netCharge: Protein Charge Calculation, Net Charge

In idpr: Profiling and Analyzing Intrinsically Disordered Proteins in R

Description

This function will determine the net charge of a peptide using the Henderson-Hasselbalch Equation. The output is a numeric value describing the total net charge or the average net charge.

Usage

netCharge(
  sequence,
  pKaSet = "IPC_protein",
  pH = 7,
  includeTermini = TRUE,
  averaged = FALSE
)

Arguments

sequence	amino acid sequence as a character string or vector of individual residues. alternatively, a character string of the path to a .fasta / .fa file
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.
pH	numeric value, 7.0 by default. The environmental pH used to calculate residue charge.
includeTermini	Logical value, TRUE by default. This determines how the calculation handles the N- and C- terminus. includeTermini determines if the calculation will use the charge of the amine and carboxyl groups at the ends of the peptide (When TRUE). These charges are ignored when includeTermini = FALSE.
averaged	logical value. FALSE by default. When averaged = FALSE, the total net charge is returned. When averaged = TRUE, the total net charge is averaged by the sequence length. This gives a value of -1 to +1.

Value

numeric value. Either the net charge or average net charge, depending on the value of the averaged argument

See Also

pKaData for residue pKa values and citations. See hendersonHasselbalch for charge calculations.

Other charge functions: chargeCalculationGlobal(), chargeCalculationLocal(), hendersonHasselbalch()

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 a character string
 # of the path to the file.

#Calculate the Net Charge
netCharge(aaString,
          averaged = FALSE)
netCharge(aaVector,
          averaged = FALSE)

#Calculate the Average Net Charge
netCharge(aaString,
          averaged = TRUE)
netCharge(aaVector,
          averaged = TRUE)

#Change the pH
netCharge(aaString,
          pH = 8)
netCharge(aaString,
          pH = 7)
netCharge(aaString,
          pH = 5.5)

#Specify which pKa set to use
netCharge(aaString,
          pKaSet = "IPC_protein") #Default
netCharge(aaString,
          pKaSet = "IPC_peptide")
netCharge(aaString,
          pKaSet = "Dawson")
netCharge(aaString,
          pKaSet = "EMBOSS")

#Should the termini be included in charge calculations?
netCharge(aaString,
          includeTermini = TRUE) #Default
netCharge(aaString,
          includeTermini = FALSE)

Example output

[1] -0.1898971
[1] -0.1898971
[1] -0.009494853
[1] -0.009494853
[1] -0.8887975
[1] -0.1898971
[1] 0.669778
[1] -0.1898971
[1] 0.04533928
[1] -0.01434495
[1] 0.1865899
[1] -0.1898971
[1] -0.1819816

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