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EMBOSS: octanol |
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.
% octanol Input sequence: sw:opsd_human Graph type [x11]:Click here to see the results.
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) |
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.
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:
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 |