sni.scan()

Description

Scans the indicated protein in search of S-nitrosylation sites

Usage

sni.scan(up_id)

Arguments

up_id a character string corresponding to the UniProt ID.

Value

Returns a dataframe where each row corresponds to a modifiable residue.

References

Huang et al. Nucleic Acids Res. 2019 47:D298-D308.

See Also

ac.scan(), meto.scan(), ni.scan(), gl.scan(), ub.scan(), su.scan(), dis.scan(), ptm.scan(), me.scan(), p.scan(), reg.scan()

Details

S-Nitrosylation is the covalent attachment of a nitric oxide group (-NO) to cysteine thiol within a protein to form an S-nitrosothiol (SNO). S-nitrosylation has diverse regulatory roles in bacteria, yeast and plants and in all mammalian cells.

The package ptm provides a function, sni.scan(), that assists in the identification of S-nitrosylation sites in a given protein. The UniProt ID of the protein of interest must be passed as argument. For instance, to scan the protein vimentin, we can proceed as follows:

First, you need to search for the UniProt ID. If the protein in question is found into MetOSite, you can search the ID:

id <- meto.list('Vimentin')$prot_id
id

## [1] "P08670"

Otherwise, go to the UniProt page to search for the ID.

Then,

sni.scan(id)

##       up_id organism modification database
## 4138 P08670       NA     C328-Sni    dbPTM