[Myotox] Myotoxin-II sequence

Wed Sep 7 06:42:43 MDT 2022

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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