[Demelerlab] updates to the UltraScan SOMO residue definitions

[Jason Zhu]

Hi Mattia,

Thanks for the questions! Here are my responses.

1. I did use the values from the 1994 paper that you listed. The values are
for 25°C so they are not corrected for 20°C.

2. Phi 5 in the proposed NMR model is N-Me Cha. XXX in the x-ray derived
model is also N-Me Cha. Would Xaa work as an acceptable 3 letter
abbreviation for N-Me Cha? I am happy to correct the residue naming
accordingly for both the NMR and x-ray pdbs if Xaa works!

3. I do have glycine where it is labeled as SAR and have corrected the SAR
accordingly to GLY (attached).

Best,
Jason

On Thu, Jul 27, 2023 at 9:37 AM Mattia Rocco <mattia.rocco at quipo.it> wrote:

> Hello Jason,
>
> I have started the coding for your residues, and I have a few questions
> for you.
>
> 1-In using the Durchschlag's values (I assume the Prog. Coll. Polym. Sci.
> 1994 paper), did you correct them for 20 °C? Because most are for 25 °C. I
> just need to know it, because all values in US-SOMO are at 20 °C.
>
> 2-I had no problems for Ornithine, which is a shorter version of Lysine...
> ;-) But I would need the real name for "Phi 5", and I don't see any N-Me
> Cha in the PDBs that Bo sent me. Is that the "XXX" residue? In that case,
> we need to pick a better three-characters name for it... ;-)
>
> 3-In those PDBs, there is "SAR", so I believe a proper psv should be
> computed also for this residue. If you have glycine, then the "SAR" residue
> should be changed to "GLY". Since US-SOMO somo.residue files are then
> distributed to the community, they should contain properly coded
> residues... ;-)
>
> Best - Mattia
>
>
> Il 2023-07-10 20:21 Jason Zhu ha scritto:
>
> Hi Mattia, Emre, and Borries,
>
> You should be able to use the following values for the non-canonical amino
> acids in the meantime. I assumed (-H2O) in determining the MW and partial
> specific volumes for the 2 non-canonical amino acids based on Helmut
> Durchschlang's papers.
>
> Ornithine:
> MW (g/mol): 114.2
> Partial Specific Volume (mL/g): 0.7795446
>
> N-Methyl cyclohexylalanine (N-Me Cha):
> MW (g/mol): 167.3
> Partial Specific Volume (mL/g): 0.90342716
>
> I would use the N-Me Cha values for Phi 5. For SAR at residue 13, I would
> use the MW and PSV for glycine instead. The analog that I based my NMR PDB
> model off of (PDB ID: 5v63) had sarcosine (N-methylglycine) where I have
> glycine.
>
> Hope that helps and please let me know if there's anything else you need!
> Jason
>
>
> On Mon, Jul 10, 2023 at 9:37 AM Mattia Rocco <mattia.rocco at quipo.it>
> wrote:
>
> 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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