[Demelerlab] updates to the UltraScan SOMO residue definitions

[Mattia Rocco]

Hello Bo,

nice to read from you! I am currently away, I will be back in Genova a 
week from today, and I'll have a look at this residue coding task. I do 
not expect it to be difficult, especially if calculations of the psv of 
the non-coded residues are already available. In the meantime, you and 
your collaborators can use the approximate method, just enter the 
correct global psv and MW in the appropriate fields (Emre can point them 
out to you).

Take care - 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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