[Demelerlab] updates to the UltraScan SOMO residue definitions

[Borries Demeler]

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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