structuralTendency: Structural Tendency of Amino Acid Residues

In idpr: Profiling and Analyzing Intrinsically Disordered Proteins in R

Description

Each amino acid residue has a tendency to impact the order / disorder of the amino acid sequence. Some residues are disorder promoting, meaning they tend to favor disorder over ordered structures. These are typically hydrophilic, charged, or small residues. Order promoting residues tend to be aliphatic, hydrophobic, aromatic, or form tertiary structures. Disorder neutral residues neither favor order nor disordered structures.

Usage

structuralTendency(
  sequence,
  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"),
  printCitation = FALSE
)

Arguments

sequence	amino acid sequence as a single character string, a vector of single characters, or an AAString object. It also supports a single character string that specifies the path to a .fasta or .fa file.
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. These definitions are from Uversky (2013).
printCitation	logical, FALSE by default. When printCitation = TRUE, a citation to Uversky, V. N. (2013) is printed. This is the paper categorizing the structural impact of each residue that is used as the default settings.

Value

a data frame containing each residue from the sequence matched with its structural tendency, defined by disorderPromoting, disorderNeutral, and orderPromoting. For convenient plotting see structuralTendencyPlot.

References

Uversky, V. N. (2013). A decade and a half of protein intrinsic disorder: Biology still waits for physics. Protein Science, 22(6), 693-724. https://doi.org/10.1002/pro.2261.
Kulkarni, Prakash, and Vladimir N. Uversky. "Intrinsically disordered proteins: the dark horse of the dark proteome." Proteomics 18.21-22 (2018): 1800061. https://doi.org/10.1002/pmic.201800061.

See Also

Other structural tendency: structuralTendencyPlot()

Examples

#Amino acid sequences can be character strings
aaString <- "ACDEFGHIKLMNPQRSTVWY"
#Amino acid sequences can also be character vectors
aaVector <- c("A", "C", "D", "E", "F",
              "G", "H", "I", "K", "L",
              "M", "N", "P", "Q", "R",
             "S", "T", "V", "W", "Y")
#Alternatively, .fasta files can also be used by providing
##The path to the file as a character string

exampleDF <- structuralTendency(aaString)
head(exampleDF)
exampleDF <- structuralTendency(aaVector)
head(exampleDF)

#This example shows if a user changes the default definition of residues.
##These residues are labeled as such from Dunker et al (2001),
##"Intrinsically disordered protein."
exampleDF <- structuralTendency(aaString,
               disorderPromoting = c("A", "R", "G", "Q", "S", "P", "E", "K"),
               disorderNeutral = c("H", "M", "T", "D"),
               orderPromoting = c("W", "C", "F", "I", "Y", "V", "L", "N"))
head(exampleDF)

idpr documentation built on Dec. 26, 2020, 6 p.m.