ptm.plot: Plot Values of a Property and PTM Sites Along the Protein Sequence

Description

Represents the values of a property and show the PTM sites along a protein sequence.

Usage

ptm.plot(up_id, pdb = "", property, ptm, dssp = 'compute',
                window = 1, sdata = FALSE, ...)

Arguments

up_id

a character string for the UniProt ID of the protein of interest.

pdb

Optional argument to indicate the PDB and chain to be used (i.e. '1u8f.O'). If we leave this argument empty, the function will make the election for us whenever possible.

property

a character string indicating the property of interest. It should be one of 'sasa', 'acc', 'dpx', 'entropy7.aa','entropy7.codon', 'entropy100.aa', 'entropy100.codon', 'eiip', 'volume', 'polarizability', 'avg.hyd', 'pi.hel', 'a.hel', 'b.sheet', 'B.factor', or 'own'.

ptm

a character vector indicating the PTMs of interest. It should be among: 'ac' (acetylation), 'me' (methylation), 'meto' (sulfoxidation), 'p' (phosphorylation), 'ni' (nitration), 'su' (sumoylation) or 'ub' (ubiquitination), 'gl' (glycosylation), 'sni' (S-nitrosylation),'reg' (regulatory), 'dis' (disease).

dssp

character string indicating the method to compute DSSP. It should be either 'compute' or 'mkdssp'.

window

positive integer indicating the window size for smoothing with a sliding window average (default: 1, i.e. no smoothing).

sdata

logical, if TRUE save a Rda file with the relevant data in the current directory.

...

when the user want to use his/her own amino acid index, it can be passed as a named vector.

Value

This function returns either one or two plots related to the chosen property along the primary structure, as well as the computed data if sdata has been set to TRUE.

Details

If the property 'own' is selected, a named vector with the own index for the 20 amino acids should be passed as argument. Currently the supported properties are:

sasa: Solvent-accessible surface area (3D)
acc: Accessibility (3D)
dpx: Depth (3D)
volume: Normalized van der Waals volume (1D)
mutability: Relative mutability, Jones 1992, (1D)
helix: Average relative probability of helix, Kanehisa-Tsong 1980,(1D)
beta-sheet: Average relative probability of beta-sheet, Kanehisa-Tsong 1980, (1D)
pi-helix: Propensity of amino acids within pi-helices, Fodje-Al-Karadaghi 2002, (1D)
hydropathy: Hydropathy index, Kyte-Doolittle 1982, (1D)
avg.hyd: Normalized average hydrophobicity scales, Cid et al 1992, (1D)
hplc: Retention coefficient in HPLC at pH7.4, Meek 1980, (1D)
argos: Hydrophobicity index, Argos et al 1982, (1D)
eiip: Electron-ion interaction potential, Veljkovic et al 1985, (1D)
polarizability: Polarizability parameter, Charton-Charton 1982, (1D)
entropy7.aa: Shannon entropy based on 7 species and protein sequences (EVO)
entropy100.aa: Shannon entropy based on 100 species and protein sequences (EVO)
entropy7.condon: Shannon entropy based on 7 species and codon sequences (EVO)
entropy100.codon: Shannon entropy based on 100 species and codon sequences (EVO)

For 3D properties such as sasa, acc or dpx, for which different values can be obtained depending on the quaternary structure, we first compute the property values for each residue in the whole protein and plotted them against the residue position. Then, the value for this property is computed in the isolated chain (a single polypeptide chain) and in a second plot, the differences between the values in the whole protein and the chain are plotted against the residue position.

Examples

Run this code

# NOT RUN {
ptm.plot('P04406', property = 'sasa', window = 10, ptm = 'meto')
# }
# NOT RUN {
ptm.ptm('P04406', property = 'dpx', ptm = c('meto', 'p'))
# }