[Chimera-users] Phosphorylation

[Elaine Meng]

Hi Greg,
The SwissSidechain database doesn't include phosphorylated (natural) residues, nor do our standard rotamer libraries.  

In Chimera you can use the Build Structure tool (under Tools... Structure Editing) to build a phosphate onto the existing sidechain atom-by-atom with the Modify Structure section, or if you have a phosphate and the protein as separate models, to stick the phosphate onto the protein using the Join Models section.

<http://www.cgl.ucsf.edu/chimera/1.5.3/docs/ContributedSoftware/editing/editing.html#modify>
<http://www.cgl.ucsf.edu/chimera/1.5.3/docs/ContributedSoftware/editing/editing.html#join>

Example of atom-by-atom: you would first add hydrogens. For serine, you would select the OH hydrogen (Ctrl-click on it) and in the Modify Structure panel, change it to P, 4 bonds, tetrahedral, Apply (you might also want to change the atom name and residue name).  That would give all the atoms you need, but it is still necessary to change the hydrogens on the P to O.  Select the three hydrogens on P (Ctrl-click, Shift-Ctrl-click, Shift-Ctrl click) then use Modify Structure to make them element O, 1 bond.  Apply.  Be aware the bond lengths are only approximate.  You can also rotate a bond: Ctrl-doubleclick on it, choose Rotate Bond, use the resulting Adjust Torsions tool.

<http://www.cgl.ucsf.edu/chimera/1.5.3/docs/ContributedSoftware/structuremeas/structuremeas.html#adjust>

A third approach is to superimpose an already phosphorylated residue that is present in some other structure onto the unphosphorylated residue in your structure, write the coordinates of the phosphorylated residue "relative to" your structure, and then manually text-edit the PDB file of your structure to swap the phosphorylated residue coordinates for the unphosphorylated.

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

On Jan 6, 2012, at 10:27 PM, Tombline, Gregory wrote:

> Hi
> I noticed the script/plugin for no natural amino acids...
> Is it possible to substitute phosphorylated residues?
> Ie.   and see the phosphate
> Thanks,
> Greg