[Demelerlab] updates to the UltraScan SOMO residue definitions

[Borries Demeler]

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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