hendersonHasselbalch {idpr} | R Documentation

## Henderson-Hasselbalch Equation

### 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")

[Package idpr version 1.2.0 Index]