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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 Displays protein hydropathy 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
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 standard output
-filter boolean Read standard input, write 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
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| 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) | |||
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
//
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![[octanol results]](octanol.1.octanol.gif)
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.
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 |
|---|---|
| backtranambig | Back translate a protein sequence to ambiguous codons |
| backtranseq | Back translate a protein sequence |
| charge | Protein charge plot |
| checktrans | Reports STOP codons and ORF statistics of a protein |
| compseq | Count 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 |
| mwcontam | Shows molwts that match across a set of files |
| 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 |