amyloid peptides and alzheimer’s...
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Name________________________
StarBiochem
Ver.5‐D.SinhaandL.Alemán 1
AmyloidPeptidesandAlzheimer’sExerciseLearningObjectivesInthisexercise,youwilluseStarBiochem,aprotein3D‐viewer,toexplore:• thestructureoftheamyloidpeptidesthatcontributetothedevelopmentofAlzheimer’sdisease• theprocessbywhichthesepeptidesareproduced
BackgroundAlzheimer’sdisease(AD),aneurodegenerativediseaseofthebrain,isthemostcommoncauseofdementia.ADcanbedividedintotwoformsdependingonthemodeofinheritance:familialAD(FAD),thegeneticallyinheritedform,andsporadicAD(SAD),theformthatshowsnogeneticinheritance.FADisassociatedwithearlyonsetofthedisease,affectingindividualsasearlyas30‐60yearsold,whereasSADtypicallydevelopsafterage65.ADismorecommoninwomenthanmenforanygivenagegroup.AmolecularhallmarkofADistheformationofamyloidpeptideswhichclustertogethertoformamyloidplaquesinthebrain.ThedensityoftheseplaquesshowsadirectcorrelationwiththeprogressionofAD.Amyloidpeptidesareformedbytheprogressivecleavageoftheamyloidprecursorprotein(APP)bysecretaseenzymeslocatedinneuronalmembranes.Amyloidpeptidesforminsideneuronsbutexerttheirdamagingeffectswhentransportedintotheextracellularenvironment,aphenomenonthatisobservedonlyinADpatients.Extracellulartransportofamyloidpeptidesandtheformationofamyloidplaquescauseneuronaldeathduetoinflammationand/orformationofneurofibrillarytangles(NFTs).NFTsareformedbytheaggregationofphosphorylatedtauproteins.Thetauprotein,initsunphosphorylatedstate,stabilizesmicrotubuleswhicharerequiredfortransportofmoleculesalongthelengthofneurons.PhosphorylatedtaudoesnotstabilizemicrotubulesbutinsteadbindstoothertauproteinstoformNFTs.AccumulationofNFTsresultsinneuronalcelldeath.
GettingstartedwithStarBiochem• TobeingusingStarBiochem,pleasenavigateto:http://web.mit.edu/star/biochem.• ClickontheStartbuttontolaunchtheapplication.• ClickTrustwhenapromptappearsaskingifyoutrustthecertificate.• InthetopmenuunderFileclickonOpen/Import,select“1IYT”andclickOpen.• Repeatthesestepstoimportthefollowingstructuresinseparatewindows:“1BA4”,“2ONA”,“2OKZ”and“1HZ3”whilekeepingtheotherstructuresopened.
Amyloidpeptidesandplaquesarerepresentedamongthesestructures.Thecurrentwayyouareviewingthesestructuresisbyseeingeachbondintheproteindrawnasaline(“bondsonly”view).
Name________________________
StarBiochem
Ver.5‐D.SinhaandL.Alemán 2
Practicechangingtheviewpointofthisproteinintheviewwindow: Mac PCTOROTATE
clickanddragthemouse left‐clickanddragthemouse
TOMOVEUP/DOWNRIGHT/LEFT
apple‐clickanddragthemouse right‐clickanddragthemouse
TOZOOM
option‐clickanddragthemouse Alt‐left‐clickanddragthemouse
Takeamomenttolookatthestructureoftheseamyloidpeptidesandplaques(1IYT,1BA4,2ONA,2OKZ,and1HZ3)fromvariousanglesinthis“bondsonly”view.Beforeproceedingtoanswerthequestions,youcanreviewthebasicstructuresandtermsonthenextpagewhichyoucanrefertoduringthisexercise.
Name________________________
StarBiochem
Ver.5‐D.SinhaandL.Alemán 3
PROTEINSTRUCTUREBASICSEachproteinhasthefollowingthreelevelsofproteinstructure:PrimarystructureListstheaminoacidsthatmakeupaprotein’ssequence,butdoesnotdescribeitsshape.SecondarystructureDescribesregionsoflocalfoldingthatformaspecificshape,likeahelix,asheet,oracoil.TertiarystructureDescribestheentirefoldedshapeofawholeproteinchain.Inaddition,someproteinsinteractwiththemselvesorwithotherproteinstoformlargerproteinstructures.HowtheseproteinsinteractandfoldtoformalargerproteincomplexistermedQuaternarystructure.
CHEMICALSTRUCTURESOFTHEAMINOACIDSThe20aminoacidsshareacommonbackboneandaredistinguishedbydifferent‘R’groups,highlightedinvariouscolorsbelow.
Name________________________
StarBiochem
Ver.5‐D.SinhaandL.Alemán 4
1Howmanymonomers/chainsdoyouseeinthecurrentviewforeachofthesestructures?• ClickonStructure.• ClickonPrimary.Theaminoacidsofeachpolypeptidechainarehighlightedbyaspecificcolorandcanbedistinguishedfromthoseofotherpolypeptidechains.
• Todistinguishbetweenthedifferentmonomersthattogethermakeupeachofthesestructures,underStructureclickonQuaternary.ClickonChain.
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2Carefullylookattheaminoacidsequenceofeachstructure.Writedownthesequencethatiscommonamongallfourstructures.Hint:Foreachofthesecrystalstructures,clickonPrimary.
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3Biologicalreactionsaremulti‐stepcascadesofevents.Theendproductofonereactionstepbecomesthestartingsubstrateofthenextstep.Eachstepinthecascadeiscatalyzedbyaspecificenzyme.Theformationofamyloidplaquesfromamyloidpeptidesisanexampleofamulti‐stepbiologicalreaction.
a)Basedontheprimarystructuresofthesepeptides,arrangethesestructuressequentiallytoreflectthecascadethatleadstoamyloidplaqueformation.Hint:Allofthesestructuresarederivedbythecleavageofamyloidprecursorprotein.
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b)Howmanyenzymesmightbeinvolvedincatalyzingallthestepsofthiscascade?Assumethateachstepinthecascadeiscatalyzedbyonlyonespecificenzyme.
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c)Describewhathappensateachstepinthecascade.
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Name________________________
StarBiochem
Ver.5‐D.SinhaandL.Alemán 5
4Wewillnowanalyzethesecondarystructureofthesepeptides.• Foreachwindow,gotoView.• ClickonResetMolecule.• UnderStructure,clickonSecondary.• ExplorethedifferentsecondarystructuresfoundwithinthesecrystalstructuresbyindividuallyclickingonthedifferentchoicesthatappearwithintheShowRibbonsbox.
a)Whichsecondarystructureisabsentinallofthesecrystalstructures?
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b)Whichsecondarystructureispresentinallofthesecrystalstructures?
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c)Whichistheonlysecondarystructurepresentintheamyloidprecursorpeptide?
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d)Whichsecondarystructureispresentexclusivelyintheamyloidplaques?
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5Letusanalyzethenatureoftheaminoacidsthatcomprisethesepeptidestobetterunderstandtheenvironmentinwhichtheyreside.• GotoView.• ClickonResetMolecule.• WithinStructure,clickonTertiary.• ClickonthedifferentoptionsprovidedwithintheColorbyresiduebox.
a)Arrangethepeptides,indescendingorderbasedontheirdifferenceinpolarity(polar>>>nonpolar).
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b)Itishypothesizedthatsomeofthesepeptidesremaininsideneuronsafterbeingproduced.ThepresenceofthesestructuresinneuronsisnotregardedasanindexofAD.Whichofthesestructuresrepresenttheamyloidpeptidesthatresideinsideneurons?Explainyouranswer.
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Name________________________
StarBiochem
Ver.5‐D.SinhaandL.Alemán 6
c)Thepeptidesthatyouhaveidentifiedinquestion5(b)containacentralcluster:N‐Leu‐Val‐Phe‐Phe‐Ala‐C.Circletheoptionthatbestdescribesthenatureofthiscluster.
AnswerPolar Non‐polar Hydrophilic Hydrophobic
d)Withinthisclusteridentifytheaminoacid(s)that“Valine”interactswithandstatethetypeofinteractionbetweenthem.Yourchoicesare‘hydrogenbond’,‘ionicbonds’,‘peptidebonds’,‘hydrophobicinteraction’OR‘vanderWaalsforces’.
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e)Incontrasttothestructuresyouidentifiedinquestion5(b),thereareothertypesofamyloidpeptidesthataretransportedfromtheinsideofbrainneuronstotheoutside,wheretheyformamyloidplaques.Identifythisstructureandprovideanexplanationforhowthesepeptidescanresideintheaqueousextracellularenvironment.
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f)Whatisthemostcommoninteractionthatmayexistbetweenthepeptidesthatmakeupamyloidplaques?
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6Besidesamyloidplaqueformation,anotherkeyfeatureobservedinADisthephosphorylationandclusteringofthetauprotein.• OpenanewwindowofStarbiochem.• Inthetoppanel,underFileclickonOpen/Import.• Typein“2Ol9.”• ClickOpen.
Ofthetwentyessentialaminoacidresidues,indicatewhichonescanbephosphorylatedinthetauprotein.Hint:youcanrefertotheaminoacidchemicalstructurechartatthebeginningofthisexercise.
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Name________________________
StarBiochem
Ver.5‐D.SinhaandL.Alemán 7
7Basedonwhatyouhavelearnedfromthisexercise,ifyouweretodesignatreatmentstrategy,whatprocesswouldyoutargettopreventtheonsetandprogressionofAD?ProposethreetreatmentstrategiesandexplainhoweachwillpreventtheonsetorprogressionofAD.
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KeywordsCascade,familial,sporadic,type‐IIdiabetes,dementia,enzymes,amyloidplaques,andamyloidpeptides.Thoughtquestions1HIVpatientsareoftenreportedtodevelopdementiawithsimilarcharacteristicstothatobservedinAD.Proposeanexplanationforthisobservation.2WhatdothemechanismthatleadstotheonsetofADandthemechanismthatleadstotheonsetofpriondiseaseshaveincommon?3PeoplewithDown’ssyndromedevelopADatamuchearlierage.Explainwhy.