[Demelerlab] updates to the UltraScan SOMO residue definitions

[Mattia Rocco]

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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