Name________________________
StarBiochem
Ver.1‐MR
1
LysozymeExerciseBackgroundInthisexercise,youwilluseStarBiochem,aprotein3‐Dviewer,toexplorethestructureoftheproteinlysozyme.Lysozymedegradesthecellwallsofbacteria,andisfoundinhumantears.GettingstartedwithStarBiochem• TogettoStarBiochem,pleasenavigateto:http://web.mit.edu/star/biochem.• ClickontheStartbuttontolaunchtheapplication.• ClickTrustwhenapromptappearsaskingifyoutrustthecertificate.• InthetopmenuunderFileclickonOpen/Importandselect“1GXX”andclickonOpen.
Youarenowviewingthestructureoflysozyme,witheachbondintheproteindrawnasaline.Practicechangingtheviewpointofthisproteinintheviewwindow:
Mac PCTOROTATE
clickanddragthemouse left‐clickanddragthemouse
TOMOVEUP/DOWNRIGHT/LEFT
apple‐clickanddragthemouse right‐clickanddragthemouse
TOZOOM
option‐clickanddragthemouse Alt‐left‐clickanddragthemouse
Takeamomenttolookatthestructureoflysozyme(1GXX)fromvariousanglesinthis"bondsonly"view.Beforeproceedingtoanswerthequestions,reviewthebasicstructuresandtermsonthenextpagewhichyoucanrefertoduringthisexercise.
Name________________________
StarBiochem
Ver.1‐MR
2
PROTEINSTRUCTUREBASICSEachproteinhasthefollowingthreelevelsofproteinstructure:PrimarystructureListstheaminoacidsthatmakeupaprotein’ssequence,butdoesnotdescribeitsshape.SecondarystructureDescribesregionsoflocalfoldingthatformaspecificshape,likeahelix,asheet,oracoil.TertiarystructureDescribestheentirefoldedshapeofawholeproteinchain.Inaddition,someproteinsinteractwiththemselvesorwithotherproteinstoformlargerproteinstructures.HowtheseproteinsinteractandfoldtoformalargerproteincomplexistermedQuaternarystructure.
CHEMICALSTRUCTURESOFTHEAMINOACIDSThe20aminoacidsshareacommonbackboneandaredistinguishedbydifferent‘R’groups,highlightedinvariouscolorsbelow.
Name________________________
StarBiochem
Ver.1‐MR
3
ProteinStructureQuestions1Otherthanhydrogen,proteinscontainfouradditionalatoms,Carbon,Nitrogen,Oxygen,andSulfur.Whichofthesefouratomsismostrarelyfoundinproteins?• ClickonViewControls.• UnderAtoms,clickonDraw.Underthisview,eachatomintheproteinisshown.Carbonisgrey,Nitrogenisblue,Oxygenisred,andSulfurisyellow.Note:hydrogenisnotshown.
Answer
2Howmanyofthesulfursintheproteinareclearlyexposedonthesurfaceofthisprotein?• ClickonViewControls.• WithinAtomsboxclickonFillSpace.Thisshowsaspace‐fillingviewoftheproteinsothatyoucanseehowmuchspaceistakenupbyeachatom.
Answer
3Nowexplorelysozyme’ssecondarystructure.
a)Howmanyhelicesareinonelysozymeprotein?• ClickonViewandchooseResetMolecule.• GotoStructureandclickonSecondary.• ClickonHelices.
Answer
b)Whichstructurepredominatesinthelysozymeprotein,helicalshapesorsheet‐likeshapes?• UnderSecondary,clickonSheetsandcomparethiswithyouranswertoparta).
Answer
4Whicharemorecommoninlysozyme,acidicaminoacidsorunchargedpolaraminoacids?• ClickonViewandchooseResetMolecule.• GotoStructureandclickonTertiary.• ClickonbothAcidicandPolartohighlighttheacidicandthepolaraminoacidswithintheprotein.
Answer
Name________________________
StarBiochem
Ver.1‐MR
4
5Lysozymeconsistsof129aminoacids.Listinorderthe12aminoacidsnumbered4through15inlysozyme.• ClickonViewandchooseResetMolecule.• GotoStructureandclickonPrimary.
Answer
6These12aminoacidsmakeupahelixinlysozyme.Howmanyfullturnsofthehelix(i.e.360° turns)doyouseeinthisonehelix?• ClickonViewandchooseResetMolecule.• GotoStructureandclickonSecondary.• UnderHelixSelectionclickontheboxnextto"1".Thiswillselectalltheaminoacidsinthefirsthelixinlysozyme,whichturnsouttobethe12aminoacidsyoulistedabove.
• ClosetheStructurepanelandopentheViewControlspanel.IntheViewControlspanel,movetheUnselectedtransparencyslidertozero.Thismakesalltheaminoacidsyouhavenotselecteddisappear.
• SettheSidechaintransparencyslidertozero.• UnderAtomsclickontheDraw.Rotatethehelixtolookatitfromavarietyofviewpoints.
Answer
7Everyaminoacidismadeupoftwoparts,thebackbone(whichissharedbyallaminoacids,andconsistsofanaminogroupboundtoacentralcarbonboundtoacarboxylgroup)andasidechain(whichisdifferentforeachofthe20aminoacids).DothesidechainsoftheaminoacidsinahelixpointINTOorOUTofthecenterofthehelix?• Rotatethehelixsothatyoulookdownthecenteraxisofthehelix.• ClickonViewControlsandmovethesliderlabeledSidechainbackandforth,toturnthesidechainsonandoff.
Answer
8Howmanyprolinesareinonelysozymeprotein?• ClickonViewandchooseResetMolecule..• GotoSelectionControlsandclickonSelectresiduebytype.Thisallowsyoutoseewhereeachofthetwentyaminoacids/residuesareintheprotein.
• ClickonProline.Answer
