Re: [ccp4bb] CCP4BB vs COVID19

[Jonathan Cooper]

 A bit off-topic, and not wishing to tempt fate, of course, here are the No. 
cases by date for two typical outer-London boroughs (of absolutely no 
particular interest to me ;-), one about 4 times bigger than the other: 
http://u.cubeupload.com/jbcooper/2020032316h22m13s.png
Could I be forgiven for seeing a bit of a plateau there? I saw an article 
yesterday saying you could only make the global numbers slope-off by taking 
logs on the Y-axis - the age-old adage that logs will flatten everything!! I 
haven't had to do that in this case. I'll be more crystallographic next time. 
On Sunday, 22 March 2020, 20:26:51 GMT, Darren Hart  
wrote:  
 
  Structure of 2019-nCov RNA polymerase:
 
https://www.biorxiv.org/content/10.1101/2020.03.16.993386v1.full.pdf+html
 
 Here we report the cryo-EM structure of 2019-nCoV full-length nsp12 in complex 
with cofactors nsp7 and nsp8 at a resolution of 2.9-Å...A comparative analysis 
to show how remdesivir binds to this polymerase is also provided. 
 
 Darren
 
 
 
 On 22/03/2020 19:18, Nikolay Dobrev wrote:
  
 
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 
  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 | facebook.com/embl.org | youtube.com/user/emblmedia
 Visit 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/
     
My paper in Medical Hypotheses 
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 

Re: [ccp4bb] External: [ccp4bb] Fwd: [ccp4bb] CCP4BB vs COVID19

[Gihan Ketawala]

Guys, Thanks for all the help. I figured out what's wrong with the sequence 
file. 
I had accedently entered an "X' to one of the sub-chains.

Cheeres !
Gihan




To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1

Re: [ccp4bb] CCP4BB vs COVID19

[Darren Hart]

Structure of 2019-nCov RNA polymerase:

https://www.biorxiv.org/content/10.1101/2020.03.16.993386v1.full.pdf+html

/Here we report the cryo-EM structure of 2019-nCoV full-length nsp12 in 
complex with cofactors nsp7 and nsp8 at a resolution of 2.9-Å...A 
comparative analysis to show how remdesivir binds to this polymerase is 
also provided. /


Darren



On 22/03/2020 19:18, Nikolay Dobrev wrote:

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

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" mailto:jmhol...@lbl.gov>>
*À: *"CCP4BB" mailto:CCP4BB@JISCMAIL.AC.UK>>
    *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/


My paper in /Medical Hypotheses
/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
mailto:jmhol...@lbl.gov>> wrote:

You might think that as a structu

Re: [ccp4bb] CCP4BB vs COVID19

[Tristan Croll]

For what it’s worth, I’ve spent the last few days going over most of the 
existing COVID-19 related structures and rebuilding/re-refining wherever I 
considered necessary. The resulting models along with some basic explanatory 
notes are at 
https://drive.google.com/drive/folders/1S5qJtCnK00NrcbwwBNgImUMewhiBkyPa?usp=sharing.
 Some commentary on things I found can also be found in my Twitter thread at 
https://twitter.com/crolltristan/status/1241317484235554823?s=21. Normally I 
shy away from meddling with other people’s new models without invitation - but 
if ever there was a time to make an exception, this is it. Please feel free to 
use these for whatever purpose you like, and to improve on them further if you 
can. Tomorrow I’ll start personally contacting the individual authors to see if 
they’re willing to update their PDB entries.

Wishing the best of good health to all!

Tristan
 

 

> On 20 Mar 2020, at 22:59, 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
> 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.  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 

Re: [ccp4bb] CCP4BB vs COVID19

[Patrick Shaw Stewart]

James, there are lots of quite simple experiments that would be could be
done, but I can't get anyone to think seriously about the problem - let
alone do the experiments.

The attitude seems to be, "it can't be as simple as you suggest - someone
would have noticed it".

* Has anyone measured virulence vs temperature in cell culture?*


This isn't what you've got in mind, but yes, it was noticed that the
viruses that establish persistent infections of cell cultures (and they
have to be less aggressive to do that) often *spontaneously* become
temperature sensitive.  And, conversely, temperature-sensitive viruses that
are grown at low temp but in conditions where they can multiply fast, often
spontaneously lose their initial temperature-sensitivity.  Refs in my
paper.  Thse are all experiments that were done "by accident".

In influenza a temperature-driven switch has been seen, switching between
translation (high temp) and replication (low temp).  See the link below for
figures - described in words in my paper, below.

Best wishes

Patrick


Figures showing the "switch":
https://www.douglas.co.uk/f_ftp1/Seminar_by_Patrick_Shaw_Stewart_-_a_few_slides_for_Bill.pdf
Paper: http://douglas.co.uk/f_ftp1/ShawStewart_final_1-s2.pdf
Easy read part 1, about seasonality: https://oldwivesandvirologists.blog/
Easy read part 2 about Covid:
https://oldwivesandvirologists.blog/Covid-19-and-the-trade-off-model-of-selection/


_


>From my paper:


*The temperature sensitivity of viral transcription*

Most laboratory respiratory viruses are propagated at 37 C, which may
result in the rapid
loss of ts characters, especially since viruses mutate very rapidly when
they are introduced
to new hosts. If, however, temperature sensitivity is a common feature of
wild respiratory
viruses, we might expect to see remnants of temperature sensitivity in the
biochemistry
of laboratory strains. It turns out that such remnants are quite common.
For several
decades virologists have found that maximum RNA transcription in influenza
viruses occurs
below normal body temperature. In 1977, Plotch and Krug [61] reported that
the greatest
activity of the RNA polymerase of WSN virus was at 30–32 C. This is similar
to the optimum
temperature of the polymerase of influenza C, which is 33 C [62,63].
Ulmanen et al. [64]
found that the rate of transcription by detergent-treated WSN viruses
(influenza A) was about
10 times greater at 33 C than at 39.5 C, and also that the binding of a
cleaved primer cap
(the ‘‘A13 fragment”) to the viral cores was ‘‘unexpectedly” much weaker at
39.5 C than at
33 C. Scholtissek and Rott [65] showed that the optimum for the polymerase
of the
Rostock strain of fowl plague virus was 36 C, five degrees below chickens’
normal body
temperature (41 C). At least two reports show that temperature affects the
balance between
transcription and viral replication. Kashiwagi et al. looked at the effect
of temperature on
RNA production for five varied influenza A strains [66]. For all strains,
vRNA unexpectedly
decreased when the temperature was increased from 37 C to 42 C. The PA
subunit of the
viral polymerase caused this thermal sensitivity. In another interesting
study, Dalton et al.
showed that the production of mRNA by the PR8 influenza strain is favored
at a higher
temperature (41 C), with very little vRNA being produced at that
temperature [67]. A plasmid-
based recombinant system showed that as the incubation temperature
increased from 31 C
to 39 C the amount of replicative RNA products (c- and vRNA) decreased and
a greater
accumulation of mRNA was observed. The cRNA that is used as a template to
make the
vRNA formed a complex with the polymerase that was particularly
heat-labile, showing rapid
dissociation even at 37 C. The authors suggested that the ‘‘switch” that
regulates the
transition from transcription to replication is dependent on temperature,
but made no
comments about how shifts in the host’s body or respiratory tract
temperature may influence
this transition.





On Sun, Mar 22, 2020 at 3:38 PM James Holton  wrote:

> 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 

Re: [ccp4bb] CCP4BB vs COVID19

[Nikolay Dobrev]

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 

Re: [ccp4bb] CCP4BB vs COVID19

[DUMAS Philippe (IGBMC)]

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 



BQ_BEGIN

[ 
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 < [ mailto:jmhol...@lbl.gov | 
jmhol...@lbl.gov ] > wrote: 

BQ_BEGIN
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 sa

Re: [ccp4bb] CCP4BB vs COVID19

[James Holton]

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/


My paper in /Medical Hypotheses
/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
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 

Re: [ccp4bb] CCP4BB vs COVID19

[James Holton]

Well, look at that!  I had missed that one.  Thank you Dan.

Ahh, those Ig folds.  They are like dougnuts.  Is there anything they 
can't do?


Interesting that Tan et al. arrived at their conclusions from a very 
different line of evidence.  They seem to have missed the covariance 
with the silent site pointed out by Tang et al.?


1xak is from original SARS, and I must say not great statistics despite 
being at 1.8A.  Still, it is a start.


From the literature cited by Tan et al. it appears ORF8 has been 
suspected as pathogenic for some time, but for widely different 
reasons.  One paper says it is a transcription factor that up-regulates 
chaperones, another says it is a secreted imunosuppressor.


So, my question remains: why haven't we solved it yet?

-James Holton
MAD Scientist

On 3/21/2020 9:12 AM, Rigden, Dan wrote:


Hi James


5o32I is not a homolog of ORF8 - the BLAST e-value is insignificant. 
In fact, rather than the EGF-like fold of 5o32I, ORF8 has an Ig-like 
fold similar to ORF7 (for which there is a structure; 1xak).



https://toolkit.tuebingen.mpg.de/jobs/2717885_1


I must say I got quite excited seeing that until I noticed this 
pre-print which tells the whole story very nicely, including that key 
position 84



https://www.biorxiv.org/content/10.1101/2020.03.04.977736v1

Best wishes

Dan


*From:* CCP4 bulletin board  on behalf of 
Patrick Shaw Stewart 

*Sent:* 21 March 2020 15:41:17
*To:* CCP4BB@JISCMAIL.AC.UK
*Subject:* Re: [ccp4bb] CCP4BB vs COVID19

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/


My paper in /Medical Hypotheses
/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 <mailto:jmhol...@lbl.gov>> 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 th

Re: [ccp4bb] CCP4BB vs COVID19

[Chandra]

hi

There are developments in cyclic and constrained peptides

see for example J Am Chem Soc. 
<https://www.ncbi.nlm.nih.gov/pubmed/30768253#>2019 Mar 
13;141(10):4167-4181.


hope it helps


On 22/3/2020 8:01 pm, Abhishek Anan wrote:

Dear all,

Not directly related to the discussion but does anyone know of a
antiretroviral protease inhibitor that is a peptide? I am new to the
topic and read that peptides suffer from bioavailability issues. Are
there any workarounds?

best,
Abhishek


On 3/21/20, Rigden, Dan  wrote:

Hi James


5o32I is not a homolog of ORF8 - the BLAST e-value is insignificant. In
fact, rather than the EGF-like fold of 5o32I, ORF8 has an Ig-like fold
similar to ORF7 (for which there is a structure; 1xak).


https://toolkit.tuebingen.mpg.de/jobs/2717885_1


I must say I got quite excited seeing that until I noticed this pre-print
which tells the whole story very nicely, including that key position 84


https://www.biorxiv.org/content/10.1101/2020.03.04.977736v1


Best wishes

Dan


From: CCP4 bulletin board  on behalf of Patrick Shaw
Stewart 
Sent: 21 March 2020 15:41:17
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] CCP4BB vs COVID19


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/

My paper in Medical Hypotheses
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
mailto:jmhol...@lbl.gov>> 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
My question is: how can this test be m

Re: [ccp4bb] CCP4BB vs COVID19

[Abhishek Anan]

Dear all,

Not directly related to the discussion but does anyone know of a
antiretroviral protease inhibitor that is a peptide? I am new to the
topic and read that peptides suffer from bioavailability issues. Are
there any workarounds?

best,
Abhishek


On 3/21/20, Rigden, Dan  wrote:
> Hi James
>
>
> 5o32I is not a homolog of ORF8 - the BLAST e-value is insignificant. In
> fact, rather than the EGF-like fold of 5o32I, ORF8 has an Ig-like fold
> similar to ORF7 (for which there is a structure; 1xak).
>
>
> https://toolkit.tuebingen.mpg.de/jobs/2717885_1
>
>
> I must say I got quite excited seeing that until I noticed this pre-print
> which tells the whole story very nicely, including that key position 84
>
>
> https://www.biorxiv.org/content/10.1101/2020.03.04.977736v1
>
>
> Best wishes
>
> Dan
>
> 
> From: CCP4 bulletin board  on behalf of Patrick Shaw
> Stewart 
> Sent: 21 March 2020 15:41:17
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] CCP4BB vs COVID19
>
>
> 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/
>
> My paper in Medical Hypotheses
> 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
> mailto:jmhol...@lbl.gov>> 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
> straight

Re: [ccp4bb] External: [ccp4bb] Fwd: [ccp4bb] CCP4BB vs COVID19

[Michel Fodje]

In Ascoidea asiatica where CUG is translated as both Leu and Ser.
Mühlhausen S., Schmitt H.D., Pan K.T., Plessmann U., Urlaub H., Hurst L.D., 
Kollmar M. Endogenous stochastic decoding of the CUG codon by competing Ser- 
and Leu-tRNAs in Ascoidea asiatica. Curr. Biol. 2018; 28:2046-2057.

Perhaps, this is not a mutation at all but points to the origin of this virus.

/Michel.

From: CCP4 bulletin board  On Behalf Of Carter, Charlie
Sent: March 21, 2020 7:48 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: External: [ccp4bb] Fwd: [ccp4bb] CCP4BB vs COVID19




Begin forwarded message:

From: "charles w carter, jr" mailto:cwcar...@ad.unc.edu>>
Subject: Re: [ccp4bb] CCP4BB vs COVID19
Date: March 21, 2020 at 8:07:53 AM EDT
To: James Holton mailto:jmhol...@lbl.gov>>

Brilliant post, James. Thanks so much!

I also find what you describe interesting, because of work done by a colleague, 
Manuel Santos, who showed that in fungi,

The CUG codon is decoded in vivo as serine and not leucine in Candida albicans
MAS Santos, MF Tuite
Nucleic acids research 23 (9), 1481-1486

I may be hallucinating, but I recall something to the effect that this genetic 
ambiguity also related to the ability of Candida to adapt to life in high 
concentrations of SDS.

Charlie

On Mar 20, 2020, at 6:59 PM, James Holton 
mailto:jmhol...@lbl.gov>> 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
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.  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

Re: [ccp4bb] CCP4BB vs COVID19

[Rigden, Dan]

Hi James


5o32I is not a homolog of ORF8 - the BLAST e-value is insignificant. In fact, 
rather than the EGF-like fold of 5o32I, ORF8 has an Ig-like fold similar to 
ORF7 (for which there is a structure; 1xak).


https://toolkit.tuebingen.mpg.de/jobs/2717885_1


I must say I got quite excited seeing that until I noticed this pre-print which 
tells the whole story very nicely, including that key position 84


https://www.biorxiv.org/content/10.1101/2020.03.04.977736v1


Best wishes

Dan


From: CCP4 bulletin board  on behalf of Patrick Shaw 
Stewart 
Sent: 21 March 2020 15:41:17
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] CCP4BB vs COVID19


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/

My paper in Medical Hypotheses 
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 
mailto:jmhol...@lbl.gov>> 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
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 bioinform

Re: [ccp4bb] CCP4BB vs COVID19

[Patrick Shaw Stewart]

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/


My paper in *Medical Hypotheses *
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
> 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.  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.  

[ccp4bb] Fwd: [ccp4bb] CCP4BB vs COVID19

[Carter, Charlie]

Begin forwarded message:

From: "charles w carter, jr" mailto:cwcar...@ad.unc.edu>>
Subject: Re: [ccp4bb] CCP4BB vs COVID19
Date: March 21, 2020 at 8:07:53 AM EDT
To: James Holton mailto:jmhol...@lbl.gov>>

Brilliant post, James. Thanks so much!

I also find what you describe interesting, because of work done by a colleague, 
Manuel Santos, who showed that in fungi,

The CUG codon is decoded in vivo as serine and not leucine in Candida albicans
MAS Santos, MF Tuite
Nucleic acids research 23 (9), 1481-1486

I may be hallucinating, but I recall something to the effect that this genetic 
ambiguity also related to the ability of Candida to adapt to life in high 
concentrations of SDS.

Charlie

On Mar 20, 2020, at 6:59 PM, James Holton 
mailto:jmhol...@lbl.gov>> 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
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.  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 homolog

Re: [ccp4bb] CCP4BB vs COVID19

[Boy]

The best way against COVID19 is staying at home, staying at home, and
staying at home.

Nothing else.

On Fri, Mar 20, 2020, 5:59 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
> 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.  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=1
>



To unsubscribe from the CCP4BB list, click the following link:

Re: [ccp4bb] CCP4BB vs COVID19

[Clemens Vonrhein]

Dear James,

On Fri, Mar 20, 2020 at 03:59:01PM -0700, James Holton wrote:
> 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.

This is a very good example of why we all are trying to get raw
diffraction data deposited as soon as possible to the publication and
deposition of a structure. It highlights the potential benefit of
revisting some important structures right at the level of the raw
data. The paper says

  Diffraction data were collected at European Synchrotron Radiation
  Facility (ESRF) and Swiss Light Source at Paul Scherrer Institute
  (SLS-PSI). Diffraction data were processed by XDS and
  AIMLESS. Crystals of C3b–miniFH–FI exhibited space group P1 and
  diffracted to a resolution of 3.8 Å. However, the diffraction data
  was highly anisotropic. The data were therefore truncated to 4.2-Å
  resolution and rescaled using the Diffraction Anisotropy Server.

Obviously, that was state-of-the-art in 2015 (data collection) and
2017 (publication) - but maybe new methods could indeed do better on
this already existing structure if the raw data became
available. Maybe nothing will change in terms of structure quality and
(most importantly) structure interpretation ... who knows.

We've contacted the authors - who were very quick and extremely
helpful in providing us with raw images for some other deposited
project from their lab a few weeks ago, so expect and hope for a
similar response when/if the data can be located.

> Good luck to you all, and stay healthy.

Ditto!

Cheers

Clemens

-- 

*--
* Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com
* Global Phasing Ltd., Sheraton House, Castle Park 
* Cambridge CB3 0AX, UK   www.globalphasing.com
*--



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1

Re: [ccp4bb] CCP4BB vs COVID19

[Paula Salgado]

Same for Newcastle University, particularly our Faculty of Medical Sciences but 
colleagues and labs from across the University.

There are also several efforts to get scientists to help:

http://crowdfightcovid19.org/volunteers

Thanks to all those trying to help!

Paula



On 21 Mar 2020, at 11:53, David Briggs  wrote:


For general interest,

The Francis Crick institute in London is offering facilities to public health 
England, and over 300 Crick scientists have volunteered to help with testing.

https://www.crick.ac.uk/news/2020-03-19_francis-crick-institute-offers-assistance-in-emergency-coronavirus-testing

--
Dr David C. Briggs
Senior Laboratory Research Scientist
Signalling and Structural Biology Lab
The Francis Crick Institute
London, UK
==
about.me/david_briggs


From: CCP4 bulletin board  on behalf of David Waterman 

Sent: Saturday, March 21, 2020 11:12:36 AM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: Re: [ccp4bb] CCP4BB vs COVID19

Liz Tunbridge's lab at Oxford are offering PCR machines and expertise to help 
fill the testing shortfall in the UK (see 
https://www.wired.co.uk/article/coronavirus-uk-testing-key-workers<https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.wired.co.uk%2Farticle%2Fcoronavirus-uk-testing-key-workers=02%7C01%7C%7Cde0d51b4b5e54708671d08d7cd88cc25%7C4eed7807ebad415aa7a99170947f4eae%7C0%7C0%7C637203859739921917=M4TnA9YFRaRkCO%2B7MtI1prS615g8Ff0VWWnrMWArv8s%3D=0>).
 This is a worthy initiative, if it is accepted (logistics are the main 
problem). The structural biology community is pretty good with this too. 
Perhaps there are some opportunities to help out here, for those who can still 
get to their wet labs?

-- David


On Fri, 20 Mar 2020 at 22:59, James Holton 
mailto:jmhol...@lbl.gov>> 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://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.cdc.gov%2Fcoronavirus%2F2019-nCoV%2Flab%2Findex.html=02%7C01%7C%7Cde0d51b4b5e54708671d08d7cd88cc25%7C4eed7807ebad415aa7a99170947f4eae%7C0%7C0%7C637203859739921917=nLlQqA10Uh5JWPRACl5ofZotvzRhTR0XimeWiNCZ4GI%3D=0>
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.d

Re: [ccp4bb] CCP4BB vs COVID19

[David Briggs]

For general interest,

The Francis Crick institute in London is offering facilities to public health 
England, and over 300 Crick scientists have volunteered to help with testing.

https://www.crick.ac.uk/news/2020-03-19_francis-crick-institute-offers-assistance-in-emergency-coronavirus-testing

--
Dr David C. Briggs
Senior Laboratory Research Scientist
Signalling and Structural Biology Lab
The Francis Crick Institute
London, UK
==
about.me/david_briggs


From: CCP4 bulletin board  on behalf of David Waterman 

Sent: Saturday, March 21, 2020 11:12:36 AM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: Re: [ccp4bb] CCP4BB vs COVID19

Liz Tunbridge's lab at Oxford are offering PCR machines and expertise to help 
fill the testing shortfall in the UK (see 
https://www.wired.co.uk/article/coronavirus-uk-testing-key-workers<https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.wired.co.uk%2Farticle%2Fcoronavirus-uk-testing-key-workers=02%7C01%7C%7Cde0d51b4b5e54708671d08d7cd88cc25%7C4eed7807ebad415aa7a99170947f4eae%7C0%7C0%7C637203859739921917=M4TnA9YFRaRkCO%2B7MtI1prS615g8Ff0VWWnrMWArv8s%3D=0>).
 This is a worthy initiative, if it is accepted (logistics are the main 
problem). The structural biology community is pretty good with this too. 
Perhaps there are some opportunities to help out here, for those who can still 
get to their wet labs?

-- David


On Fri, 20 Mar 2020 at 22:59, James Holton 
mailto:jmhol...@lbl.gov>> 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://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.cdc.gov%2Fcoronavirus%2F2019-nCoV%2Flab%2Findex.html=02%7C01%7C%7Cde0d51b4b5e54708671d08d7cd88cc25%7C4eed7807ebad415aa7a99170947f4eae%7C0%7C0%7C637203859739921917=nLlQqA10Uh5JWPRACl5ofZotvzRhTR0XimeWiNCZ4GI%3D=0>
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://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdx.doi.org%2F10.1093%2Fnsr%2Fnwaa036=02%7C01%7C%7Cde0d51b4b5e54708671d08d7cd88cc25%7C4eed7807ebad415aa7a99170947f4eae%7C0%7C0%7C637203859739931914=g%2Fv1diPmPWKEo%2Frw371ZRUgl%2BGEGJHxGj6kaSLxjAas%3D=0>.
  Search for
"T8517

Re: [ccp4bb] CCP4BB vs COVID19

[David Waterman]

Liz Tunbridge's lab at Oxford are offering PCR machines and expertise to
help fill the testing shortfall in the UK (see
https://www.wired.co.uk/article/coronavirus-uk-testing-key-workers). This
is a worthy initiative, if it is accepted (logistics are the main problem).
The structural biology community is pretty good with this too. Perhaps
there are some opportunities to help out here, for those who can still get
to their wet labs?

-- David


On Fri, 20 Mar 2020 at 22:59, 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
> 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.  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
>
> 

[ccp4bb] CCP4BB vs COVID19

[James Holton]

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
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.  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=1