R/charge.R

In Peptides: Calculate Indices and Theoretical Physicochemical Properties of Protein Sequences

#' @export charge
#' @importFrom utils data
#' @title Compute the theoretical net charge of a protein sequence
#' @description This function computes the net charge of a protein sequence based on the Henderson-Hasselbalch equation described by Moore, D. S. (1985). The net charge can be calculated at defined pH using one of the 9 pKa scales availables: \code{Bjellqvist}, \code{Dawson}, \code{EMBOSS}, \code{Lehninger}, \code{Murray}, \code{Rodwell}, \code{Sillero}, \code{Solomon} or \code{Stryer}.
#' @param seq An amino-acids sequence
#' @param pH A pH value
#' @param pKscale A character string specifying the pKa scale to be used; must be one of \code{"Bjellqvist"}, \code{"Dawson"}, \code{"EMBOSS"}, \code{"Lehninger"}, \code{"Murray"}, \code{"Rodwell"}, \code{"Sillero"}, \code{"Solomon"} or \code{"Stryer"}
#' @author Original by Daniel Osorio <dcosorioh@tamu.edu>, C++ code optimized by Luis Pedro Coelho <luis@luispedro.org>
#' @references
#' Kiraga, J. (2008) Analysis and computer simulations of variability of isoelectric point of proteins in the proteomes. PhD thesis, University of Wroclaw, Poland.
#'
#' Bjellqvist, B., Hughes, G.J., Pasquali, Ch., Paquet, N., Ravier, F., Sanchez, J.Ch., Frutige,r S., Hochstrasser D. (1993) The focusing positions of polypeptides in immobilized pH gradients can be predicted from their amino acid sequences. Electrophoresis, 14:1023-1031.
#'
#' Dawson, R. M. C.; Elliot, D. C.; Elliot, W. H.; Jones, K. M. Data for biochemical research. Oxford University Press, 1989; p. 592.
#'
#' EMBOSS data are from http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/iep.html.
#'
#' Nelson, D. L.; Cox, M. M. Lehninger Principles of Biochemistry, Fourth Edition; W. H. Freeman, 2004; p. 1100.
#'
#' Murray, R.K., Granner, D.K., Rodwell, V.W. (2006) Harper's illustrated Biochemistry. 27th edition. Published by The McGraw-Hill Companies.
#'
#' Rodwell, J. Heterogeneity of component bands in isoelectric focusing patterns. Analytical Biochemistry, 1982, 119 (2), 440-449.
#'
#' Sillero, A., Maldonado, A. (2006) Isoelectric point determination of proteins and other macromolecules: oscillating method. Comput Biol Med., 36:157-166.
#'
#' Solomon, T.W.G. (1998) Fundamentals of Organic Chemistry, 5th edition. Published by Wiley.
#'
#' Stryer L. (1999) Biochemia. czwarta edycja. Wydawnictwo Naukowe PWN.
#'
#' @examples # COMPARED TO EMBOSS PEPSTATS
#' # http://emboss.bioinformatics.nl/cgi-bin/emboss/pepstats
#' # SEQUENCE: FLPVLAGLTPSIVPKLVCLLTKKC
#' # Charge   = 3.0
#'
#' charge(seq= "FLPVLAGLTPSIVPKLVCLLTKKC",pH= 7, pKscale= "Bjellqvist")
#' # [1] 2.737303
#' charge(seq= "FLPVLAGLTPSIVPKLVCLLTKKC",pH= 7, pKscale= "EMBOSS")
#' # [1] 2.914112
#' charge(seq= "FLPVLAGLTPSIVPKLVCLLTKKC",pH= 7, pKscale= "Murray")
#' # [1] 2.907541
#' charge(seq= "FLPVLAGLTPSIVPKLVCLLTKKC",pH= 7, pKscale= "Sillero")
#' # [1] 2.919812
#' charge(seq= "FLPVLAGLTPSIVPKLVCLLTKKC",pH= 7, pKscale= "Solomon")
#' # [1] 2.844406
#' charge(seq= "FLPVLAGLTPSIVPKLVCLLTKKC",pH= 7, pKscale= "Stryer")
#' # [1] 2.876504
#' charge(seq= "FLPVLAGLTPSIVPKLVCLLTKKC",pH= 7, pKscale= "Lehninger")
#' # [1] 2.87315
#' charge(seq= "FLPVLAGLTPSIVPKLVCLLTKKC",pH= 7, pKscale= "Dawson")
#' # [1] 2.844406
#' charge(seq= "FLPVLAGLTPSIVPKLVCLLTKKC",pH= 7, pKscale= "Rodwell")
#' # [1] 2.819755
#'
#' # COMPARED TO YADAMP
#' # http://yadamp.unisa.it/showItem.aspx?yadampid=845&x=0,7055475
#' # SEQUENCE: FLPVLAGLTPSIVPKLVCLLTKKC
#' # CHARGE pH5: 3.00
#' # CHARGE pH7: 2.91
#' # CHARGE pH9: 1.09

#' charge(seq= "FLPVLAGLTPSIVPKLVCLLTKKC",pH= 5, pKscale= "EMBOSS")
#' # [1] 3.037398
#' charge(seq= "FLPVLAGLTPSIVPKLVCLLTKKC",pH= 7, pKscale= "EMBOSS")
#' # [1] 2.914112
#' charge(seq= "FLPVLAGLTPSIVPKLVCLLTKKC",pH= 9, pKscale= "EMBOSS")
#' # [1] 0.7184524
#'
#' # JUST ONE COMMAND
#' charge(seq= "FLPVLAGLTPSIVPKLVCLLTKKC",pH= seq(from = 5,to = 9,by = 2), pKscale= "EMBOSS")
#' # [1] 3.0373984 2.9141123 0.7184524

charge<- function(seq, pH = 7, pKscale = "Lehninger") {
  seq <- toupper(seq)
  pKscale <- names(AAdata$pK)[pmatch(pKscale,names(AAdata$pK))]
  if(is.na(pKscale)){
    stop("The selected pK scale is not available. pKscale must be one of: 'Bjellqvist','Dawson', 'EMBOSS', 'Lehninger', 'Murray', 'Rodwell', 'Sillero', 'Solomon', or 'Stryer'.")
  }
  if(!is.numeric(pH)){
    stop("The pH must be numeric.")
  }
  if(length(seq) == 1 || length(pH) == 1){
    return(unlist(chargeList(seq = seq,pH = pH, pKscale = pKscale)))
  } else {
    return(chargeList(seq = seq,pH = pH, pKscale = pKscale))
  }
}