octanol

Function

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

Command line arguments


Input file format

octanol reads any protein sequence USA.

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.

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.

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.

Author(s)

History

Target users

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