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Hogle.)of RobertGrant,StephanCrainic,by x-raycrystallographyand areknown in atomicdetail.(CourtesyManyStructuresin CellsAre Capableof Self-AssemblyThe information for forming many of the complex assemblies of macromolecules in cells must be contained in the subunits themselves,because purified subunits can spontaneously assemble into the final structure under theappropriate conditions. The first large macromolecular aggregateshown to becapable of self-assembly from its component parts was tobacco mosaic uirus(TMV). This virus is a long rod in which a cylinder of protein is arranged arounda helical RNA core (Figure 3-32).
If the dissociated RNA and protein subunits aremixed together in solution, they recombine to form fully active viral particles.The assembly process is unexpectedly complex and includes the formation ofdouble rings of protein, which serve as intermediates that add to the growingviral coat.Another complex macromolecular aggregate that can reassemble from itscomponent parts is the bacterial ribosome. This structure is composed of about55 different protein molecules and 3 different rRNA molecules.
Incubating theindividual components under appropriate conditions in a test tube causesthemto spontaneously re-form the original structure. Most importantly, such reconstituted ribosomes are able to catalyze protein s),'nthesis.As might be expected,the reassembly of ribosomes follows a specific pathway: after certain proteinshave bound to the RNA, this complex is then recognized by other proteins, andso on, until the structure is complete.It is still not clear how some of the more elaborate self-assemblyprocessesare regulated. Many structures in the cell, for example, seem to have a precisely150Chaoter3: ProteinsFigure3-31 The structureof a sphericalvirus.In manyviruses,identicalproteinsubunitspacktogetherto createasphericalshell(a capsid)that enclosesthe viralgenome,composedof eitherRNAor DNA(seealsoFigure3-30).Forgeometricreasons/no morethan 60identicalsubunitscan packtogetherin apreciselysymmetricway.lf slightirregularitiesareallowed,however,moresubunitscan be usedto producea largercapsidthat retainsicosahedralsymmetry.Thetomato bushystuntvirus(TBSV)shownhere,for example,is a sphericalvirusabout33 nm in diameterformedfrom 180identicalcopiesof a 386aminoacidcapsidproteinplusan RNAgenomeof 4500nucleotides.To constructsuchalargecapsid,the proteinmust be abletofit into threesomewhatdifferentenvironments,eachof which is differentlycoloredin the virusparticleshownhere.The postulatedpathwayof assemblyisshown;the precisethree-dimensionalstructurehasbeendeterminedby x-raydiffraction.(Courtesyof SteveHarrison.)dimerp r o j e c t i n gd o m a i ns h e l ld o m a i nc o n n e c t i n ga r mR N A - b i n d i ndgo m a i n{-c a p s i dp r o t e i nmonomers n o w na sribbonmodel20nmdefined length that is many times greater than that of their component macromolecules.
How such length determination is achieved is in many casesa mystery. Three possible mechanisms are illustrated in Figure 3-33. In the simplestFigure3-32 The structureof tobaccomosaicvirus(TMV).(A)An electronmicrographof the viralparticle,whichconsistsof a singlelong RNAmoleculeenclosedin a cylindricalproteincoatcomposedof identicalproteinsubunits.(B)A modelshowingpart of the structureof TMV.Asingle-strandedRNAmoleculeof 6395nucleotidesis packagedin a helicalcoatconstructedfrom 2130 copiesof a coat protein158 aminoacidslong.Fullyinfectiveviralparticlescan self-assemblein a testtube from ourifiedRNAand proteinmolecules.(A,courtesyof RobleyWilliams;B,courtesyofRichardJ. Feldmann.)151THESHAPEAND STRUCTUREOF PROTEINSt( A ) A S 5 E M B LOYN C O R E( B ) A C C U M U L A T ESDT R A I N(C) VERNIEMR ECHANIsMFigure3-33 Threemechanismsof length determination for large protein(A)Coassemblyassemblies.alongan elongatedcoreproteinor otherofmacromoleculethat actsasa measuringdevice.(B)Terminationassemblybecauseof strainthat accumulatesin the polymericstructureasadditionalsubunitsareadded,so that beyonda certainlengththe energylarge.requiredto fit anothersubunitonto the chainbecomesexcessively(C)A verniertype of assembly,in whichtwo setsof rodlikemoleculesdifferingin lengthform a staggeredcomplexthat growsuntiltheirendsexactlymatch.The namederivesfrom a measuringdevicebasedon thesameprinciple,usedin mechanicalinstruments.case,a long core protein or other macromolecule provides a scaffold that determines the extent of the final assembly.
This is the mechanism that determinesthe length of theTMVparticle, where the RNA chain provides the core. Similarly,a core protein is thought to determine the length of the thin filaments in muscle, as well as the length of the long tails of some bacterial viruses (Figure 3-34).AssemblyFactorsOftenAid the Formationof ComplexBiologicalStructuresNot all cellular structures held together by noncovalent bonds self-assemble.Amitochondrion, a cilium, or a myofibril of a muscle cell, for example, cannotform spontaneously from a solution of its component macromolecules.
In thesecases, part of the assembly information is provided by special enzymes andother proteins that perform the function of templates, guiding construction buttaking no part in the final assembled structure.Even relatively simple structures may lack some of the ingredients necessaryfor their ovrn assembly. In the formation of certain bacterial viruses, for example, the head, which is composed of many copies of a single protein subunit, isassembled on a temporary scaffold composed of a second protein.
Becausethesecond protein is absent from the final viral particle, the head structure cannotspontaneously reassemble once it has been taken apart. Other examples areknornrnin which proteolltic cleavage is an essential and irreversible step in thenormal assembly process.This is even the case for some small protein assemblies, including the structural protein collagen and the hormone insulin (Figure3-35). From these relatively simple examples,it seems certain that the assemblyof a structure as complex as a mitochondrion or a cilium will involve temporaland spatial ordering imparted by numerous other cell components.Figure3-34 An electron micrographof bacteriophagelambda.The tip ofthe virustail attachesto a soecificproteinon the surfaceof a bacterialcell,afterwhichthe tightlypackagedDNAin the headis injectedthroughthetail into the cell.Thetail hasa preciselength,determinedby themechanismshownin Figure3-33A.152Chapter3: ProteinsproinsulinFigure3-35 Proteolyticcleavageininsulinassembly.The polypeptidehormoneinsulincannotspontaneouslyre-formefficientlyif its disulfidebondsaredisrupted.lt is synthesizedas a largerprotein (proinsufin)that is cleaved by aproteolyticenzymeafter the proteinchainhasfoldedinto a specificshape.Excisionof part of the proinsulinpolypeptidechain removessomeof theinformationneededfor the oroteintofold spontaneouslyinto its normalconformation.Onceinsulinhasbeendenaturedand its two polypeptidechainshaveseparated,its abilitytoreassembleis lost.I1,,i1,.,,r,..11."0,,,,"0reduction irreversiblyseoaratesthe two chainsSH+tr5SHSu m m a r yA protein molecule'samino acid sequencedetermines its three-dimensional conformation.
Noncoualentinteractions betweendffirent parts of the polypeptide chain stabilize itsfolded structure. The amino acids with hydrophobic side chains tend to cluster in the interior of the molecule, and local hydrogen-bond interactions betweenneighboring peptide bondsgiue rise to a helicesand B sheets.Globular regions,known as domains, are the modular units from which manyproteins are constructed;such domains generally contain 4u3s0 amino acids. smallproteins typically consistof only a single domain, while large proteins areformed fromseueraldomains linked together by uarious lengths of polypeptide chain, some ofwhich can be relatiuelydisordered.As proteins haueeuolued,domains hauebeenmodified and combined with other domains to construct new proteins.
Thusfar, about g00dffirent ways of folding up a domain haue been obserued,among more than 20,000known protein structures.Proteinsare brought togetherinto larger structuresby the samenoncoualentforcesthat determine protein folding. Proteins with binding sitesfor their own surface canassembleinto dimers, closedrings, spherical shells,or helical polymers.Although mixtures of proteins and nucleic acids can assemblespontaneously into complex structures in a test tube, many biological assemblyprocessesinuolue irreuersiblesteps.Consequently,not all structures in the cell are capable of spontaneous reassemblyafterthey haue beendissociatedinto their component par6.PROTEINFUNCTIONwe have seen that each type of protein consists of a precise sequence of aminoacids that allows it to fold up into a particular three-dimensional shape, or conformation.
But proteins are not rigid lumps of material. They often have preciselyengineered moving parts whose mechanical actions are coupled to chemicalevents. It is this coupling of chemistry and movement that gives proteins theextraordinary capabilities that underlie the dynamic processesin living cells.PROTEINFUNCTION153In this section,we explainhow proteinsbind to other selectedmoleculesand how their activity dependson suchbinding.We showthat the ability to bindto other molecules enables proteins to act as catalysts,signal receptors,switches,motors,or tiny pumps.The exampleswe discussin this chapterby nomeansexhaustthe vastfunctionalrepertoireof proteins.Youwill encounterthespecializedfunctionsof many other proteinselsewherein this book, basedonsimilarprinciples.All ProteinsBindto OtherMoleculesA protein molecule's physical interaction with other molecules determines itsbiological properties.
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