user manual - University of Athens Biophysics Laboratory
Contents
1. PLASMIC 9999 jaspi all pi H t A LS eR rege Po Ra poole arene G EXTRACELLULAR Additional sequence features namely signal peptides post translational modifications giycosylation sites and lipid bindings can be handled from the Tool Bar Ilustration 13 and whenever visible are marked with special symbols Illustration 14 By pressing the painter s right bution while the representation area is focused a pop up menu appears Illustration 19 Several appearance options may be configured using this E Show Residue Names Hide Residue Names C by Electastatie Potential by Hydrophobic Potential Background Color Annotation cyan TransMembrane Region Style gt 5 mne Anha value Red Yellow Green orange oe rack Maio 19 Semisespanded popup mena e Residue Names radio buttons switch toggle the visibility of the aminoacid type names along the peptide chain For example output shown in Illustration 18 demonstrates the Show Residue Names enabled The Coloring submenu carries the coloring options which may be applied to the peptide chain These are gt coloring by Electrostatic Potential according to the electrical charge assuming pH 7 by using blue far positive red for negative and gray for uncharged residues gt coloring by Hydrophobic Potential based on an ad hoc hydrophobicity scale Illus2. TMRPres2D High quality visual representation of transmembrane protein models Version 0 91 User s manual Ioannis C Spyropoulos Theodore D Liakopoulos Pantelis G Be wos J H Department of Cell Biology and Biophysics Faculty of Biology University of Athens miopolis Athens 157 01 Greece The Application Workspace The Application Workspace is divided into 3 prts usteation 1 The Menu Bar where the user can handle the basic iopulexport procedures The Too Bar where you can accomplish non disfiguring scaling of the image and adjust various appearance options The Representation Panel where the actual image resides and all user interaction takes place r a i The Menu Bar The Menu Bar is always visible and consists of three menus File Export About File menu The File menu provides various available methods of data input to the aplication The Input submenu includes 4 options corresponding ta different datasources SwissProt SwissProt entries may be loaded from the local disc Illustration 2 if available or pasted into the appropriate text area Illustration 4 Finally an entry can Illustration 3 ees fee Ee ARES ID seas momen so 11 3 30 04 6 39 PM Dartturnan sp 5 KB3 30 04 6 40 PU O ompa ecot sa 10 KB 3 30 04 6 39 PM Beene aie F ae ioraa 1 Wad for lading Setara or a a eal eT F
3. e button et oma same ea ee 2 Paste vour sone in plan et or FASTA forma ICEY UNCOMRRK VOCERO FOINA VCTICAONOCANE Ja PIGTESVARANSATFOELCRPICEFSRTHN TLNAP GVLAENPDNEAMILLTGLLT I CYEESAMYNKIFTONVNLCFMYSGFYKCSVENIETEEDECITSERLCINNOT KEG P OYGGIN PIGESGNISGART CAVC DOAT TOEVINPQIAPYGN LENA feee raneren cuta AA is Dber i segen ne ane Sequence ei Mirain 0 Tet Tora or gc deped poen egene ad tricrmcnlrane dares Consequently another input area should be activated Illustration 11 You may define the transmembrane segments by specifying their boundaries using the pull down menus provided named From and To A new segment should be added each time the Add new segment button is pressed You can remove the last segment by pressing the Remove segment button once For each transmembrane segment a number on the left colored blue serves as an index while a number on the right colored green shows its length TT D Define a name eptiorad 2 Paste your sequence in plain text oF FASTA format CCR INCAPERE SRETAN ONAT AAGA E PAF AALAN ALC VEF GARN PKTCSATLYSWVTYGE NARITE WALIS TEV AR ANSETE CRP ICEFSRTEMTLNAP CYLAENPDIFAVWULTCLLT GV KESAMYNKIFTCINVLVLGE MVS CPYKGSVKNNWQLTEEDFGNTSGRLCLNNDTKEG f CYSAAL TIMP TEC LONNSFLPDAEK HY GEGA TA AY CSUC ALSASLLCSMFPHPR PANARD CLLEKFLANVNORTKTPNAT UASC AVANMAFLOLKPLVOLNSIETLLAY l Ami ce Define tm segments i rr
4. f visualizing transmembrane segments that is as alpha helices or as beta strands The default style which is selected everytime a model is loaded is the helix style The Alpha value submenu adjusts the level of transparency of the depicted peptide chain High alpha values correspond to low transparency while Low alpha values correspond to high transparency By moving the pointer within the representation area while the pointers left button is pressed the user can move the image towards a desired direction
5. he TMHMM 20 web sever at Bip ww cbs diu dk services TMHMM Please note that the Extensive output form option should have has been selected Copy the results of TMHMM prediction meo rie E raa Sept fre or stg Re TIN pat ad ie aT apee Finally OR bnon han be peed PRED TMBB Results from the PRED TMBB prediction algorithm transmembrane topology predictions for bet barel outer membrane proteins can be used to feed the data input process with the required information llastation 9 A valid way to provide a PRED TMBB result would be to copy and paste the whole webpage containing a prediction as provided by the PRED TMBB server BE nip bioinformatics bil voa gr PRED TMBB Copy the results of PRED_TMBE prediction fA Hidden Markow Madel metho capabile of predicting ane discriminat Discrimination score Senuence scared avale of 2 894 whic The cifference beween the value and the threshold indicates the possi INamecme terti method E D en E Oe 122455789012345678901234567290123 156789012745578 0000 MKT AAAY ALAGFATVAQAAPKDNT INT GAKLC WSOYHL User defined Input may be provided by manually filling a special input form illustration 10 The procedure consists of the following steps You may optionally enter a name for the sequence The sequence required should be entered in the appropriate text area in plain text or FASTA format When finished you should press the Apply sequenc
6. le af plain et comaining the desired entry Hd davea p and pres the Open ato Siss Prot Entry from WER Copy ne Ewy arne UD or the Accession Nurnberiac cf ane SwissProt ertry ctr1_ human Cancel Beview entry Mera 9 Taps for Tar aea aede ae Fam Te vee IT re doa TD Acceso ner Taman of he ots the wer ean pe fr dad Rese entry Border tire ey int eter aeration d Copy one SwissProt entry FFT 30 ines are required D ONPALECOL STANDARD PRT 346 AA eg Jac Po2934 DT 71 Jul 2986 Rel 61 Creates DT 21 Jul 1986 Rel A1 Last sequence updats IoT 28 Mar 2004 Ral d3 Last amoradon update IDE Guer maribrane protein A precursor Cuter membrane protain I IGN OMPA OR TOLC OR TUT OR CON OR B0957 OR Z1307 ORECSL los Escherichia col and los Escherichia coli 0 157 H7 O Baneris Preteanacera Carraarateabactei Enerabarterale Se eT TH oe emer rao aps fort pase an Sata rat ey pao Ar pas The war tol pres he TOR huton 4 PIR PIR entries may only be fetched from the web Illustration 5 by providing the appropriate ID b PIR Entry rom WEB Copyrtne Entr Name 40 of one PIR emv rato 9 Taps for far dodo 2 PIR emirs am te NED Aper prove he 183005 the entry th ser con prees YOR fr doverla MR or PRED TMR2 prediction algorithms can be used to provide the application with the required information Ulustration 6 A valid way to provide a PRED TMR or PRED TMR2
7. ndly button several appearance parameters should be modified gt the background color is set to white gt the color of the transmembrane segment boundary indexes is set to black 2 the color of the peptide chain is set to back With these changes you can produce an image capable to be printed exactly as it appears on the sereen When the button is unpressed the old appearance options and colors are restored m gt Msration 14 Symbols Jor aditional Seumee data 3 Greom lation te Lipid iads Pat iranslanional modreation 8 K i representing adie tand borcen nun Hecho i A i There is a polymorphism which replaces a small sized residue A with a medium sized residue V pray Mhsration 16 Thic text bax contains am annotation Jar a residue Phe direction of he at haz the above example lef Each of the toggle buttons mentioned above may appear in one of 3 potential states illustration 17 Unselected Selected Disabled whenever the corresponding feature is not present in the input data Sona ie eee ee ee Unicoi Selected and Disable repose The Representation Panel The Representation Panel should become visible afler a protein has been loaded It contains the actual image The panel may hold several panes each one containing an image model You may switch between models by selecting the corresponding tab lustratio 18 SEER AON ERA STH ATR OREO cyTO
8. om 36 0 tesz v e gt momar to 82 L gt From 103 0 Yer 123m w From 247 To 267 Add new segment Remove segmen rrr Sequence tengin 629 Maraon 11 apa for for flag acd rote segues along wi a enamine our resting the Clear hutan all input elde are reret By pring he OK ato he rove doa Vl be tuned Export menu The Expo menu provides the option of saving an imagelmodel of a protein using several vector based formats namely Encapsuleated PostScript eps PostScript ps Portable Document Format pdf and Scalable Vector Graphies svg Alternatively pictures may be exported using the popular bitmap image formats JPEG and PNG llustration 12 This option is enabled only when an image is available enean Browse Encapsulated PostScript ep eni enst eps0 onions mi Protograpners Exper Croup Format 1P Joes Portable Document Format pab Portable Network Graphis Format Gpng PNG rassom eos RAW image craw alahle Vector Graphics sv svab Martian 12 The expor window from the ErecHEP Jeva Library From here ome may let he erable format and name of th output fle ar xet same ade opin About menu The Abou menu contains information about the authors and copyright of the application The Tool Bar The Tool Bar should appears after a protein has been loaded Illustration 13 It consists ofthe following element
9. result would be to copy and paste the whole webpage containing the output as provided by the respective web Servers available at bitpuibiophvsics bioLuongePRED TMR and nip biophysics biol wa ee PRED TMIRD Copy the results of PRED_TMR prediction PRED TME Prediction or Transmerrbrane renons m proeime ISecuence CTR HUMAN S S 2 4 5 E 12345678901234567890134567890 1234567890123456781 a 0000 MGEKYLLNIGQQM LARV rae 0 Inpa ort pante Te PRED THE out Falls OK Pato as proved HMMTOP Results from the HMMTOP prediction algorithm can be used to feed the data input process with the required information llstation 7 A valid way to provide an HMMTOP result would be to copy and paste the whole webpage containing the output as provided by the HMMTOP 2 web sever at nip ww enzim huhmmtop index html Copy the results of HMMTOP prediction seq FGYGLWHSEE ASLDADOART PDCNIDACK 628 bred HAP i Mn Iryou are going to use these resis In your work please ce CETusrayand Simon 1986 Mol lol 283 489 505 CE Tusn cy and Simon C001 Bioinformatics 17 843 850 Marae Tepe forn for petan he DAT TOP output Finally OR Paton st be prenre TMHMM Results from the TMHMM prediction algorithm can be used to fed the data input process with the required information Illustation 8 A valid way to provide a TMHMM result would be to copy and paste the whole webpage containing the output as provided by t
10. s eee E eer cn esraion 3The ToolBar consists o several gle ations and sie tht co the appearance of the op Seale slider When you move the knob to the right the sealing factor is increased and when you move it to the left the scaling factor is reduced Signal Peptide toggle button If signal peptide data are available the Signal Peptide toggle button appears enabled When the button is activated the signal peptide of the protein appears as a magents colored chain Post translational modifications toggle button When you activate this button special symbols lustration 14 should appear under residues for which post translational modification data are available Glyeasylation sites toggle button When you activate this button glycosylation symbols Illustration 14 should appear above residues for which glycosylation data are available ig of lipid moiety toggle button When this button i activated lipid binding symbols Illustration 14 should appear at known lipid binding residues in the chain Disulfide bonds toggle button When you activate this button a bridge Ilustration 15 would appear between any two residues known to be connected with a disulfide bond Annotation toggle button When you activate this button any defined annotation labels Illustration 16 should become visible Printer Friendly toggle button When you activate the Printer Frie
11. tration 20 by using a gradation from yellow to blue gt applying a uniform user defined color on the protein chain sree 20 Coloring Py rope potential The hydrophobicity values assumed for the 20 aminoacid residue types are listed below Aminoseld Hydrophobicity value Phenylalanine F oxo Isoleucine D ona Leucine L 0612 Tryptophan W ossz Valine V 0363 Methionine M 0407 Alanine A oaz Cysteine C oasa Glycine ou Tyrosine V 0073 Threonine T 019 Serine S 0216 Proline P 0316 isin 0 0930 Asparagine N asu Glutamine Q 1300 Asari acid D asn Glutamic acid E 2083 Arginine R 2088 Lysine an The Background Color submenu opens a window to choose the background color iustation 21 Tosa 1 Wind se a color fore bacaran The Annotation submenu opens the annotation input form Illustration 22 from which residue annotations can be added The desired residue can be selected from the pull down list The selection of any residue leads to the appearence of the annotaton s message Gf available in the text area Four radio buttons declare the direction of the bows depiction Ilastration 16 Any modifications are applied when the Submit button is pressed coeeee sine a Frere 1 a pomerans veneer TA ee on S upoerten types is Maren 15 Mr eonig Dr da For ng The TransMembrane Region Style submenu toggles between two styles o
Download Pdf Manuals
Related Search