirus pathogenesis and virulence in young and aged mouse models of human disease. J Virol 86:884–897. doi:https://doi.org/10.1128/JVI.05957-11

Gordon CJ, Tchesnokov EP, Feng JY, Porter DP, Gotte M (2020a) The antiviral compound remdesivir potently inhibits RNA-dependent RNA polymerase from Middle East respiratory syndrome coronavirus. J Biol Chem 295:4773–4779. doi:https://doi.org/10.1074/jbc.AC120.013056

Gordon DE et al (2020b) A SARS-CoV-2 protein interaction map reveals targets for drug repurposing. Nature 583:459–468. https://doi.org/10.1038/s41586-020-2286-9

Hafsa NE, Arndt D, Wishart DS (2015) CSI 3.0: a web server for identifying secondary and super-secondary structure in proteins using NMR chemical shifts. Nucleic Acids Res 43:W370–W377. doi:https://doi.org/10.1093/nar/gkv494

Hansen DF, Vallurupalli P, Lundstrom P, Neudecker P, Kay LE (2008) Probing chemical shifts of invisible states of proteins with relaxation dispersion NMR spectroscopy: How well can we do? J Am Chem Soc 130:2667–2675. doi:https://doi.org/10.1021/ja078337p

Jin Z et al (2020) Structure of Mpro from SARS-CoV-2 and discovery of its inhibitors. Nature 582:289–293. doi:https://doi.org/10.1038/s41586-020-2223-y

Kovermann M, Rogne P, Wolf-Watz M (2016) Protein dynamics and function from solution state NMR spectroscopy. Q Rev Biophys 49: e6.

Littler DR, Gully BS, Colson RN, Rossjohn J (2020) Crystal structure of the SARS-CoV- 2 non-structural protein 9, nsp9. iScience 23:101258. https://doi.org/10.1016/j.isci.2020.101258

Marklund EG, Benesch JL (2019) Weighing-up protein dynamics: the combination of native mass spectrometry and molecular dynamics simulations. Curr Opin Struct Biol 54:50–58. doi:https://doi.org/10.1016/j.sbi.2018.12.011

Ponnusamy R, Moll R, Weimar T, Mesters JR, Hilgenfeld R (2008) Variable oligomerization modes in coronavirus non-structural protein 9. J Mol Biol 383:1081–1096. doi:https://doi.org/10.1016/j.jmb.2008.07.071

Rossi P et al (2010) A microscale protein NMR sample screening pipeline. J Biomol NMR 46:11–22. doi:https://doi.org/10.1007/s10858-009-9386-z

Shaheen S et al (2020) Solution structure for an Encephalitozoon cuniculi adrenodoxin-like protein in the oxidized state. Protein Sci 29:809–817. https://doi.org/10.1002/pro.3818

Sharma D, Rajarathnam K (2000) 13C NMR chemical shifts can predict disulfide bond formation. J Biomol NMR 18:165–171. https://doi.org/10.1023/A:1008398416292

Sutton G et al (2004) The nsp9 replicase protein of SARS-coronavirus, structure and functional insights. Structure 12:341–353. doi:https://doi.org/10.1016/j.str.2004.01.016

Szyperski T, Yeh D, Sukumaran D, Moseley H, Montelione G (2002) Reduced-dimensionality NMR spectroscopy for high-throughput protein resonance assignment. Proc Natl Acad Sci USA 99:8009–8014

Tan YJ, Lim SG, Hong WJ (2005) Characterization of viral proteins encoded by the SARS-coronavirus genome. Antivir Res 65:69–78. doi:https://doi.org/10.1016/j.antiviral.2004.10.001

Wu F et al (2020) A new coronavirus associated with human respiratory disease in China. Nature 579:265–269. https://doi.org/10.1038/s41586-020-2008-3

Zuiderweg ERP (2002) Mapping protein-protein interactions in solution by NMR spectroscopy. Biochemistry 41:1–7