isoelectric

Estimate isoelectric point for amino acid sequence

Syntax

pI = isoelectric(SeqAA)
[pI Charge] = isoelectric(SeqAA)

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

Arguments

SeqAAAmino acid sequence. Enter a character string or a vector of integers from the table Mapping Amino Acid Letter Codes to Integers. Examples: 'ARN' or [1 2 3].
PKValsValueString specifying a file name or path and file name of a PK file containing a table of pK values for amino acids, which .isoelectric uses to estimate the isoelectric point (pI) of an amino acid sequence. For an example of a PK file format, type edit Emboss.pK in the MATLAB® command line.
ChargeValueProperty to select a specific pH for estimating charge. Enter a number between 0 and 14. Default is 7.2.
ChartValueControls the plotting a graph of charge versus pH. Enter true or false.

Description

pI = isoelectric(SeqAA) returns the estimated isoelectric point (pI) for an amino acid sequence using the following pK values:

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

The isoelectric point is the pH at which the protein has a net charge of zero.

[pI Charge] = isoelectric(SeqAA) returns the estimated isoelectric point (pI) for an amino acid sequence and the estimated charge for a given pH (default is typical intracellular pH 7.2).

The estimates are 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.


isoelectric(..., 'PropertyName', PropertyValue,...)
defines optional properties using property name/value pairs.

isoelectric(..., 'PKVals', PKValsValue) uses pK values stored in a PKValValues, a PK file, to estimate the isoelectric point (pI) of an amino acid sequence. For an example of a PK file format, type edit Emboss.pK in the MATLAB command line.

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

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

Examples

% Get a sequence from PDB.
pdbSeq = getpdb('1CIV', 'SequenceOnly', true)
% 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 calculate
% its charge at pH 7.3 (typical blood pH).
gpSeq = getgenpept('AAB39602')
[pI Charge] = isoelectric(gpSeq, 'Charge', 7.38)

See Also

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