idprofile: IDp PRofile From idpr Package
In wmm27/idpr: Profiling and Analyzing Intrinsically Disordered Proteins in R

idprofile

R Documentation

IDp PRofile From idpr Package

Description

The IDPRofile is a summation of many features of the idpr package, conveniently grouped into one function for quick analysis. This combines many plotting functions in this package. These include:
chargeHydropathyPlot
chargeCalculationLocal
scaledHydropathyLocal
structuralTendencyPlot
foldIndexR
All of the above linked functions only require the sequence argument to output plots of characteristics associated with IDPs. The function also includes options for IUPred functions. The function does one of the following based on user-specified parameters:
iupred
iupredAnchor
iupredRedox
The IUPred function used depends on the argument of iupredType. All require the UniProt Accession to make a proper connection to the IUPred2A REST API. If the UniProt Accession is not specified, the IUPred plot is skipped.

Usage

idprofile(
  sequence,
  uniprotAccession = NA,
  proteinName = NA,
  iupredType = "long",
  window = 9,
  foldIndexWindowSize = 51,
  pH = 7,
  foldIndex_pH = 7,
  pKaSet = "IPC_protein",
  structuralTendencyType = "bar",
  structuralTendencySummarize = FALSE,
  disorderPromoting = c("P", "E", "S", "Q", "K", "A", "G"),
  disorderNeutral = c("D", "T", "R"),
  orderPromoting = c("M", "N", "V", "H", "L", "F", "Y", "I", "W", "C")
)

Arguments

`sequence`	amino acid sequence as a single character string or vector of single characters. It also supports a single character string that specifies the location of a .fasta or .fa file.
`uniprotAccession`	character string specifying the UniProt Accession of the protein of interest. Used to fetch predictions from IUPreds REST API. Default is NA. Keep as NA if you do not have a UniProt Accession.
`proteinName`	character string, optional. Used to add protein name to the title in ggplot.
`iupredType`	character string specifying the type of IUPred2 prediction to retrieve. Can be c("long", "short", "glob", "anchor", "redox"). "long" by default. "long", "short", and "glob" use the `iupred` function and specify the type of plot. Both "redox" and "anchor" use "long" for predictions, but are context dependent. "anchor" uses `iupredAnchor` to get predictions of disorder with IUPred2 and predictions of induced folding based on ANCHOR2 predictions (Shown with a red line). "redox" uses `iupredRedox` to make predictions of disorder based on environmental conditions. Regions of predicted environmental sensitivity are highlighted. See the respective functions for more details. This is skipped if uniprotAccession = NA.
`window`	a positive, odd integer. 9 by default. Sets the size of sliding window, must be an odd number. The window determines the number of residues to be analyzed and averaged for each position along the sequence. For chargeCalculationLocal and scaledHydropathyLocal.
`foldIndexWindowSize`	a positive, odd integer. 51 by default. Sets the size of sliding window, must be an odd number. The window determines the number of residues to be scored and averaged for each position along the sequence.
`pH`	numeric value, 7.0 by default. The environmental pH used to calculate residue charge.
`foldIndex_pH`	numeric value, 7.0 by default. The environmental pH used to calculate residue charge. FoldIndex specifically uses pH = 7.0 in settings and thus, is distinct from changing pH in the other calculations.
`pKaSet`	A character string or data frame. "IPC_protein" by default. Character string to load specific, preloaded pKa sets. c("EMBOSS", "DTASelect", "Solomons", "Sillero", "Rodwell", "Lehninger", "Toseland", "Thurlkill", "Nozaki", "Dawson", "Bjellqvist", "ProMoST", "Vollhardt", "IPC_protein", "IPC_peptide") Alternatively, the user may supply a custom pKa dataset. The format must be a data frame where: Column 1 must be a character vector of residues named "AA" AND Column 2 must be a numeric vector of pKa values.
`structuralTendencyType`	a character string specifying the type of plot the `structuralTendencyPlot` should output. Can be "bar" or "pie". Equivalent argument to graphType= in the linked function. "bar" by default.
`structuralTendencySummarize`	a logical value specifying the `structuralTendencyPlot` should be summarized into broad categories. Equivalent argument to summarize= in the linked function. FALSE by default
`disorderPromoting, disorderNeutral, orderPromoting`	character vectors of individual residues to be matched with the input sequence. Defaults: disorderPromoting = c("P", "E", "S", "Q", "K", "A", "G") orderPromoting = c("M", "N", "V", "H", "L", "F", "Y", "I", "W", "C") disorderNeutral = c("D", "T", "R") It is not recommended to change these. Arguments passed to `structuralTendencyPlot`

Details

Described in McFadden, W. M., & Yanowitz, J. L. (2022). idpr: A package for profiling and analyzing Intrinsically Disordered Proteins in R. PloS one, 17(4), e0266929

Value

4 or 5 plots, depending if a UniProt Accession is provided.

Citations for each Plot

chargeHydropathyPlot
- Kozlowski, L. P. (2016). IPC – Isoelectric Point Calculator. Biology Direct, 11(1), 55. https://doi.org/10.1186/s13062-016-0159-9
- Kyte, J., & Doolittle, R. F. (1982). A simple method for displaying the hydropathic character of a protein. Journal of molecular biology, 157(1), 105-132.
- Uversky, V. N. (2016). Paradoxes and wonders of intrinsic disorder: Complexity of simplicity. Intrinsically Disordered Proteins, 4(1), e1135015. https://doi.org/10.1080/21690707.2015.1135015
- Uversky, V. N., Gillespie, J. R., & Fink, A. L. (2000). Why are “natively unfolded” proteins unstructured under physiologic conditions?. Proteins: structure, function, and bioinformatics, 41(3), 415-427. https://doi.org/10.1002/1097-0134(20001115)41:3<415::AID-PROT130>3.0.CO;2-7
- If a pKa set is specified, see pKaData
chargeCalculationLocal
- Kozlowski, L. P. (2016). IPC – Isoelectric Point Calculator. Biology Direct, 11(1), 55. https://doi.org/10.1186/s13062-016-0159-9
- If a pKa set is specified, see pKaData
scaledHydropathyLocal
- Kyte, J., & Doolittle, R. F. (1982). A simple method for displaying the hydropathic character of a protein. Journal of molecular biology, 157(1), 105-132.
structuralTendencyPlot
- Uversky, V. N. (2013). A decade and a half of protein intrinsic disorder: Biology still waits for physics. Protein Science, 22(6), 693-724. doi:10.1002/pro.2261
foldIndexR
- Prilusky, J., Felder, C. E., et al. (2005). FoldIndex: a simple tool to predict whether a given protein sequence is intrinsically unfolded. Bioinformatics, 21(16), 3435-3438.
- Uversky, V. N., Gillespie, J. R., & Fink, A. L. (2000). Why are “natively unfolded” proteins unstructured under physiologic conditions?. Proteins: structure, function, and bioinformatics, 41(3), 415-427. https://doi.org/10.1002/1097-0134(20001115)41:3<415::AID-PROT130>3.0.CO;2-7
- Also see citations for hydrapthy and charge plots above
iupred, iupredAnchor, iupredRedox
- Bálint Mészáros, Gábor Erdős, Zsuzsanna Dosztányi, IUPred2A: context-dependent prediction of protein disorder as a function of redox state and protein binding, Nucleic Acids Research, Volume 46, Issue W1, 2 July 2018, Pages W329–W337, https://doi.org/10.1093/nar/gky384
- Erdős, G., & Dosztányi, Z. (2020). Analyzing protein disorder with IUPred2A. Current Protocols in Bioinformatics, 70, e99. https://doi.org/10.1002/cpbi.99

Examples

#For most functions, a protein sequence is all that is needed.

#The UniProt ID is optional but recommended for IUPred results.
proteinID <- "P04637"
p53Seq <- idpr:::TP53Sequences[2]
## Not run: 
idprofile(
  sequence = p53Seq,
  uniprotAccession = proteinID)


#changing the iupred to redox
## and getting a pie chart for structuralTendency.
idprofile(
  sequence = p53Seq,
  uniprotAccession = proteinID,
  pKaSet = EMBOSS,
  iupredType = "redox",
  structuralTendencyType = "pie")

## End(Not run)

wmm27/idpr documentation built on Jan. 12, 2023, 8:45 a.m.