Abstract
A detergent-free protocol for purification of the coronavirus prefusion S-protein using styrene-maleic acid copolymer (SMA) was developed. Expression of the S-protein was carried out in HEK293T cells. Two solubilization methods were used to purify and prepare the S-protein for microscopy: in NP-40 detergent and as part of SMA. The resulting preparations were examined in an electron microscope, and the particles of purified S-proteins were classified. Analysis of two-dimensional projections of the particles showed that the use of lipodiscs for solubilization leads to lower mobility of the purified protein on the substrate compared to the protein in the detergent, which may further contribute to obtaining higher resolutions when studying the structure of membrane proteins.
REFERENCES
Kudriavtsev, A.V., Vakhrusheva, A.V., Novoseletsky, V.N., Bozdaganyan, M.E., Shaitan, K.V., Kirpichnikov, M.P., and Sokolova, O.S., Immune escape associated with RBD omicron mutations and SARS-CoV-2 evolution dynamics, Viruses, 2022, vol. 14, no. 8, p. 1603. https://doi.org/10.3390/v14081603
Bozdaganyan, M.E., Shaitan, K.V., Kirpichnikov, M.P., Sokolova, O.S., and Orekhov, P.S., Computational analysis of mutations in the receptor-binding domain of SARS-CoV-2 spike and their effects on antibody binding, Viruses, 2022, vol. 14, no. 2, p. 295. https://doi.org/10.3390/v14020295
Li, F., Structure, function, and evolution of coronavirus spike proteins, Annu. Rev. Virol., 2016, vol. 3, no. 1, pp. 237–261. https://doi.org/10.1146/annurev-virology-110615-042301
Shang, J., Ye, G., Shi, K., Wan, Yu., Luo, C., Aihara, H., Geng, Q., Auerbach, A., and Li, F., Structural basis of receptor recognition by SARS-CoV-2, Nature, 2020, vol. 581, no. 7807, pp. 221–224. https://doi.org/10.1038/s41586-020-2179-y
Palsdottir, H. and Hunte, C., Lipids in membrane protein structures, Biochim. Biophys. Acta, Biomembr., 2004, vol. 1666, nos. 1–2, pp. 2–18. https://doi.org/10.1016/j.bbamem.2004.06.012
Dörr, J.M., Scheidelaar, S., Koorengevel, M.C., Dominguez, J.J., Schäfer, M., Van Walree, C.A., and Killian, J.A., The styrene–maleic acid copolymer: A versatile tool in membrane research, Eur. Biophys. J., 2016, vol. 45, no. 1, pp. 3–21. https://doi.org/10.1007/s00249-015-1093-y
Turoňová, B., Sikora, M., Schürmann, C., Ha-gen, W.J.H., Welsch, S., Blanc, F.E.C., Von Bülow, S., Gecht, M., Bagola, K., Hörner, C., Van Zandbergen, G., Landry, J., De Azevedo, N.T.D., Mosalaganti, S., Schwarz, A., Covino, R., Mühlebach, M.D., Hummer, G., Krijnse Locker, J., and Beck, M., In situ structural analysis of SARS-CoV-2 spike reveals flexibility mediated by three hinges, Science, 2020, vol. 370, no. 6513, pp. 203–208. https://doi.org/10.1126/science.abd5223
Garavito, R.M. and Ferguson-Miller, S., Detergents as tools in membrane biochemistry, J. Biol. Chem., 2001, vol. 276, no. 35, pp. 32403–32406. https://doi.org/10.1074/jbc.r100031200
Lichtenberg, D., Ahyayauch, H., and Goñi, F.M., The mechanism of detergent solubilization of lipid bilayers, Biophys. J., 2013, vol. 105, no. 2, pp. 289–299. https://doi.org/10.1016/j.bpj.2013.06.007
Popot, J.-L., Althoff, T., Bagnard, D., Banères, J.-L., Bazzacco, P., Billon-Denis, E., Catoire, L.J., Champeil, P., Charvolin, D., Cocco, M.J., Crémel, G., Dahmane, T., De La Maza, L.M., Ebel, C., Gabel, F., Giusti, F., Gohon, Y., Goormaghtigh, E., Guittet, E., Kleinschmidt, J.H., Kühlbrandt, W., Le Bon, C., Martinez, K.L., Picard, M., Pucci, B., Sachs, J.N., Tribet, C., Van Heijenoort, C., Wien, F., Zito, F., and Zoonens, M., Amphipols from A to Z, Annu. Rev. Biophys., 2011, vol. 40, no. 1, pp. 379–408. https://doi.org/10.1146/annurev-biophys-042910-155219
Rigaud, J.-L. and Lévy, D., Reconstitution of membrane proteins into liposomes, Methods in Enzymology, Elsevier, 2003, vol. 372, pp. 65–86. https://doi.org/10.1016/s0076-6879(03)72004-7
Ritchie, T.K., Grinkova, Y.V., Bayburt, T.H., Denisov, I.G., Zolnerciks, J.K., Atkins, W.M., and Sligar, S.G., Reconstitution of membrane proteins in phospholipid bilayer nanodiscs, Liposomes, Part F, Düzgünes, N. and Dugoni, A.A., Eds., Methods in Enzymology, vol. 464, Elsevier, 2009, pp. 211–231. https://doi.org/10.1016/s0076-6879(09)64011-8
Knowles, T.J., Finka, R., Smith, C., Lin, Yu-P., Dafforn, T., and Overduin, M., Membrane proteins solubilized intact in lipid containing nanoparticles bounded by styrene maleic acid copolymer, J. Am. Chem. Soc., 2009, vol. 131, no. 22, pp. 7484–7485. https://doi.org/10.1021/ja810046q
Karlova, M.G., Voskoboynikova, N., Gluhov, G.S., Abramochkin, D., Malak, O.A., Mulkidzhanyan, A., Loussouarn, G., Steinhoff, H.-J., Shaitan, K.V., and Sokolova, O.S., Detergent-free solubilization of human Kv channels expressed in mammalian cells, Chem. Phys. Lipids, 2019, vol. 219, pp. 50–57. https://doi.org/10.1016/j.chemphyslip.2019.01.013
Punjani, A., Rubinstein, J.L., Fleet, D.J., and Bruba-ker, M.A., cryoSPARC: Algorithms for rapid unsupervised cryo-EM structure determination, Nat. Methods, 2017, vol. 14, no. 3, pp. 290–296. https://doi.org/10.1038/nmeth.4169
Zhong, F., Zhong, Z.Y., Liang, S., and Li, X.J., High expression level of soluble SARS spike protein mediated by adenovirus in HEK293 cells, World J. Gastroenterol., 2006, vol. 12, no. 9, p. 1452. https://doi.org/10.3748/wjg.v12.i9.1452
Cai, Yo., Zhang, J., Xiao, T., Peng, H., Sterling, S.M., Walsh, R.M., Rawson, S., Rits-Volloch, S., and Chen, B., Distinct conformational states of SARS-CoV-2 spike protein, Science, 2020, vol. 369, no. 6511, pp. 1586–1592. https://doi.org/10.1126/science.abd4251
Wrapp, D., Wang, N., Corbett, K.S., Goldsmith, J.A., Hsieh, Ch.-L., Abiona, O., Graham, B.S., and McLellan, J.S., Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation, Science, 2020, vol. 367, no. 6483, pp. 1260–1263. https://doi.org/10.1126/science.abb2507
Choi, Ye.K., Cao, Yi., Frank, M., Woo, H., Park, S.-J., Yeom, M.S., Croll, T.I., Seok, C., and Im, W., Structure, dynamics, receptor binding, and antibody binding of the fully glycosylated full-length SARS-CoV-2 spike protein in a viral membrane, J. Chem. Theory Comput., 2021, vol. 17, no. 4, pp. 2479–2487. https://doi.org/10.1021/acs.jctc.0c01144
Pramanick, I., Sengupta, N., Mishra, S., Pandey, S., Girish, N., Das, A., and Dutta, S., Conformational flexibility and structural variability of SARS-CoV2 S protein, Structure, 2021, vol. 29, no. 8, pp. 834.e5–845.e5. https://doi.org/10.1016/j.str.2021.04.006
Yao, H., Song, Yu., Chen, Yo., Wu, N., Xu, J., Sun, C., Zhang, J., Weng, T., Zhang, Z., Wu, Z., Cheng, L., Shi, D., Lu, X., Lei, J., Crispin, M., Shi, Yi., Li, L., and Li, S., Molecular architecture of the SARS-CoV-2 virus, Cell, 2020, vol. 183, no. 3, pp. 730.e13–738.e13. https://doi.org/10.1016/j.cell.2020.09.018
Song, Yu., Yao, H., Wu, N., Xu, J., Zhang, Z., Peng, C., Li, S., Kong, W., Chen, Yo., Zhu, M., Wang, J., Shi, D., Zhao, C., Lu, X., Echavarría galindo, M., and Li, S., In situ architecture and membrane fusion of SARS-CoV-2 Delta variant, Proc. Natl. Acad. Sci. U. S. A., 2023, vol. 120, no. 18, p. e2213332120. https://doi.org/10.1073/pnas.2213332120
ACKNOWLEDGMENTS
We thank A.V. Moiseenko for assistance in conducting electron microscopic studies.
Funding
The study was carried out with the financial support of the Moscow State University Development Program (project no. 23A-Sh04-01) using the Three-Dimensional Electron Microscopy and Spectroscopy unique set-up of Moscow State University.
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Mamaeva, N.Y., Derkacheva, N.I., Gasanova, D.A. et al. Stabilization of Full-Length S-Protein of SARS-Cov-2 Coronavirus in SMA Polymer for Electron Microscopy Study. Moscow Univ. Biol.Sci. Bull. 78 (Suppl 1), S22–S27 (2023). https://doi.org/10.3103/S0096392523700165
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DOI: https://doi.org/10.3103/S0096392523700165