[Demelerlab] updates to the UltraScan SOMO residue definitions

[Jason Zhu]

Hi Borries and Mattia,

Sure thing! I would be happy to help out with the development and testing
of the beadmodels program and I don't mind waking up early in the morning!
My schedule is flexible outside of Mondays noon - 1 pm, and Wednesdays 10 -
11 am/1 - 2 pm.

Best,
Jason

On Tue, Jul 25, 2023 at 8:10 AM Borries Demeler <demeler at gmail.com> wrote:

> Hello James and Jason,
> would you like to be involved in the development and testing of a program
> that can build beadmodels from arbitrary residues in molecular structures
> and predict their PSVs? Mattia is in Italy, which is +9 hours, so this may
> limit available time for conference calls, but maybe either Mattia is
> available in the evening or you guys don't mind getting up early ;)
> Let me know if you want to be involved and I will schedule a meeting.
> -Borries
>
> On Mon, Jul 24, 2023 at 1:33 PM Mattia Rocco <mattia.rocco at quipo.it>
> wrote:
>
>> Hi Bo - excellent! :-) From my previous interactions with Saeed, I
>> believe he would be an excellent fit for the job, with help/assistance from
>> the other people already involved! Let's set up that meeting at a time of
>> your convenience. Me, except for Fridays, I'm usually pretty much
>> available... ;-)
>>
>> Best - Mattia
>>
>> Il 2023-07-24 18:26 Borries Demeler ha scritto:
>>
>> Hi Mattia,
>> thanks so much for doing this. I would be *very* interested in having a
>> program for not only predicting the bead models for different groups, but
>> also the vbar calculations in an automated way. James Nowick has already
>> used Helmut Durchschlag's paper to predict PSV for various amyloid peptide
>> mimics, and has experience on how to use this program. Saeed in our
>> group is a MD molecular modeling expert as well as an expert UltraScan
>> programmer, I am thinking he would be perfect to develop such a module for
>> UltraScan. But we would need some scientific help on how to develop the
>> algorithm, if you and Emre could assist on this end then we could use some
>> of the delta-linked ornithin residues as examples, since James has already
>> worked them out for the PSV.
>>
>> We may need a Zoom call with you and Emre at some point to get us started
>> with the envisioned program.
>>
>> Thanks very much, -Borries
>>
>> On Mon, Jul 24, 2023 at 2:11 AM Mattia Rocco <mattia.rocco at quipo.it>
>> wrote:
>>
>> Dear Bo,
>>
>> apologies, I totally forgot of your request last week, when I returned to
>> Genova. While I will now have a look at it, I seize this occasion to
>> inquire with you if you would be keen to approach this issue from a
>> programming side. That is, develop a way of semi-automatically code, with
>> just an user supervision, for non-coded residues in US-SOMO. I would
>> suggest to first start with the most important part, the calculation of the
>> psv, which would also be very welcomed by the SAXS community. After all,
>> Durchschlag & Zipper great work should be amenable to be coded in a
>> program, relieving scientists from a demanding "manual" work.
>>
>> For instance, would be the person that did calculate the psv for your
>> unnatural amino-acids be willing to explore such a project? We could set-up
>> a Zoom meeting to discuss strategies and potential implementations... I
>> believe that a coding developed for the psv calculation would have many of
>> the features needed to also code a new residue for US-SOMO. After all, it
>> is likely that I would quit offering such a service in a not-too-distant
>> future... ;-)
>>
>> All the best - Mattia
>>
>>
>> Il 2023-07-09 23:52 Borries Demeler ha scritto:
>>
>> Hi Mattia and Emre:
>> We are working with the Nowick group from UCalifornia, Irvine, to study
>> synthetic amyloid peptide mimics which include several non-canonical amino
>> acids. Loading Xray and NMR generated PDBs into SOMO causes several errors
>> due to these discrepancies:
>>
>>
>> Encountered the following warnings with your PDB structure:
>>
>> Chain B Molecule 1 Residue ORN 1: Non-coded residue.
>>
>> Chain B Molecule 1 Residue PHI 5: Non-coded residue.
>>
>> Chain B Molecule 1 Residue ORN 9: Non-coded residue.
>>
>> Chain B Molecule 1 Residue SAR 13: Non-coded residue.
>>
>>
>>
>> ...and various downstream issues with chain breaks resulting from these
>> unknown residues. I suspect that due to the small size of these peptides we
>> want to be as accurate as possible to represent the residues correctly,
>> since they are likely extending into the solvent interface. Of great
>> interest in amyloid research is the structure & function of small soluble
>> oligomers, so this is what we are trying to investigate by AUC, NMR and
>> X-ray, and being able to simulate expected oligomers by US-SOMO would be a
>> great plus.
>>
>>
>>
>> Can you please update the residue definition list for US-SOMO so these
>> AAs are properly recognized? I think this would be a great and novel use of
>> US-SOMO!
>>
>>
>>
>> I have attached a number of PDB files from oligomeric structures of one
>> of these peptides derived from NMR and Xray that were generated by Jason
>> Zhu (Cc'ed) from James Nowick's lab, and since I am no expert in PDB
>> formats, perhaps you and Jason can collaborate to get the residues added,
>> and allow us to load them correctly?
>>
>>
>>
>> We would be happy to include you in the manuscript author list for your
>> help with the simulation. The s, D and frictional ratios would be directly
>> compared with AUC data. Also, James has already worked out the partial
>> specific volumes for these non-canonical amino acids using Helmut
>> Durchschlag's papers. He can provide you with these values.
>>
>>
>>
>> Thanks so much, -Borries
>>
>>
>>
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