Dear all, I assume most of you are aware of the EMBL-EBI datahub which was set up in January to provide essential virus research data to all scientists, but in case someone missed it I would like to share the link: https://www.ebi.ac.uk/ena/pathogens/covid-19 (https://www.ebi.ac.uk/ena/pathogens/covid-19) You can find all relevant data, from COVID-19 genome sequencing data up to x-ray and cryo-EM structures of relevant proteins. Stay healthy, Nikolay Nikolay Dobrev Scientific Officer, Protein Expression and Purification Core Facility EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany T +49 6221 387 8633 | M +49 173 684 0532 twitter.com/EMBLorg (http://twitter.com/EMBLorg) | facebook.com/embl.org (http://facebook.com/embl.org) | youtube.com/user/emblmedia (http://youtube.com/user/emblmedia) Visit www.embl.org/events (http://www.embl.org/events) for a complete list of all EMBL events. On Sun, Mar 22, 2020 at 17:26, DUMAS Philippe (IGBMC) wrote: Relevant to the discussion: * Cell, Vol. 110, 551–561, September 6, 2002, Copyright 2002 by Cell Press An RNA Thermosensor Controls Expression of Virulence Genes in Listeria monocytogenes * Bacterial RNA thermometers: molecular zippers and switches Jens Kortmann and Franz Narberhaus NATURE REVIEWS | MICROBIOLOGY VOLUME 10 | APRIL 2012 | 255 *An RNA Thermometer Activity of the West Nile Virus Genomic 30-Terminal Stem-Loop Element Modulates Viral Replication Eciency during Host Switching Viruses 2020, 12, 104; doi:10.3390/v12010104 * Temperature triggers immune evasion by Neisseria meningitidis
Edmund Loh1*, Elisabeth Kugelberg2*, Alexander Tracy1, Qian Zhang2, Bridget Gollan2, Helen Ewles2, Ronald Chalmers3, Vladimir Pelicic2 & Christoph M. Tang1,2 Nature (2013) Philippe Dumas ------------------------------------ De: "James Holton" À: "CCP4BB" Envoyé: Dimanche 22 Mars 2020 16:38:28 Objet: Re: [ccp4bb] CCP4BB vs COVID19 Thank you Patrick, RNA structure is still structural biology, so I think relevant here. It seems to me that RNA as a thermometer would be an easy hypothesis to test? Has anyone measured virulence vs temperature in cell culture? The 3D structure of the genome is no doublt important. I wouldn't want to try crystallizing the whole thing, but I wonder if this might be an excellent target for cryoEM? A challenge for that "we can classify our way out of anything" philosophy? And the result would most certainly be interesting. -James Holton MAD Scientist On 3/21/2020 8:41 AM, Patrick Shaw Stewart wrote: James, this isn't conventional structural biology, but may be of interest, and I haven't been able get any mainstream virologists to think about it. The protein sequences are obviously of interest, but so are the RNA sequences at both ends of the Covid genome, which have conserved secondary structure. A few years ago a paper came out suggesting that wild-type influenza has multiple "RNA thermometers", which may play an important role in the tropism of influenza. Similar mechanisms may exist in other respiratory viruses, including Covid. My take on this, and the relevant papers, are below. Good luck to everyone and stay well, Patrick https://oldwivesandvirologists.blog/Covid-19-and-the-trade-off-model-of-selection/ (https://oldwivesandvirologists.blog/Covid-19-and-the-trade-off-model-of-selection/) My paper in Medical Hypotheses http://douglas.co.uk/f_ftp1/ShawStewart_final_1-s2.pdf (http://douglas.co.uk/f_ftp1/ShawStewart_final_1-s2.pdf) Narberhaus, Franz, Torsten Waldminghaus, and Saheli Chowdhury. "RNA thermometers." FEMS microbiology reviews 30.1 (2006): 3-16. Chursov, Andrey, et al. "Specific temperature-induced perturbations of secondary mRNA structures are associated with the cold-adapted temperature-sensitive phenotype of influenza A virus." RNA biology 9.10 (2012): 1266-1274. Yang, Dong, and Julian L. Leibowitz. "The structure and functions of coronavirus genomic 3′ and 5′ ends." Virus research 206 (2015): 120-133. On Fri, Mar 20, 2020 at 10:59 PM James Holton wrote: You might think that as a structural biologist you won't be able to do much about COVID-19 anytime soon, but that is not true. Yes, real-world therapeutics and vaccines take time, but we have already seen just how fast we can get started. There are 21 PDBs already and some even have bound ligands. Good job Frank et al. BTW! And my personal thanks to all of you out there who are already hard at work on this. I believe this forum is an ideal place to share information and ideas on the structural biology of SARS-CoV-2 as we move forward. It's a big virus, but there are not that many proteins in it. If all of us independently do the same bioinformatics and literature searches and end up trying exactly the same thing in every lab all over the world, then that would be more than unfortunate. To that end, I am personally interested on ORF8 for reasons I will go into below. Has anyone tried to solve it yet? What happened? Didn't express? Bad diffraction? What? Do tell. Some of us, as you may have heard, are stuck at home, our beamlines and labs dark while we shelter-in-place. That doesn't mean our hands are tied. We are still allowed to think. The fraction of the human race that has a snowball's chance in Hades of figuring out this bug is very very small. Structure may be your main skill set, but you are still a biologist. Do you know how to run a PCR machine? Do you know how to pipette? You might think that anybody can do it, but that is really not the case. Ever trained a new student on sterile technique? How many days did that take? Now remember that your student was no dummy and already studying biology. Everyone reading this will make an excellent volenteer at the very least. I'm not saying this to belittle the average human, only to say that we scientists, moving in the circles we do, often forget that we have uncommon capabilities. For example, I also believe we can be useful in assay development. The void left by the dearth and delay of test results has been filled with fear, and that is a big problem. The tests, as defined, are straightforward, but also extremely regimented like any good laboratory protocol should be. The US CDC's instructions for academic labs are here: https://www.cdc.gov/coronavirus/2019-nCoV/lab/index.html (https://www.cdc.gov/coronavirus/2019-nCoV/lab/index.html) My question is: how can this test be made faster, using more commonplace supplies, in high-throughput mode and still valid? Not just for clinical but for academic use? I think more than a few people on this list could be regarded as experts in making a complex biochemical task faster, more efficient, high-throughput and nonetheless valid. Yes, there are other people who do virus testing for a living, but right now they are all rather busy. Maybe if we put our minds to it we can help? As for why ORF8. I am basing my interest on the bioinformatics done in this article: https://dx.doi.org/10.1093/nsr/nwaa036 (https://dx.doi.org/10.1093/nsr/nwaa036). Search for "T8517C" and you will find what I'm talking about. The authors found two "types" of SARS-CoV-2. They call them "S" and "L" because the only conserved amino acid change involved is S84L in ORF8. The "S" type is believed to be the ancestor of "L". What is interesting is how tightly linked this mutation is to a silent mutation on the other end of the genome: the "L" type has a faster codon for Ser in ORF1. Such tight coupling (r^2=0.945) means there must be significant selective pressure preventing both of these mutations occurring in the same virus at the same time. That, I believe, is interesting. Espeically since they are so far apart I expect this selective pressure might work in trans: as in a super-infection. That is, the S and L genome types may interfere with each other. The authors fall short of claiming evidence of interference upon super-infection, and indeed they have already been criticised for calling "L" the "aggressive" type. But it is still interesting and points a finger at ORF8. ORF8 has only one homolog in the PDB: 5o32 with 25% identity over a stretch of 60 residues. This homologous region contains the S84L site (Val I544 in 5o32). I had a quick look and appears to be a cavity-filling mutation to me. Not very big, but maybe something could fit in there. To be sure we'd need a structure of ORF8. Good luck to you all, and stay healthy. -James Holton MAD Scientist ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 (https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1) -- patr...@douglas.co.uk (mailto:patr...@douglas.co.uk) Douglas Instruments Ltd. Douglas House, East Garston, Hungerford, Berkshire, RG17 7HD, UK Directors: Patrick Shaw Stewart, Peter Baldock, Stefan Kolek http://www.douglas.co.uk (http://www.douglas.co.uk) Tel: 44 (0) 148-864-9090 US toll-free 1-877-225-2034 Regd. England 2177994, VAT Reg. GB 480 7371 36 ------------------------------------ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 (https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1) ------------------------------------ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 (https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1) ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
