EMBOSS: octanol

| octanol

## Function

Draw a White-Wimley protein hydropathy plot

## Description

octanol draws a hydropathy plot for an input protein sequence. This plots the free energy difference calculated for windows over the protein sequence, of the residues in water compared to two lipid environments: i. Octanol (equivalent to inside a lipid bilayer). ii. The interface of a synthetic lipid bilayer. Free energy differences are calculated for each position in a window of 19 residues by default, about the size of a membrane spanning alpha-helix. The energy values for each residue are summed to get two values for each window. By default, the value plotted is the free energy difference between the interface and octanol environments, which is the best indicator of the location of probable transmembrane regions. Command line options allow the display of the octanol and interface values, or hiding the difference values. The experimental free energy values for the water-interface and water-octanol transitions are read from a datafile (`Ewhite-wimley.dat`)

## Usage

Here is a sample session with octanol

    % octanol
    Draw a White-Wimley protein hydropathy plot
    Input protein sequence: tsw:opsd_human
    Graph type [x11]: ps

    Created octanol.ps

Go to the input files for this example
Go to the output files for this example

## Command line arguments

       Standard (Mandatory) qualifiers:
      [-sequence]          sequence   Protein sequence filename and optional
                                      format, or reference (input USA)
      [-graph]             xygraph    [$EMBOSS_GRAPHICS value, or x11] Graph type
                                      (ps, hpgl, hp7470, hp7580, meta, cps, x11,
                                      tekt, tek, none, data, xterm, png, gif)

       Additional (Optional) qualifiers:
       -datafile           datafile   [Ewhite-wimley.dat] White-Wimley data file
       -width              integer    [19] Window size (Integer from 1 to 200)
       -octanolplot        boolean    [N] Display the octanol plot
       -interfaceplot      boolean    [N] Display the interface plot
       -[no]differenceplot boolean    [Y] Display the difference plot

       Advanced (Unprompted) qualifiers: (none)
       Associated qualifiers:

       "-sequence" associated qualifiers
       -sbegin1            integer    Start of the sequence to be used
       -send1              integer    End of the sequence to be used
       -sreverse1          boolean    Reverse (if DNA)
       -sask1              boolean    Ask for begin/end/reverse
       -snucleotide1       boolean    Sequence is nucleotide
       -sprotein1          boolean    Sequence is protein
       -slower1            boolean    Make lower case
       -supper1            boolean    Make upper case
       -sformat1           string     Input sequence format
       -sdbname1           string     Database name
       -sid1               string     Entryname
       -ufo1               string     UFO features
       -fformat1           string     Features format
       -fopenfile1         string     Features file name

       "-graph" associated qualifiers
       -gprompt2           boolean    Graph prompting
       -gdesc2             string     Graph description
       -gtitle2            string     Graph title
       -gsubtitle2         string     Graph subtitle
       -gxtitle2           string     Graph x axis title
       -gytitle2           string     Graph y axis title
       -goutfile2          string     Output file for non interactive displays
       -gdirectory2        string     Output directory

       General qualifiers:
       -auto               boolean    Turn off prompts
       -stdout             boolean    Write first file to standard output
       -filter             boolean    Read first file from standard input, write
                                      first file to standard output
       -options            boolean    Prompt for standard and additional values
       -debug              boolean    Write debug output to program.dbg
       -verbose            boolean    Report some/full command line options
       -help               boolean    Report command line options. More
                                      information on associated and general
                                      qualifiers can be found with -help -verbose
       -warning            boolean    Report warnings
       -error              boolean    Report errors
       -fatal              boolean    Report fatal errors
       -die                boolean    Report dying program messages

Standard (Mandatory) qualifiers | Allowed values | Default
--- | --- | ---
[-sequence] (Parameter 1) | Protein sequence filename and optional format, or reference (input USA) | Readable sequence | Required
[-graph] (Parameter 2) | Graph type | EMBOSS has a list of known devices, including ps, hpgl, hp7470, hp7580, meta, cps, x11, tekt, tek, none, data, xterm, png, gif | EMBOSS_GRAPHICS value, or x11
Additional (Optional) qualifiers | Allowed values | Default
-datafile | White-Wimley data file | Data file | Ewhite-wimley.dat
-width | Window size | Integer from 1 to 200 | 19
-octanolplot | Display the octanol plot | Boolean value Yes/No | No
-interfaceplot | Display the interface plot | Boolean value Yes/No | No
-[no]differenceplot | Display the difference plot | Boolean value Yes/No | Yes
Advanced (Unprompted) qualifiers | Allowed values | Default
(none)

## Input file format

octanol reads any protein sequence USA.

### Input files for usage example

'tsw:opsd_human' is a sequence entry in the example protein database 'tsw'

### Database entry: tsw:opsd_human

    ID   OPSD_HUMAN              Reviewed;         348 AA.
    AC   P08100; Q16414; Q2M249;
    DT   01-AUG-1988, integrated into UniProtKB/Swiss-Prot.
    DT   01-AUG-1988, sequence version 1.
    DT   20-MAR-2007, entry version 91.
    DE   Rhodopsin (Opsin-2).
    GN   Name=RHO; Synonyms=OPN2;
    OS   Homo sapiens (Human).
    OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
    OC   Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
    OC   Catarrhini; Hominidae; Homo.
    OX   NCBI_TaxID=9606;
    RN   [1]
    RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    RX   MEDLINE=84272729; PubMed=6589631;
    RA   Nathans J., Hogness D.S.;
    RT   "Isolation and nucleotide sequence of the gene encoding human
    RT   rhodopsin.";
    RL   Proc. Natl. Acad. Sci. U.S.A. 81:4851-4855(1984).
    RN   [2]
    RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    RA   Suwa M., Sato T., Okouchi I., Arita M., Futami K., Matsumoto S.,
    RA   Tsutsumi S., Aburatani H., Asai K., Akiyama Y.;
    RT   "Genome-wide discovery and analysis of human seven transmembrane helix
    RT   receptor genes.";
    RL   Submitted (JUL-2001) to the EMBL/GenBank/DDBJ databases.
    RN   [3]
    RP   NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    RC   TISSUE=Retina;
    RG   The German cDNA consortium;
    RL   Submitted (JUN-2003) to the EMBL/GenBank/DDBJ databases.
    RN   [4]
    RP   NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    RX   PubMed=15489334; DOI=10.1101/gr.2596504;
    RG   The MGC Project Team;
    RT   "The status, quality, and expansion of the NIH full-length cDNA
    RT   project: the Mammalian Gene Collection (MGC).";
    RL   Genome Res. 14:2121-2127(2004).
    RN   [5]
    RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-120.
    RX   PubMed=8566799; DOI=10.1016/0378-1119(95)00688-5;
    RA   Bennett J., Beller B., Sun D., Kariko K.;
    RT   "Sequence analysis of the 5.34-kb 5' flanking region of the human
    RT   rhodopsin-encoding gene.";
    RL   Gene 167:317-320(1995).
    RN   [6]
    RP   REVIEW ON RP4 VARIANTS.
    RX   MEDLINE=94004905; PubMed=8401533;
    RA   Al-Maghtheh M., Gregory C., Inglehearn C., Hardcastle A.,
    RA   Bhattacharya S.;

      [Part of this file has been deleted for brevity]

    FT                                /FTId=VAR_004816.
    FT   VARIANT     209    209       V -> M (effect not known).
    FT                                /FTId=VAR_004817.
    FT   VARIANT     211    211       H -> P (in RP4).
    FT                                /FTId=VAR_004818.
    FT   VARIANT     211    211       H -> R (in RP4).
    FT                                /FTId=VAR_004819.
    FT   VARIANT     216    216       M -> K (in RP4).
    FT                                /FTId=VAR_004820.
    FT   VARIANT     220    220       F -> C (in RP4).
    FT                                /FTId=VAR_004821.
    FT   VARIANT     222    222       C -> R (in RP4).
    FT                                /FTId=VAR_004822.
    FT   VARIANT     255    255       Missing (in RP4).
    FT                                /FTId=VAR_004823.
    FT   VARIANT     264    264       Missing (in RP4).
    FT                                /FTId=VAR_004824.
    FT   VARIANT     267    267       P -> L (in RP4).
    FT                                /FTId=VAR_004825.
    FT   VARIANT     267    267       P -> R (in RP4).
    FT                                /FTId=VAR_004826.
    FT   VARIANT     292    292       A -> E (in CSNBAD1).
    FT                                /FTId=VAR_004827.
    FT   VARIANT     296    296       K -> E (in RP4).
    FT                                /FTId=VAR_004828.
    FT   VARIANT     297    297       S -> R (in RP4).
    FT                                /FTId=VAR_004829.
    FT   VARIANT     342    342       T -> M (in RP4).
    FT                                /FTId=VAR_004830.
    FT   VARIANT     345    345       V -> L (in RP4).
    FT                                /FTId=VAR_004831.
    FT   VARIANT     345    345       V -> M (in RP4).
    FT                                /FTId=VAR_004832.
    FT   VARIANT     347    347       P -> A (in RP4).
    FT                                /FTId=VAR_004833.
    FT   VARIANT     347    347       P -> L (in RP4; common variant).
    FT                                /FTId=VAR_004834.
    FT   VARIANT     347    347       P -> Q (in RP4).
    FT                                /FTId=VAR_004835.
    FT   VARIANT     347    347       P -> R (in RP4).
    FT                                /FTId=VAR_004836.
    FT   VARIANT     347    347       P -> S (in RP4).
    FT                                /FTId=VAR_004837.
    SQ   SEQUENCE   348 AA;  38893 MW;  6F4F6FCBA34265B2 CRC64;
         MNGTEGPNFY VPFSNATGVV RSPFEYPQYY LAEPWQFSML AAYMFLLIVL GFPINFLTLY
         VTVQHKKLRT PLNYILLNLA VADLFMVLGG FTSTLYTSLH GYFVFGPTGC NLEGFFATLG
         GEIALWSLVV LAIERYVVVC KPMSNFRFGE NHAIMGVAFT WVMALACAAP PLAGWSRYIP
         EGLQCSCGID YYTLKPEVNN ESFVIYMFVV HFTIPMIIIF FCYGQLVFTV KEAAAQQQES
         ATTQKAEKEV TRMVIIMVIA FLICWVPYAS VAFYIFTHQG SNFGPIFMTI PAFFAKSAAI
         YNPVIYIMMN KQFRNCMLTT ICCGKNPLGD DEASATVSKT ETSQVAPA
    //

## Output file format

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

### Output files for usage example

### Graphics File: octanol.ps

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.

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

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).

For each amino acid residue in the protein, the free energy difference of the residue in lipid and water environments is measured in two ways. The first is the free energy difference between the protein in water and the protein associated with the interface (glycerol group) of a POPC (palmitoyloleoylphosphocholine) bilayer. The second is the free energy difference of the protein in water and the protein in 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 probable 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.

## 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
--- | ---
backtranambig | Back-translate a protein sequence to ambiguous nucleotide sequence
backtranseq | Back-translate a protein sequence to a nucleotide sequence
charge | Draw a protein charge plot
checktrans | Reports STOP codons and ORF statistics of a protein
compseq | Calculate the composition of unique words in sequences
emowse | Search protein sequences by digest fragment molecular weight
freak | Generate residue/base frequency table or plot
iep | Calculate the isoelectric point of proteins
mwcontam | Find weights common to multiple molecular weights files
mwfilter | Filter noisy data from molecular weights file
pepinfo | Plot amino acid properties of a protein sequence in parallel
pepstats | Calculates statistics of protein properties
pepwindow | Draw a Kyte-Doolittle hydropathy plot for a protein sequence
pepwindowall | Draw Kyte-Doolittle hydropathy plot for a protein alignment
wordcount | Count and extract unique words in DNA sequence(s)

## Author(s)

Ian Longden (il © sanger.ac.uk)
Sanger Institute, 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

None