[phenixbb] covalently modified proteins

Nigel W. Moriarty nwmoriarty at lbl.gov
Fri Mar 16 10:41:49 PDT 2007


Covalently bound ligands is an active area at the moment.  It is 
possible using the latest CCI-Apps and the interface will improve in the 
near future.

If you have a modified amino acid in the PDB which contains the rest of 
the protein and you have modified the residue name (or in the near 
future, you have non-standard atoms in the modified residue) you can run

elbow.builder protein_modified_amino.pdb --do-all

which will scan the PDB file for residues it does not recognise and 
generate a restraints library.  You can then

phenix.refine data.mtz protein_modified_amino.pdb elbow.XXX.all.cif

to tell the refinement about the restrains for your modified amino 
acid.  The refinement attempts to  include the modified amino acid in 
the backbone based on the atom names (C, N, CA, O).  You should check 
that this occurs and let me know in the event that it fails.

I'm also working on a scheme were by you can have the modified amino 
acids in other formats.


Marcelo Carlos Sousa wrote:

>I have followed with interest the discussions regarding refinement of  
>proteins with ligands. I wonder if Pavel or anybody else could  
>comment on the refinement of proteins with covalently attached  
>ligands. I am currently handling that in CNS as I know how to write  
>the patches. Is this possible in phenix? Coudl it be handled by  
>generating a "new amino acid" like say a Cys with beta mercapto  
>ethanol attached and then get the program to link this "new amino  
>acid" via normal peptide bonds with the rest of the protein? What  
>about a capped N-terminus? can we make the "new amino acid" say N- 
>acetyl-Gly and get the program to put this at the N-terminus?
>Any help is appreciated.
>Marcelo C. Sousa, Ph.D.
>Department of Chemistry and Biochemistry
>Cristol Chemistry Building. Room 100
>215 UCB
>University of Colorado at Boulder
>Boulder, CO 80309
>Phone: (303) 735 4341
>Fax: (303) 492 5894
>phenixbb mailing list
>phenixbb at phenix-online.org

Nigel W. Moriarty
Building 64R0246B, Physical Biosciences Division
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709
Fax   : 510-486-5909
Email : NWMoriarty at LBL.gov
Web   : CCI.LBL.gov

More information about the phenixbb mailing list