EMBOSS: iep


Program iep

Function

Calculates the isoelectric point of a protein

Description

This calculates the isoelectric point of a protein from its amino acid composition assuming that no electrostatic interactions change the propensity for ionization.

Adjusting the pH of an aqueous protein solution to the point where the numbers of positive and negative charges on the protein are equal brings the protein to its isoelectric point. This is often the point of lowest solubility, presumably because it is the point at which there are fewest intermolecular repulsions, so that the molecules tend to form aggregates.

The application can make a plot of the ionization curve with respect to pH and can write an output file of the data.

Usage

Here is a sample session with iep.

% iep sw:laci_ecoli
Output file [laci_ecoli.iep]:

Command line arguments

   Mandatory qualifiers (* if not always prompted):
  [-sequencea]         seqall     Sequence database USA
*  -graph              xygraph    Graph type
*  -outfile            outfile    Output file name

   Optional qualifiers: (none)
   Advanced qualifiers:
   -plot               bool       Plot charge vs pH
   -[no]report         bool       Write results to a file
   -step               float      pH step value
   -amino              integer    Number of N-termini
   -[no]termini        bool       Include charge at N and C terminus

   General qualifiers:
  -help                bool       report command line options. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose


Mandatory qualifiers Allowed values Default
[-sequencea]
(Parameter 1)
Sequence database USA Readable sequence(s) Required
-graph Graph type EMBOSS has a list of known devices, including postscript, ps, hpgl, hp7470, hp7580, meta, colourps, cps, xwindows, x11, tektronics, tekt, tek4107t, tek, none, null, text, data, xterm, png EMBOSS_GRAPHICS value, or x11
-outfile Output file name Output file <sequence>.iep
Optional qualifiers Allowed values Default
(none)
Advanced qualifiers Allowed values Default
-plot Plot charge vs pH Yes/No No
-[no]report Write results to a file Yes/No Yes
-step pH step value Number from 0.010 to 1.000 .5
-amino Number of N-termini Any integer value 1
-[no]termini Include charge at N and C terminus Yes/No Yes

Input file format

Any protein sequence USA.

Output file format

This is the output file from the example:
For each pH point it gives the number of bound electrons and the charge.


IEP of LACI_ECOLI from 1 to 360
Isoelectric Point = 6.8820

   pH     Bound    Charge
  1.00    81.96    37.96
  1.50    81.89    37.89
  2.00    81.65    37.65
  2.50    80.91    36.91
  3.00    78.79    34.79
  3.50    73.70    29.70
  4.00    65.15    21.15
  4.50    56.73    12.73
  5.00    51.75     7.75
  5.50    49.36     5.36
  6.00    47.63     3.63
  6.50    45.56     1.56
  7.00    43.59    -0.41
  7.50    42.27    -1.73
  8.00    41.22    -2.78
  8.50    39.87    -4.13
  9.00    38.26    -5.74
  9.50    36.24    -7.76
 10.00    33.03   -10.97
 10.50    28.46   -15.54
 11.00    23.58   -20.42
 11.50    19.41   -24.59
 12.00    15.19   -28.81
 12.50     9.75   -34.25
 13.00     4.64   -39.36
 13.50     1.75   -42.25
 14.00     0.59   -43.41

Data files

None.

Notes

None.

References

None.

Warnings

None.

Diagnostic Error Messages

None.

Exit status

0 if successfull.

Known bugs

None.

See also

Program nameDescription
backtranseqBack translate a protein sequence
chargeProtein charge plot
checktransReports STOP codons and ORF statistics of a protein sequence
compseqCounts the composition of dimer/trimer/etc words in a sequence
emowseProtein identification by mass spectrometry
mwfilterFilter noisy molwts from mass spec output
octanolDisplays protein hydropathy
pepinfoPlots simple amino acid properties in parallel
pepstatsProtein statistics
pepwindowDisplays protein hydropathy
pepwindowallDisplays protein hydropathy of a set of sequences

Author(s)

This application was written by Alan Bleasby (ableasby@hgmp.mrc.ac.uk)

History

Completed 1st August 1999.

Target users

This program is intended to be used by everyone and everything, from naive users to embedded scripts.

Comments