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The switch helix seems to serve as a latch thatadheresto a specific site in another domain of the molecule, holding the proteinin a "shut" conformation. The conformational change triggered by GTP hydrolysis causesthe switch helix to detach, allowing separatedomains of the proteinto swing apart, through a distance of about 4 nm. This releasesthe bound IRNAmolecule, allowing its attached amino acid to be used (Figure 3-75).Notice in this example how cells have exploited a simple chemical changethat occurs on the surface of a small protein domain to create a movement 50times larger.Dramatic shape changesof this type also causethe verylarge movements that occur in motor proteins, as we discuss next.MotorProteinsProduceLargeMovementsin CellsWe have seen that conformational changes in proteins have a central role inenzyrne regulation and cell signaling.
We now discuss proteins whose majorfunction is to move other molecules. These motor proteins generate the forcesresponsible for muscle contraction and the crawling and swimming of cells.Motor proteins also power smaller-scaleintracellular movements: they help tomove chromosomes to opposite ends of the cell during mitosis (discussedinChapter 17),to move organellesalong molecular tracks within the cell (discussedsite oftRNAbindingGTPbindingsiteswitchhelix(A)(B)(A)The three-dimensionalstructureof EF-TuwithFigure3-75 The large conformationalchange in EF-Tucausedby GTPhydrolysis.is the switchhelix,which movesafterGTPlixprotein,itsandRasGTPbound.The domainat the top hasa structuresimilarto the(B)Thechangein the conformationof the switchhelixin domain1 causesdomains2 and 3 to rotateas a singleunit by about90"hydrolysis.toward the viewer,which releasesthe IRNAthat was shown bound to this structurein Figure3-74.
(A,adaptedfrom H. Berchtoldet al.,NotureLtd.B,courtesyof MathiasSprinzland RolfHilgenfeld')from MacmillanPublishers365:126-132,1993.With permission182Chapter3: Proteinsin chapter 16), and to move enzyrnes along a DNA strand during the synthesisof a new DNA molecule (discussed in chapter 5). All these fundamental processesdepend on proteins with moving parts that operate as force-generatingmachines.How do these machines work? In other words, how do cells use shapechanges in proteins to generate directed movements? If, for example, a proteinis required to walk along a narrow thread such as a DNA molecule, it can do thisby undergoing a series of conformational changes,such as those shor,rrnin Figure 3-76. But with nothing to drive these changes in an orderly sequence,theyare perfectly reversible, and the protein can only wander randomly back andforth along the thread.
we can look at this situation in another way. Since thedirectional movement of a protein does work, the laws of thermodynamics (discussed in chapter 2) demand that such movement use free energy from someother source (otherwise the protein could be used to make a perpetual motionmachine). Therefore, without an input of energy,the protein molecule can onlywander aimlessly.How can the cell make such a series of conformational changes unidirectional? To force the entire cycle to proceed in one direction, it is enough to makeany one of the changes in shape irreversible. Most proteins that are able to walkin one direction for long distances achieve this motion by coupling one of theconformational changes to the hydrolysis of anATp molecule bound to the protein.
The mechanism is similar to the one iust discussed that drives allostericFigure3-76 An allosteric"walking"protein. Although its three differentconformationsallow it to wanderrandomlybackand forth while boundtoa threador a filament,the protein cannotmoveuniformlyin a singledirection.In the model shorrrmin Figure 3-zz, Nlp binding shifts a motor protein fromconformation I to conformation 2.The bound ATp is then hydrolyzed to produce ADP and inorganic phosphate (PJ, causing a change from conformation 2Many motor proteins generate directional movement in this general way,including the muscle motor protein myosin, which walks along actin filamenisto generatemuscle contraction, and the kinesinproteins that walk along microtubules (both discussedin chapter l6).
These movements can be rapid:iome ofthe motor proteins involved in DNA replication (the DNA helicises) propelthemselves along a DNA strand at rates as high as 1000nucleotides p". second.Membrane-BoundTransportersHarnessEnergyto pumpMoleculesThroughMembranesHYDROLYSISwe have thus far seen how allosteric proteins can act as microchips (cdk and Srckinases),as assembly factors (EF-Tu),and as generatorsof mechanical force andmotion (motor proteins). Allosteric proteins can also harness energy derivedfrom ATP hydrolysis, ion gradients, or electron transport processesto pump specific ions or small molecules acrossa membrane.
we consider one ex€rrnptetrere;others will be discussedin Chapter ll.The ABC transporters constitute an important class of membrane-boundpump proteins. In humans at least 48 different genesencode them. These transporters mostly function to export hydrophobic molecules from the cytoplasm,Figure3-77 An allostericmotor protein.The transitionbetweenthreedifferentconformationsincludesa stepdrivenby the hydrolysisof a boundATPmolecule,and this makesthe entirecycleessentiallyirreversible.Byrepeatedcycles,the proteinthereforemovescontinuouslyto the rightalongthe thread.direction ofmovement183PROTEINFUNCTIONm e m b r a n e - s p a n n i nsgu b u n i t slipidbilayerCYTOSOLFigure3-78 The ABC(ATP-bindingcassette)transporter,a protein machinethat pumps large hydrophobic moleculesthrough a membrane.(A)The bacterialBtuCDprotein,whichimportsvitamin812into E coli usingthe energyofATPofThe bindingof two moleculeshydrolysis.ATPclampstogetherthe two ATP-bindingThe structureis shownin its ADPsubunits.bound state,wherethe channelto thespacecan be seento be openextracellularbut the gateto the cytosolremainsclosed.(B)Schematicof substrateillustrationIn bacteria,pumpingby ABCtransporters.the bindingof a substratemoleculeto thefaceof the proteincomplexextracellulartriggersATPhydrolysisfollowed by ADPgate;whichopensthe cytoplasmicrelease,the pump is then resetfor anothercycle.Ineucaryotes,an oppositeprocessoccurs,to be pumpedcausingsubstratemoleculesout ofthe cell.(A,adaptedfrom K.P.Locher,Curr.
Ooin. Struct.Biol. 14:426-441,2004'from Elsevier.)With permissionA T P - b i n d i n sgu b u n i t sABCTRANSPORTERA EUCARYOTIC(B) A BACTERIALABCTRANSPORTERs u b s t r a t em o l e c u l el:,CI'TOSOLsubstratemolecule,\2P{;\ATP-bindingserving to remove toxic molecules at the mucosal surface of the intestinal tract,for example, or at the blood-brain barrier. The study of ABC transporters is ofintense interest in clinical medicine, because the overproduction of proteins inthis class contributes to the resistance of tumor cells to chemotherapeuticdrugs. And in bacteria, the same tlpe of proteins primarily function to importessential nutrients into the cell.The ABC transporter is a tetramer, with a pair of membrane-spanning subunits linked to a pair of ATP binding subunits located just below the plasmamembrane (Figure 3-78A).
As in other exampleswe have discussed,the hydrolysis of the bound ATP molecules drives conformational changes in the protein,transmitting forces that cause the membrane-spanning subunits to move theirbound molecules acrossthe lipid bilayer (Figure 3-788).Humans have invented many different types of mechanical pumps, and itshould not be surprising that cells also contain membrane-bound pumps thatfunction in other ways.
Among the most notable are the rotary pumps thatcouple the hydrolysis of ATP to the transport of H* ions (protons). These pumpsresemble miniature turbines, and they are used to acidify the interior of lysosomes and other eucaryotic organelles.Like other ion pumps that create ion gradients, they can function in reverseto catalyzethe reactionADP + Pr-+ ATB if thegradient acrosstheir membrane of the ion that they transport is steep enough.One such pump, the ATP slrrthase, harnessesa gradient of proton concentration produced by electron transport processesto produce most of the AIPused in the living world. This ubiquitous pump has a central role in energy conversion, and we shall discussits three-dimensional structure and mechanism inChapter 14.+zrizi.:#Mi184Chapter3: ProteinsProteinsOftenFormLargeComplexesThatFunctionas proteinMachines <ACTT><ATCG>Large proteins formed from many domains are able to perform more elaboratefunctions than small, single-domain proteins.
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