As we all know by now, the most pressing current concern about the ongoing pandemic is the potential for emergence of immune-escape variants. With that in mind, I'm very happy to have had the chance to contribute to this important work: (1/6)
nature.com/articles/s4158…
A major multi-centre effort including @tylernstarr, @jbloom_lab, @Vir_Biotech, @jchodera, @ivyzhang__, @W_Glass and many others, this work assesses a wide panel of antibodies against the SARS-CoV-2 spike for potency, breadth and potential for immune escape. (2/6)
While the potency of many existing antibodies is dramatically reduced by mutations tolerated by the virus itself, the great news is that a few show high potency against most or all known sarbecoviruses. (3/6)
That suggests that their epitopes are trapped by evolution - that is, mutations that escape antibody binding also significantly reduce the fitness of the virus itself. Excellent news for ongoing clinical treatment and potentially for design of next-generation vaccines. (4/6)
In situations like the current pandemic time is of the essence, and the research must be done both fast and well. My contribution was to use ISOLDE to quickly finalise the reported RBD-antibody crystal structures starting from initial molecular replacement models. (5/6)
A great team effort, and a sign of hope for the future. While it seems unlikely this virus will ever go away completely, I'm more and more confident that this and similar work will help to relegate it to the status of "just another common cold". (fin)

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More from @CrollTristan

8 Feb
A more extreme illustration of the problem: yes, this is a single residue (JSG, found in 6s8h and 6mhu). What it actually *is* is E. coli lipopolysaccharide (LPS) - how it appears in the database is {deep breath}:
(2~{r},4~{r},5~{r},6~{r})-6-[(1~{r})-1,2-bis(oxidanyl)ethyl]-2-[(2~{r},4~{r},5~{r},6~{r})-6-[(1~{r})-1,2-bis(oxidanyl)ethyl]-5-[(2~{s},3~{s},4~{r},5~{r},6~{r})-6-[(1~{s})-1,2-bis(oxidanyl)ethyl]-4-[(2~{r},3~{s},4~{r},5~{s},6~{r})-6-[(1~{s})-2-[(2~{s},3~{s},4~{s},5~{s},6~{r})-...
...6-[(1~{s})-1,2-bis(oxidanyl)ethyl]-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-1-oxidanyl-ethyl]-3,4-bis(oxidanyl)-5-phosphonooxy-oxan-2-yl]oxy-3-oxidanyl-5-phosphonooxy-oxan-2-yl]oxy-2-carboxy-2-[[(2~{r},3~{s},4~{r},5~{r},6~{r})-5-[[(3~{r})-3-dodecanoyloxytetradecanoyl]amino]-6-...
Read 7 tweets
2 Feb
As is becoming increasingly common these days, the pace of reality has well outstripped that of the scientific publication cycle. Still, I'd like to share this with you: sciencedirect.com/science/articl… (1/14)
Unless you've been entirely disconnected for the last month or three, the core message (that immunity-escaping variants of SARS-CoV-2 are developing and need to be watched) should come as no surprise. This work focuses on one of the first such mutants identified, N439K. (2/14)
At the time of submission, the N439K variant had been spotted in 34 different countries and had arisen independently multiple times, suggesting at least some gain of fitness over the wild-type virus. (3/14)
Read 14 tweets
6 Aug 20
ISOLDE 1.0 is finally live! To get it, just install ChimeraX 1.0 from rbvi.ucsf.edu/chimerax/downl…, then go to Tools/More Tools..., find ISOLDE and click Install. In the thread, I'll give a quick recap of what ISOLDE is, followed by a rundown of what's new. (1/17)
So what is ISOLDE? In brief, it's an interactive environment for (re)building atomic models into medium-low-density crystallographic and cryo-EM maps using GPU-accelerated interactive molecular dynamics. That's a bit of a mouthful, so here's a video demo in the next tweet. (2/17)
This example (found this morning) shows the correction of an out-by-one error in a beta strand (residues 306-318 of 3mca chain B). Like all videos in this thread, it's an actual-speed screen capture. Key features to note: (3/17)
Read 17 tweets
27 Jul 20
In all cryo-EM maps of the SARS-CoV-2 spike protein density for the N-terminal domain has been really rubbishy, with modelling only really possible based on somewhat-weak homology to the original SARS equivalent... until now. (1/12)
On the left: a better-resolved region from this domain in 6vxx - general path of the backbone is fine, but sidechains are uninterpretable without outside info. The outer surface loops devolve to complete rubbish. On the right, the same site from 6zge. Clear, unambiguous (2/12)
So what caused this enormous difference in quality? I asked the authors (from the lab of Steve Gamblin at the Crick), and their honest answer was that they weren't sure - but they pointed me at this intriguing preprint from Christiane Schaffitzel: biorxiv.org/content/10.110… (3/12)
Read 12 tweets
21 Mar 20
I was going to wait until Monday to organise and release my current set of SARS-CoV-2 structure rebuilds, but given that I woke up with a bit of a cough (don't worry, nothing serious yet) I figured better safe than sorry. Link in next post, and previous tweets collated in thread:
Link to models: drive.google.com/drive/folders/…. Each folder also contains a short set of notes covering what I considered the most important changes/issues. I'll add the previous threads discussing each model below, and add new ones as I do them.
Read 16 tweets

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