This application is currently a simple command-line wrapper for the KinaseMover. It simulates the activity of a virtual kinase on a Pose by modifying (a) residue(s) at biologically relevant sequon positions into a PHOSPHORYLATION VariantType. It performs no further refinement or algorithmic steps.
Many proteins in nature are post-translationally modified, yet deposited structures often have their PTMs absent or removed. Kinases are enzymes that perform the transfer of a phosphate group from ATP to an substrate peptide/protein. The phosphorylation application allows a user to simulate the action of a virtual kinase enzyme on a "substrate" — the loaded .pdb structure. The virtual phosphorylation may be a biologically real transfer or entirely hypothetical or constructed.
One can use the phosphorylation application to quickly phosphorylate a protein at biologically relevant O positions, depending on the virtual enzyme selected for the application. Further applications can be used to refine the output structure(s) in preparation for other protocols.
General Options
| Group | Flag | Description | Type |
|---|---|---|---|
| in:path | s | Name of the .pdb file to process. |
String |
| enzymes | species | Set the species name of this simulated enzyme. The default value is h_sapiens. |
String |
| enzymes | enzyme | Set the specific enzyme name of this simulated enzyme. The default value is generic. |
String |
| enzymes | efficiency | Set the efficiency of the this simulated enzyme, where 1.0 is 100%. The default value is read from the database. | Real |
| out | nstruct | Number of times to process each input .pdb file. |
Integer |
Details
Setting the species name limits the behavior of the simulated kinase used in this application to consensus sequences used by the homolog found in the given species. A species name must be in the format e_coli or h_sapiens, (note the underscores,) which must also correspond to a directory in the Rosetta database, e.g., database/virtual_enzymes/kinases/h_sapiens/. If not set, h_sapiens is assumed.
If set, the simulated enzyme used in this application will use specific enzymatic details for this reaction from the database. If the species name has not been set, a "generic" enzyme from the kinase family is assumed. An enzyme name must be as listed in an appropriate enzyme file in database/virtual_enzymes/kinases/<species_name_>.
The generic H. sapiens kinase is a highly promiscuous kinase that transfers phopshate group to any Ser or Thr residue on a struture with 100% efficiency.
See EnzymaticMover#Enzyme Data Files for information on how to format your own enzymatic data for other kinases.
phosphorylation -s input/2DEF.pdb -nstruct 1
The phosphorylation application can be found in /Rosetta/main/source/src/apps/public/post-translational_modification/phosphorylation.cc.
A demo for the phosphorylation application can be found in /Rosetta/main/tests/integration/tests/phosphorylation/.
Labonte JWLabonte@jhu.edu