[chimerax-users] phosphorylation

[Elaine Meng]

Hi Fabian!
There are a few ways... what is easiest depends on whether you are familiar with text-editing PDB format or using the Build Structure tool.   However, I suspect that the easiest for you currently would be to use method (3) below in Chimera.  It is not available in ChimeraX.

(1) add/modify atoms to the sidechain manually in a stepwise process and change residue name using Build Structure (in ChimeraX menu under Tools... Structure Editing, use the Modify Structure part).
<https://rbvi.ucsf.edu/chimerax/docs/user/tools/buildstructure.html#modify>

(2) open a separate PDB file with the modified residue (phosphoserine or phosphothreoine), superimpose on existing residue backbone atoms, save modified residue PDB "relative to" your protein, then manually with text-editor substitute in the coordinates of the newly saved PDB of the modified residue into the PDB of the original structure.  May also need to renumber atoms, edit residue name, etc. 

(3) only available in Chimera (not ChimeraX):  install the SwissSideChain plugin and then use it to "mutate" the serine to SEP or SEP2 and the threonine to TPO or TPO2 (see second link below for explanation of residue names).  The plugin creates a new command "swapnaa" for doing the mutation.

Plugin and installation:
<https://swisssidechain.ch/visualization/chimera.php>

List of non-natural amino acids available via this plugin:
<https://www.swisssidechain.ch/browse/family/table.php?family=all>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco


> On Dec 21, 2022, at 5:49 AM, Fabian Glaser via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> Dear experts,
> 
> I would like to mutate a ser and a thr to phospo-serine and phospho-threonine, what is the easiest way to do it?
> 
> Thanks a lot,
> 
> fabian
> 
> --------------------------
> Fabian Glaser, PhD
> 
> Structural and Computational Biology Unit
> The Lorry I. Lokey Center for Life Sciences and Engineering
> Technion - Israel Institute of Technology, Haifa, Israel