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<p>Hi everyone, hope you are all fine<br>
</p>
<p>I wish I could be of more help in discussing the interesting
ideas on the structural data, both the NMR experiments and the MD
simulations (by the way, fantastic images Francisco!) but
unfortunately my biological/biomedical background is insufficent,
and therefore I am mostly expecting your specialized steering on
this - sorry!</p>
<p>hope to obtain more protein and send it soon...<br>
</p>
<p>all the best</p>
<p>Bruno</p>
<p><br>
</p>
<p>+++</p>
<p><br>
</p>
<div class="moz-cite-prefix">On 6/9/2020 10:04 PM, Francisco
Gomes-Neto wrote:<br>
</div>
<blockquote type="cite"
cite="mid:CAK2jCfK3mi6n929C2S2Nuiu-g-A+Wk+FORKqh6GGL7gT6bjCkA@mail.gmail.com">
<meta http-equiv="content-type" content="text/html; charset=UTF-8">
<div dir="ltr">Hello all
<div>Find attached a small report for a starting ideia, a MD
simulation of Myotoxin-II interacting with free SDS molecules</div>
<div>Would be great hear your questions, comments and
suggestions<br>
Best regards <br>
Francisco<br>
</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">Em seg., 8 de jun. de 2020 às
17:20, Borries Demeler <<a href="mailto:demeler@gmail.com"
moz-do-not-send="true">demeler@gmail.com</a>> escreveu:<br>
</div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px
0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">FOr
me the most interesting part would be to learn the structural<br>
arrangement of the SDS molecules around the protein, and how
it changes<br>
the protein itself, vs. how does it change the conformation of
the<br>
protein in the presence of SDS so that it goes from monomer to
dimer?<br>
<br>
THis is the central question we are trying to answer. If this
is not the<br>
type of information we can get readily, what other information
can be<br>
obtained that would give us more coarse-grained information?<br>
<br>
Thanks, -Borries<br>
<br>
P.S. please reply to <a
href="mailto:myotox@biophysics.uleth.ca" target="_blank"
moz-do-not-send="true">myotox@biophysics.uleth.ca</a> so
everyone gets to see<br>
your response. Bruno and Ana may have some additional ideas as
to what <br>
we could get out of the NMR experiments. Please feel free to
tune in...<br>
<br>
<br>
On Mon, Jun 08, 2020 at 07:46:42PM +0000, Montina, Tony wrote:<br>
> Hello all,<br>
> I agree with Paul. An idea of what you are looking for in
this first paper would be helpful in guiding the NMR
experimental work.<br>
> Tony<br>
> <br>
> _______________________________________________<br>
> Tony Montina<br>
> Director, Science Operations<br>
> Director, Magnetic Resonance Facility<br>
> Instructor, Department of Chemistry and Biochemistry<br>
> Faculty of Arts and Science<br>
> The University of Lethbridge<br>
> Lethbridge, Alberta, Canada, T1K 3M4<br>
> Office: 1-403-394-3927<br>
> Lab: 1-403-329-2230<br>
> <br>
> From: Hazendonk, Paul <<a
href="mailto:paul.hazendonk@uleth.ca" target="_blank"
moz-do-not-send="true">paul.hazendonk@uleth.ca</a>><br>
> Sent: June 8, 2020 1:32 PM<br>
> To: Borries Demeler <<a
href="mailto:demeler@gmail.com" target="_blank"
moz-do-not-send="true">demeler@gmail.com</a>>; Montina,
Tony <<a href="mailto:tony.montina@uleth.ca"
target="_blank" moz-do-not-send="true">tony.montina@uleth.ca</a>><br>
> Cc: Henrickson, Amy <<a
href="mailto:amy.henrickson@uleth.ca" target="_blank"
moz-do-not-send="true">amy.henrickson@uleth.ca</a>><br>
> Subject: Re: Myotoxin-II<br>
> <br>
> I think we need to ask ourselves what type of structural
insights are the most important for this particular story.
This will help us set the goals for the level of strucural
information sought. Some may be achieved with partial
imformation other may require us to do a complete spectral
assignment. The ammount of work required, hence time, would be
dramatically different.<br>
> Sent from Outlook Mobile<<a
href="https://aka.ms/blhgte" rel="noreferrer"
target="_blank" moz-do-not-send="true">https://aka.ms/blhgte</a>><br>
> <br>
> ________________________________<br>
> From: Montina, Tony <<a
href="mailto:tony.montina@uleth.ca" target="_blank"
moz-do-not-send="true">tony.montina@uleth.ca</a><mailto:<a
href="mailto:tony.montina@uleth.ca" target="_blank"
moz-do-not-send="true">tony.montina@uleth.ca</a>>><br>
> Sent: Sunday, June 7, 2020 12:04:01 PM<br>
> To: Borries Demeler <<a
href="mailto:demeler@gmail.com" target="_blank"
moz-do-not-send="true">demeler@gmail.com</a><mailto:<a
href="mailto:demeler@gmail.com" target="_blank"
moz-do-not-send="true">demeler@gmail.com</a>>>;
Hazendonk, Paul <<a href="mailto:paul.hazendonk@uleth.ca"
target="_blank" moz-do-not-send="true">paul.hazendonk@uleth.ca</a><mailto:<a
href="mailto:paul.hazendonk@uleth.ca" target="_blank"
moz-do-not-send="true">paul.hazendonk@uleth.ca</a>>><br>
> Cc: Henrickson, Amy <<a
href="mailto:amy.henrickson@uleth.ca" target="_blank"
moz-do-not-send="true">amy.henrickson@uleth.ca</a><mailto:<a
href="mailto:amy.henrickson@uleth.ca" target="_blank"
moz-do-not-send="true">amy.henrickson@uleth.ca</a>>><br>
> Subject: RE: Myotoxin-II<br>
> <br>
> Hello Borries,<br>
> I believe that Mike used most of the sample that Amy gave
him to make up the myotoxin in D2O and PBS.<br>
> It would probably be worthwhile to ask Bruno to send
more, as we will want to prepare the NMR samples under several
conditions.<br>
> For example, we might want a sample (as you suggested)
with SDS, we might want another sample with H2O and D2O (for
exchange purposes), etc.<br>
> Amy would have a better idea of how much she just gave
us, but I would suggest two to three times that amount.<br>
> Does that work<br>
> Tony<br>
> <br>
> _______________________________________________<br>
> Tony Montina<br>
> Director, Science Operations<br>
> Director, Magnetic Resonance Facility<br>
> Instructor, Department of Chemistry and Biochemistry<br>
> Faculty of Arts and Science<br>
> The University of Lethbridge<br>
> Lethbridge, Alberta, Canada, T1K 3M4<br>
> Office: 1-403-394-3927<br>
> Lab: 1-403-329-2230<br>
> <br>
> -----Original Message-----<br>
> From: Borries Demeler <<a
href="mailto:demeler@gmail.com" target="_blank"
moz-do-not-send="true">demeler@gmail.com</a><mailto:<a
href="mailto:demeler@gmail.com" target="_blank"
moz-do-not-send="true">demeler@gmail.com</a>>><br>
> Sent: June 5, 2020 4:23 PM<br>
> To: Hazendonk, Paul <<a
href="mailto:paul.hazendonk@uleth.ca" target="_blank"
moz-do-not-send="true">paul.hazendonk@uleth.ca</a><mailto:<a
href="mailto:paul.hazendonk@uleth.ca" target="_blank"
moz-do-not-send="true">paul.hazendonk@uleth.ca</a>>><br>
> Cc: Montina, Tony <<a
href="mailto:tony.montina@uleth.ca" target="_blank"
moz-do-not-send="true">tony.montina@uleth.ca</a><mailto:<a
href="mailto:tony.montina@uleth.ca" target="_blank"
moz-do-not-send="true">tony.montina@uleth.ca</a>>>;
Henrickson, Amy <<a href="mailto:amy.henrickson@uleth.ca"
target="_blank" moz-do-not-send="true">amy.henrickson@uleth.ca</a><mailto:<a
href="mailto:amy.henrickson@uleth.ca" target="_blank"
moz-do-not-send="true">amy.henrickson@uleth.ca</a>>><br>
> Subject: Re: Myotoxin-II<br>
> <br>
> Caution: This email was sent from someone outside of the
University of Lethbridge. Do not click on links or open
attachments unless you know they are safe. Please forward
suspicious emails to <a href="mailto:phishing@uleth.ca"
target="_blank" moz-do-not-send="true">phishing@uleth.ca</a><mailto:<a
href="mailto:phishing@uleth.ca" target="_blank"
moz-do-not-send="true">phishing@uleth.ca</a>>.<br>
> <br>
> Tony/Amy, Paul mentioned that we could do this experiment
in the presence of SDS. How much material would we need and
how much do we still have on hand? If we don't have enough we
should contact Bruno and ask him to milk some more snakes :)
-b.<br>
> <br>
> <br>
> On Fri, Jun 05, 2020 at 07:02:11PM +0000, Hazendonk, Paul
wrote:<br>
> > Hi Borries<br>
> ><br>
> > We have a 1D proton that makes sense to me now. We
have some T1 data. I am waiting for the T2 and DOSY results.
Mike could you updaye us on when these will be done.<br>
> ><br>
> > Cheers<br>
> ><br>
> > Paul<br>
> ><br>
> > Sent from Outlook Mobile<<a
href="https://aka.ms/blhgte" rel="noreferrer"
target="_blank" moz-do-not-send="true">https://aka.ms/blhgte</a>><br>
> ><br>
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-- <br>
<div dir="ltr" class="gmail_signature">
<div dir="ltr">
<div>-- </div>
<div>Francisco Gomes Neto</div>
<div>Pesquisador Assistente</div>
<div>Laboratório de Toxinologia</div>
<div>Instituto Oswaldo Cruz</div>
<div>Pavilhão Ozório de Almeida, Sala 5</div>
<div>Fundação Oswaldo Cruz-FIOCRUZ</div>
<div>Ave. Brasil, 4365 - Manguinhos</div>
<div>Caixa Postal 926</div>
<div>CEP 21040-900</div>
<div>Rio de Janeiro, RJ, Brasil.</div>
<div>Tel.: (55-21) 2562-1263</div>
<div>Fax : (55-21) Lab. 2562-1410</div>
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<pre class="moz-quote-pre" wrap="">_______________________________________________
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<pre class="moz-signature" cols="72">--
Bruno Lomonte, Ph.D.
Instituto Clodomiro Picado
Universidad de Costa Rica
San José, 11501
COSTA RICA
<a class="moz-txt-link-abbreviated" href="mailto:bruno.lomonte@ucr.ac.cr">bruno.lomonte@ucr.ac.cr</a>
tel. +506 2511 7888
cel. +506 8392 0012
</pre>
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