おおざっぱな SARS CoV-2 S protein のメモ

【注意】当時なけなしの知識で資料をかきあつめたメモ。たしか、開裂の仕方の図がこうでない可能性があって非公開にした気がするので、図は当てにしないで下さい。いまはもっと詳しい図がいっぱいあるんじゃなかろうか？このあと忙しくなってアップデートしてません。すまんです。

論文を読むための予習用自習。Class I fusion protein の様式はインフルエンザHEの知見が主になっていて、S1/S2の関係とか、S2の展開のモデルとかはインフルエンザHEから推測されているもの、という理解。実験でS1/S2をプロテアーゼ処理で開裂→S2の6HB構造の間の時間分解がうまくできる方法がないみたいで、あんまり見えていない感。

資料

書式は揃ってません。自分勉強用なのでちょっと違う話が混ざってても許して。

Scientific Americanの図の裏付け研究が解説されているすごい記事。サイエンスイラストレーターなら読むべき。
"How I Built a 3-D Model of the Coronavirus for Scientific American"
https://www.scientificamerican.com/article/how-i-built-a-3-d-model-of-the-coronavirus-for-scientific-american/?fbclid=IwAR0_pZB3zQfk5MSUTUzXY2SOPTe4z0y2YZxZm2239TxWLO6tt5NBWBmauKA

プレプリントだが再構築してる。
Developing a Fully-glycosylated Full-length SARS-CoV-2 Spike Protein Model in a Viral Membrane
Hyeonuk Woo, Sang-Jun Park, Yeol Kyo Choi, Taeyong Park, Maham Tanveer, Yiwei Cao, Nathan R. Kern, Jumin Lee, Min Sun Yeom, Tristan I. Croll, Chaok Seok, Wonpil Im
bioRxiv 2020.05.20.103325; doi: https://doi.org/10.1101/2020.05.20.103325
This article is a preprint and has not been certified by peer review

ウイルスの fusion protein の総説。
White JM, Delos SE, Brecher M, Schornberg K. Structures and mechanisms of viral membrane fusion proteins: multiple variations on a common theme. Critical reviews in biochemistry and molecular biology. 2008;43(3):189–219. Epub 2008/06/24. pmid:18568847; PubMed Central PMCID: PMC2649671.
https://www.tandfonline.com/doi/full/10.1080/10409230802058320

S1とS2が切れてからFPが宿主細胞の膜に刺さると記述してるやつ↓
Heald-Sargent, T.; Gallagher, T. Ready, Set, Fuse! The Coronavirus Spike Protein and Acquisition of Fusion Competence. Viruses 2012, 4, 557-580.
https://doi.org/10.3390/v4040557

同じく、S1とS2が切れてからFPが宿主細胞の膜に刺さると記述してるやつ↓
Yuan, Y., Cao, D., Zhang, Y. et al. Cryo-EM structures of MERS-CoV and SARS-CoV spike glycoproteins reveal the dynamic receptor binding domains. Nat Commun 8, 15092 (2017). https://doi.org/10.1038/ncomms15092

Xia, S., Zhu, Y., Liu, M. et al. Fusion mechanism of 2019-nCoV and fusion inhibitors targeting HR1 domain in spike protein. Cell Mol Immunol (2020). https://doi.org/10.1038/s41423-020-0374-2

Xia, S., Liu, M., Wang, C. et al. Inhibition of SARS-CoV-2 (previously 2019-nCoV) infection by a highly potent pan-coronavirus fusion inhibitor targeting its spike protein that harbors a high capacity to mediate membrane fusion. Cell Res 30, 343–355 (2020). 
https://doi.org/10.1038/s41422-020-0305-x

M. Alejandra Tortorici, David Veesler,
Chapter Four - Structural insights into coronavirus entry,
Editor(s): Félix A. Rey,
Advances in Virus Research, Academic Press, Volume 105, 2019, Pages 93-116, ISSN 0065-3527, ISBN 9780128184561, Academic Press, 
https://doi.org/10.1016/bs.aivir.2019.08.002.Pages 93-116, ISSN 0065-3527, ISBN 9780128184561,
https://doi.org/10.1016/bs.aivir.2019.08.002

Shang J, Wan Y, Liu C, Yount B, Gully K, Yang Y, et al. (2020) Structure of mouse coronavirus spike protein complexed with receptor reveals mechanism for viral entry. PLoS Pathog 16(3): e1008392. https://doi.org/10.1371/journal.ppat.1008392

Biochemical Analysis of Coronavirus Spike Glycoprotein Conformational Intermediates during Membrane Fusion
Miyuki Kawase, Michiyo Kataoka, Kazuya Shirato, Shutoku Matsuyama
Journal of Virology Sep 2019, 93 (19) e00785-19; DOI: 10.1128/JVI.00785-19
https://jvi.asm.org/content/93/19/e00785-19

SARS CoV のS1の折りたたみなど。
Cryo-EM structure of the SARS coronavirus spike glycoprotein in complex with its host cell receptor ACE2
Song W, Gui M, Wang X, Xiang Y (2018) Cryo-EM structure of the SARS coronavirus spike glycoprotein in complex with its host cell receptor ACE2. PLOS Pathogens 14(8): e1007236. https://doi.org/10.1371/journal.ppat.1007236

Class I fusion protein では一番良く調べられている（と書いてあったよ）インフルエンザウイルスの Hemagglutinin という fusion protein がバネのように開く話。
Hui Qiao, Sandra L. Pelletier, Lucas Hoffman, Jill Hacker, R. Todd Armstrong, Judith M. White; Specific Single or Double Proline Substitutions in the “Spring-loaded” Coiled-Coil Region of the Influenza Hemagglutinin Impair or Abolish Membrane Fusion Activity . J Cell Biol 15 June 1998; 141 (6): 1335–1347. doi: https://doi.org/10.1083/jcb.141.6.1335

Felix A. Rey, and Shee-Mei Lok 
Common Features of EnvelopedViruses and Implications for Immunogen Design for Next-Generation Vaccines
Cell, Volume 172, Issue 6, March 8, 2018, 1319 - 1334
https://doi.org/10.1016/j.cell.2018.02.054

Receptor Binding and Membrane Fusion in Virus Entry: The Influenza Hemagglutinin
John J. Skehel and Don C. Wiley
Annual Review of Biochemistry 2000 69:1, 531-569
https://www.annualreviews.org/doi/10.1146/annurev.biochem.69.1.531

ClassI fusion protein はインフルエンザの Hemagglutinin が一番良く調べられているというのでいろいろ見ていったら、昨今はインフルエンザはバネのように開くんじゃなくて、一度にコイルドコイルがほどけちゃうという話が…。まあ、Hemagglutinin の話だからいいんですけど。
Structural monitoring of a transient intermediate in the hemagglutinin fusion machinery on influenza virions
M. A. Benhaim1, V. Mangala Prasad1, View ORCID ProfileN. K. Garcia1, View ORCID ProfileM. Guttman1 and View ORCID ProfileK. K. Lee1,2,3,*
Science Advances 29 Apr 2020:
Vol. 6, no. 18, eaaz8822
DOI: 10.1126/sciadv.aaz8822
https://doi.org/10.1126/sciadv.aaz8822

サイエンスイラストレーション制作会社の人のナイスまとめ。
https://falconierivisuals.com/?p=916

HR2はstalkである件。
Immunogenicity and structures of prefusion MERS S
Jesper Pallesen, Nianshuang Wang, Kizzmekia S. Corbett, Daniel Wrapp, Robert N. Kirchdoerfer, Hannah L. Turner, Christopher A. Cottrell, Michelle M. Becker, Lingshu Wang, Wei Shi, Wing-Pui Kong, Erica L. Andres, Arminja N. Kettenbach, Mark R. Denison, James D. Chappell, Barney S. Graham, Andrew B. Ward, Jason S. McLellan
Proceedings of the National Academy of Sciences Aug 2017, 114 (35) E7348-E7357; DOI: 10.1073/pnas.1707304114

C-I-TASSER
https://zhanglab.ccmb.med.umich.edu/COVID-19/

CHARMM-GUI
http://www.charmm-gui.org/?doc=archive&lib=covid19

Amaro Lab