Stress adaptation signature into the functional units of spike, envelope, membrane protein and ssRNA of SARS-CoV-2

Document Type : Original article

Authors

1 Post Graduate Department of Biotechnology, Oriental Institute of Science and Technology, Vidyasagar University, Midnapore, 721102, West Bengal, India

2 Post-Graduate Department of Biotechnology, Molecular informatics Laboratory, Oriental Institute of Science and Technology, Vidyasagar University, Midnapore, West Bengal, India

Abstract

Pandemic coronavirus causes respiratory, enteric and sometimes neurological diseases. Proteome data of individual coronavirus strains were already reported. Here we investigated of SARS-CoV-2 ssRNA and protein of spike, envelope and membrane to determine stress adaptation profile. Thermodynamic properties, Physicochemical behaviour and, amino acid composition along with their RMSD value was analysed. Thermodynamic index of SARS-CoV2 spike, envelope and membrane ssRNA is unstable in higher temperature. Presence of higher proportion of polar with positive and negative charged amino acid residues into spike (S), envelope (E) and membrane (M) protein indicate the lower stress adaptability pattern. Our study represented several unstable pockets into S, E and M proteins of SARS-CoV-2 against different abiotic stresses, specifically higher in spike protein. Contact with heat through solvent may denature the architectural network of SARS-CoV-2 spike, envelope and membrane ssRNA and structural protein. The stress instability index of SARS-CoV-2 and the interactome profile of its transmembrane proteins may help to reveal novel factors for inhibiting SARS-CoV-2 growth.

Keywords

References

  1. Zhong, NS, Zheng BJ, Li YM., Poon, Xie ZH, Chan KH, Li PH, Tan SY, Chang Q, Xie JP, Liu XQ, Xu J, Li DX., Yuen KY, Peiris, Guan Y. Epidemiology and cause of severe acute respiratory syndrome (SARS) in Guangdong, People's Republic of China, in February, 2003. Lancet 2003;362:1353-1358.
  2. Llanes A, Restrepo CM, Caballero Z, Rajeev S, Kennedy MA, Lleonart R. Betacoronavirusgenomes: How genomic information has been used to deal with past outbreaks and the COVID-19 pandemic. Int J Mol Sci 2020;21:4546.
  3. Woo Chan JF, Kok KH, Zhu Z, Chu H, Wang To KK, Yuan S, Yuen KY. Genomic characterization of the 2019 novel human-pathogenic coronavirus isolated from a patient with atypical pneumonia after visiting Wuhan. Emerg Microbes Infect 2020;9:221-236.
  4. Wu F, Zhao S, Yu B, Chen YM, Wang W, Song ZG, Hu Y, Tao ZW, Tian JH., Pei YY, Yuan ML, Zhang YL, Dai FH, Liu Y, Wang QM, Zheng JJ, Xu L, Holmes EC, Zhang YZ. A new coronavirus associated with human respiratory disease in China. Nature 2020;579:265-269.
  5. Katen S, Zlotnick A. The thermodynamics of virus capsid assembly. Methods Enzymol 2009;455:395-417.
  6. Lei J, Kusov Y, Hilgenfeld R. Nsp3 of coronaviruses: Structures and functions of a large multi-domain protein. Antiviral Res 2018;149:58-74.
  7. Wang C, Zheng X, Gai W, Zhao Y, Wang H, Wang H, Feng N, Chi H, Qiu B, Li N, Wang T, Gao Y, Yang S, Xia X. MERS-CoV virus-like particles produced in insect cells induce specific humoural and cellular imminity in rhesus macaques. Oncotarget 2017;8:12686-12694.
  8. Li F. Structure, function, and evolution of coronavirus spike proteins. Annu Rev Virol 2016; 3:237-261.
  9. Kirchdoerfer RN, Cottrell CA, Wang N, Pallesen J, Yassine HM, Turner HL, Corbett KS, Graham BS, McLellan JS, Ward AB. Pre-fusion structure of a human coronavirus spike protein.  Nature 2016;531:118-121.
  10. Walls AC, Tortorici MA, Frenz B, Snijder J, Li W, Rey FA, DiMaio F, Bosch BJ, Veesler D. Glycan shield and epitope masking of a coronavirus spike protein observed by cryo-electron microscopy. Nat Struct Mol Biol 2016;23:899-905.
  11. Lin SC, Leng CH, Wu SC. Generating stable Chinese hamster ovary cell clones to produce a truncated SARS-CoV spike protein for vaccine development. Biotechnol Prog 2010;26: 1733-1740.
  12. He Y, Li J, Heck S, Lustigman S, Jiang S. Antigenic and immunogenic characterization of recombinant baculovirus-expressed severe acute respiratory syndrome coronavirus spike protein: implication for vaccine design. J Virol 2006;80:5757-5767.
  13. Hoffmann M, Kleine-Weber H, Schroeder S, Krüger N, Herrler T, Erichsen S, Schiergens T S, Herrler G, Wu NH, Nitsche A, Müller MA., Drosten C, Pöhlmann S. SARS-CoV-2 cell entry depends on ACE2 and TMPRSS2 and is blocked by a clinically proven protease inhibitor. Cell 2020;181:271–280.e8.
  14. Reinke LM, Spiegel M, Plegge T, Hartleib A, Nehlmeier I, Gierer S, Hoffmann M, Hofmann-Winkler H, Winkler M, Pöhlmann S. 2017. Different residues in the SARS-CoV spike protein determine cleavage and activation by the host cell protease TMPRSS2. PLoS One 2017;12:e0179177.
  15. Simmons G, Zmora P, Gierer S, Heurich A, Pöhlmann S. Proteolytic activation of the SARS-coronavirus spike protein: cutting enzymes at the cutting edge of antiviral research. Antiviral Res 2013;100;605-614.
  16. Belouzard S, Chu VC, Whittaker GR. Activation of the SARS coronavirus spike protein via sequential proteolytic cleavage at two distinct sites. Proc Natl Acad Sci USA 2009;106: 5871-5876.
  17. Madu IG, Roth SL, Belouzard S, Whittaker GR. Characterization of a highly conserved domain within the severe acute respiratory syndrome coronavirus spike protein S2 domain with characteristics of a viral fusion peptide. J Virol 2009;83:7411-7421.
  18. Arndt AL, Larson BJ, Hogue BG. A conserved domain in the coronavirus membrane protein tail is important for virus assembly. J Virol 2010;84:11418-11428.
  19. Corse E, Machamer CE. The cytoplasmic tails of infectious bronchitis virus E and M proteins mediate their interaction. Virology 2003;312:25-34.
  20. Neuman BW, Kiss G, Kunding AH, Bhella D, Baksh MF, Connelly S, Droese B, Klaus JP, Makino S, Sawicki SG, Siddell SG, Stamou DG, Wilson IA, Kuhn P, Buchmeier MJ. A structural analysis of M protein in coronavirus assembly and morphology. J Struct Biol 2011;174:11-22.
  21. Kuo L, Hurst KR, Masters PS. Exceptional flexibility in the sequence requirements for coronavirus small envelope protein function. J Virol 2007;81:2249-2262.
  22. Schoeman D, Fielding BC. Coronavirus envelope protein: current knowledge. Virol J 2019; 16:69.
  23. Nieto-Torres JL, Verdiá-Báguena C, Castaño-Rodriguez C, Aguilella VM, Enjuanes L. Relevance of viroporin ion channel activity on viral replication and pathogenesis. Viruses 2015;7;3552-3573.
  24. de Haan CA, Rottier PJ. Molecular interactions in the assembly of coronaviruses. Adv Virus Res 2005;64:165-230.
  25. Hogue BG, Machamer CE. Coronavirus structural proteins and virus assembly. In: Nidoviruses. Perlman S, Gallagher T, Snijder E, ASM Press, Washington, DC, 12, 179–200.
  26. Zhang L, Jackson CB, Mou H, Ojha A, Peng H, Quinlan BD, Rangarajan ES, Pan A, Vanderheiden A, Suthar MS, Li W, Izard T, Rader C, Farzan M, Choe H. SARS-CoV-2 spike-protein D614G mutation increases virion spike density and infectivity. Nature Communications 2020;11:6013.
  27. Boson B, Legros V, Zhou B, Siret E, Mathieu C, Cosset FL, Lavillette D, Denolly S. The SARS-CoV-2 envelope and membrane proteins modulate maturation and retention of the spike protein, allowing assembly of virus-like particles.  J Biol Chem 2021;296:100111.
  28. Panja AS, Bandopadhyay B, Maiti S. Protein thermostability is owing to their preferences to non-polar smaller volume amino acids, variations in residual physico-chemical properties and more salt-bridges. PLoS One 2015;10:e0131495.
  29. Panja AS, Maiti S, Bandyopadhyay B. Protein stability governed by its structural plasticity is inferred by physicochemical factors and salt bridges. Scientific Reports 2020;10:1822.
  30. Horikoshi K. Alkaliphiles: some applications of their products for biotechnology. Microbiol Mol Biol Rev 1999;63:735-750.
  31. Chen L, Brügger K, Skovgaard M, Redder P, She Q, Torarinsson E, Greve B, Awayez M, Zibat A, Klenk HP, Garrett RA. The genome of Sulfolobus acidocaldarius, a model organism of the Crenarchaeota. J Bacteriol 2005;187:4992-4999.
  32. Gruber AR, Lorenz R, Bernhart SH, Neuböck R, Hofacker IL. The Vienna RNA websuite. Nucleic Acids Res 2008;36(Web Server issue):W70-W74.
  33. Lorenz R, Bernhart SH, Höner Zu Siederdissen C, Tafer H, Flamm C, Stadler PF, Hofacker IL. ViennaRNA Package 2.0. Algorithms Mol Biol 2011;6:26.
  34. Zuker M. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 2003;31:3406-3415.
  35. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 2011;28:2731-2739.
  36. Anandakrishnan R, Aguilar B, Onufriev AV. H++ 3.0: automating pK prediction and the preparation of biomolecular structures for atomistic molecular modeling and simulations. Nucleic Acids Res 2012;40(Web Server issue):W537-W541.
  37. Abraham MJ, Murtola T, Schulz R, Pall S, Smith JC, Hess B, Lindahl E. GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers. SoftwareX 2015;1-2:19-25.
  38. Biasini M, Bienert S, Waterhouse A, Arnold K, Studer G, Schmidt T, Kiefer F, Gallo Cassarino T, Bertoni M, Bordoli L, Schwede T. SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information. Nucleic Acids Res 2014;42(Web Server issue):W252-W258.
  39. Dereeper A, Guignon V, Blanc G, Audic S, Buffet S, Chevenet F, Dufayard JF, Guindon S, Lefort V, Lescot M, Claverie JM, Gascuel O. Phylogeny.fr: robust phylogenetic analysis for the non-specialist. Nucleic Acids Res 2008;36(Web Server issue):W465-W469.
  40. Popovic M, Minceva M. Thermodynamic insight into viral infections 2: empirical formulas, molecular compositions and thermodynamic properties of SARS, MERS and SARS-CoV-2 (COVID-19) viruses. Heliyon 2020;6;e04943.
  41. Flint SJ, Enquist LW, Racaniello VR., Skalka AM. third ed. II. Wiley; Hoboken, NJ: 2009. Principles of Virology.
  42. Tuladhar E, Bouwknegt M, Zwietering MH, Koopmans M, Duizer E. Thermal stability of structurally different viruses with proven or potential relevance to food safety. J Appl Microbiol 2012;112:1050-1057.
  43. Chin A, Chu J, Perera M, Hui K, Yen HL, Chan M, Peiris M, Poon L. Stability of SARS-CoV-2 in different environmental conditions. Lancet Microbe 2020;1:e10.
  44. Van Doremalen N, Bushmaker T, Morris DH, Holbrook MG, Gamble A, Williamson BN, Tamin A, Harcourt JL, Thornburg NJ, Gerber SI, Lloyd-Smith JO, de Wit E, Munster VJ. Aerosol and surface stability of SARS-CoV-2 as compared with SARS-CoV-1. N Engl J Med 2020;382:1564-1567.
  45. Nazari M, Kurdi M, Heerklotz H. Classifying surfactants with respect to their effect on lipid membrane order. Biophys J 2012;102:498-506.
  46. Prince AM, Horowitz B, Brotman B. Sterilisation of hepatitis and HTLV-III viruses by exposure to tri(n-butyl)phosphate and sodium cholate. Lancet 1986;1:706-710.
  47. Xu X, Chen P, Wang J, Feng J, Zhou H, Li X, Zhong W, Hao P. Evolution of the novel coronavirus from the ongoing Wuhan outbreak and modeling of its spike protein for risk of human transmission. Sci China Life Sci 2020;63:457-460.
  48. Li F, Li W, Farzan M, Harrison SC. Structure of SARS coronavirus spike receptor-binding domain complexed with receptor. Science 2005;309:1864-1868.
  49. Grifoni A, Sidney J, Zhang Y, Scheuermann RH, Peters B, Sette A. A sequence homology and bioinformatic approach can predict candidate targets for immune responses to SARS-CoV-2. Cell Host Microbe 2020;27:671-680.e2.
  50. Enayatkhani M, Hasaniazad M, Faezi S, Gouklani H, Davoodian P, Ahmadi N, Einakian M A, Karmostaji A, Ahmadi K. Reverse vaccinology approach to design a novel multi-epitope vaccine candidate against COVID-19: An in silico study. J Biomol Struct Dyn 2021;39: 2857-2872.

Files

Share

How to cite

Statistics