This application is currently a simple command-line wrapper for the GlycosyltransferaseMover. It simulates the activity of a virtual GT or OST on a Pose by adding (a) carbohydrate residue(s) at biologically relevant sequon positions. 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. Glycosylation is the most prevalent of all PTMs. The glycosyltransfer application allows a user to simulate the action of a virtual glycosyltransferase (GT) or oligosacharyltransferase (OST) enzyme on a "substrate" — the loaded .pdb structure. The virtual transferase may be a biologically real transferase or entirely hypothetical or constructed.
One can use the glycosyltransfer application to quickly glycosylate a protein at biologically relevant N, O, or C positions or extend a current glycan tree, depending on the virtual enzyme selected for the application. Further applications, such as the GlycanTreeModeler, 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 |
| in | include_sugars | Set whether or not carbohydrate residues will be loaded into Rosetta. The default value is false. | Boolean |
| 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
The application will fail if the -include_sugars flag is not set.
Setting the species name limits the behavior of the simulated glycosyltransferase 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/glycosyltransferases/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 glycosyltransferase family is assumed. An enzyme name must be as listed in an appropriate enzyme file in database/virtual_enzymes/glycosyltransferases/<species_name_>.
The generic H. sapiens glycosylatransferase is an OST that transfers α-D-Manp-(1→3)-[α-D-Manp-(1→6)]-β-D-Manp-(1→4)-β-D-GlcpNAc-(1→4)-β-D-GlcpNAc- (man3) to the Asn residue of any NX(S/T) sequons on a struture with 100% efficiency.
See EnzymaticMover#Enzyme Data Files for information on how to format your own enzymatic data for other glycosyltransferases.
glycosyltransfer -s input/1ABC.pdb -include_sugars -enzymes:species h_sapiens -enzymes:enzyme OGT -nstruct 5
The glycosyltransfer application can be found in /Rosetta/main/source/src/apps/public/post-translational_modification/glycosyltransfer.cc.
A demo for the glycosyltransfer application can be found in /Rosetta/main/tests/integration/tests/glycosylation/.
Labonte JWLabonte@jhu.edu