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From: Re: Authors: EuropeanBiophysicsJournalDOI10.1007/s00249-005-0461-4 Elasticvibrationsinseamlessmicrotubules PortetTuszyskiHogueDixon

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EuropeanBiophysicsJournal DOI10.1007/s00249-005-0461-4

Article

Elastic vibrations in seamless microtubules

S.Portet()J.A.TuszyskiC.HogueJ.M.Dixon S.PortetC.Hogue TheSamuelLunenfeldResearchInstitute,Room1060,MountSinaiHospital,600Univercity Avenue,Toronto,ON,Canada,M5G1X5 J.A.Tuszyski DepartmentofPhysics,UniversityofAlberta,Edmonton,AB,Canada,T6G2J1 J.M.Dixon DepartmentofPhysics,UniversityofWarwick,Coventry,CV47AL,UK S.Portet E-mail:sportet@mshri.on.ca

Received:14July2004/Revised:18December2004/Accepted:18December2004

AbstractParameterscharacterizingelasticpropertiesofmicrotubules,measuredinseveralrecent experiments,reflectananisotropiccharacter.Wedescribethemicroscopicdynamicalproperties ofmicrotubulesusingadiscretemodelbasedonanappropriatelatticeofdimers.Adoptinga harmonicapproximationforthedimerdimerinteractionsandestimatingthelatticeelasticconstants, wemakepredictionsregardingvibrationdispersionrelationsandvibrationpropagationvelocities. Vibrationfrequenciesandvelocitiesareexpressedasfunctionsoftheelasticconstantsandofthe geometricalcharacteristicsofthemicrotubules.Weshowthatvibrationswhichpropagatealong theprotofilamentdososignificantlyfasterthanthosealongthehelix. KeywordsMicrotubuleMicrotubulestructureMicrotubuledynamicsLatticeElasticvibrations

Introduction
Microtubules(MTs)areproteinsorganizedinanetworkthatisinterconnectedwithmicrofilaments andintermediatefilamentstoformthecytoskeleton.Eachoftheproteinfibershasspecificphysical

propertiesandstructuressuitableforitsroleinthecell.MTsarelong,hollow,cylindricalobjects madeupofprotofilamentsinteractinglaterally,andconsistingoflongitudinallystacked,-tubulin heterodimers;longitudinalandlateralbondsexhibitdifferentstrengths(VanBurenetal.2002).In vivoMTshavetypically13protofilamentsbut,forexample,15protofilamentMTsarefoundin Caenorhabditis elegans.Ungeretal.(1990)observedinvitroMTswithanumberofprotofilaments rangingfrom8to16dependingontheassemblyconditions.TheMTstructurecanberepresented byahelicalsurfacelatticeinterruptedbymismatcheswhicharecalledseams(ChrtienandWade 1991).Toaccommodatedifferentnumbersofprotofilamentsthewholelatticeisrotatedto compensatetheextraprotofilamentsandtoabsorbthemismatch(Rayetal.1993).InthecellMTs arenormallyorganizedinanasterradiatingnearthenucleustowardsthecellperiphery.MTsare involvedinanumberoffunctionsofthecell,suchascellshapemaintenance,mitosisandplayan importantroleinintracellulartransport.Theyformthemitoticspindlesforthesegregationof chromosomesduringcelldivision,andtheyaresupportsfordirectionaltransportdrivenbymotor proteins.MTsarehighlydynamicpolymers,characterized,forexample,bydynamicinstabilities, successiveperiodsofgrowthandshrinkage.Underspecificconditionstreadmillingmayoccur, whereadditionofheterodimersatoneendofanMTandreleaseattheotherendtakeplaceatthe samerate. Therehavebeenanumberofexperimentalstudiesinrecentyearsdealingwiththevarious aspectsoftheelasticityofMTs.Bybiologicalstandards,MTsarerigidpolymerswithalarge persistencelengthof6mm(Boal2002).FromJanmeysexperiments(Janmeyetal.1991),MTs sufferalargerstrainforasmallstresscomparedwitheithermicrofilamentsorintermediate filaments.TherupturestressforMTsisverysmallandtypicallyisonlyabout0.40.5N/m2 (Janmeyetal.1991).Fromtheliterature,wecanobservethattheshearandYoungsmoduliare significantlydifferent,whichreflectsstructuralanisotropyofthematerial(Kisetal.2002).An anisotropicmaterialhasphysicalcharacteristicswithdifferentvalueswhenmeasurementsare madeinseveraldirectionswithinthesamematerial:e.g.,valuesoftheYoungsmodulusranging from106to109N/m2canbefoundintheliterature(Kisetal.2002;TolomeoandHolley1997). AfewalreadyavailabledynamicalelasticpropertiesofMTsarelistedinTable1althoughmany morearestilltobedetermined.Inconnectionwiththisitisworthnotingthatthereareseveral papersintheliteraturedealingwithstaticandelasticproperties(Jnosietal.1998)andthe vibrationalpropertiesofcytoskeletonfilamentsand,inparticular,MTvibrations.Elasticvibrations ofsubunitsaroundtheirequilibriumpositionsinalatticehavebeencalledphononsintheliterature (Pokornyetal.1997;Sirenkoetal.1996b). 2

Sirenkoetal.(1996b)studiedtheoreticallythevibrationalpropertiesofMTsbyadoptinga continuummediumapproximationincylindricalgeometryforanisotropicmaterial.Bydescribing filamentsaselasticshellsimmersedinwater,theyidentifiedseveralmodesofvibrationradial, torsionalandlongitudinalwiththeattendantdispersionrelations.Theirpredictedphononvelocities rangedfromapproximately200to600m/s.Inasequelpaper(Sirenkoetal.1996a)theseauthors arrivedatahigherestimateofthephononvelocities,namely8001,300m/s.Theyalsopredicted theexistenceofaninfinitesetofhelicalwaveswithparabolicdispersionrelations.Whilethese resultsareveryusefulinidentifyingthemostlikelymodesofvibrationalpropagation,theystill awaitexperimentalconfirmation.ThestructureofMTsishighlyheterogeneous,andboth experimentalmeasurementsandtheoreticalanalysesindicateahighlyanisotropicdynamical picture(Kisetal.2002).Thus,webelievethatadiscreteapproachisnotonlyadequate,butitalso allowstheexpressionofMTstructuralanisotropyinanaturalway. [Table1willappearhere.Seeendofdocument.] Pokornyetal.(1997)attemptedtofinddispersionrelationsbasedonamonatomiclinearchain modelrepresentingindividualprotofilamentsmadeupofmonomers,andbyusingadditivity propertiestheydescribedanMTandconcludedthatphononfrequenciesintherange10710101/s canbeexpected.TheyalsoshowedthattheenergycanbesuppliedbythehydrolysisofGTP. OurapproachwillgofurtherthantheworkofPokornyetal.(1997)bymodelingthestructure ofMTsbyacylinderunfoldedintoaplanarlattice of tubulin dimerssatisfyingappropriateboundary conditionsinaccordancewiththeessentialgeometricalpropertiesofMTs.Thestructural transformationtoaccommodatedifferentnumbersofprotofilamentsistherotationofthewhole lattice(ChrtienandWade1991),withoutmodifyingtheinterprotofilamentinteractions. Consequentlythelocalgeometryofthelattice,(i.e.,longitudinalandlateralinteractionsbetween dimers)ispreserved.Hence,fromthecanonicallatticedescribinga13-protofilamentMT,we deducethegeneraldimensionsofthelatticeofdimersrepresentinganMTindependentlyofthe numberofprotofilaments.Fromthislattice,wedevelopamicroscopicmodelofclassicalvibration modestostudythedynamicsofdimerswithintheMTsurface(excludingradialoscillations).We estimatedispersionrelationsbyusingheterogeneouselasticcoefficientsthatreflecttheanisotropic characterofMTs.Theelasticcoefficientvaluesareobtainedfrommoleculardynamicssimulations oftubulintubulininteractions(Septetal.2003)andfromexperimentaldata(dePabloetal.2003). Ourpredictedvibrationfrequenciesandcorrespondingvelocities,whichareexpressedasfunctions ofelasticconstantsandstructuralpropertiesofMTs,areinthesamerangeasthoseestimatedby Sirenkoetal.(1996a,1996b),andslightlylargerthanthoseestimatedbyPokornyetal.(1997). 3

Althoughnoexperimentshaveyetbeenperformedtovalidatethesepredictions,theyareclearly withintodaysexperimentalcapabilities.Thus,byusingrecentlypublishedinformationregarding elasticpropertiesandthemoleculargeometryofMTswedescribeatamicroscopiclevelthe dynamicalelasticpropertiesofMTsbyaccountingfortheiranisotropy.

Modeling
Intheliterature,theoreticalandexperimentaldatacanbefoundforanMTdescriptionusinga latticeofmonomers(Amos1995;ChrtienandWade1991),butrarelybyalatticeofdimers (MetozandWade1997).Chrtienandcoworkers(1991,1998)havegivenprecisedescriptions ofMTstructuresintermsofasurfacelatticecomposedoftubulinmonomersinthelattice accommodation model.InanMTwith13protofilaments,theprotofilamentsareparalleltothe MTaxisformingahollowcylinder(ChrtienandWade1991).Tubulinmonomersarelongitudinally alignedtoformtheprotofilaments;themonomerspacingalongtheprotofilamentisb=4.05nm (Chrtienetal.1998).Eachprotofilamentisshiftedlengthwisewithrespecttoitsneighbour describingleft-handedhelicalpathwaysrunningaroundtheMTsurface.Thelongitudinalshift betweenmonomersofadjacentprotofilamentsise=0.935nm(Chrtienetal.1998).The accumulatedcircumferentialshiftis130.935nm,whichisequaltoahelixpitchof34.05nm, indicatingthatthreehelicesofmonomersarenecessarytodescribethewholeMTsurface(Chrtien etal.1998).Theseparationbetweenprotofilamentsisd=5.13nm(Chrtienetal.1998).The 13-protofilamentand3-starthelixMTistheso-calledcanonicalMT. Thereexistsanimportantvariabilityinthenumberofprotofilaments(Ungeretal.1990).MTs accommodatedifferentnumbersofprotofilamentsbyskewingtheirprotofilaments(Langford 1980),withoutmodifiyingtheirlateralinteractions.Thestructuralalterationisequivalenttothe rotationofthewholeprotofilamentsheetbyananglethatcanbeexpressedasafunctionofthe numberofprotofilamentsN,thenumberofhelicesSconstitutingtheMT,theseparationbetween protofilamentsd,thelongitudinalshiftbetweenadjacentprotofilamentse,andthespacingbetween subunitsb(Chrtienetal.1998):

(1)

Thus,theinteractionsbetweenprotofilamentsarelocallypreservedinMTs.Inotherwords,the localgeometry,i.e.,thesubunitneighbourhoodgeometry,isindependentoftheprotofilament

numbers(Rayetal.1993).ThenumberofprotofilamentsonlyinfluencestheMTradiusr(see Fig.7inChrtienetal.1998)andtheskewangle.Hence,thelocalgeometryofthesubunit neighbourhoodcanbededucedfromthegeometryofthecanonicalMT. TostudythedimervibrationsinsidetheMTwall,weusealatticemodelofdimerswhichis consideredtobeaseriesofcoupledoscillatorswhoseequilibriumpositionsrepresentthegeometry oftheMT.

Lattice of dimers
Thelongitudinalinterdimerinteractionsareverysimilartothosebetweenmonomerswithina dimer.However,anextraelectrostaticinteractionexistsbetweenmonomersthatdoesnotoccur betweendimers.Thiscomponentaffectsthestrengthoflongitudinalintradimerinteractions (Nogales1999),whicharestrongerthanlongitudinalinterdimerinteractions(Nogalesetal.1999). Furthermore,thebasicsubunitfortheMTassemblyisnotthemonomerbutthedimer. Consequently,weassumelongitudinalintradimerinteractionstobestructurallystableinsidethe MTwall,andweinvestigatethevibrationdynamicsofdimersinsidetheMTsurface. AseamlessMTcanbemodeledasathree-dimensionalhelicallatticeofdimers(Fig.1a)(Metoz andWade1997).Weconsiderdimersaspointsattheircentersofmass(Fig.1b).Thepitchof helicesthatrunaroundtheMTwallisproportionaltotheequilibriumdistance,b,betweenadjacent dimersalongaprotofilament.HencepitchisequaltoSb,whereSrepresentsthenumberofhelices necessarytodescribeawholeMTsurface(Fig.1b).Helicesarewelldefinedbyapitch,Sb,and

aradius,r,andarecharacterizedbytheradiusofcurvatureexpressedas

.From

helicalgeometry,wecancalculatethedimensionsofthedimerneighbourhoodinthelattice. Weopenthethree-dimensionallatticealongthelengthofaprotofilament,paralleltotheMT axisasweconsidera13-protofilamentMT,andunrollittoobtainatwo-dimensionalplanarlattice ofdimers.Thecharacteristicdimensionsofthetwo-dimensionalplanarlatticearisedirectlyfrom thethree-dimensionallatticegeometry;hence,allequilibriumanglesanddistancesbetween neighbouringdimersarepreserved(Figs.1c,2a).Byconstructionandfromtheradiusofcurvature ofhelices,weobtaintheequilibriumdistance,a,separatingadjacentdimersalongagivenhelix orlayer(Fig.2a):

(2)

AsweconsiderthegeometryofthecanonicalMT,thenumberofprotofilamentsisN=N0=13 anditsradiusisr=r0.Furthermore,thecanonicalMThas3-starthelicesofmonomers(Chrtien andWade1991),whichcorrespondstoS=S0=2helicesofdimers.Fromthehelixangle(inthe helicalstructure,theanglebetweenarowofdimersandthehorizontal),arctan(Sb/2r),wecalculate theequilibriumdistance,d,betweenadjacentprotofilaments,andtheequilibriumlongitudinal shift,e,betweenadjacentprotofilaments(Fig.2a):

Thenotationisasbefore.Protofilamentsinteractlaterallywithalateralspacingd.Each

(3)

protofilamentisshiftedlengthwisebyewithrespecttoitsneighbour.Dimensionsofthedimer neighbourhoodinthelatticearelistedinTable2. [Table2willappearhere.Seeendofdocument.] Tocalculatethepositionvector,Rij,inthetwo-dimensionalplane,ofadimerthatbelongsto theprotofilamentiandtothelayerofdimersjinathree-dimensionalstructurerepresentingthe canonicalMT,weusethemapping

(4)

Inthethree-dimensionalhelicalstructure,irepresentstheprotofilament(1iN),andjisthe indexofthedimerlayerintheMT(1j).Inthetwo-dimensionalplanarlattice,iisrelatedtothe y-position,jtothex-position:thex-axisisparalleltotheprotofilamentaxis(Fig.2a).InEq.4the functionFrac[]isthefractionalvaluefunction;inthefirstcoordinate,itisusedtoidentifythe layer,whileintheseconditdesignateswhichprotofilamentoftheMTtheparticulardimerbelongs to.Theneighbourhoodofadimerinthethree-dimensionalhelicallattice(Fig.1b)ispreservedin thetwo-dimensionalplanargeometryowingtotheperiodicitiesimpliedbytheuseofthefunction Frac[].Hence,inthetwo-dimensionalplanarlattice,fortwoadjacentdimersDi,jandDi,j+1along thesameprotofilament,wehaveRi,j+1=Ri,j+b,andfortwoadjacentdimersDi,jandDi+1,jalongthe

samelayerorhelix,Ri+1,j=Ri,j+a.Subsequently,Ri+1,j+1=Ri,j+a+b.Vectorsaandbarethelattice vectors, and (Fig.2).

Fig.1Geometricalmodelofamicrotubule(MT).HerethecanonicalMTisusedasanexample.aAnMT isalong,hollowcylinderwithawallmadeupofNprotofilamentsconsistingofcylindricaltubulindimers longitudinallystacked.bAnMTisathree-dimensionalhelicallatticemadeupofthecentersofmassofthe dimers.Centersofmassofthedimersarealignedwithaspacingbtoformtheprotofilamentsthatrun lengthwisealongthewall.Eachprotofilamentisshiftedlengthwisewithrespecttoitsneighbourdescribing helicalpathwaysaroundtheMT.EachhelixhasaradiusrandapitchSb,whereSisthenumberofhelices necessarytodescribethewholeMTsurface.Thegreyandblack helicesdepicttwohelicesrunningaround theMTwall.cThetwo-dimensionallatticeofdimers:thethree-dimensionallatticeislongitudinallyopened andflattened.Arrowsrepresenttheprotofilamentaxis.

Fig.2Geometricalcharacteristicsoftheplanarlatticeofdimers.Thex-axisistheprotofilamentaxis representedbyarrowsinFig.1.aLatticerepresentingthecanonicalMT,wherea=(e,d)andb=(b,0).The longitudinalshiftbetweentwoadjacentprotofilamentsise.Heredrepresentsthedistancebetweentwo adjacentprotofilaments,andbisthedistancebetweentwoadjacentdimersalongagivenprotofilament. ParametervaluesaregiveninTable2.Bondsinthelatticedescribethenearest-neighbourdimersininteraction withagivendimer.bTheneighbourhoodsystemofagivendimerDi,j.cThecanonicalMTlatticeisshown inblackandthelatticeforanMTmadeupof15protofilamentsandthreehelices(correspondingtothe 15-protofilamentand5-starthelixMTinthemonomerlattice)isinGray.Toaccommodatethetwoextra protofilamentsthelatticeisrotatedbyanangle.

Fornoncanonicalstructures,thevectorposition,Ri,j,mustberotatedbyanangle,givenin Eq.1withtheparametersofthedimerlatticetoresolvethemismatchinducedbyextra protofilaments.

Governing equations
Byconnectingadjacentdimersoftheplanarlatticebyspringswithheterogeneouselasticconstants (Fig.2),wemodelanMTbyalatticewithanisotropicelasticproperties.Thisprovidesaframework tostudythevibrationaldynamicsofdimerswithintheMTsurface. TostudytheinternalMTdynamics,wemodelthesmalldisplacementsofdimers,insidethe MTwall,fromanequilibriumposition.Anystretchingorcompressionofanybondbetween nearest-neighbourdimers(Fig.2a)inthelatticewillresultinarestoringforceobeyingHookes law.Wedenotethevectordisplacement,ui,j,ofthedimerDi,jintheorthogonalcoordinatesystem (x,y)(Fig.2a)by

(5)

wherexi,j(t)andyi,j(t)denotesmalldisplacementsfromequilibriumofthedimer,Di,j,inthedirections alongtheprotofilament(x)andorthogonaltoit(y),respectively(Fig.2a).Inthethree-dimensional helicalstructure,xi,j(t)correspondstolongitudinaldisplacementsfromequilibrium,andyi,j(t)are analogoustoangulardisplacements(Sirenkoetal.1996a). Asthedeviationsfromequilibriumaresmall,weapproximatetheelasticpotentialenergy,i,j, ofadimer,Di,j,asaharmonicpotential.Then,i,j,hastheform

whereki+l,j+misthe(l,m)elementofthecontactmatrix,Ki,j,forthedimer,Di,j,definedbythe neighbourhoodsystemshowninFig.2b.Hence,thematrix,Ki,j,hastheform

(6)

(7)

wherekhistheelasticconstantalongthemainhelix,kpistheelasticconstantalongaprotofilament, andkaistheelasticconstantalongtheantihelix(Fig.2b).Thevaluesoftheelasticconstantskh, kpandkaareassumedtobedifferentfromeachother.Thisassumptiondirectlyresultsinanelastic latticeanisotropythatiswelldocumentedintheliterature(Kisetal.2002),althoughprecise numericalmagnitudesoftheseconstantsareyetunknown. UsingNewtonssecondlawofmotionandtheelasticpotentialenergy(Eq.6,wefindthetwo CartesiancomponentsoftheequationofmotionforthedimerDi,jtobe

and

(8)

wheremisthemassofadimer.FromEqs.5,8and9weobtain

(9)

(10)

TheboundaryconditionsareuN,j=u0,j+S,becausedimersDN,jandD1,j+Sareadjacentalongagiven helixtopreservethehelicalpathwaysrunningaroundMTs. AccordinglywelookforwavelikesolutionsofEq.10oftheform

(11)

where isanarbitraryvectoramplitude,afrequency,katwo-dimensionalwave-vectorwith componentskxandky,and ishe osition t p vectorofthedimerDi,j.Herethepositionvector,Ri,j,resultsfromarotationofthecorresponding canonicalstructurepositionvectorbyangle.WesubstituteEq.11intoEq.10tofindtheassociated dispersionrelationbetweenandkgivenby

(12)

ForanMNorthogonaltwo-dimensionallatticerepresentingthecanonicalstructurecomposed ofMdimersalongthex-direction,andNdimersalongthey-direction,thewave-vectors,k,may bedefinedby(Kittel1956)

(13)

wherep=1...Nandq=1...M.ToconsiderMTswithadifferentnumberofprotofilamentswemust rotatethewave-vectorbyanangle.Sothegeneralexpressionofthevector,k,isdefinedby

where(seeEq.1)istheskewanglefromtheaxisoftheMT. Forourslantedlattice,thewave-vectorsaresuchthat

(14)

10

(15)

wheretheangleisthecomplementaryangleofthehelixangle, Thecomponent isrelatedtotheprotofilamentdirection,and

. isrelatedtotheorientation

ofhelices.TheparameterMisproportionaltothenumberofhelices,S,runningaroundtheMT wall. SubstitutingthepreviousexpressionsfromEqs.14and15intoEq.12givesthedispersion relationbetweenand :

Forsmallp,qwenotethatp,q0inEq.16.Theythereforerepresentacousticvibrational modes.

(16)

Byestimatingthegradientofp,qinspecificdirections,weobtainthegroupvelocityofvibrations propagatingalongtheprotofilamentandalongthehelix.Thevelocityoflongitudinalvibrations alongprotofilamentsis

Thevelocityofvibrationsalongthehelixis

(17)

(18)

Thevelocitiesofvibrations(alongprotofilamentsandalonghelices)dependonlyontheelastic constants,kp,khandka,andthemass,m,oftubulindimers.Theyalsodependandonthestructural

11

propertiesofMTsdeterminedbytheskewangleandthehelixangle.Inthethree-dimensional helicalstructure,atamacroscopiclevel,thelongitudinalvibrationsalongprotofilamentscorrespond tolongitudinalvibrationsoftheMT,andvibrationsalonghelicestotorsionalvibrationsofthe MT.

Results
Elastic constants
Longitudinalinteractionsbetweendimershavepolar,hydrophobicandelectrostaticcomponents (Nogalesetal.1998).Thecontactinterfaceishighlycomplementaryinshape;hence,vander Waalsinteractionsareimportant.Lateralinteractions(betweenand)havemoreimportant electrostaticcharacterthanlongitudinalinteractions(Nogalesetal.1999).Thelateralcontacts betweentubulindimersinneighbouringprotofilamentshaveadecisiveroleforMTdynamics, stability,rigidityandarchitecture(Meurer-Grobetal.2001;Nogalesetal.1999).Tubulindimers arerelativelystronglyboundinthelongitudinaldirection(alongprotofilaments),whilethelateral interactionbetweenprotofilamentsismuchweaker(Kisetal.2002;Nogales1999;Septetal. 2003);hence,kp>kh,ka.Whileallthelongitudinalintraprotofilamentinteractionsareassumedto bethesame,thelateralinteractionsbetweentheprotofilamentsareknowntobedifferent(Liet al.2002)dependingondirection;hence,khka. Tuszynskietal.(2005)havedonemoleculardynamicscomputationstostudytheelectrostatic propertiesoftubulinheterodimers.Septetal.(2003)performedacomputationofthe protofilamentprotofilamentbindingfreeenergyasafunctionofthelongitudinalshiftalongthe protofilamentaxis.Thedatapublishedinthislatterworkindicatethepresenceoftwostable equilibriumpositionsthatcorrespondtoMTlatticetypesAandB.Theyalsodiscriminatethe polarandelectrostaticcontributiontothefreebindingenergy.Wehaveprocessedthepotential diagrampublishedbySeptetal.(2003)intheirFig.1inordertoevaluatethecorrespondingelastic coefficientinaharmonicapproximationaroundthepotentialminimum.Wefoundthevaluetobe k4N/m. DePabloetal.(2003)estimatedexperimentallybyradialindentationofMTswithascanning forcemicroscopetipanelasticconstantvaluerelatedtolateralinteractionsbetweenprotofilaments. Indentations,inducedbythenanometer-sizedtippositionedonthetopofanMT,resultinalinear elasticresponsewiththeelasticconstantk=0.1N/m.

12

TheestimateofSeptetal.(2003)correspondstointeractionsbetweentwoprotofilamentswhen oneisslidalongitslengthagainsttheotherthatiskeptfixed,theprotofilamentprotofilament shiftalongtheprotofilamentaxis.However,theestimatesofdePabloetal.(2003)correspondto aradialdependenceoftheforceonthedistancetothecentreoftheMT.

Vibration dynamics
Whilewehavenodirectexperimentalevidenceatpresenttoclaimtheanisotropyintheelastic coefficientska,khandkp,itismoreprudenttoallowtheseparameterstodifferfromeachother. Toapproximatelyrepresenttheanisotropy,wejudiciouslychosekp=4.5N/m,kh=0.1N/mand ka=0.01N/m.Themassofthedimeristakentobem=1.831022kg.

Fig.3DispersionrelationsforthecanonicalMT.Thecurvelabeledlongitudinalrepresentsthedispersion relationforvibrationspropagatingalongprotofilaments.Frequenciescanyield310111/s.Thecurvelabeled transverseisthedispersionrelationforvibrationspropagatingalonghelices.Frequenciescanreach510101/s.

DispersionrelationsalongtheprotofilamentandhelixdirectionsarerepresentedinFig.3. Frequenciesreach310111/salongtheprotofilamentdirection,andonly510101/salongthehelix direction.Bothlongitudinalandtransversemodesareacoustical(Fig.3).Thecorresponding propagationvelocitiesrangebetween145and1,260m/s,wherethesmallestvelocityisrelatedto thehelixdirectionandthelargesttotheprotofilamentdirection.Therangeofpropagationvelocities isinaccordancewiththepreviouslypredictedvalues(Pokornyetal.1997;Sirenkoetal.1996a, 1996b).OurfrequenciesareslightlyhigherthanthepredictedfrequenciesofPokornyetal.(1997) (Table1).Theseresults,however,arestillsubjecttoexperimentaldetermination.Itisnoteworthy

13

thatthevibrationswhichpropagatealongtheprotofilamentdososignificantlyfasterthanthose alongthehelix,vx>vy(Table3). [Table3willappearhere.Seeendofdocument.] InFig.4werepresenttheeffectsofthestructuralpropertiesofMTs(numberofprotofilaments andhelices)onthevibrationvelocities.Thevibrationvelocitiesalongtheprotofilamentandhelix directionsareverysensitivetothenumberofprotofilamentsandtothenumberofhelices.The numberofhelices,S,hasalargerinfluencethanthenumberofprotofilaments.FurthermoreShas amajorinfluencewhenthenumberofprotofilamentsisverysmall,i.e.,N=8.

Fig.4Theeffectsofstructuralparametersonvibrationvelocitiesalongtheprotofilamentandhelixdirections. Velocitiesofvibrations,asafunctionofthenumberofprotofilamentsandofhelices,alongtheprotofilament andhelixdirections,respectively

InTable3wegiveourestimatesofthefrequencies,velocitiesandwavelengthsalongthe directionoftheprotofilamentsandofthehelices.

Discussion
FromthehelicalstructureofMTs,wedevelopedaplanarlatticeofdimersthatareconsideredto becoupledoscillatorsvibratingaboutequilibriumpositions.Theuseofadiscretemodelwas necessarytoobtainvibrationdispersionrelationsaccountingforthegeometricalpropertiesofMTs andparticularsofproteinproteininteractions.Ourplanarlatticeofdimerswithoutaseamrespects thegeometricalpropertiesofMTs.Equationsofmotionfordimerswerederivedandanansatzof harmonicsolutionsfoundwhichsatisfytheperiodicboundaryconditions.Weobtaineddispersion relationsforanumberofvibrationalacousticmodesandthecorrespondingpropagationvelocities. Wegiveexplicitexpressionsforvibrationfrequenciesandvelocities,alongbothprotofilament 14

andhelixdirections.Thesequantitiesarefunctionsofonlyelasticconstantsandstructural parametersofMTs. Thus,fromtheplanarlatticeweareabletostudyvibrationmodesofdimersalongprotofilament andhelixdirections,whichrespectivelycorrespondtothelongitudinalandtorsionalmodesof vibrationsofdimersinsidetheMTwall.Itisnoteworthythatthevibrationswhichpropagatealong theprotofilamentdososignificantlyfasterthanthosealongthehelix.Wealsoobserveastrong dependenceofthemicroscopicvibrationalpropertiesofMTsonthenumberofprotofilamentsand ofhelices.Finally,ourpredictedvibrationalfrequenciesandcorrespondingvelocitiesareinthe samerangeasthoseestimatedbySirenkoetal.(1996a,1996b),andslightlylargerthanthose estimatedbyPokornyetal.(1997)(Table1). Thisworkwaspossibleowingtoarecentlyobtainedexperimentalbodyofdatacomingfrom severalgroupsanddescribinganumberofphysicalandstructuralpropertiesofMTs(dePabloet al.2003;Kisetal.2002;Nogales1999;Septetal.2003).ThemostmarkedaspectofMTsobserved wastheanisotropiccharacterofMTelasticitythatisreflectedintheheterogeneityofelastic coefficients.Theoreticalestimatesoftheelasticconstantsrequiredknowledgeofthetubulin dimerdimerinteractionpotentialorrelevantexperimentaldata.Withtheknowledgeofparticular interactionstrengthsbetweentwoneighbouringdimers,resultingfromthe protofilamentprotofilamentshiftingalongtheMTaxis(Septetal.2003)orduringtheradial indentationsofMTs(dePabloetal.2003),asguidance,weobtainedroughestimatesofthe molecularelasticconstantsalongthreedifferentdirectionsontheMTsurface.Thesevalueswere usedforthemodelingofthevibrationaldynamics. Inthisworkwereguidedbyearlierworksthatexploredboththecontinuummediumapproach toacylindricalhollowstructure(Sirenkoetal.1996a)andaone-dimensionalapproximationto thecalculationofphonondispersion(Pokornyetal.1997).Nevertheless,webelievethatneither thecontinuummodelnortheone-dimensionalapproximationisadequateowingtotheheterogeneity oftheMTstructure.However,theknowledgeofseveralmodesofvibrationaswellasthepredicted dispersionrelationsandphononvelocitieswereveryusefulinourmodeling.Theradialmotions arenotdescribedinourmodel(SirenkoandDutta2001).Intermsofthecontinuummedium approximation,ourMTwouldbeacylinderwithafixedradius. Theviscosityofthesurroundingsolution(invitro)orofcytoplasm(invivo)mayaffectvibrations bydampingthemout(FosterandBaish2000).FosterandBaishcalculatedtherelaxationtime causedbyviscousdampingtobeinthenanosecondregion.Foroursmallestpredictedfrequency, weobtainaperiod2ordersofmagnitudesmallerthantherelaxationtime.Furthermore,Pokorny 15

(2004)hasshownthattheviscousdampingeffectsduetothecytoplasmviscositycanbeminimized bytheioncondensationaroundtheMT.Thus,inourmodel,theviscousdampingeffectsare neglected. OurlatticeofdimerswithoutmismatchcanbeclassifiedasaB-typelatticewherelateralcontacts aremadebetweenandsubunits.ThislatticetypeispredominantlyobservedinMT structures;however,MTscanpossessaseaminwhichlateralcontactsexistbetweenheterologous subunits.Inourdynamicalmodel,theseamcouldbedescribedbydifferentelasticconstantsfor theboundarynodestomodeldifferencesofenergyoccurringatthesecontacts.Butnochangewill occurinthegeometricalmodel.Thisaspectstillrequiresfurtherattention. AcknowledgementsS.P.andC.H.weresupportedbyGenomeCanada,theOntarioR&DChallenge FundandtheCanadianInstitutesofHealthResearch.J.T.wassupportedbygrantsfromNSERC andMITACS.J.M.D.wouldliketothankthestaffandmembersofthePhysicsDepartmentofthe UniversityofAlbertaforalltheirkindnessandthoughtfulnessduringhisstay.

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SirenkoYM,StroscioMA,KimKW(1996b)PhysRevE53:1003 SirenkoYM,DuttaM(2001)Phononsinnanostructures.CambridgeUniversityPress,London TolomeoJA,HolleyMC(1997)BiophysJ73:2241 TuszynskiJA,BrownJA,CrawfordE,CarpenterEJ,NipMLA,DixonJM,SataricMV(2005)MathComp Model(toappear) UngerE,BohmKJ,VaterW(1990)ElectronMicroscRev3:355 VanBurenV,OddeDJ,CassimerisL(2002)ProcNatlAcadSciUSA9:6035

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Table1Dynamicalelasticpropertiesofmicrotubules(MTs)
10710101/s(Pokornyetal.(1997) 200600m/s(Sirenkoetal.1996b) 1001,000m/s(Pokornyetal.1997) 8001,300m/s(Sirenkoetal.1996a)

Phononfrequencies Phononvelocities

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Table2Parametervalueswhich,usedinEq.4,givethetwo-dimensionalplanarlatticesofdimersinaccordancewiththeMTsgeometryandwithnomismatchasshowninFigs.1c

and2a
b 2 8 16 6.01 Pitch a e 1.24

N0 d 5.88

r0

S0

13

12

N0andS0representthenumberofprotofilamentsandhelicesinthecanonicalMT.Itsradiusr0andthepitch(S0b)characterizethehelicesdefiningthecanonicalMT.bisthedistancebetweentwoadjacent subunitsalongthesameprotofilament.a,dandearecalculatedbyEqs.2and3.Valuesofr0,b,pitch,a,dandeareexpressedinnanometers.

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Table3Estimatesoffrequencies,velocitiesvandwavelengthsalongtheprotofilamentdirection(labelledx)andalongthehelicalpathway(labelledy)forfourMTs

S=2 A

N=13

N=15

x=3.1510111/s vx=1,256m/s x=3.9109m x=3.1510111/s vx=1,237m/s x=3.9109m

y=4.810101/s vy=147m/s y=3109m y=510101/s vy=151m/s y=3109m

S=3 C

N=13

N=15

x=3.1510111/s vx=1,222(m/s) x=3.8109m x=3.1510111/s vx=1,263m/s x=4109m

y=4.810101/s vy=197(m/s) y=4.1109m y=510101/s vy=167m/s y=3.3109m

AthecanonicalMT(N=13andS=2),BtheMTwith15protofilamentsandtwohelices,CtheMTwith13protofilamentsandthreehelices[threehelicesinthedimerlatticecorrespondsto5-starthelices inthemonomerlattice(Chrtienetal.1998)]andDtheMTwith15protofilamentsandthreehelices

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