hendersonHasselbalch: Henderson-Hasselbalch Equation

In idpr: Profiling and Analyzing Intrinsically Disordered Proteins in R

Description

This function calculates the ionic charge of a residue at a specific pH when given the pKa. pH = pKa + log([A-] / [HA]) Known, charged residues are accepted as well as the protein termini and general property to allow customized calculations. The output is a ratio comparing acid to conjugate base for acidic residues or a ratio comparing conjugate base to acid for basic residues.

Usage

hendersonHasselbalch(pKa, pH = 7, residue)

Arguments

pKa	numeric value. The point where A- = HA.
pH	numeric value. The pH of the environment. 7.0 by default
residue	individual character or character string. accepted values are the exact aa c("C", "D", "E", "H", "K", "R", "Y"), termini c("COOH","COO","NH2","NH3"), or a general property c("acid", "base", "negative", "positive").

Value

a numeric value giving the ratio of charged to uncharged residues.

See Also

pKaData for residue pKa values and citations. See other charge functions for use.

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

Examples

#Calculating Lysine charge using the EMBOSS pKa data
EMBOSS_pKa <- pKaData[, 1:2]
EMBOSS_pKa

Lys_pKa <- EMBOSS_pKa[EMBOSS_pKa$AA == "K", ]
Lys_pKa$EMBOSS #This is Lysines pKa

hendersonHasselbalch(
  pKa = as.numeric(Lys_pKa$EMBOSS),
  pH = 7.0,
  residue = "K")

#residue = supports general properties as well
hendersonHasselbalch(
  pKa = as.numeric(Lys_pKa$EMBOSS),
  pH = 7.0,
  residue = "base")

hendersonHasselbalch(
  pKa = as.numeric(Lys_pKa$EMBOSS),
  pH = 7.0,
  residue = "positive")

#CALCULATIONS ARE DEPENDENT ON RESIDUE PROPERTY!
hendersonHasselbalch(
  pKa = as.numeric(Lys_pKa$EMBOSS),
  pH = 7.0,
  residue = "acid") #Inaccurate Description

#You can also calculate charge at different pHs
hendersonHasselbalch(
  pKa = as.numeric(Lys_pKa$EMBOSS),
  pH = 5.5,
  residue = "K")
hendersonHasselbalch(
  pKa = as.numeric(Lys_pKa$EMBOSS),
  pH = 8,
  residue = "K")

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