[Myotox] Myotoxin-II
Borries Demeler
demeler at gmail.com
Wed Jun 10 20:23:12 MDT 2020
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
> > > >
> > > > Sent from Outlook Mobile<https://aka.ms/blhgte>
> > > >
> > _______________________________________________
> > Myotox mailing list
> > Myotox at biophysics.uleth.ca <mailto:Myotox at biophysics.uleth.ca>
> > http://demeler7.uleth.ca/mailman/listinfo/myotox
> >
> >
> >
> > --
> > --
> > 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
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> >
> >
> > _______________________________________________
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> > Myotox at biophysics.uleth.ca
> > http://demeler7.uleth.ca/mailman/listinfo/myotox
>
> --
> 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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