EMBOSS: octanol

| ## EMBOSS: octanol

# Program octanol

## Function

Displays protein hydropathy

## Description

Protein sequences that form transmembrane regions are assumed to have a thermodynamic preference for a hydrophobic environment (inside the membrane lipid bilayer), rather than an aqueous environment in water.

The free energy change for each amino acid residue between a lipid and a water environment can be measured experimentally, and the values for peptides can be shown to be additive (White and Wimley 1999).

The octanol program calculates two free energy differences.

The first is the free energy difference between solution in water and association with the interface (glycerol group) of a POPC (palmitoyloleoylphosphocholine) bilayer.

The second is the free energy difference between water and octanol, equivalent to the environment inside a lipid bilayer.

Residues which can be buried inside a lipid bilayer must be in a region of the peptide where most residues show a free energy difference in favour of being in an octanol environment or at least being in the lipid/water interface region.

White and Wimley (1999) showed that a sliding window of either free energy difference will indicate the location of probably transmembrane regions, but that the best indicator is the difference between the two values, which is the free energy difference between the interface and octanol environments.

The free energies are calculated over a sliding window of 19 residues, about the size of a membrane spanning alphahelix. The energy values for each residue are added over the window.

## Usage

Here is a sample session with octanol.

    % octanol
    Input sequence: sw:opsd_human
    Graph type [x11]:

Click here to see the results.

## Command line arguments

       Mandatory qualifiers:
      [-sequencea]         sequence   Sequence USA
      [-graph]             xygraph    Graph type

       Optional qualifiers:
       -datafile           datafile   White-Wimley data file (Ewhite-wimley.dat)
       -width              integer    window size
       -octanolplot        bool       Display the octanol plot
       -interfaceplot      bool       Display the interface plot
       -[no]differenceplot bool       Display the difference plot

       Advanced qualifiers: (none)
       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 USA | Readable sequence | Required
[-graph] (Parameter 2) | 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
Optional qualifiers | Allowed values | Default
-datafile | White-Wimley data file (Ewhite-wimley.dat) | Data file | Ewhite-wimley.dat
-width | window size | Integer from 1 to 200 | 19
-octanolplot | Display the octanol plot | Yes/No | No
-interfaceplot | Display the interface plot | Yes/No | No
-[no]differenceplot | Display the difference plot | Yes/No | Yes
Advanced qualifiers | Allowed values | Default
(none)

## Input file format

Any protein sequence.

## Output file format

octanol draws a graph showing the free energy calcuated over a sliding window.

The line on the default plot is the difference between the interface and octanol free energy calculations. Command line options allow the display of the interface and octanol values, or hiding the difference values.

In the example, the human opsin protein has 7 transmembrane regions: 37-61, 74-98, 114-133, 153-176, 203-230, 253-276 and 285-309. Each is about 20 residues in length, which is also the gap between tick marks on the sequence axis. All have energetic preferences for being in the lipid (octanol) enviroment - shown as being above the zero line - or have at least no clear preference.

Running octanol with all three plots:

    % octanol -interface -octanol
    Input sequence: tsw:opsd_human
       Graph type [x11]:

gives a graph with the water-interface and water-octanol plots (link to the output). For those regions where the diference plot is close to zero, both the other two plots are above the line, showing a preference for either the octanol or the interface membrane environments rather than water.

## Data files

File Ewhite-wimley.dat contains the experimental free energy values for the water-interface and water-octanol transitions.

EMBOSS data files are distributed with the application and stored in the standard EMBOSS data directory, which is defined by the EMBOSS environment variable EMBOSS_DATA.

To see the available EMBOSS data files, run:

    % embossdata -showall

To fetch one of the data files (for example 'Exxx.dat') into your current directory for you to inspect or modify, run:

    % embossdata -fetch -file Exxx.dat

Users can provide their own data files in their own directories. Project specific files can be put in the current directory, or for tidier directory listings in a subdirectory called ".embossdata". Files for all EMBOSS runs can be put in the user's home directory, or again in a subdirectory called ".embossdata".

The directories are searched in the following order:

- . (your current directory)
- .embossdata (under your current directory)
- ~/ (your home directory)
- ~/.embossdata

## Notes

None.

## References

1. White S.H. and Wimley W.C. (1999) "Membrane protein folding and stability: physical principles" Ann. Rev.Biophys. Biomol. Struct. 28:319-365.

## Warnings

None.

## Diagnostic Error Messages

None.

## Exit status

It always exits with status 0.

## Known bugs

None.

## See also

Program name | Description
--- | ---
backtranseq | Back translate a protein sequence
charge | Protein charge plot
checktrans | Reports STOP codons and ORF statistics of a protein sequence
compseq | Counts the composition of dimer/trimer/etc words in a sequence
emowse | Protein identification by mass spectrometry
freak | Residue/base frequency table or plot
iep | Calculates the isoelectric point of a protein
mwfilter | Filter noisy molwts from mass spec output
pepinfo | Plots simple amino acid properties in parallel
pepstats | Protein statistics
pepwindow | Displays protein hydropathy
pepwindowall | Displays protein hydropathy of a set of sequences

## Author(s)

This application was written by Ian Longden (il@sanger.ac.uk) Informatics Division, The Sanger Centre, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.

## History

## Target users

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

## Comments