Protein Visualization 1 Bioinformatics Lab 7: Protein Visualization The primary objectives are: Learn how to search and use

use the PDB and Entrez structure databases !nderstand PDB entry and structure analysis tools Learn how to view and manipulate protein structures usin" #n$D and the %wiss PDB

To start the lab &'ll demonstrate the use o( the %wiss PDB structure viewer 1. View the structure o( 1)*# (rom the PDB database %wiss PDB viewer +ou should see a ,dou"hnut, molecule #lic-in" on the view pane while holdin" down the '#trl' -ey brin"s up command menus E.plore the viewin" options/ color options/ etc 0otice that (irst you need to select a portion o( the structure/ then pic- a command to chan"e the display o( the selected item The startin" ima"e is a 'cartoon' view #olor the molecule by secondary structure/ ma-e the water visible/ rotate so the ,hole, is obvious/ and ta-e a ,picture, P)%TE 1E2E 2. a. 3easure the appro.imate size o( this multi4protein comple. 5ive (i"ures (or the lon"est dimension 6across the hole7 and thic-ness 6ed"e on so the hole is not visible7 b. 0ow e.amine the size o( the hole 3easure the appro.imate distance across the ,hole, 5ive the distance between the atoms that you measured c. &s this ,hole, appro.imately lar"e enou"h (or a D0) molecule8 6%tructure 1D1$ lin-ed above shows D0) 7 5ive a brie( answer

d. & would li-e you to thin- in a very physical way about biolo"ical problems )ssume that somehow/ you have to "et this ,clamp, around the very middle o( a very lon" D0) molecule Propose two alternate ways that one could "o (rom havin" the ,clamp, and the ,D0) thread, separate to havin" the clamp around the middle o( the thread e. 1ow many protein chains ma-e up this structure8 3. %earch (or structure 1D#9 in PDB a. View the pdb structure (ile 6the lin- near the structure &D7 :hat protein is this8 b. :hat is the resolution o( the structure8 c. :hat atoms or molecules other than standard amino acids in the polypeptide chain does this structure contain8 d. View the 2amachandran plot (or this protein 6PDB le(t hand side lin- to 5eometry 4; 3olProbity 2amachandran Plot7 E.cludin" "lycine/ proline/ and pre4proline/ which amino acid6s7 is in the disallowed re"ion8

Protein Visualization < Bioinformatics e. Try to trace the chain (rom 04terminus to #4terminus 1ow many helices does this molecule contain by your count8 )ccordin" to the annotation in the pdb (ile/ how many helices are present8 f. &s the lar"est B4sheet in the protein predominantly parallel or anti4parallel8

g. E.amine the lar"est B4sheet in this protein 1ow many strands does it contain8 4. a. 0ow use #n$D= 1 to view structural ali"nments o( two proteins with related $D structures and related se>uences ) simple e.ample is PDB &D <+2%/ the human hemo"lobin #ompare this structure to human myo"lobin 61)937 and Drosophila melano"aster "lobin 6<B?@7 !se #n$D to visualize both a spatial ali"nment )0D to project the se>uence ali"nment onto the $D structures Do the se>uence ali"ned portions appear to ali"n in space8 b. Aor the hemo"lobin4myo"lobin ali"nment e.amine the insertion in the myo"lobin se>uence %elect the se>uence to hi"hli"ht it in the $D viewin" window :here does this insertion occur in the protein8 &s this insertion in a re"ion o( secondary structure8 c. Aor the hemo"lobin4myo"lobin structural ali"nment/ e.amine the heme bindin" poc-et Aind the parts o( the heme bindin" poc-et that di((er most between these two proteins 5ive the re"ion6s7 o( the ali"nment that di((er the most/ use <+2% amino acid positions to describe the re"ion6s7 d. Aor the human4(ly ali"nment/ e.amine the heme bindin" poc-et Describe chan"es in the secondary structure surroundin" the heme 0otice also that the loop re"ions at the outer ed"e o( the heme bindin" poc-et show structural chan"es Ainally/ e.plore some wonder(ul #hime4based biochemical tutorials Bne o( my (avorites is the D0) polymerase tutorials This is a valuable/ (un/ but optional e.ercise Internet Resources: PDB Entrez %tructure #n$D = 1 Tutorial E3ol Basic #ommands E3ol Guic- 5uide E3ol #onsole #ommands 1D1$ in PDB #hime4based tutorials http:CCwww rcsb or"CpdbChomeChome do http:CCwww ncbi nlm nih "ovCsitesCentrez8dbDstructure http:CCwww ncbi nlm nih "ovC%tructureC#0$DCcn$dtut shtml http:CCwww pdb or"CrobohelpCmolecularFviewersC interactiveFviewersCjmolinteraction htm http:CCwww rcsb or"CpdbstaticCtutorialsCviewersCGuic-Emol sw( http:CCchemapps stola( eduCjmolCdocsC http:CCwww rcsb or"CpdbCe.ploreCe.plore do8structure&dD1D1$ http:CCmolvis sdsc eduCvisresCready4to4useCtitles jspHD

u!!lementar" #ools and $ata: %wiss PDB Viewer #n$D = 1 Viewer Airst5lance E3olI #n$D hemo"lobin4myo"lobin ali"nment #n$D 1sFhemo4DmF"lobin ali"nment