N-terminal acetyltransferases (NATs) are used in Nature to acetylayte the terminal amino group of a peptide chain.
The N-terminal_acetylation application allows a user to simulate the action of a virtual NAT enzyme on a "substrate" — the loaded .pdb structure. The virtual transferase may be a biologically real transferase or entirely hypothetical or constructed.
This application is currently a simple command-line wrapper for the NTerminalAcetyltransferaseMover. It simulates the activity of a virtual NAT on a Pose by modifying the N-terminal residue at biologically relevant sequon positions into a ACETYLATED_NTERMINUS_VARIANT VariantType. It performs no further refinement or algorithmic steps.
One can use the N-terminal_acetylation application to quickly acetylate a protein at biologically relevant 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
| Froup | 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 acetyltransferase 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/N-terminal_acetyltransferases/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 DNA methyltransferase family is assumed. An enzyme name must be as listed in an appropriate enzyme file in database/virtual_enzymes/DNA_methyltransferases/<species_name_>.
The generic H. sapiens N-terminal acetyltransferase is acetylates any N-terminus with 100% efficiency.
See EnzymaticMovers#Enzyme Data Files for information on how to format your own enzymatic data for other N-terminal acetyltransferases. (Note that the sequon for an N-terminal virtual enzyme should begin with <, as in <(A/S/T/C); otherwise, the Mover will needlessly scan the entire Pose sequence.)
N-terminal_acetylation -s input/1ABC.pdb -enzymes:species h_sapiens -enzymes:efficiency 0.50 -nstruct 3
The N-terminal_acetylation application can be found in /Rosetta/main/source/src/apps/public/post-translational_modification/N-terminal_acetylation.cc.
A demo for the N-terminal_acetylation application can be found in /Rosetta/main/tests/integration/tests/N-terminal_acetylation/.
Labonte JWLabonte@jhu.edu