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.

Answer

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.

Answer

KeywordsCascade,familial,sporadic,type‐IIdiabetes,dementia,enzymes,amyloidplaques,andamyloidpeptides.Thoughtquestions1HIVpatientsareoftenreportedtodevelopdementiawithsimilarcharacteristicstothatobservedinAD.Proposeanexplanationforthisobservation.2WhatdothemechanismthatleadstotheonsetofADandthemechanismthatleadstotheonsetofpriondiseaseshaveincommon?3PeoplewithDown’ssyndromedevelopADatamuchearlierage.Explainwhy.