[Demelerlab] updates to the UltraScan SOMO residue definitions

[Borries Demeler]

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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