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)
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
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
Germany
Tel.: +49 (0) 89 2180 77716
https://www.cup.lmu.de/oc/schneider/
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?
Cheers,
Seth
------------------------------------------------------------------------
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:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=1
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
https://www.jiscmail.ac.uk/policyandsecurity/
