本帖最后由 choi 于 4-1-2021 08:03 编辑
(2) Ryan Cross, The Tiny Tweak Behind COVID-19 Vaccines; Prepandemic coronavirus research by Jason McLellan and Barney Graham led to a trick for stabilizing the prefusion form of spike proteins. Chemical & Engineering News (c&en; "a weekly news magazine published by the American Chemical Society": en.wikipedia.org), Sept 29, 2020.
https://cen.acs.org/pharmaceutic ... ind-COVID-19/98/i38
Quote:
(a) "Scientists believe that for COVID-19 vaccines to be effective, our immune systems must develop antibodies that prevent this fusion [with neutralizing antibodies physically shrouding the part of S protein that would dock to the (cellular) receptor]. Such antibodies must target the spike protein in its aptly named prefusion conformation. Unfortunately for vaccine developers, spike proteins are liable to spring from their stubby prefusion shape into their elongated postfusion form on a hair trigger.
"Fortuitously, Graham and a former postdoc, Jason McLellan, devised a solution to this problem before the pandemic. Through a bit of structural biology [structural biology determine the 3-dimentional structure of a molecule] and persistent protein engineering, McLellan discovered that adding two prolines—the most rigid of the 20 amino acids—to a key joint of a vaccine's spike protein could stabilize the structure's prefusion shape. This 2P [two-proline] mutation worked in preclinical studies of Graham and Moderna's MERS vaccine, so they applied it to Moderna's COVID-19 vaccine.
(b) About Respiratory syncytial virus (RSV): " * * * There's still no vaccine available.
In 1966, a decade after RSV was discovered [in 1955], US National Institutes of Health researchers began testing an RSV vaccine made of a virus killed with formalin—an aqueous solution of formaldehyde. The trial was a disaster, McLellan says. Although infants who got the vaccine developed antibodies against the virus, they were not protected from infection. Instead, the vaccine seemed to make the disease worse. Some 80% of infants who got the shot were hospitalized after an RSV infection, compared with 5% of infants in the control group. Two vaccinated babies died from the infection. The tragedy tainted the RSV vaccine field for decades.
"Scientists now know that RSV infects and fuses with human cells using its F protein, which, like coronavirus spike proteins, shape-shifts during infection. The F protein is far more unstable than spike proteins, and in 2016 Graham reported that formalin inactivation leaves the viruses coated with postfusion F. Our immune systems can make antibodies against postfusion F, but they aren't very good ones.
(c) "McLellan joined NIAID [National Institute of Allergy and Infectious Diseases (whose head has been Anthony Fauci), a division of National Institute of Health (NIH)] as a postdoc in Peter Kwong's lab in 2008 to do that work [structural biology] with HIV, but he soon realized he was up against the hardest test case for these protein-engineering principles. [Barney] Graham, who, as the deputy director of NIAID's Vaccine Research Center, worked in the same building, encouraged McLellan to work with him [as Graham's postdoc] on RSV. If they could find a way to modify the F protein and keep it locked in its prefusion form, they might have a shot at creating a successful RSV vaccine.
"Figuring out exactly what the prefusion F protein looked like was their first challenge. McLellan and Graham decided to look for antibodies that neutralize RSV but don't bind postfusion F. Such antibodies were likely binding to prefusion F, they reasoned, and could thus be used to lock the protein down [which can mean to purify the prefusion F, or as here, to get 3-d of both prefusion F and antibody together (without separating the two first)]. Doing so would allow McLellan, a trained X-ray crystallographer, to capture a snapshot of the prefusion F and antibody bound together. The team found three highly potent neutralizing antibodies that fit the bill.
(d) "As McLellan was starting his own lab at Dartmouth College in 2013, the recently emerged MERS coronavirus was top of mind. No one had ever solved the structure of a full coronavirus spike protein. These proteins are similar to the F protein on RSV but a whopping 2.5 times as large.
"Despite many attempts, and even with outside help, the scientists couldn’t get the MERS spike protein to cooperate. So McLellan, Graham, and their collaborator at Scripps Research, Andrew Ward, turned to a different coronavirus, HKU1 [first discovered in Hong kong in 2004 but is found to be prevalent worldwide; I am clueless about U in HKU1]. The virus, which causes the common cold, was safer to work with and better at sitting still while its picture was being taken. In 2016, Ward's lab used a technique called cryogenic electron microscopy to capture the structure of the HKU1 spike.
(e) " * * * This 2P mutation enabled McLellan and Ward to solve the MERS prefusion spike structure in 2017 (Proc. Natl. Acad. Sci. U.S.A., DOI: 10.1073/pnas.1707304114). Graham began working with Moderna to make an mRNA vaccine for MERS using the 2P mutation that same year.
"Once the genetic sequence of SARS-CoV-2 was released this January [in 2020], Graham's lab, collaborating with McLellan's lab, was able to compare its genome with those of SARS and MERS, pinpoint the code corresponding to that bent spring [where 2P would be swapped], and then add the 2P mutation to lock the SARS-CoV-2 spike in its prefusion conformation.
(f) "One of the COVID-19 vaccine front-runners, produced by AstraZeneca, doesn't even use it [2P].
My comment:
(a) Regarding quotation (a).
(i) hair-trigger (n): "a gun trigger so adjusted as to permit the firearm to be fired by a very slight pressure"
https://www.merriam-webster.com/dictionary/hair-trigger
(ii) "prolines—the most rigid of the 20 amino acids"
proline
https://en.wikipedia.org/wiki/Proline
View structure in the table to the right and you will see that the proline can not turn around (there is no axis to turn, that is).
(b) Regarding quotation (b).
(i) respiratory syncytial virus
https://en.wikipedia.org/wiki/Respiratory_syncytial_virus
("is the single most common cause of respiratory hospitalization in infants, reinfection remains common throughout the lifetime [meaning that antibodies, if any, are useless] * * * its name is derived from the large syncytia that form when infected cells fuse together. * * * Following inoculation of the nose or eyes, RSV infects ciliated columnar epithelial cells of the upper and lower airway")
(A) RSV is paramyxovirus (not coronavirus), whose members includes mumps, measle, and rubella
https://en.wikipedia.org/wiki/Rubella
(Rash "usually starts on the face and spreads to the rest of the body. The rash is sometimes itchy and is not as bright as that of measles. * * * Only humans are infected. * * * The name "rubella" is from Latin and means little red. It was first described as a separate disease by German physicians in 1814 resulting in the name 'German measles' ")
(B) English dictionary:
* rubella (n; From Latin [adjective masculine] rubellus reddish, diminutive of [adjective masculine] ruber red)
https://en.wiktionary.org/wiki/rubella
The corresponding Latin noun (masculine) for red is rubor.
(C) RSV is not coronavirus. It just happens that RSV's extracellular domain undergoes pre- and post- fusion transformation and was used for study that phenomenon, which then paved the way for research of coronavirus's S protein.
(D) Griffiths CD et al, IGF1R Is an Entry Receptor for Respiratory Syncytial Virus. Nature 583: 615 (2020)
https://www.nature.com/articles/s41586-020-2369-7
(Abstract: "Nucleolin is an entry coreceptor for RSV [footnote 2 pointed to a 2011 Nature Medicine report] * * * These findings [reported here] reveal a mechanism of virus entry in which receptor engagement and signal transduction bring the coreceptor to viral particles at the cell surface")
The coreceptor is nucleolin, which usually stays inside nucleus.
The article is placed behind paywall. Here is the conceptual scheme (which is novel):
Carlos Castellanos, RSV and IGF1R: More Than Just a Scratch on the 'Cell' Surface. Breaking Down Biology, June 21, 2020
https://www.breakingdownbio.com/ ... he-cell-surfacenbsp
(iii) syncytium (n; plural syncytia (due to lts Latin root); etymology: New Latin, from syn- + cyt-)
https://www.merriam-webster.com/dictionary/syncytium
(pronunciation)
(c) Regarding quotation (c).
Peter Kwong, PhD
Chief, Structural Biology Section[,] Vaccine Research Center[, NIAID]
https://www.niaid.nih.gov/resear ... ral-biology-section
(d) Regarding quotation (d).
"In 2016, Ward's lab used a technique called cryogenic electron microscopy to capture the structure of the HKU1 spike."
Kirchdoerfer RN et al, Pre-fusion structure of a human coronavirus spike protein. Nature 531: 118 (2016).
https://www.nature.com/articles/nature17200
There is no need to read it, because S protein of coronavirus family are all similar. Science published (1), only due to widespread interest in Covid-19.
(e) Regarding quotation (e).
"This 2P mutation enabled McLellan and Ward to solve the MERS prefusion spike structure in 2017"
The link connected:
Pallesen J et al (Jason S McLellan being the last author), Immunogenicity and Structures of a Rationally Designed Prefusion MERS-CoV Spike Antigen. Proc Nat Acad Sci 114: E7348 (Aug 29, 2017).
https://www.pnas.org/content/114/35/E7348
There is no need to read this article. What you have to know is that 2P was needed to study protein (here MERS perfusion S) structure, simply because crystallography was used, together with cryo-EM. Cryo-EM, when used alone, does not need 2P, as shown in both (1) and Bing Chen's article at (f)(i)(C) below.
(f) Now I am going to discuss the first two figures in (2).
(i) The top figure has a legend that read: "Harvard Medical School virologist Bing Chen determined prefusion and postfusion structures of the SARS-CoV-2 spike protein. The spike sheds a subunit and elongates during fusion with a human cell."
(A) "Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the virus that causes coronavirus disease 2019 (COVID-19)." en.wikipedia.org for "severe acute respiratory syndrome coronavirus 2."
(B) The top figure demonstrates a trimer with each protomer painted a different color (red, green and blue).
(C) The top figure is from
Cai Y et al (Bing Chen is the last author), Distinct Conformational States of SARS-CoV-2 Spike Protein. Science 369: 1586 (Sept 25, 2020).
https://pubmed.ncbi.nlm.nih.gov/32694201/
There is no need to read this Science article.
(ii) The middle figure's legend reads, "The prefusion form of the F protein of respiratory syncytial virus revealed two sites, colored red and orange, that the most potent neutralizing antibodies bind to. These sites], having been shed,] are not found on postfusion F."
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