[Myotox] Myotoxin-II

Montina, Tony tony.montina at uleth.ca
Thu Jun 11 06:32:11 MDT 2020 

Hi Borries
Currently I am free all day Thursday except from 9-10am. On Friday I am free from 8am to noon.
Let me know what time you determine
Tony

Tony Montina
Director, Science Operations
Director, Magnetic Resonance Facility
Faculty of Arts and Science
Instructor, Department of Chemistry and Biochemistry
University of Lethbridge
SA6214, Science Commons
4401 University Drive West
Lethbridge, Alberta, Canada, T1K3M4
Office: 1-403-394-3927
Lab: 1-403-329-2230

This message has been sent from my mobile device so please ignore any autocorrect or typing errors.

On Jun 10, 2020, at 8:23 PM, Borries Demeler <demeler at gmail.com> wrote:

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 phishing at uleth.ca.

Hi everyone,
thanks for your feedback, and I think we should schedule a zoom meeting
for later next week to discuss the NMR results and the MD results from
Francisco. In particular, I would like to know if any of the discoveries
by Francisco can be supported by the NMR data. Paul, could you please
review the MD results Francisco sent earlier?
Francisco's original message and attachments can be found in the mailing list archives:
https://biophsyics.uleth.ca/pipermail/myotox/2020-June/000066.html
In particular, is there anything that NMR could say about the angle
between the monomers changing when SDS is added? Could you say anything
about the distribution of the SDS molecules around the protein,
interactions of acyl chains with particular hydrophobic residues shown
in Francisco's structures, any anything else you think could be
supportive. The more of our data match, the more informative it would
be. Of course, we also want to know discrepancies, if you can tell those
from your data.

Please send me your availability for Thursday or Friday next week and
I'll schedule a zoom conference. This would be a good opportunity for
all of us to get together and discuss what we have so far and what else
would be needed to finish the paper.

Thanks, -Borries

On Wed, Jun 10, 2020 at 07:32:42PM -0600, Bruno Lomonte wrote:
Hi everyone, hope you are all fine

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!

hope to obtain more protein and send it soon...

all the best

Bruno


+++


On 6/9/2020 10:04 PM, Francisco Gomes-Neto wrote:
Hello all
Find attached a small report for a starting ideia, a MD simulation of
Myotoxin-II interacting with free SDS molecules
Would be great hear your questions, comments and suggestions
Best regards
Francisco

Em seg., 8 de jun. de 2020 às 17:20, Borries Demeler <demeler at gmail.com
<mailto:demeler at gmail.com>> escreveu:

   FOr me the most interesting part would be to learn the structural
   arrangement of the SDS molecules around the protein, and how it
   changes
   the protein itself, vs. how does it change the conformation of the
   protein in the presence of SDS so that it goes from monomer to dimer?

   THis is the central question we are trying to answer. If this is
   not the
   type of information we can get readily, what other information can be
   obtained that would give us more coarse-grained information?

   Thanks, -Borries

   P.S. please reply to myotox at biophysics.uleth.ca
   <mailto:myotox at biophysics.uleth.ca> so everyone gets to see
   your response. Bruno and Ana may have some additional ideas as to
   what
   we could get out of the NMR experiments. Please feel free to tune
   in...


   On Mon, Jun 08, 2020 at 07:46:42PM +0000, Montina, Tony wrote:
Hello all,
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.
Tony

_______________________________________________
Tony Montina
Director, Science Operations
Director, Magnetic Resonance Facility
Instructor, Department of Chemistry and Biochemistry
Faculty of Arts and Science
The University of Lethbridge
Lethbridge, Alberta, Canada, T1K 3M4
Office: 1-403-394-3927
Lab: 1-403-329-2230

From: Hazendonk, Paul <paul.hazendonk at uleth.ca
   <mailto:paul.hazendonk at uleth.ca>>
Sent: June 8, 2020 1:32 PM
To: Borries Demeler <demeler at gmail.com
   <mailto:demeler at gmail.com>>; Montina, Tony <tony.montina at uleth.ca
   <mailto:tony.montina at uleth.ca>>
Cc: Henrickson, Amy <amy.henrickson at uleth.ca
   <mailto:amy.henrickson at uleth.ca>>
Subject: Re: Myotoxin-II

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.
Sent from Outlook Mobile<https://aka.ms/blhgte>

________________________________
From: Montina, Tony <tony.montina at uleth.ca
   <mailto:tony.montina at uleth.ca><mailto:tony.montina at uleth.ca
   <mailto:tony.montina at uleth.ca>>>
Sent: Sunday, June 7, 2020 12:04:01 PM
To: Borries Demeler <demeler at gmail.com
   <mailto:demeler at gmail.com><mailto:demeler at gmail.com
   <mailto:demeler at gmail.com>>>; Hazendonk, Paul
   <paul.hazendonk at uleth.ca
   <mailto:paul.hazendonk at uleth.ca><mailto:paul.hazendonk at uleth.ca
   <mailto:paul.hazendonk at uleth.ca>>>
Cc: Henrickson, Amy <amy.henrickson at uleth.ca
   <mailto:amy.henrickson at uleth.ca><mailto:amy.henrickson at uleth.ca
   <mailto:amy.henrickson at uleth.ca>>>
Subject: RE: Myotoxin-II

Hello Borries,
I believe that Mike used most of the sample that Amy gave him to
   make up the myotoxin in D2O and PBS.
It would probably be worthwhile to ask Bruno to send more, as we
   will want to prepare the NMR samples under several conditions.
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.
Amy would have a better idea of how much she just gave us, but I
   would suggest two to three times that amount.
Does that work
Tony

_______________________________________________
Tony Montina
Director, Science Operations
Director, Magnetic Resonance Facility
Instructor, Department of Chemistry and Biochemistry
Faculty of Arts and Science
The University of Lethbridge
Lethbridge, Alberta, Canada, T1K 3M4
Office: 1-403-394-3927
Lab: 1-403-329-2230

-----Original Message-----
From: Borries Demeler <demeler at gmail.com
   <mailto:demeler at gmail.com><mailto:demeler at gmail.com
   <mailto:demeler at gmail.com>>>
Sent: June 5, 2020 4:23 PM
To: Hazendonk, Paul <paul.hazendonk at uleth.ca
   <mailto:paul.hazendonk at uleth.ca><mailto:paul.hazendonk at uleth.ca
   <mailto:paul.hazendonk at uleth.ca>>>
Cc: Montina, Tony <tony.montina at uleth.ca
   <mailto:tony.montina at uleth.ca><mailto:tony.montina at uleth.ca
   <mailto:tony.montina at uleth.ca>>>; Henrickson, Amy
   <amy.henrickson at uleth.ca
   <mailto:amy.henrickson at uleth.ca><mailto:amy.henrickson at uleth.ca
   <mailto:amy.henrickson at uleth.ca>>>
Subject: Re: Myotoxin-II

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 phishing at uleth.ca
   <mailto:phishing at uleth.ca><mailto:phishing at uleth.ca
   <mailto:phishing at uleth.ca>>.

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.


On Fri, Jun 05, 2020 at 07:02:11PM +0000, Hazendonk, Paul wrote:
Hi Borries

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.

Cheers

Paul

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--
--
Francisco Gomes Neto
Pesquisador Assistente
Laboratório de Toxinologia
Instituto Oswaldo Cruz
Pavilhão Ozório de Almeida, Sala 5
Fundação Oswaldo Cruz-FIOCRUZ
Ave. Brasil, 4365 - Manguinhos
Caixa Postal 926
CEP 21040-900
Rio de Janeiro, RJ, Brasil.
Tel.: (55-21) 2562-1263
Fax : (55-21) Lab. 2562-1410


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--
Bruno Lomonte, Ph.D.
Instituto Clodomiro Picado
Universidad de Costa Rica
San José, 11501
COSTA RICA

bruno.lomonte at ucr.ac.cr
tel. +506  2511 7888
cel. +506  8392 0012


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