PROTEINMODELING
1. DESCRIPTION:Studentswillusecomputervisualizationandonlineresourcestoconstructphysicalmodelsofproteins.
For2016-17,studentswillmodelproteinsinvolvedinswineflu(H1N1),withafocusontwoproteinsinvolvedin
infectivity:Hemagglutinin(H)andNeuraminidase(N).
ATEAMOFUPTO:3IMPOUND:YesAPPROXIMATETIME:50minutesforPartsII&III
2. EVENTPARAMETERS:Pre-buildmodelswillbeimpounded.
a. Eachteammaybringuptoonedouble-sided,8.5”x11”pageofhandwrittennotes.
b. Studentsmustbringwritinginstruments(pencil/penfortheexamandmarkerformarkingthetoobers)anda
metricrulerwithcmmarks.
c. Supervisorswillprovideallothermaterialsforon-sitemodelconstructionandtest.(Internetaccessnotpermitted)
3. THECOMPETITION:Thiseventhasthreeparts:pre-buildmodel,on-sitebuildmodel,&exam.
a. PartI:ThePre-BuildModel.StudentswillusetheprogramJmol/JSmol,(seeweb-resources)tovisualizeamodelofa
specificproteinbasedonatomiccoordinatedata,freelyaccessiblefromtheRCSBProteinDataBank
(http://www.rcsb.org).For2016-17,studentswillconstructamodelofresidues1-160ofchainBofthehemagglutinin
protein,basedonthecoordinatedatafoundinthe5HMG.pdbfile,whichcanbedownloadedforfreefromtheRCSB
ProteinDataBank(www.rcsb.org)..TheroleofthisproteinininfluenzainfectionisdescribedintheApril2006RCSB
MoleculeoftheMonthfeature(http://dx.doi.org/10.2210/rcsb_pdb/mom_2006_4)byDavidGoodsell.Aconstructed
modelofthisproteinwillbebroughttoallcompetitions;asthecompetitionlevelincreases,thescoringrubricsforthe
pre-buildmodelwillreflecthigherexpectationsformodelaccuracy,detailandenhancements.
b. Thefinalpre-buildmodelmustbebasedonthealphacarbonbackbonedisplayoftheprotein,usingascaleof2cm
peraminoacid.StudentsmayuseMini-Toobers®,orothercomparablebendablematerial(e.g.,KwikTwists,12gauge
dimensionalhousewire,etc.),tomanuallyfoldtheirpre-buildmodel.3DprintingtechnologiesmayNOTbeusedto
buildtheproteinbackbone,butMAYbeusedforcreativeadditions.Themodelmustbesufficientlysturdythatjudges
canpickitupandrotateitforjudging.Studentswillusematerialsoftheirownchoosingtoaddfunctionallyrelevant
featurestotheirmodel(e.g.selectedaminoacidsidechains,DNAorassociatedmolecules).Additionstothemodel
shouldhighlightthesignificanceofstructuretofunctionoftheprotein.Studentsmustexplaintheircreative
additionsona4”x6”notecard,intheformofatablewith3columns,headed:1)Whatisdisplayed2)Howitis
displayed,3)whyitisimportant.Explanationsshouldbeclearandconcise.Asignificantportionofthescorewillbe
derivedfromtheseadditionalfeatures.Prebuildmodelswithalladditionsmustfitwithina2x2x2ftspace.Students
mustdelivertheirpre-buildmodeland4”x6”notecardforimpounding.Theymaypickupallpre-buildmodelsafter
thecompetition.
c. PartII:TheOn-SiteModel.Duringtheon-sitecompetition,studentswillbuildaphysicalmodelofaselectedregionof
aspecificproteinusingmaterialsprovidedbytheeventsupervisor.Web-basedresourceslistedbelowwillprovide
backgroundinformationaboutthemoleculesforalllevelsofcompetitions.
d. StudentswillutilizeacomputerprovidedwiththeJmol/JSmolapplicationatthecompetition.Eachteammustutilize
onlyoneoftheidenticalcomputersprovidedatthecompetitionwiththeappropriatecoordinatefilesonittoguide
theirmodelconstruction.Allconstructionmaterialsforthemodel(Mini-Toobers®,aminoacidsidechains,crosslinkers
andplasticredandblueendcaps)willbeprovided.Anymodelnothandedtothejudgesbytheendofthe
competitiontimewillnotbeacceptedforscoring.
e. PartIII:TheOn-SiteWrittenExamwillbemultiplechoice/shortanswerquestionsaddressingprinciplesofchemistry
thatdriveproteinfoldingandthestructure/functionrelationshipofthemodeledproteins.
4. SCORING:40%oftheeventscorewillbebasedonthepre-buildproteinmodel(PartI),30%ontheon-sitebuild(PartII)
and30%onthewrittenexam(PartIII).Thepre-buildproteinmodelwillbescoredbasedontheaccuracyandscaleof
thesecondarystructures,aswellastheadditionstothemodel(e.g.sidechains,DNAorassociatedmolecules).Additions
thatdonotsupportthemolecularstorywillnotreceivecredit.Theon-sitebuildproteinmodelwillbescoredbasedon
accuracyoffoldingthemodelandpositioningspecificaminoacidsidechains.Theexamwillbescoredforaccuracy.Ties
willbebrokenusingidentifiedquestionsfromthewrittenexam.
RecommendedResources:Materialforthestudents,coachesandjudgeswillbeavailableontheScienceOlympiad
Webpage-atMSOECBM(http://cbm.msoe.edu/scienceOlympiad/index.php)andRCSBPDB
(http://pdb101.rcsb.org/events/science-olympiad);RCSBPDBHomepage(www.rcsb.org)andPDB-101resources
(http://www.rcsb.org/pdb-101).TheMini-Toobers®areaproductof3DMolecularDesigns.MaterialsforthePre-buildcan
beobtainedfromhttp://www.3dmoleculardesigns.com.
THISEVENTISSPONSOREDBY:TheMilwaukeeSchoolofEngineering
ScienceOlympiadFeaturedTrialEventRulesfor2016-2017;ProteinModelingC;v.June30,2016
©ScienceOlympiad,Inc.2017