Research Article
BibTex RIS Cite

The Effects of SARS CoV-2 nsp13 Mutations on the Structure and Stability of Helicase in Chinese Isolates

Year 2022, , 11 - 17, 30.06.2022
https://doi.org/10.26650/EurJBiol.2022.1061858

Abstract

Objective: Coronavirus Disease 2019 (COVID19) is a viral disease caused by Severe Acute Respiratory Syndrome Coronavirus-2 (SARS CoV-2). The high mutation propensity of the SARS CoV-2 genome is one of the biggest threats to the long-term validity of treatment options. Helicases are anti-viral targets because of the vital role they play in the viral life cycle. In this study, changes in the protein structure caused by SARS CoV-2 nsp13 mutations were investigated to contribute to the development of effective antiviral drugs. Materials and Methods: Genome data of 298 individuals located in the China location were examined. The mutant model was built using deep learning algorithms. Model quality assessment was done with QMEAN. Protein stability analyses were performed with DynaMut2 and Cutoff Scanning Matrix stability. Changes in substrate affinity were performed with Haddock v2.4. Results: In this study, twenty-eight mutations in nsp13 were identified (23 sense, 5 missense). The changes in protein structure caused by the five missense mutations (Leu14Phe, Arg15Ser, Arg21Ser, Leu235Phe, Ala454Thr) were modeled. The mutations caused a decrease in the stability of SARS CoV-2 helicase (-0.99, -1.66, -1.15, -0.54, and -0.73 for Leu14Phe, Arg15Ser, Arg21Ser, Leu235Phe, Ala454Thr, respectively). The mutations reduced the helicase's affinity to the substrate. The docking scores for wild-type and mutant helicase were -84.4±1.4 kcal.mol-1 and -71.1±6.7 kcal.mol-1, respectively. Conclusion: Helicase mutations caused a decrease in the protein stability and nucleic acid affinity of the SARS CoV-2 helicase. The results provide important data on the development of potential antivirals and the effect of mutation on the functions of viral proteins.

Thanks

Genome data of Chinese isolates were obtained from the NCBI Virus database. Thanks to the NCBI Virus database for its open-source data sharing policy.

References

  • 1. Singhal T. A Review of Coronavirus Disease-2019 (COVID-19). Indi- an J Pediatr 2020; 87: 281-6.
  • 2. Zhou P, Yang X Lou, Wang XG, Hu B, Zhang L, Zhang W, et al. A pneumonia outbreak associated with a new coronavirus of proba- ble bat origin. Nature 2020; 579: 270-3.
  • 3. Worldometer. Coronavirus case report. WwwWorldometersInfo/ Coronavirus 2022.
  • 4. Wu F, Zhao S, Yu B, Chen YM, Wang W, Song ZG, et al. A new corona- virus associated with human respiratory disease in China. Nature 2020; 579: 265-9.
  • 5. Zito Marino F, De Cristofaro T, Varriale M, Zannini G, Ronchi A, La Mantia E, et al. Variable levels of spike and ORF1ab RNA in post-mortem lung samples of SARS-CoV- 2-positive subjects: com- parison between ISH and RT-PCR. Virchows Arch 2022: 1-11.
  • 6. Finkel Y, Mizrahi O, Nachshon A, Weingarten-Gabbay S, Morgen- stern D, Yahalom-Ronen Y, et al. The coding capacity of SARS- CoV-2. Nature 2021; 589: 125-30.
  • 7. Habtemariam S, Nabavi SF, Banach M, Berindan-Neagoe I, Sarkar K, Sil PC, et al. Should We Try SARS-CoV-2 Helicase Inhibitors for COVID-19 Therapy? Arch Med Res 2020; 51: 733-5.
  • 8. Singleton MR, Dillingham MS, Wigley DB. Structure and mecha- nism of helicases and nucleic acid translocases. Annu Rev Biochem 2007; 76: 23-50.
  • 9. Ahmad S, Waheed Y, Ismail S, Bhatti S, Abbasi SW, Muhammad K. Structure-based virtual screening identifies multiple stable bind- ing sites at the RecA domains of SARS-CoV-2 helicase enzyme. Molecules 2021; 26: 1446.
  • 10. Akbulut E. Mutations in the SARS CoV-2 spike protein may cause functional changes in the protein quaternary structure. Turkish J Biochem 2021; 46: 137-44.
  • 11. Akbulut E. Comparative Genomic and Proteomic Analysis of SARS CoV-2 - with Potential Mutation Probabilities and Drug Targeting. Erzincan Univ J Sci Technol 2020; 13: 1187-97.
  • 12. Zahradník J, Marciano S, Shemesh M, Zoler E, Harari D, Chiaravalli J, et al. SARS-CoV-2 variant prediction and antiviral drug design are enabled by RBD in vitro evolution. Nat Microbiol 2021; 6: 1188-98.
  • 13. Katoh K. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res 2002; 30: 3059-66.
  • 14. Mount DW. Using BLOSUM in sequence alignments. Cold Spring Harb Protoc 2008; 3: pdb-top39.
  • 15. Jones DT, Taylor WR, Thornton JM. The rapid generation of muta- tion data matrices from protein sequences. Bioinformatics 1992; 8: 275-82.
  • 16. Kumar S, Stecher G, Li M, Knyaz C, Tamura K. MEGA X: Molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol 2018; 35: 1547-9.
  • 17. Mirdita M, Ovchinnikov S, Steinegger M. ColabFold - Making pro- tein folding accessible to all. BioRxiv 2021: 2021.08.15.456425.
  • 18. Newman JA, Douangamath A, Yadzani S, Yosaatmadja Y, Aimon A, Brandão-Neto J, et al. Structure, mechanism and crystallographic fragment screening of the SARS-CoV-2 NSP13 helicase. Nat Com- mun 2021; 12.
  • 19. Benkert P, Biasini M, Schwede T. Toward the estimation of the abso- lute quality of individual protein structure models. Bioinformatics 2011; 27: 343-50.
  • 20. Rose AS, Bradley AR, Valasatava Y, Duarte JM, Prlic A, Rose PW. NGL viewer: Web-based molecular graphics for large complexes. Bioin- formatics 2018; 34: 3755-8.
  • 21. Xu J, Zhang Y. How significant is a protein structure similarity with TM-score = 0.5? Bioinformatics 2010; 26: 889-95.
  • 22. Rodrigues CHM, Pires DEV, Ascher DB. DynaMut2: Assessing changes in stability and flexibility upon single and multiple point missense mutations. Protein Sci 2021; 30: 60-9.
  • 23. Pires DEV, Ascher DB, Blundell TL. MCSM: Predicting the effects of mutations in proteins using graph-based signatures. Bioinformat- ics 2014; 30: 335-42.
  • 24. Pires DEV, de Melo-Minardi RC, dos Santos MA, da Silveira CH, San- toro MM, Meira W. Cutoff Scanning Matrix (CSM): Structural classi- fication and function prediction by protein inter-residue distance patterns. BMC Genomics, vol. 12, Springer; 2011, p. 1–11.
  • 25. Pires DEV, De Melo-Minardi RC, Da Silveira CH, Campos FF, Meira W. ACSM: Noise-free graph-based signatures to large-scale recep- tor-based ligand prediction. Bioinformatics 2013; 29: 855-61.
  • 26. Jubb HC, Higueruelo AP, Ochoa-Montaño B, Pitt WR, Ascher DB, Blundell TL. Arpeggio: A Web Server for Calculating and Visualising Interatomic Interactions in Protein Structures. J Mol Biol 2017; 429: 365-71.
  • 27. Van Zundert GCP, Rodrigues JPGLM, Trellet M, Schmitz C, Kastritis PL, Karaca E, et al. The HADDOCK2.2 Web Server: User-Friendly In- tegrative Modeling of Biomolecular Complexes. J Mol Biol 2016; 428: 720-5.
  • 28. Chen J, Malone B, Llewellyn E, Grasso M, Shelton PMM, Olinares PDB, et al. Structural Basis for Helicase-Polymerase Coupling in the SARS-CoV-2 Replication- Transcription Complex. Cell 2020; 182: 1560-1573.e13.
  • 29. Leulier F, Parquet C, Pili-Floury S, Ryu JH, Caroff M, Lee WJ, et al. IK- Kepsilon and TBK1 are essential components of the IRF3 signaling pathway. Nat Immunol 2003; 4: 478-84. doi: 10.1038/ni922.
  • 30. Xia H, Cao Z, Xie X, Zhang X, Chen JYC, Wang H, et al. Evasion of Type I Interferon by SARS-CoV-2. Cell Rep 2020; 33: 108234.
  • 31. Nguyen TT, Chang SC, Evnouchidou I, York IA, Zikos C, Rock KL, et al. Structural basis for antigenic peptide precursor processing by the endoplasmic reticulum aminopeptidase ERAP1. Nat Struct Mol Biol 2011; 18: 604-13.
  • 32. Wu S, Tian C, Liu P, Guo D, Zheng W, Huang X, et al. Effects of SARS- CoV-2 mutations on protein structures and intraviral protein–pro- tein interactions. J Med Virol 2021; 93: 2132-40. 33. Akbulut E, Kar B. SARS CoV-2 nsp1 Mutasyonlarının Protein Yapıda Ortaya Çıkardığı Değişimler. Int J Pure Appl Sci 2020; 6: 68-76.
  • 34. Farkas C, Fuentes-Villalobos F, Garrido JL, Haigh J, Barría MI. Insights on early mutational events in SARS-CoV-2 virus reveal founder ef- fects across geographical regions. PeerJ 2020; 2020: e9255.
  • 35. Garvin MR, T. Prates E, Pavicic M, Jones P, Amos BK, Geiger A, et al. Potentially adaptive SARS-CoV-2 mutations discovered with novel spatiotemporal and explainable AI models. Genome Biol 2020; 21: 1-26.
  • 36. Alouane T, Laamarti M, Essabbar A, Hakmi M, Bouricha EM, Che- mao-Elfihri MW, et al. Genomic diversity and hotspot mutations in 30,983 SARS-CoV-2 genomes: Moving toward a universal vaccine for the “confined virus”? Pathogens 2020; 9: 1-19.
  • 37. Akbulut E. SARS CoV-2 Spike Glycoprotein Mutations and Changes in Protein Structure. Trak Univ J Nat Sci 2020; 22: 1-11.
  • 38. Matyášek R, Kovařík A. Mutation patterns of human SARS-CoV-2 and bat RATG13 coronavirus genomes are strongly biased towards C>U transitions, indicating rapid evolution in their hosts. Genes (Basel) 2020; 11: 1-13.
  • 39. Wang R, Hozumi Y, Zheng YH, Yin C, Wei GW. Host immune re- sponse driving SARS-CoV-2 evolution. Viruses 2020; 12: 1095.
  • 40. Seyran M, Takayama K, Uversky VN, Lundstrom K, Palù G, Sherchan SP, et al. The structural basis of accelerated host cell entry by SARS- CoV-2†. FEBS J 2021; 288: 5010-20.
  • 41. Feroza B, Banerjee AK, Tripathi PP, Ray U. Two mutations P/L and Y/C in SARS-CoV-2 helicase domain exist together and influence helicase RNA binding. BioRxiv 2020.
  • 42. Jen J, Wang YC. Zinc finger proteins in cancer progression. J Biomed Sci 2016; 23: 1-9.
  • 43. Iuchi S. Three classes of C2H2 zinc finger proteins. Cell Mol Life Sci 2001; 58: 625-35.
  • 44. Filippova GN, Ulmer JE, Moore JM, Ward MD, Hu YJ, Neiman PE, et al. Tumor-associated zinc finger mutations in the CTCF transcrip- tion factor selectively alter its DNA-binding specificity. Cancer Res 2002; 62: 48-52.
  • 45. Takaku M, Grimm SA, Roberts JD, Chrysovergis K, Bennett BD, My- ers P, et al. GATA3 zinc finger 2 mutations reprogram the breast cancer transcriptional network. Nat Commun 2018; 9: 1-14.
  • 46. Munro D, Ghersi D, Singh M. Two critical positions in zinc finger domains are heavily mutated in three human cancer types. PLoS Comput Biol 2018; 14: e1006290.
  • 47. Ma J, Chen Y, Wu W, Chen Z. Structure and Function of N-Terminal Zinc Finger Domain of SARS-CoV-2 NSP2. Virol Sin 2021; 36: 1104- 12.
  • 48. Ma Y, Wu L, Shaw N, Gao Y, Wang J, Sun Y, et al. Structural basis and functional analysis of the SARS coronavirus nsp14-nsp10 complex. Proc Natl Acad Sci U S A 2015; 112: 9436-41.
  • 49. Halder UC. Predicted antiviral drugs Darunavir, Amprenavir, Rimantadine and Saquinavir can potentially bind to neutralize SARS-CoV-2 conserved proteins. J Biol Res 2021; 28: 1-58.
  • 50. Berta D, Badaoui M, Martino SA, Buigues PJ, Pisliakov A V., Elgho- bashi-Meinhardt N, et al. Modelling the active SARS-CoV-2 helicase complex as a basis for structure-based inhibitor design. Chem Sci 2021; 12: 13492-505.
Year 2022, , 11 - 17, 30.06.2022
https://doi.org/10.26650/EurJBiol.2022.1061858

Abstract

References

  • 1. Singhal T. A Review of Coronavirus Disease-2019 (COVID-19). Indi- an J Pediatr 2020; 87: 281-6.
  • 2. Zhou P, Yang X Lou, Wang XG, Hu B, Zhang L, Zhang W, et al. A pneumonia outbreak associated with a new coronavirus of proba- ble bat origin. Nature 2020; 579: 270-3.
  • 3. Worldometer. Coronavirus case report. WwwWorldometersInfo/ Coronavirus 2022.
  • 4. Wu F, Zhao S, Yu B, Chen YM, Wang W, Song ZG, et al. A new corona- virus associated with human respiratory disease in China. Nature 2020; 579: 265-9.
  • 5. Zito Marino F, De Cristofaro T, Varriale M, Zannini G, Ronchi A, La Mantia E, et al. Variable levels of spike and ORF1ab RNA in post-mortem lung samples of SARS-CoV- 2-positive subjects: com- parison between ISH and RT-PCR. Virchows Arch 2022: 1-11.
  • 6. Finkel Y, Mizrahi O, Nachshon A, Weingarten-Gabbay S, Morgen- stern D, Yahalom-Ronen Y, et al. The coding capacity of SARS- CoV-2. Nature 2021; 589: 125-30.
  • 7. Habtemariam S, Nabavi SF, Banach M, Berindan-Neagoe I, Sarkar K, Sil PC, et al. Should We Try SARS-CoV-2 Helicase Inhibitors for COVID-19 Therapy? Arch Med Res 2020; 51: 733-5.
  • 8. Singleton MR, Dillingham MS, Wigley DB. Structure and mecha- nism of helicases and nucleic acid translocases. Annu Rev Biochem 2007; 76: 23-50.
  • 9. Ahmad S, Waheed Y, Ismail S, Bhatti S, Abbasi SW, Muhammad K. Structure-based virtual screening identifies multiple stable bind- ing sites at the RecA domains of SARS-CoV-2 helicase enzyme. Molecules 2021; 26: 1446.
  • 10. Akbulut E. Mutations in the SARS CoV-2 spike protein may cause functional changes in the protein quaternary structure. Turkish J Biochem 2021; 46: 137-44.
  • 11. Akbulut E. Comparative Genomic and Proteomic Analysis of SARS CoV-2 - with Potential Mutation Probabilities and Drug Targeting. Erzincan Univ J Sci Technol 2020; 13: 1187-97.
  • 12. Zahradník J, Marciano S, Shemesh M, Zoler E, Harari D, Chiaravalli J, et al. SARS-CoV-2 variant prediction and antiviral drug design are enabled by RBD in vitro evolution. Nat Microbiol 2021; 6: 1188-98.
  • 13. Katoh K. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res 2002; 30: 3059-66.
  • 14. Mount DW. Using BLOSUM in sequence alignments. Cold Spring Harb Protoc 2008; 3: pdb-top39.
  • 15. Jones DT, Taylor WR, Thornton JM. The rapid generation of muta- tion data matrices from protein sequences. Bioinformatics 1992; 8: 275-82.
  • 16. Kumar S, Stecher G, Li M, Knyaz C, Tamura K. MEGA X: Molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol 2018; 35: 1547-9.
  • 17. Mirdita M, Ovchinnikov S, Steinegger M. ColabFold - Making pro- tein folding accessible to all. BioRxiv 2021: 2021.08.15.456425.
  • 18. Newman JA, Douangamath A, Yadzani S, Yosaatmadja Y, Aimon A, Brandão-Neto J, et al. Structure, mechanism and crystallographic fragment screening of the SARS-CoV-2 NSP13 helicase. Nat Com- mun 2021; 12.
  • 19. Benkert P, Biasini M, Schwede T. Toward the estimation of the abso- lute quality of individual protein structure models. Bioinformatics 2011; 27: 343-50.
  • 20. Rose AS, Bradley AR, Valasatava Y, Duarte JM, Prlic A, Rose PW. NGL viewer: Web-based molecular graphics for large complexes. Bioin- formatics 2018; 34: 3755-8.
  • 21. Xu J, Zhang Y. How significant is a protein structure similarity with TM-score = 0.5? Bioinformatics 2010; 26: 889-95.
  • 22. Rodrigues CHM, Pires DEV, Ascher DB. DynaMut2: Assessing changes in stability and flexibility upon single and multiple point missense mutations. Protein Sci 2021; 30: 60-9.
  • 23. Pires DEV, Ascher DB, Blundell TL. MCSM: Predicting the effects of mutations in proteins using graph-based signatures. Bioinformat- ics 2014; 30: 335-42.
  • 24. Pires DEV, de Melo-Minardi RC, dos Santos MA, da Silveira CH, San- toro MM, Meira W. Cutoff Scanning Matrix (CSM): Structural classi- fication and function prediction by protein inter-residue distance patterns. BMC Genomics, vol. 12, Springer; 2011, p. 1–11.
  • 25. Pires DEV, De Melo-Minardi RC, Da Silveira CH, Campos FF, Meira W. ACSM: Noise-free graph-based signatures to large-scale recep- tor-based ligand prediction. Bioinformatics 2013; 29: 855-61.
  • 26. Jubb HC, Higueruelo AP, Ochoa-Montaño B, Pitt WR, Ascher DB, Blundell TL. Arpeggio: A Web Server for Calculating and Visualising Interatomic Interactions in Protein Structures. J Mol Biol 2017; 429: 365-71.
  • 27. Van Zundert GCP, Rodrigues JPGLM, Trellet M, Schmitz C, Kastritis PL, Karaca E, et al. The HADDOCK2.2 Web Server: User-Friendly In- tegrative Modeling of Biomolecular Complexes. J Mol Biol 2016; 428: 720-5.
  • 28. Chen J, Malone B, Llewellyn E, Grasso M, Shelton PMM, Olinares PDB, et al. Structural Basis for Helicase-Polymerase Coupling in the SARS-CoV-2 Replication- Transcription Complex. Cell 2020; 182: 1560-1573.e13.
  • 29. Leulier F, Parquet C, Pili-Floury S, Ryu JH, Caroff M, Lee WJ, et al. IK- Kepsilon and TBK1 are essential components of the IRF3 signaling pathway. Nat Immunol 2003; 4: 478-84. doi: 10.1038/ni922.
  • 30. Xia H, Cao Z, Xie X, Zhang X, Chen JYC, Wang H, et al. Evasion of Type I Interferon by SARS-CoV-2. Cell Rep 2020; 33: 108234.
  • 31. Nguyen TT, Chang SC, Evnouchidou I, York IA, Zikos C, Rock KL, et al. Structural basis for antigenic peptide precursor processing by the endoplasmic reticulum aminopeptidase ERAP1. Nat Struct Mol Biol 2011; 18: 604-13.
  • 32. Wu S, Tian C, Liu P, Guo D, Zheng W, Huang X, et al. Effects of SARS- CoV-2 mutations on protein structures and intraviral protein–pro- tein interactions. J Med Virol 2021; 93: 2132-40. 33. Akbulut E, Kar B. SARS CoV-2 nsp1 Mutasyonlarının Protein Yapıda Ortaya Çıkardığı Değişimler. Int J Pure Appl Sci 2020; 6: 68-76.
  • 34. Farkas C, Fuentes-Villalobos F, Garrido JL, Haigh J, Barría MI. Insights on early mutational events in SARS-CoV-2 virus reveal founder ef- fects across geographical regions. PeerJ 2020; 2020: e9255.
  • 35. Garvin MR, T. Prates E, Pavicic M, Jones P, Amos BK, Geiger A, et al. Potentially adaptive SARS-CoV-2 mutations discovered with novel spatiotemporal and explainable AI models. Genome Biol 2020; 21: 1-26.
  • 36. Alouane T, Laamarti M, Essabbar A, Hakmi M, Bouricha EM, Che- mao-Elfihri MW, et al. Genomic diversity and hotspot mutations in 30,983 SARS-CoV-2 genomes: Moving toward a universal vaccine for the “confined virus”? Pathogens 2020; 9: 1-19.
  • 37. Akbulut E. SARS CoV-2 Spike Glycoprotein Mutations and Changes in Protein Structure. Trak Univ J Nat Sci 2020; 22: 1-11.
  • 38. Matyášek R, Kovařík A. Mutation patterns of human SARS-CoV-2 and bat RATG13 coronavirus genomes are strongly biased towards C>U transitions, indicating rapid evolution in their hosts. Genes (Basel) 2020; 11: 1-13.
  • 39. Wang R, Hozumi Y, Zheng YH, Yin C, Wei GW. Host immune re- sponse driving SARS-CoV-2 evolution. Viruses 2020; 12: 1095.
  • 40. Seyran M, Takayama K, Uversky VN, Lundstrom K, Palù G, Sherchan SP, et al. The structural basis of accelerated host cell entry by SARS- CoV-2†. FEBS J 2021; 288: 5010-20.
  • 41. Feroza B, Banerjee AK, Tripathi PP, Ray U. Two mutations P/L and Y/C in SARS-CoV-2 helicase domain exist together and influence helicase RNA binding. BioRxiv 2020.
  • 42. Jen J, Wang YC. Zinc finger proteins in cancer progression. J Biomed Sci 2016; 23: 1-9.
  • 43. Iuchi S. Three classes of C2H2 zinc finger proteins. Cell Mol Life Sci 2001; 58: 625-35.
  • 44. Filippova GN, Ulmer JE, Moore JM, Ward MD, Hu YJ, Neiman PE, et al. Tumor-associated zinc finger mutations in the CTCF transcrip- tion factor selectively alter its DNA-binding specificity. Cancer Res 2002; 62: 48-52.
  • 45. Takaku M, Grimm SA, Roberts JD, Chrysovergis K, Bennett BD, My- ers P, et al. GATA3 zinc finger 2 mutations reprogram the breast cancer transcriptional network. Nat Commun 2018; 9: 1-14.
  • 46. Munro D, Ghersi D, Singh M. Two critical positions in zinc finger domains are heavily mutated in three human cancer types. PLoS Comput Biol 2018; 14: e1006290.
  • 47. Ma J, Chen Y, Wu W, Chen Z. Structure and Function of N-Terminal Zinc Finger Domain of SARS-CoV-2 NSP2. Virol Sin 2021; 36: 1104- 12.
  • 48. Ma Y, Wu L, Shaw N, Gao Y, Wang J, Sun Y, et al. Structural basis and functional analysis of the SARS coronavirus nsp14-nsp10 complex. Proc Natl Acad Sci U S A 2015; 112: 9436-41.
  • 49. Halder UC. Predicted antiviral drugs Darunavir, Amprenavir, Rimantadine and Saquinavir can potentially bind to neutralize SARS-CoV-2 conserved proteins. J Biol Res 2021; 28: 1-58.
  • 50. Berta D, Badaoui M, Martino SA, Buigues PJ, Pisliakov A V., Elgho- bashi-Meinhardt N, et al. Modelling the active SARS-CoV-2 helicase complex as a basis for structure-based inhibitor design. Chem Sci 2021; 12: 13492-505.
There are 49 citations in total.

Details

Primary Language English
Journal Section Research Articles
Authors

Ekrem Akbulut 0000-0002-7526-9835

Publication Date June 30, 2022
Submission Date January 23, 2022
Published in Issue Year 2022

Cite

AMA Akbulut E. The Effects of SARS CoV-2 nsp13 Mutations on the Structure and Stability of Helicase in Chinese Isolates. Eur J Biol. June 2022;81(1):11-17. doi:10.26650/EurJBiol.2022.1061858