7kdh Citations

D614G Mutation Alters SARS-CoV-2 Spike Conformation and Enhances Protease Cleavage at the S1/S2 Junction.

Abstract

The severe acute respiratory coronavirus 2 (SARS-CoV-2) spike (S) protein is the target of vaccine design efforts to end the coronavirus disease 2019 (COVID-19) pandemic. Despite a low mutation rate, isolates with the D614G substitution in the S protein appeared early during the pandemic and are now the dominant form worldwide. Here, we explore S conformational changes and the effects of the D614G mutation on a soluble S ectodomain construct. Cryoelectron microscopy (cryo-EM) structures reveal altered receptor binding domain (RBD) disposition; antigenicity and proteolysis experiments reveal structural changes and enhanced furin cleavage efficiency of the G614 variant. Furthermore, furin cleavage alters the up/down ratio of the RBDs in the G614 S ectodomain, demonstrating an allosteric effect on RBD positioning triggered by changes in the SD2 region, which harbors residue 614 and the furin cleavage site. Our results elucidate SARS-CoV-2 S conformational landscape and allostery and have implications for vaccine design.

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  1. Native, engineered and de novo designed ligands targeting the SARS-CoV-2 spike protein. Costa CFS, Barbosa AJM, Dias AMGC, Roque ACA. Biotechnol Adv 59 107986 (2022)

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Reviews citing this publication (52)

  1. Mechanisms of SARS-CoV-2 entry into cells. Jackson CB, Farzan M, Chen B, Choe H. Nat Rev Mol Cell Biol 23 3-20 (2022)
  2. The biological and clinical significance of emerging SARS-CoV-2 variants. Tao K, Tzou PL, Nouhin J, Gupta RK, de Oliveira T, Kosakovsky Pond SL, Fera D, Shafer RW. Nat Rev Genet 22 757-773 (2021)
  3. SARS-COV-2 Variants: Differences and Potential of Immune Evasion. Hirabara SM, Serdan TDA, Gorjao R, Masi LN, Pithon-Curi TC, Covas DT, Curi R, Durigon EL. Front Cell Infect Microbiol 11 781429 (2021)
  4. Proteolytic activation of SARS-CoV-2 spike protein. Takeda M. Microbiol Immunol 66 15-23 (2022)
  5. SARS-CoV-2 one year on: evidence for ongoing viral adaptation. Peacock TP, Penrice-Randal R, Hiscox JA, Barclay WS. J Gen Virol 102 (2021)
  6. Mutations and Evolution of the SARS-CoV-2 Spike Protein. Magazine N, Zhang T, Wu Y, McGee MC, Veggiani G, Huang W. Viruses 14 640 (2022)
  7. From delta to Omicron: S1-RBD/S2 mutation/deletion equilibrium in SARS-CoV-2 defined variants. Papanikolaou V, Chrysovergis A, Ragos V, Tsiambas E, Katsinis S, Manoli A, Papouliakos S, Roukas D, Mastronikolis S, Peschos D, Batistatou A, Kyrodimos E, Mastronikolis N. Gene 814 146134 (2022)
  8. Emerging SARS-CoV-2 Variants of Concern (VOCs): An Impending Global Crisis. Thye AY, Law JW, Pusparajah P, Letchumanan V, Chan KG, Lee LH. Biomedicines 9 1303 (2021)
  9. SARS-CoV-2 Omicron variant: Immune escape and vaccine development. Ao D, Lan T, He X, Liu J, Chen L, Baptista-Hon DT, Zhang K, Wei X. MedComm (2020) 3 e126 (2022)
  10. Molecular characteristics, immune evasion, and impact of SARS-CoV-2 variants. Sun C, Xie C, Bu GL, Zhong LY, Zeng MS. Signal Transduct Target Ther 7 202 (2022)
  11. Mutations of SARS-CoV-2 spike protein: Implications on immune evasion and vaccine-induced immunity. Mengist HM, Kombe Kombe AJ, Mekonnen D, Abebaw A, Getachew M, Jin T. Semin Immunol 55 101533 (2021)
  12. Functional importance of the D614G mutation in the SARS-CoV-2 spike protein. Jackson CB, Zhang L, Farzan M, Choe H. Biochem Biophys Res Commun 538 108-115 (2021)
  13. SARS-CoV-2 spike protein: pathogenesis, vaccines, and potential therapies. Almehdi AM, Khoder G, Alchakee AS, Alsayyid AT, Sarg NH, Soliman SSM. Infection 49 855-876 (2021)
  14. D614G mutation and SARS-CoV-2: impact on S-protein structure, function, infectivity, and immunity. Bhattacharya M, Chatterjee S, Sharma AR, Agoramoorthy G, Chakraborty C. Appl Microbiol Biotechnol 105 9035-9045 (2021)
  15. Expression and characterization of SARS-CoV-2 spike proteins. Schaub JM, Chou CW, Kuo HC, Javanmardi K, Hsieh CL, Goldsmith J, DiVenere AM, Le KC, Wrapp D, Byrne PO, Hjorth CK, Johnson NV, Ludes-Meyers J, Nguyen AW, Wang N, Lavinder JJ, Ippolito GC, Maynard JA, McLellan JS, Finkelstein IJ. Nat Protoc 16 5339-5356 (2021)
  16. Immune Escape Associated with RBD Omicron Mutations and SARS-CoV-2 Evolution Dynamics. Kudriavtsev AV, Vakhrusheva AV, Novosеletsky VN, Bozdaganyan ME, Shaitan KV, Kirpichnikov MP, Sokolova OS. Viruses 14 1603 (2022)
  17. Evolution of the SARS-CoV-2 genome and emergence of variants of concern. Safari I, Elahi E. Arch Virol 167 293-305 (2022)
  18. Structural Plasticity and Immune Evasion of SARS-CoV-2 Spike Variants. Ghimire D, Han Y, Lu M. Viruses 14 1255 (2022)
  19. Swine Enteric Coronavirus: Diverse Pathogen-Host Interactions. Yan Q, Liu X, Sun Y, Zeng W, Li Y, Zhao F, Wu K, Fan S, Zhao M, Chen J, Yi L. Int J Mol Sci 23 3953 (2022)
  20. The virological impacts of SARS-CoV-2 D614G mutation. Wang C, Zheng Y, Niu Z, Jiang X, Sun Q. J Mol Cell Biol 13 712-720 (2021)
  21. Physicochemical effect of the N501Y, E484K/Q, K417N/T, L452R and T478K mutations on the SARS-CoV-2 spike protein RBD and its influence on agent fitness and on attributes developed by emerging variants of concern. Pondé RAA. Virology 572 44-54 (2022)
  22. Shooting at a Moving Target-Effectiveness and Emerging Challenges for SARS-CoV-2 Vaccine Development. Günl F, Mecate-Zambrano A, Rehländer S, Hinse S, Ludwig S, Brunotte L. Vaccines (Basel) 9 1052 (2021)
  23. Proteases and variants: context matters for SARS-CoV-2 entry assays. Stevens CS, Oguntuyo KY, Lee B. Curr Opin Virol 50 49-58 (2021)
  24. The Future of the COVID-19 Pandemic: How Good (or Bad) Can the SARS-CoV2 Spike Protein Get? Nugent MA. Cells 11 855 (2022)
  25. COVID-19 Research: Lessons from Non-Human Primate Models. Albrecht L, Bishop E, Jay B, Lafoux B, Minoves M, Passaes C. Vaccines (Basel) 9 886 (2021)
  26. Cardiovascular protective properties of oxytocin against COVID-19. Wang SC, Wang YF. Life Sci 270 119130 (2021)
  27. Molecular Level Dissection of Critical Spike Mutations in SARS-CoV-2 Variants of Concern (VOCs): A Simplified Review. Joshi N, Tyagi A, Nigam S. ChemistrySelect 6 7981-7998 (2021)
  28. Recent progress on the mutations of SARS-CoV-2 spike protein and suggestions for prevention and controlling of the pandemic. Li X, Zhang L, Chen S, Ji W, Li C, Ren L. Infect Genet Evol 93 104971 (2021)
  29. Antibody-mediated immunity to SARS-CoV-2 spike. Errico JM, Adams LJ, Fremont DH. Adv Immunol 154 1-69 (2022)
  30. Protein structure-based in-silico approaches to drug discovery: Guide to COVID-19 therapeutics. Gupta Y, Savytskyi OV, Coban M, Venugopal A, Pleqi V, Weber CA, Chitale R, Durvasula R, Hopkins C, Kempaiah P, Caulfield TR. Mol Aspects Med 91 101151 (2023)
  31. COVID-19: Mechanistic Model of the African Paradox Supports the Central Role of the NF-κB Pathway. Kircheis R, Schuster M, Planz O. Viruses 13 1887 (2021)
  32. The origins of COVID-19 pandemic: A brief overview. Hao YJ, Wang YL, Wang MY, Zhou L, Shi JY, Cao JM, Wang DP. Transbound Emerg Dis 69 3181-3197 (2022)
  33. Epidemiology and Characteristics of SARS-CoV-2 Variants of Concern: The Impacts of the Spike Mutations. Cocherie T, Zafilaza K, Leducq V, Marot S, Calvez V, Marcelin AG, Todesco E. Microorganisms 11 30 (2022)
  34. Evolution of the SARS-CoV-2 Omicron spike. Parsons RJ, Acharya P. Cell Rep 42 113444 (2023)
  35. Molecular variants of SARS-CoV-2: antigenic properties and current vaccine efficacy. Rayati Damavandi A, Dowran R, Al Sharif S, Kashanchi F, Jafari R. Med Microbiol Immunol 211 79-103 (2022)
  36. S Protein, ACE2 and Host Cell Proteases in SARS-CoV-2 Cell Entry and Infectivity; Is Soluble ACE2 a Two Blade Sword? A Narrative Review. Nejat R, Torshizi MF, Najafi DJ. Vaccines (Basel) 11 204 (2023)
  37. SARS-CoV-2 Virology. Li Y, Li JZ. Infect Dis Clin North Am 36 251-265 (2022)
  38. Mechanism and evolution of human ACE2 binding by SARS-CoV-2 spike. Wrobel AG. Curr Opin Struct Biol 81 102619 (2023)
  39. Novel coronavirus mutations: Vaccine development and challenges. Luo WR, Wu XM, Wang W, Yu JL, Chen QQ, Zhou X, Huang X, Pan HF, Liu ZR, Gao Y, He J. Microb Pathog 173 105828 (2022)
  40. The spike glycoprotein of highly pathogenic human coronaviruses: structural insights for understanding infection, evolution and inhibition. Qiao S, Zhang S, Ge J, Wang X. FEBS Open Bio 12 1602-1622 (2022)
  41. Mutations in the SARS-CoV-2 spike receptor binding domain and their delicate balance between ACE2 affinity and antibody evasion. Xue S, Han Y, Wu F, Wang Q. Protein Cell 15 403-418 (2024)
  42. Strategies for the Production of Molecular Animations. Werner E. Front Bioinform 2 793914 (2022)
  43. The effects of amino acid substitution of spike protein and genomic recombination on the evolution of SARS-CoV-2. Fang L, Xu J, Zhao Y, Fan J, Shen J, Liu W, Cao G. Front Microbiol 14 1228128 (2023)
  44. Towards Quantum-Chemical Level Calculations of SARS-CoV-2 Spike Protein Variants of Concern by First Principles Density Functional Theory. Ching WY, Adhikari P, Jawad B, Podgornik R. Biomedicines 11 517 (2023)
  45. Molecular and Clinical Investigation of COVID-19: From Pathogenesis and Immune Responses to Novel Diagnosis and Treatment. Kashani NR, Azadbakht J, Ehteram H, Kashani HH, Rajabi-Moghadam H, Ahmad E, Nikzad H, Hosseini ES. Front Mol Biosci 9 770775 (2022)
  46. SARS-CoV-2 Spike-Mediated Entry and Its Regulation by Host Innate Immunity. Yu S, Hu H, Ai Q, Bai R, Ma K, Zhou M, Wang S. Viruses 15 639 (2023)
  47. Mutational dynamics of SARS-CoV-2: Impact on future COVID-19 vaccine strategies. Faraji N, Zeinali T, Joukar F, Aleali MS, Eslami N, Shenagari M, Mansour-Ghanaei F. Heliyon 10 e30208 (2024)
  48. Cryo-electron microscopy in the study of virus entry and infection. Dutta M, Acharya P. Front Mol Biosci 11 1429180 (2024)
  49. Host Cell Proteases Involved in Human Respiratory Viral Infections and Their Inhibitors: A Review. Lubinski B, Whittaker GR. Viruses 16 984 (2024)
  50. Molecular and structural insights into SARS-CoV-2 evolution: from BA.2 to XBB subvariants. Yajima H, Nomai T, Okumura K, Maenaka K, Genotype to Phenotype Japan (G2P-Japan) Consortium, Ito J, Hashiguchi T, Sato K. mBio 15 e0322023 (2024)
  51. Potential impacts of SARS-CoV-2 on parathyroid: current advances and trends. Murugan AK, Alzahrani AS. Endocrine 81 391-408 (2023)
  52. Significance of Artificial Intelligence in the Study of Virus-Host Cell Interactions. Elste J, Saini A, Mejia-Alvarez R, Mejía A, Millán-Pacheco C, Swanson-Mungerson M, Tiwari V. Biomolecules 14 911 (2024)

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