isoelectric

Estimate isoelectric point for amino acid sequence

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    Syntax

    pI = isoelectric(SeqAA)
    [pI,ChargePH] = isoelectric(SeqAA)
    ___ = isoelectric(___,Name=Value)

    Description

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

    • Nterm = 8.6

    • K = 10.8

    • R = 12.5

    • H = 6.5

    • D = 3.9

    • E = 4.1

    • C = 8.5

    • Y = 10.1

    • Cterm = 3.6

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

    [pI,ChargePH] = 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(___,Name=Value) specifies additional options using one or more name-value arguments. Use any arguments from the previous syntaxes.

    example

    Examples

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    Open Live Script

    Calculate the isoelectric point using the pK values stored in a PK file and plot the charge against the pH for a short sequence. 

    isoelectric("PQGGGGWGQPHGGGWGQPHGGGGWGQGGSHSQG", ...
            PKVals="Emboss.pK",CHART=true)

    Figure contains an axes object. The axes object with xlabel pH, ylabel Net Charge contains 144 objects of type line, text.

    ans = 
7.8109

    Estimate its charge at a specific pH.

    [pI,ChargePH] = ...
    isoelectric("PQGGGGWGQPHGGGWGQPHGGGGWGQGGSHSQG",Charge=7.3)
    pI = 
7.8109

    ChargePH = 
0.3629

    Input Arguments

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    Amino acid sequence, specified as a character vector, string, or a vector of integers from the table Mapping Amino Acid Letter Codes to Integers.

    Example: "ARN"

    Example: [1 2 3]

    Data Types: char | string | double

    Name-Value Arguments

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    Specify optional pairs of arguments as Name1=Value1,...,NameN=ValueN, where Name is the argument name and Value is the corresponding value. Name-value arguments must appear after other arguments, but the order of the pairs does not matter.

    Example: isoelectric("PQGGGGWGQPHGGGWGQPHGGGGWGQGGSHSQG",PKVals="Emboss.pK",CHART=true)

    PK file name or path and file name, specified as a character vector or a string. PK file contains 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 window.

    Data Types: char | string

    Specific pH for estimating charge, specified as a number between 0 and 14.

    Data Types: double

    Control for plotting a graph of charge versus pH, specified as true or false. Set this value to true to return a graph plotting the charge of the protein versus the pH of the solvent.

    Data Types: logical

    Output Arguments

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    Estimated isoelectric point for an amino acid sequence, returned as number.

    Estimated charge for a given pH, returned as number between 0 and 14.

    Version History

    Introduced in R2006a

    See Also

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