[Demelerlab] updates to the UltraScan SOMO residue definitions

[Mattia Rocco]

Hi Jason. No, the ANISOU field is automatically discarded on loading in 
US-SOMO. If you scroll to the top of the progress window, you will see 
what are the residue atom naming issues.

Il 2023-07-31 23:36 Jason Zhu ha scritto:

> Hi Mattia,
> 
> Thank you for pointing out those formatting issues with the PDB! I 
> tried incorporating all of your suggestions, however I'm still getting 
> errors with non-coded atoms and missing atoms. I suspect the bigger 
> issue is the "ANISOU" label on a number of the atoms and how that 
> affects the numbering of the atoms. The "ANISOU" labeled atoms have the 
> same number as the preceding atom. Manually relabeling them isn't 
> feasible as all of the "CONECT" numbers would change accordingly.
> 
> I will talk to Adam in our lab who solved the crystal structure and see 
> if he can re-export the PDB file from Phenix refine so that it is more 
> compatible with SOMO. Let me get back to you once I have more info.
> 
> Best,
> Jason
> 
> On Mon, Jul 31, 2023 at 12:35 PM Mattia Rocco <mattia.rocco at quipo.it> 
> wrote:
> 
> Hi Jason,
> 
> one thing I've noticed is that in, for instance, the trimer x-ray file, 
> ornithine is named "ORT" instead of "ORN". Plus, the ORT residues have 
> "NA" instead of "N" as the N-terminal atom, and "CQ" instead of "CA". 
> Also, the "XXX" (now MCA) has a totally different atom naming. Try 
> replacing that naming with the one I coded in the somo.residue file, 
> "HETERO" with "ATOM", and the it should work
> 
> Best - Mattia
> 
> Il 2023-07-31 20:56 Jason Zhu ha scritto:
> 
> Hi Borries, Mattia, and Emre,
> 
> I've attached the PDB files for the nmr models of the monomer, trimer, 
> and dodecamer that should be correctly labeled and compatible with 
> SOMO. I've also attached the updated residue and atom files courtesy of 
> Mattia and Emre. I'm still having some difficulties getting US-SOMO to 
> work on the xray pdb files due to how those PDB files are formatted and 
> will get back to you as soon as I figure out how to make them 
> compatible. Please feel free to reach out if you have any questions!
> 
> Best,
> Jason
> 
> On Thu, Jul 27, 2023 at 12:31 PM Mattia Rocco <mattia.rocco at quipo.it> 
> wrote:
> 
> Hi Jason,
> 
> thanks, that's makes things much easier... ;-) :-)
> 
> So, for Phi 5 / N-Me-Cha, in the PDB there are residues named ALC or 
> CHA, without the N-Methylation. We could propose MCA, apparently not 
> used for a residue [MHA is used, stands for 
> (CARBAMOYLMETHYL-CARBOXYMETHYL-AMINO)-ACETIC ACID]. What do you think?
> 
> Just an additional check for the psv: have you tried to reproduce a 
> couple of the standard amino acid residues, just to be sure? Having 
> done so countless times, I'm well aware of the potential pitfalls... 
> :-( ;-) You can pick the values to be compared from the somo.residue 
> file in US-SOMO, and the T-conversion formula is 
> psv at 20C=psv at 25C+[4.25E-04 * (20-25)]
> 
> Best - Mattia
> 
> Il 2023-07-27 20:55 Jason Zhu ha scritto:
> 
> 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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