Bioinformatics Toolbox

isoelectric

Estimate isoelectric point for amino acid sequence

Syntax

pI = isoelectric(SeqAA,)
                 'PropertyName', PropertyValue...)
[pI Charge] = isoelectric(SeqAA)

isoelectric(..., 'PKVals', PKValsValue)
isoelectric(..., 'Charge', ChargeValue)
isoelectric(..., 'Chart', ChartValue)

Arguments

`SeqAA`	Amino acid sequence. Enter a character string or a vector of integers from the table . Examples: `'ARN'` or `[1 2 3]`.
`PKVals`	Property to provide alternative pK values.
`Charge`	Property to select a specific pH for estimating charge. Enter a number between `0` and `14`. The default value is `7.2`.
`Chart`	Property to control plotting a graph of charge versus pH. Enter `true` or `false`.

Description

isoelectric estimates the isoelectric point (the pH at which the protein has a net charge of zero) for an amino acid sequence and it estimates the charge for a given pH (default is pH 7.2). The estimates skewed by the underlying assumptions that all amino acids are fully exposed to the solvent, that neighboring peptides have no influence on the pK of any given amino acid, and that the constitutive amino acids, as well as the N- and C-termini, are unmodified. Cysteine residues participating in disulfide bridges also affect the true pI and are not considered here. By default, isoelectric uses the EMBOSS amino acid pK table, or you can substitute other values using the property PKVals.

If the sequence contains ambiguous amino acid characters (b z * –), isoelectric ignores the characters and displays a warning message.
```
Warning: Symbols other than the standard 20 amino acids 
appear in the sequence.
```
If the sequence contains undefined amino acid characters (i j o) , isoelectric ignores the characters and displays a warning message.
```
Warning: Sequence contains unknown characters. These will
be ignored.
```

pI = isoelectric(Seq_AA, 'PropertyName', PropertyValue...) returns the isoelectric constant (pI) for an amino acid sequence.

isoelectric(..., 'PKVals', PKValsValue) uses the alternative pK table stored in the text file PKValValues. For an example of a pK text file, see the file Emboss.pK.

N_term 8.6
K 10.8
R 12.5
H 6.5
D 3.9
E 4.1
C 8.5
Y 10.1
C_term 3.6

isoelectric(..., 'Charge', ChargeValue) returns the estimated charge of a sequence for a given pH (ChargeValue).

isoelectric(..., 'Chart', ChartValue) when Chart is true, returns a graph plotting the charge of the protein versus the pH of the solvent.

Example

% Get a sequence from PDB and estimate the isoelectric point.
pdbSeq = getpdb('1CIV', 'SequenceOnly', true)
% then estimate its isoelectric point
isoelectric(pdbSeq)

% plot the charge against the pH for a short polypeptide sequence
isoelectric('PQGGGGWGQPHGGGWGQPHGGGGWGQGGSHSQG', 'CHART', true)

% Get the Rh blood group D antigen from NCBI and calculates
% its charge at pH 7.3 (typical blood pH)
gpSeq = getgenpept('AAB39602')
[pI Charge] = isoelectric(gpSeq, 'Charge', 7.38)

isoelectric

Syntax

Arguments

Description

Example

See Also