[Myotox] Myotoxin-II sequence

Wed Sep 7 10:44:06 MDT 2022

Dear all,

I think I have retrieved the latest figure. The determined mass was 13,760
Da.

The figure is attached, and its legend reads:

*Figure 1: Mass spectrometry*. The molecular mass of myotoxin II (50 pmol)
was determined by ESI-MS on Waters Synapt G1 mass spetrometer. Acquired
data were submitted to analysis with the MassLynx software, including
background subtraction, choice of m/z range for further processing *(panel
A)*, and deconvolution using MaxEnt 1 algorithm to generate the final mass
values *(panel B)*.

All the best,

Richard.

Richard Hemmi Valente, Dr.
Pesquisador Titular
Laboratório de Toxinologia - IOC
Fundação Oswaldo Cruz
Av Brasil 4365 - 21040-900 - Rio de Janeiro - RJ - Brasil
Skype name: rhv4u2
Tel. Fixo: +55 21 25621345
Tel. Móvel: +55 21 999855080

On Wed, Sep 7, 2022 at 9:43 AM Ana Gisele da Costa Neves Ferreira <
anagextra at gmail.com> wrote:

> Hi Borries,
> I didn't bring my computer to the beach, true vacation time. But we do
> have a MS spectrum for myotoxin-II. It was included in the first version of
> the manuscript, I think I have sent you a long time ago.
> Anyway, I'll ask my colleague Richard to send you again.
> Best regards,
> Ana
>
>
> Em ter, 6 de set de 2022 12:55, Borries Demeler <demeler at gmail.com>
> escreveu:
>
>> Thank you, Bruno, this definitely helps! BTW, I was talking about Lys-49
>> (actually, Lys-48), not His-49, I can't find a his residue close to there.
>> I was looking over the micro-heterogeneity paper, based on that, and the
>> type of MT-II you have been sending us, what would be the best molar mass
>> value to use for my calculations? We can cite this manuscript, of course.
>> Some weight average? Can you send me a number? Thanks!
>>
>> Best wishes, -Borries
>>
>> On Mon, Sep 5, 2022 at 11:19 PM Bruno Lomonte <bruno.lomonte at ucr.ac.cr>
>> wrote:
>>
>>> Hi Borries, hi all,
>>>
>>> your sequence is OK (it corresponds to P24605 in Uniprot), the reason
>>> you find His to be 48 (instead of 49) is because it is an arbitrary
>>> convention to use a numbering system that was proposed long time ago
>>> (1985) and which became kind of a jargon
>>>
>>> in order to have the "nomenclature" for the arbitrary numbering, I
>>> believe in the crystal structure 1CLP the coordinates received the
>>> consensus numbering I refer to as "jargon" (I am attaching here the 1CLP
>>> file, although I am not sure if the numbering is displayed differently
>>> in different softwares for structure visualization)
>>>
>>> in the paper reporting the deposited P24605 there was an ambiguity at
>>> position 124 during the original sequencing, it was either Leu or Phe by
>>> Edman degradation, and it was arbitrarily decided to deposit the
>>> sequence as Leu
>>>
>>> however when we obtained a good mass spectrometer to chech the intact
>>> mass (30 years later!), we finally observed that the protein we are
>>> using in recent years actually has a Phe instead of the Leu (please see
>>> attached microheterogeneity article)
>>>
>>> so you will see everything fits well - hope that this has helped to
>>> clarify your doubt (actually I should have told you this beforehand)
>>>
>>> best regards to all,
>>>
>>> Bruno
>>>
>>> ++++++++++++++++++++
>>>
>>>
>>> On 9/5/2022 2:44 PM, Borries Demeler wrote:
>>> > Hi everyone,
>>> > I'm currently writing up the AUC results, but come across an
>>> inconsistency I m hoping someone can clear up for me.
>>> > In the literature, I see myotoxin-II from Bothrops asper referred to
>>> as the class-2 myotoxin Lys-49 phospholipases.
>>> > When I look at the protein sequence (which I believe I obtained from
>>> Bruno), I see Lys (K) at position 48, not 49:
>>> >
>>> > 0001 slfelgkmil qetgknpaks ygaygcncgv lgrgkpkdat drccyvhkcc ykkltgcnpk
>>> > 0061 kdrysyswkd ktivcgenns clkelcecdk avaiclrenl ntynkkyryy lkplckkada
>>> > 0121 c
>>> >
>>> > Am I missing a residue? I found the exact same sequence in the protein
>>> database.
>>> >
>>> > Since we determined very precise sed. and diff. coefficients, I could
>>> use the precisely known molar mass from sequence
>>> > to calculate an accurate partial specific volume and anisotropy.
>>> Before I use this sequence, it would be good if someone
>>> > could confirm it. Ana, what do you get from mass spec? Do you have
>>> some mass spec data we can include in this manuscript?
>>> >
>>> > Thanks, -Borries
>>> > _______________________________________________
>>> > Myotox mailing list
>>> > Myotox at biophysics.uleth.ca
>>> > https://demeler7.uleth.ca/mailman/listinfo/myotox
>>>
>>> --
>>> Bruno Lomonte, Ph.D.
>>> Instituto Clodomiro Picado
>>> Facultad de Microbiología
>>> Universidad de Costa Rica
>>> San José, COSTA RICA
>>>
>>> tel.of. (+506) 2511 7888
>>> bruno.lomonte at ucr.ac.cr
>>> _______________________________________________
>>> Myotox mailing list
>>> Myotox at biophysics.uleth.ca
>>> https://demeler7.uleth.ca/mailman/listinfo/myotox
>>>
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