meto.list()

Description

Lists proteins found in MetOSite with names matching the keyword.

Usage

meto.list(keyword)

Arguments

keyword a character string corresponding to the keyword.

Value

This function returns a dataframe with the UniProt id, the protein name and the species, for those proteins present into MetOSite whose name contains the keyword.

References

Valverde et al. 2019. MetOSite: an integrated resource for the study of methionine residues sulfoxidation, Bioinformatics 35:48 49-4850.

Details

We have search the literature to find those protein-bound methionine residues that have been detected, either in vitro or in vivo, as MetO. All this information has been collected and published in the form of a database: MetOSite.

Thus, MetOSite is a database that provides mannually curated data related to experimentally confirmed sulfoxidation sites and the effect of such PTM on the protein properties. Currently, it contains over 7300 sites found in more than 3500 different proteins from over 20 species.

The ptm packages offers three functions that help to explore and download data from MetOSite.

meto.list (the current tutorial)
meto.scan
meto.search

Thus, if you wish to know whether your protein of interest has been described to contain MetO sites, the function meto.scan() will help you.

If, on the contrary, you’re interested on sets of proteins or MetO sites, grouped according to criteria such as functional effect, species or oxidants, then the place to go is meto.search()

Finally, the function meto.list() provides a list with the proteins found in MetOSite whose names contain the keyword provided as argument to the function.

For instance, using the word calcium as keyword:

ca <- meto.list('calcium')
head(ca)

##   prot_id                                           prot_name      prot_sp
## 1  O14983 Sarcoplasmic/endoplasmic reticulum calcium ATPase 1 Homo sapiens
## 2  O95202      Mitochondrial proton/calcium exchanger protein Homo sapiens
## 3  P09758        Tumor-associated calcium signal transducer 2 Homo sapiens
## 4  P16615 Sarcoplasmic/endoplasmic reticulum calcium ATPase 2 Homo sapiens
## 5  P23634       Plasma membrane calcium-transporting ATPase 4 Homo sapiens
## 6  P98194        Calcium-transporting ATPase type 2C member 1 Homo sapiens

In this way, the object we have named ca is a dataframe that contains tens of proteins (one per row) whose names include the word calcium. Now, if you wish, we can further explore any of them using meto.scan(). For instance, let’s say we are interested in the protein “Calcium/calmodulin-dependent protein kinase type II subunit delta”, which is found in the row 11 from the dataframe ca :

meto.scan(ca$prot_id[11])$Note

## [1] "The sulfoxidation activates the kinase in a Ca/CaM-independent fashion. In the 6BAB PDB the Met labeling can be different to the one used herein."

Note that we have only requested the ‘Note’ field. For a more detailed report, please check the documentation of the function meto.scan().