Phosphorylated PDB files

Tuesday, 15 January 2019

Phosphorylated PDB files

Sometime in human protein, a residue is phosphorylated, yet the model one gets from I-TASSER, Phyre etc. or the actual PDB structure lacks these. Here is how to add them easily and quickly with Rosetta.
There are several ways, another notable one is using Charmm-GUI PDB reader which allows the addition of phosphates and few cyanine dyes and other modifications. Here I will discuss using Rosetta as it is more flexible in the breadth of mutations.
Firstly, in the PDB file, the residues that one wants modified need to be changed. In PyMOL, it is simply a question of typing alter resi xx+yy+zz, resn='XXX' and then sort, where xx, yy and zz are the residues numbers and XXX is the three letter code of the phosphorylated equivalent, namely:

  • SER (Serine) → SEP (Phosphoserine)
  • THR (Threonine) → TPO (Phosphothreonine)
  • TYR (Tyrosine) → PTR (Phosphotyrosine)
The saved pdb file will have these residues changed in name only. The next step is to force the change in Rosetta.
Parenthetically, I have wondered about if one could add non-canonical amino acids to the mutagenesis wizard in PyMol, but it is impossible/hard/buggy.
In the terminal simply run the Rosetta score app* with pdb output enabled.

$ROSETTA/score.$ROSETTAEXT -database $ROSETTADB -s your_modded_model.pdb -out:output -no_optH false;

The file your_modded_model_0001.pdb will have the correct NCAA.

*) Note that this only works with 3.8 and above thanks to the addition of the PDB Chemical Components dictionary (CCD) business —this is normally a pain as it prevents parsing of custom params files with shared names with PDB ligands and has to be disabled with -load_PDB_components false.


Some other residues of interest are:
  • GTP —GTP (be careful as a handful of structures have GDP with odd atom names)
  • MLZ —n-methyl-lysine
  • MLY —n-dimethyl-lysine
  • M3L —n-trimethyl-lysine
  • ORN —ornithine
  • SEC —selenocysteine
  • MSE —selenomethionine
  • HCS —homocysteine
  • SLZ —thialysine
  • NLE —norleucine
  • ALO —allothreonine
  • ALN —naphthalylalanine
  • 2MR —dimethylargnine
  • CIR —citrulline

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