Hi Seth,

There might be a more straight-forward way, but here is what I would do:

- modify a native amino acid to your non-natural residue i.e. in Jligand
- assign a new three-letter code and write it out as cif and PDB file
- open the cif file in your favorite text editor and define it as L-peptide (or D-peptide), see example for ALA below (keep the exact spacing! So best copy the line from i.e. ALA)

ALA     ALA     ALANINE     L-peptide     13     6     .

- safe the cif file again.
-optional combine all cif files in one file (you can do that in CCP4)
- now open all your non-natural amino acids PDBs of your cyclic peptide in coot, move the roughly the order you want them manually and safe them - open all PDBs in your favourit texteditor, use search and replace to renumber them consecutively in the order you want them, and copy them in one PDB file in the correct order
- open the PDB file in coot
- read in the
=> since all are defined as peptides and numbered consecutively, coot should generate peptide bonds in between (there might be some hydrogen residues interfering) and RSR should work (I usually check, if the cif definitions make sense, by running a couple of circles structure idealisation in refmac with my compound/ligand etc) - now you just need to add a link to make the circle and define its geometry in the cif file

Hope that helps!

Best Sabine

Dr. Sabine Schneider
Heisenberg Research Group Leader
Ludwig-Maximilians University Munich
Department of Chemistry
Butenandtstr. 5-13
81377 Munich
Tel.: +49 (0) 89 2180 77716

On 02/09/2021 01:55, Seth Harris wrote:
Hi all,

I am increasingly dealing with large macrocycles or cyclized peptides that include unnatural amino acids or modifications. Early on my approach was to treat most of it as the native peptide scaffold, then add a few custom 'LINK' records to capture covalent bonds to some non-native moiety, and that moiety would be defined as we do for small molecule synthetic ligands. Advantage was that it was efficient for refinement of the conventional amino acid scaffold. Disadvantage, a bit cumbersome and I do find that while the covalently bonded attachment point is reasonable, the neighboring atoms to that new attachment don't always behave reliably (as in perhaps don't have the knowledge that their neighbor has something new attached which affects their space.) As our chemists got more creative, it also is tedious to sit there trying to make 5 or 6 little bits and pieces that all have to be attached to different atoms along the scaffold. Plus the bookkeeping of made up names for little extra ethylenes, halognes, and their atom name attachment points and such was pretty painful.

So, that led to approach two, which was to just let the dictionary generation happen for the whole peptide or macrocycle. This ignores knowledge that it's essentially an amino acid type of base scaffold (so a bit inefficient for purists) and just redefines all those as if it's some small molecule, albeit a relatively large version of one of those. You also lose residue number indexing, as the whole thing is typically called "LIG" with a single residue identifier, but it seems a small price to pay for the convenience of it taking care of all the sundry modifications and cyclization points, etc.

The problem I'm having is that COOT is having trouble reading or using these large .cif files. The files may be 1000 or more lines long with the hydrogens defined. I've tried dropping all hydrogens but it's still large and when I go to real space refine or do any editing to move the starting conformation of the molecule in question into the clear density for it bound to some protein, Coot basically hangs either indefinitely or for several minutes at a time at least with each attempted motion, step. Is there some memory allocation for the .cif dictionary that perhaps is limiting? I don't have a handy non-proprietary example currently, but could likely generate one if needed. Or have people had success with this approach (e.g. taking a 10-14 amino acid peptide, treat it as a SMILES string and generate a .cif for the whole thing as a single molecule and then be able to use it in real space refinement in Coot? )

I've tried a few workarounds to get the atoms pretty close and then let reciprocal space refinement do the rest, but there really aren't so many good ways to do that (Pymol's sculpting drifts, was playing with Isolde but having similar technical issues with the restraints definitions).

Thanks for thoughts, or info on Coot and large .cif dictionaries?



To unsubscribe from the COOT list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=1 <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=1>


To unsubscribe from the COOT list, click the following link:

This message was issued to members of www.jiscmail.ac.uk/COOT, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 

Reply via email to