[Demelerlab] AUC Collaboration: Sizing Amyloid Beta derived Oligomers

[Borries Demeler]

I suspect that the negative absorbance of TFA is a problem with chromatic
aberration on your nanodrop device. This may be related to a high
refractive index of TFA that distorts your measurement, if you got this
result from a 1 cm cuvette you may want to try with a shorter pathlength to
get a more accurate measurement. A negative absorbance doesn't make any
sense. Do you have a trace from 220-280 nm for TFA? It would be good to see
multiple concentration of TFA in water.
Thanks, -Borries



On Tue, Jul 18, 2023 at 1:59 PM Jason Zhu <jasonz13 at uci.edu> wrote:

> Hi Borries,
>
> Apologies for the belated response, the purifications took a bit longer
> than expected.
>
> I tried adding Tris (at pH 6.0 and pH 9.0) to 1 mM F19Cha and observed
> salting out at 10-50 mM Tris so it is not a viable additive to prevent
> non-ideal effects unfortunately.
>
> I ran nanopure water (blank), nanopure water with 0.1 % TFA (ca. 10 mM)
> and 1 mM F19Cha dissolved in nanopure water on our nanodrop. I see a slight
> negative peak when 0.1% TFA is added (run 1) and that this peptide absorbs
> strongly even at 1 mM F19Cha (run 2) on our nanodrop.
> [image: image.png]
> I have some purified F19Cha (~24 mgs) that is ready for shipping. I can
> weigh out the peptides and write out the corresponding volumes of solution
> to add for our AUC studies. What would be the best address to ship to and
> when should I ship these peptides?
>
> Best regards,
> Jason
>
> On Sun, Jul 9, 2023 at 1:23 PM Borries Demeler <demeler at gmail.com> wrote:
>
>> Hi Jason,
>> thanks for the PDB files, as I suspected we need new definitions for the
>> various non-canonical AAs. I get errors when running SOMO on the undefined
>> residues. I asked Emre from our group to suggest a way how to deal with
>> this. Presumably someone needs to edit the definitions for the unknown
>> residues. I'll give you some updates when I have them.
>>
>> Regards, -borries
>>
>> On Thu, Jul 6, 2023 at 11:37 PM Jason Zhu <jasonz13 at uci.edu> wrote:
>>
>>> Dear Borries and the Demeler lab,
>>>
>>> As a follow-up to our conversation today, I've attached my slides, PyMOL
>>> models for the crystallographic F19Cha hexamer and the proposed NMR
>>> dodecamer based on a structural analog (PDB ID: 5v63). I broke up the
>>> subunits of the crystallographic hexamer and proposed NMR dodecamer into
>>> separate pdb files to make them easier to work with.
>>>
>>> In the meantime, I'll try adding Tris to my peptide, running samples on
>>> the nanodrop, purifying more F19Cha and will keep you posted.
>>>
>>> Thanks again for setting up this meeting and having so many members of
>>> your lab attend. Please feel free to reach out if there's anything you need
>>> from our end. I look forward to working with you all! :)
>>>
>>> Kind regards,
>>> Jason
>>>
>>
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