Structure-based design of prefusion-stabilized SARS-CoV-2 spikes
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Abstract
Stabilizing the prefusion SARS-CoV-2 spike: The development of therapeutic antibodies and vaccines against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is focused on the spike (S) protein that decorates the viral surface. A version of the spike ectodomain that includes two proline substitutions (S-2P) and stabilizes the prefusion conformation has been used to determine high-resolution structures. However, even S-2P is unstable and difficult to produce in mammalian cells. Hsieh et al. characterized many individual and combined structure-guided substitutions and identified a variant, named HexaPro, that retains the prefusion conformation but shows higher expression than S-2P and can also withstand heating and freezing. This version of the protein is likely to be useful in the development of vaccines and diagnostics. Science , this issue p. 1501
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S-2P differs from the spike protein in the reference SARS-CoV-2 genome (NC_045512) by two amino acids, i.e., amino acids KV at sites 986 and 987 were replaced by PP.
“Both mRNA encodes the same S-2P protein [5,6] which differ from the spike protein in the reference SARS-CoV-2 genome (NC_045512) by two amino acids, i.e., amino acids KV at sites 986 and 987 were replaced by PP to stabilize the resulting spike protein in the prefusion state to train the host immune system to recognize the virus before its entry into the host cell [7,8].”
From Detailed Dissection and Critical Evaluation of the Pfizer/BioNTech and Moderna mRNA Vaccines (2021) · cites this paper as [7]
The supplied passage describing S-2P (section labeled Abstract; page unavailable) says it contains two consecutive proline substitutions in the S2 subunit that stabilize the prefusion spike. Our copy does not identify the original residues as KV, give positions 986 and 987, or compare the construct with reference genome NC_045512, so those specifics are not verified. (LLM, conf=0.85)
Experimental — accuracy not yet measuredSelection involved K417N/E/T for six antibodies, E484K for five, and N501Y/T/H for three; these match mutations in circulating B.1.1.17/501Y.V1, B.1.351/501Y.V2, and B1.1.28/501.V3 (P.1) variants.
“Notably, 6 of the antibodies selected for K417N, E or T, 5 selected for E484K and 3 selected for N501Y, T or H, which coincide with mutations present in the circulating B.1.1.17/501Y.V1, B.1.351/501Y.V2 and B1.1.28/501.V3 (P.1) variants that have been associated with rapidly increasing case numbers in particular locales14,17,18,36.”
From mRNA vaccine-elicited antibodies to SARS-CoV-2 and circulating variants (2021) · cites this paper as [36]
Several circulating variants linked to rapidly rising case counts are especially prevalent in the UK (B.1.1.7/501Y.V1), South Africa (B.1.351/501Y.V2), and Brazil (P.1).
“A number of circulating SARS-CoV-2 variants that have been associated with rapidly increasing case numbers and have particular prevalence in the UK (B.1.1.7/501Y.V1), South Africa (B.1.351/501Y.V2) and Brazil (P.1)14,17,18,36.”
From mRNA vaccine-elicited antibodies to SARS-CoV-2 and circulating variants (2021) · cites this paper as [36]
The S protein is considered the main antigen for vaccine design.
“Therefore, the S protein is considered the main antigen for vaccine design.228–230”
From Advances in COVID-19 mRNA vaccine development (2022) · cites this paper as [230]
The trimeric S protein on the surface of SARS-CoV-2 plays a key role in mediating host cell invasion.
“The trimeric S protein on the surface of SARS-CoV-2 plays a key role in mediating host cell invasion.”
From Advances in COVID-19 mRNA vaccine development (2022) · cites this paper as [230]
The PP substitution stabilizes the resulting spike protein in the prefusion state to train the host immune system to recognize the virus before its entry into the host cell.
“Both mRNA encodes the same S-2P protein [5,6] which differ from the spike protein in the reference SARS-CoV-2 genome (NC_045512) by two amino acids, i.e., amino acids KV at sites 986 and 987 were replaced by PP to stabilize the resulting spike protein in the prefusion state to train the host immune system to recognize the virus before its entry into the host cell [7,8].”
From Detailed Dissection and Critical Evaluation of the Pfizer/BioNTech and Moderna mRNA Vaccines (2021) · cites this paper as [7]
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Günl, F., Mecate-Zambrano, A., Rehländer, S., Hinse, S., Ludwig, S., & Brunotte, L. (2021) · Vaccines · doi:10.3390/vaccines9101052 · Cited by 27 · see citing works
Immunogenicity of novel mRNA COVID-19 vaccine MRT5500 in mice and non-human primates
Kalnin, K. V., Plitnik, T., Kishko, M., Zhang, J., Zhang, D., Beauvais, A., Anosova, N. G., Tibbitts, T., DiNapoli, J. M., Huang, P.-W. D., et al. (2020) · doi:10.1101/2020.10.14.337535 · Cited by 18 · see citing works
- Authors
- Hsieh, C.-L., Goldsmith, J. A., Schaub, J. M., DiVenere, A. M., Kuo, H.-C., Javanmardi, K., Le, K. C., Wrapp, D., Lee, A. G., Liu, Y., Chou, C.-W., Byrne, P. O., Hjorth, C. K., Johnson, N. V., Ludes-Meyers, J., Nguyen, A. W., Park, J., Wang, N., Amengor, D., Lavinder, J. J., Ippolito, G. C., Maynard, J. A., Finkelstein, I. J., & McLellan, J. S.
- Affiliations
- The University of Texas at Austin (US)
- Corresponding author
- Maynard, Jennifer A.
- Finkelstein, Ilya J.
- McLellan, Jason S.
- ORCID
- Hsieh, Ching-Lin
- Goldsmith, Jory A.
- Schaub, Jeffrey M.
- DiVenere, Andrea M.
- Kuo, Hung-Che
- Javanmardi, Kamyab
- Le, Kevin C.
- Wrapp, Daniel
- Lee, Alison G.
- Liu, Yutong
- Chou, Chia-Wei
- Byrne, Patrick O.
- Hjorth, Christy K.
- Johnson, Nicole V.
- Nguyen, Annalee W.
- Park, Juyeon
- Wang, Nianshuang
- Amengor, Dzifa
- Lavinder, Jason J.
- Ippolito, Gregory C.
- Maynard, Jennifer A.
- Finkelstein, Ilya J.
- McLellan, Jason S.
- Venue
- Science
- Published
- 2020-09-18
- Volume
- 369
- Issue
- 6510
- Pages
- 1501-1505
- ISSN
- 0036-8075 (ISSN-L)
- 1095-9203
- PMC
- PMC7402631
- OpenAlex
- W3044914269
- Cited by
- 1,303
- References
- 33
- Citations by year
- 2026: 109 · 2025: 163 · 2024: 185 · 2023: 221 · 2022: 268 · 2021: 279 · 2020: 77
- FWCI
- 27.68
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Science (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- PubMed Central (submittedVersion, cc-by-nc-nd)
- Funders
- National Science Foundation (1453358)
- National Institutes of Health (R01-AI127521, GM120554, GM124141, AI122753)
- Welch Foundation (F-1808, F-1767)
- Topics
- Health Sciences › Medicine › Infectious Diseases › SARS-CoV-2 and COVID-19 Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › vaccines and immunoinformatics approaches
- Keywords
- SARS-CoV-2 spike protein, prefusion spike, protein stabilization, structure-guided protein engineering, proline substitution, protein thermal stability, freeze-thaw stability, COVID-19 vaccine development, serological diagnosis
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Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
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