[Myotox] Myotoxin-II sequence

[Borries Demeler]

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
> > _______________________________________________
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> > 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
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> Myotox mailing list
> Myotox at biophysics.uleth.ca
> https://demeler7.uleth.ca/mailman/listinfo/myotox
>
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