Intrinsic Disorder in Histone Proteins

16 Pages·2012·4.69 MB·English

View Online / Journal Homepage / Table of Contents for this issue
Molecular Dynamic Article Links
BioSystems
Citethis:Mol.BioSyst.,2012,8,1886–1901
PAPER
www.rsc.org/molecularbiosystems
More than just tails: intrinsic disorder in histone proteins
Zhenling Peng,a Marcin J. Mizianty,a Bin Xue,b Lukasz Kurgana and
Vladimir N. Uversky*bc
Received17thMarch2012,Accepted7thApril2012
G DOI: 10.1039/c2mb25102g
2
0
1
5
B2 Manybiologicallyactiveproteinsaredisorderedasawhole,orcontainlongdisorderedregions.
M
2 Theseintrinsicallydisorderedproteins/regionsareverycommoninnature,abundantlyfoundin
C
9/ allorganisms,wheretheycarryoutimportantbiologicalfunctions.Thefunctionsofthese
3
1210 proteinscomplementthefunctionalrepertoireof‘‘normal’’orderedproteins,andmanyprotein
erta on 07 June 20bs.rsc.org | doi:10. ffpifnuuartmnnerscciienttlyniisooitcanntrashdeleaisicrnorleaetrrssdiinusneetlrstesisricanaaorclfe2tlyi0choo0den7maissvhpowiirlrsyiedtthhoedernenneepdusseicvnpflreedroioebcmtnieaotic7inoni4sdnf.6osFirsanmpunterradtcitnhiipesecsrirsc.omaWtdeoniisraenoelys,rchsdoienoemstwrr.poinAtlfehstxmiahctoaedasnaislgslebomuttrhhndbeedelsyrame.niedsIcmniensbootaherntdridsosenrsro-tlofcyuledetanhsybte,rouiwhfcniedstaonnte
bu
versity of Al2 on http://p ihpnerothetiresoitnodsni,measen,rdibzuattotiiopsnoastbtostrofalounrtsmelalayttiiononencaelosmfsahoridygihfifoecrratoviroadrniesor.uoslihgiostmoenres,futoncitnitoenrsa,ctsitoanrtsinwgitfhroDmNAandother
Uni201
d by April Introduction the Saccharomyces genome suggested that proteins containing
Downloadeublished on 12 pAhreraaovhltieietgyinahosfup(mnIrDeioqvPduasele)ernna3cn-peDdrooptsfretoirbnutieocsicntluiosergnweiccietaa.h1sll–yi5anTtarwchintheissvoieceleainpllotryrorindtiesinsiiconaprsldalyterhrtdeadiitssordraeodgenionreenowdst Sodbfieyssoiitnnredvtmroeiarnlvtsaieicrcdebdioinoivsientohrfr-oedrreermprergaieuntsilecatnstritsaoetndnusdiconirefistpthrtreiaeovncneesacllfrl’aeispdcnttaoiuorcsnslie.g4aun2ns–ifi4da4cncaFdenlotlarprseiregelxnivkaaamellilenypnglcte.oe3,
P analysis of 401 human transcription factors showed that IDRs
(IDRs) exist as dynamic conformational ensembles,4,6–11 which occupyB50%oftheentiresequenceofhumantranscription
can be collapsed-disordered (molten globule-like), partially factors.44
collapsed-disordered (pre-molten globule-like) or extended-
Another important class of DNA-binding proteins is the
disordered(coil-like).12,13Theyarehighlyabundantinvirtually
histonefamily.Histonesaresmall,highlybasicnuclearproteins
any given proteome2 and are typically involved in regulation,
thatassociatewithDNAinaspecificstoichiometrytoformthe
signaling,andcontrolpathways,14–16thereforecomplementing
nucleosome, which further contributes to the formation of the
thefunctionalrepertoireoforderedproteins.17–20Furthermore,
chromatin fiber to package the complete genome within the
many IDPs are involved in various human diseases.21 This
nucleus.Therearefiveclassesofhistonesinmammals,namely
conclusion is based on numerous case studies in which a
core histones, H2A, H2B, H3, H4, and a linker histone H1
particular IDP was shown to be associated with a particular
(orH5inavianerythrocytes,whichunlikemammalianerythro-
disease;e.g.,variouscancer-associatedproteins22–26andmany
cytes,havenuclei).Eachhistoneclasshasvariousnumbersof
proteins involved in neurodegeneration maladies,27–34 as well
variantsthatareexpressedinacellularcontext-dependentmanner.
asinsystematicbioinformaticsstudies.11,14,17,21,35–40
Activity of histones is tightly regulated via the broad range of
Intrinsic disorder was shown to be verycommon in RNA-
reversible, enzymatic posttranslational modifications (PTMs),
andDNA-bindingproteins.4,8,9,41Theresultsoftheanalysisof constitutingaspecifichistonecode.45–49Sincethemajorfunction
ofhistonesisDNAcondensationinchromatin(seebelow),these
aDepartmentofElectricalandComputerEngineering,Universityof proteinsareintimatelyinvolvedinmajorcellularprocessessuch
Alberta,Edmonton,Canada.E-mail:[email protected], as DNA damage response, X chromosome inactivation, trans-
[email protected],[email protected]
bDepartmentofMolecularMedicine,CollegeofMedicine, criptional regulation, and even formation of an epigenetic
UniversityofSouthFlorida,Tampa,FL33612,USA. memory.50–57 Several diseases and syndromes are related to
E-mail:[email protected],[email protected]; thedysregulationofhistonefunctionsandPTMs.58
Fax:[phone];Tel:[phone]
Asmentionedabove,themajorfunctionofhistoneproteins
cInstituteforBiologicalInstrumentation,RussianAcademyof
isDNApackaginginchromatin,auniqueprotein–DNAcomplex
Sciences,12901BruceB.DownsBlvd.MDC07,142290Pushchino,
MoscowRegion,Russia thattypicallycontainsabouttwiceasmuchproteinasDNA.
1886 Mol.BioSyst.,2012,8,1886–1901 Thisjournalis c TheRoyalSocietyofChemistry2012
View Online
Formation of chromatin is crucial for any eukaryotic cell, involvedinproteindimerization,whereasa1helicesandloops
since it condenses DNA to fit inside the cell nucleus. The formDNAbindingsites.Inthecrystalstructure,histonesare
efficiencyofthispackagingisveryhigh,whichisillustratedby highlyhelicalproteins, witha-helicesaccounting for65–70%
thefactthatthenearly2mlonghumanDNA,initsextended ofthetotalstructure.Only3%ofresiduescanbeassignedto
form,iscondensedtofitintoanucleuswithadiameterofonly formshortparallelb-sheets(loopsinteractions).Therestofthe
5 to 10 mm.59 This high degree of DNA condensation in loopsandtheN-terminalregionsarehighlydisordered.62,63The
chromatin is achieved via interaction with specific proteins sequence of a given histone is highly conserved from yeast to
(histones).ThestructureofchromatinwasproposedbyRoger mammals, but there is only minimal sequence identity, at the
Kornberg in 1974 based on the experiments on partial DNA levelof4–6%,betweenthehistoneproteins.64Inspiteofthis,
digestion showing that the sites accessible to the nuclease the peptide backbones of the four histone monomers overlay
attack were separated by approximately 200 base pairs, and withRMSdeviationsof1.5–2.5A˚ .62Thisisfurtherillustrated
on the beaded appearance of chromatin fibers in electron by Fig. 1A which shows that the central parts of the histone
microscopy.60 These observations led to the conclusion that proteins comprising the core octamer of the X. laevis nucleo-
G
2 DNA in chromatin is composed of repeating 200-base-pair somearewell-aligned.However,bothN-andC-terminiofthese
0
1
5 units that wrap around histone proteins forming nucleosome proteins possess high structural variability, suggesting their
2
B
M and giving the ‘‘beads on a string’’ structure of euchromatin. intrinsicallydisorderednature(seebelow).
C2 Each‘‘bead’’inthechromatinisthenucleosomecoreparticle, Histones H2A and H2B, as well as histones H3 and H4,
39/ which is the elemental subunit in the hierarchy of DNA wereshowntoheterodimerizeinahead-to-tailfashionknown
20
d by University of Alberta on 07 June 201April 2012 on http://pubs.rsc.org | doi:10.1 paetatwDfiorhheucabfiNseahctkSceaehmteikariAassnlsstariroscoecnycgaianorebnokhirvsenneiete.eltt6iigrimhcact1ctaohyioeeonsinrinnrTlsoeefmu1etthuefc4ochcooreun6lhniDseclsldreeebtotecoNacaoasfaruommmaonsycAlfemamheseeatstrprntiihaenilna(tcncyeluHaiaocrlce(fipso2nsaHluefstpAorsntkroie1rhffdus,asoo)tDcorH,iphrtntaymteNaui2hgntosirhrnetBeAttoeeoiyii,cccn,mfcocHalweooecertpr,mfswene3reoaHl,tolpprtrrptsaht1aehao.pnadv,elrenenTdite(bsdmeitHahcueHnnll1eeibeem3tunr.4s.dj6–s5cgae)e5H9lcnodoaetbtta4foihnfioaoml)sadyHu2tcfotosehnmtim2isrnerdseAoetatearoomertm–caoonffHhmcbausottteit2nehhhvoirrBrndeeeeesf, dwlIiaHiHtsconnhtaasihmn3t3neniaetsi––godhcrehHHanvhawerainaiscs44ci2hitrtcasiioiiahtmholnehennaetenthtpeyeddelrsiti4orsa-.ceoobtas-rmerohhfccetosTnaetttaepdawetnlhrkrihwimsxteeomefaoiedmtettmbenlehurHdreuiaoenstdirn2eow.st–eit6AadifaoD3fofcpl,tt–oe6thohNtaH4HorhrecsmAo2etk2foThaoAteBeHfhabhcrdd–noemoie4lHrdilhmbi–niz-gdHeHy2tsepotoahiBdem2l2amnaerABfdkbxoeoecaeiery–dreimrnisnHimnizm.tztmte6aitha2e-4orrtepter–Basaitiroa6.iaolf6ecnHIhr,nxHtnabTeti,t3lhoitem3halwn–eeenn–derHdlohssHocdsti.otio4vdwcii4rTtfrheiiiooemtoehteiinHnenehnsHtetttrrirc3ofrastae3solao–ttfum–ouiomHadottHnnnerhhene3eerdd4eesrs.,,0
Downloadehed on 12 psotafrrutthcicteulefroehuoarfschobireseteonhniessotHolvn1eedinp.rwFoihtgei.cinh1sA,thceoshncoosiwmstsmintoghneosfNtraMulcoRtnugrsaocllemuntotirotainfl fctohouenrtXac-ionrarfleyechxriiysbtsloetanNless-ttraeurrcmetutinhreaelostifatetilhsseothcfoavrtaearnrioeuucnsloeotpsocoosmtmtrepa.l6ne2stleTalhytieorentasaoilllsvmoeodfdaiinl-l
s
bli a-helixwithtwoadjacentsmallera-helicesseparatedbyloops fications,includinglysineacetylationandserinephosphorylation,
Pu (a1-L1-a2-L2-a3),62,63canbeseen.Thea2anda3helicesare that modulate the structure of chromatin.45,67 A specific
combination of posttranslational modifications creates different
biochemicalresponsesbyswitchingvariousgenetranscriptionand
other signaling events on or off.68 The histone tail-mediated
internucleosomal attraction and control of the chromatin
conformationthroughsite-specificposttranslationalmodifica-
tionsconstitutethebasisofthehistonecodehypothesis.45–49
Histone tails arethe membersofthe IDPrealm.68Overall,
theN-terminaltailsarethemostbasicregionsofthehistones.
For example, the histone fold motifs of the Xenopus laevis
proteinscontainanexcessof7and5mol%basicresiduesfor
H2AandH2B,respectively.Thetailscontainnoacidicresidues,
Fig.1 (A)NMRsolutionstructureoftheglobulardomain(residues andinclude38and45mol%basicresidues,forH2AandH2B,
41–113)oftheG.gallushistoneH1(PDBID:1GHC).Tenrepresentative respectively.69Finally,H2AandH2BhistoneshaveC-terminal
members of the conformational ensemble are shown by cartoons of sequences that extend beyond the histone fold. The H2A
different colors. (B) Structural alignment of the histone proteins C-terminal 31residuesadopta largelyextendedconformation;
formingtheX.laevisnucleosomecoreparticle(PDBID:1AOI).There the H2B C-terminal extension of 23 residues is predominantly
areeightproteinchainsinthenucleosomecoreparticle,twoH2A–H2B helical.62Thehighlydynamicnatureofhistonetailsisvisualized
heterodimersand(H3–H4) tetramer.Theseeightchainsarecolorcoded
2 by the X-ray structures of nucleosomes, where tail domains
asfollows:chainA–H3(blue);chainB–H4(red);chainC–H2A(gray);
appear to sample multiple conformations.62,70 Furthermore,
chainD–H2B(orange);chainE–H3(yellow);chainF–H4(tan);chain
somehistonetailsmayadoptspecificsecondarystructureswhile
G–H2A(silver);andchainH–H2B(green).Structuralalignmentwas
done by MultiProt (http://bioinfo3d.cs.tau.ac.il/MultiProt/).156 The boundtoalinkerDNAoracidicpatchesofcorehistones.71–73
alignedstructureswerevisualizedusingtheVMDsoftware.157Asemi- The intrinsically disordered nature of the N-terminal ‘‘tail’’
transparentbluesphereattherightsideofthefigurerepresentsvolume domains (NTDs) of the core histones and the C-terminal
potentiallyoccupiedbytheN-terminaltailsofthecorehistones. tail domains (CTDs) of linker histones, peculiarities of their
Thisjournalis c TheRoyalSocietyofChemistry2012 Mol.BioSyst.,2012,8,1886–1901 1887
View Online
amino acid compositions, and the role of disorderedness in performedasofyet.Tofillthisgap,weanalyzed2007histones
functioningandposttranslationalmodificationsofthesedomains from the Histone Database.99 The analyzed dataset included
were systemized in a review by Hansen et al.74 Based on the all members of all the five major histone classes (H1/H5: 216,
atomreplicaexchangemoleculardynamicssimulationsforeachof H2A:335,H2B:270,H3:999,andH4:187).Weshowthatthe
fourhistonetails,H4,H3,H2B,andH2A,ithasbeenconcluded majority of the histone family members were predicted to be
thatmosttailsarenotfullydisordered,butshowdistinctconfor- mostlydisordered,withintrinsicdisorderextendingfarbeyond
mational organization, containing specific flickering secondary thelimitsofmentionedNTDsofthecorehistonesandCTDsof
structuralelements.68Theseobservationsareingeneralagreement linker histones. The roles ofintrinsic disorder in the function-
withtheresultsoftheexperimentsonnucleosomesusingcircular ality of histones and their posttranslational modifications are
dichroismandacombinationofhydrogenexchangewithNMR alsodiscussed.
thatshowedthatH4/H3tailsacquiredstructuredconformations
aspartofnucleosomecoreparticles,whereasH2AandH2Bwere
foundtobeessentiallydisordered.73,75,76 Materials and methods
G
2 Thenucleosomedoesnotrepresentasimpleandstaticpackaging
0 Datasets
1
5 system,beingadynamicregulatorofDNAchemistriesinthe
2
MB nucleus,includingtranscription,replication,andrepair.77,78This Histone proteins were collected from the Histone Database99
C2 dynamicregulationisachievedviathemodificationofstability, in June 2011. This database combines proteins taken from
39/ structure,andassociationstateofthecorenucleosomeproteins. GenBank, EMBL Nucleotide Sequence Database, DDBJ
20
berta on 07 June 201ubs.rsc.org | doi:10.1 cPdfocooobiasronsrsmetpofiroec’lv’vrur.ea7emld9tadi–arv8dlite7ynuio,crHwoininton.ag8hfwt1oeat–errh8svm7ewebarrieT,tteeihnoihnnanintseauotslhrtscaaeaahtdblipatodlin-rnseieghndseoedesdfntuahcucllaetoentdnafoiosrgflesdrasieeimagnfdlooitlalgadttnlrhhointea‘bo‘ygteuxtlpahatiuderesnrotpedrparaehtondithfsseoitliitoognlidonhose.nesl8dyess7 (SP5dhDWaiRsctNtlFaoIabSAsn(saSePes-seDrPc:oshRaHtaietOnia1innT/stH;Bh,R(5ra2eeP,n)seIkHewRas2ertoeAcfr(phPe,smJr:HFaoo(op2t1veuBa)iennn,dwd)H,aceIht3nPic,aofDoioannlrBn)lsme,dcawa(tnHPethnidr4oiooc.nahttWaellitaRneerndeeopsDanordsoa-uirvctpreaiecrddseeeus)Bded,nidacdinatnateknhtnd)odet,,
d by University of AlApril 2012 on http://p lamFhsotgiurwasgurtgrtocnehpntgierutaerourmtstdeeessenoin,roowcetco,ciocitonthunnthrcaflaoeyionsnldnftibnroienagletgtdinimobh‘pne‘eubosinniusntgdcthtarfeetleadehdssretoseyauftohontmladftdhtaianpaydgtgr,igoffaaratleefesntrgoiedanrbtaitfyohmognegrmomrableadeaegncidtnaiuyiotgtlieneoosslntro’ood’fow.e8flr7.la8ass1rarA–ggol8tee7tf, sstnnhiuuumabWmmtislebbeahteerau,rrovshofoeeydffhpcsittohpshhttaeeoehicnneincetsehoiscanicainish-nlr,asseaihadnlcnolusodwnfiltldnvehhaceiaisntntetctodliTanncaashecsfb-laeutlliiesendkr.see1ssT;.atahepnpnerddo2btt(ehrt3ieeon)askcwfoodferrrormocwemosnldpleaosocptntafedescdtieinhte1ages
Downloadehed on 12 tbIenyttreasrtmaebsetlrienaogrelryde,earsHeild2yAfsot–rruHmc2teuBdreinhs,etthaeenrdopdrpeismoesnescersessoahfnisdgahl(tH,rae3srie–sHtcah4na)cr2eachttoeewtreiazrerodd- a2inn0v0de7sctnhigoaanitn-erseddaisufotnerdrdaesnrtetipncht3haeitnoesnfftroiorremmhi7ds4tao6tnassepeeftac2mi.esDil,yaaatnandsdewtt1aospinuecsrlefuoddrtmeos
blis the urea- and temperature-induced unfolding,69,88–93 with the analysisacrossdifferentkingdoms/phyla.Thisdatasetcontains
Pu conformational stability of these oligomers being dramatically proteinsthatbelongto11phyla,suchasMetazoa(1,425chains),
modulated by salt.89,90,92 The capability of purified histones to Viridiplantae (240 chains), Fungi (184 chains), Alveolata
assembleintolargewell-definedperiodicsuperstructureswiththe (90 chains), Euglenozoa (36 chains), Amoebozoa (10chains),
shapeofbentrodsandfibershasbeendescribed.94–97Infact,all Rhodophyta(7chains),Diplomonadida(6chains),Cryptophyta
individualcorehistonesandtheirmixtureswereshowntoform40 (4chains),Stramenopiles(3chains),andParabasalia(2chains).
to 80 A˚ diameter fibers under suitable in vitro conditions.94–97 Intheanalysis ofintrinsicdisorderdistributionwithindifferent
Thesefibrilshadtheappearanceofadouble-strandedcable,with phyla,westudiedthefirstfivephylathathaveasufficientnumber
intervalsof300–400A˚ betweencrossoverpoints.94–97Itwasalso of chains to warrant statistically sound calculations. Dataset2
shown that core histones are able to form amyloid-like fibrils, includes 696 chains from 30 species that were common to all
mostefficientlyundertheconditionsoflowandneutralpHinthe histoneclasses.Thisdatasetwasusedtoperformcomparative
presenceofhighsaltconcentrations.98 analysisofdisorderbetweendifferenthistoneclasses.
Systematic structural characterization of a sample of
Aminoacidcompositionanalysis
histones from calf thymus, representing a mixture of core
histones, H2A, H2B, H3, and H4, revealed that the bovine Amino acid compositional analysis was carried out using
core histones are intrinsically disordered proteins,98 which Composition Profiler100 (http://www.cprofiler.org) using the
haveextremelyhighconformationalplasticitythatallowedthem PDBSelect25101andtheDisProt102datasetsasreferencefor
toadoptanumberofdifferentconformationsdependingonthe
environmental conditions, therefore possessing a remarkable Table 1 The number of non-redundant histone sequences and the
ability to change their conformation from an ‘‘extended loose correspondingnumberofspeciesforeachclassofhistones
form’’ to a rigid globular oligomeric conformation with high
Numberofnon-redundantsequences(numberofspecies)
propensityforsubsequentaggregation.98Itwasalsomentioned
that the intrinsically disordered nature of histone NTDs and H1/H5class H2Aclass H2Bclass H3class H4class
CTDswasasubjectofseveralexperimentalandcomputational Step1 254(71) 383(105) 311(100) 1043(664) 198(122)
studies. However, the detailed computational analysis of the Step2 216(65) 335(100) 270(94) 999(657) 187(118)
Step3 155(30) 187(30) 162(30) 117(30) 75(30)
prevalenceofintrinsicdisorderinentirehistoneproteinswasnot
1888 Mol.BioSyst.,2012,8,1886–1901 Thisjournalis c TheRoyalSocietyofChemistry2012
View Online
ordered and disordered proteins, respectively. Enrichment The predictions for the entire histone family and for all
or depletion in each amino acid type was expressed as considered phyla were collated and the corresponding averages,
(C (cid:2) C )/C , i.e., the normalized excess of a given standarddeviations,andper-proteindistributionswerecomputed
s order order
residue’s content in a query dataset (C) relative to the using dataset1. We calculated the disorder content, the number
s
correspondingvalueinthedatasetoforderedproteins(C ). of disordered and MoRF segments, and the number of long
order
Amino acid types were ranked according to their increasing (consisting ofatleast30consecutiveaminoacids)disordered
disorder-promotingpotential.17 segments.Suchlongsegmentswerefoundtobeimplicatedin
protein–protein recognition.40 We counted only the segments
which included at least 4 consecutive disordered residues,
Disorderpredictions
which was consistent with.104,121 We computed the same
The prediction of disordered residues and segments was statisticsforeachhistoneclassusingdataset2.
performedusingtherecentconsensus-basedMFDpmethod.103
Calculationofsequenceconservation
This method was shown to provide high quality predictions
G
02 whencomparedtoothermoderndisorderpredictors.104,105The Wereportandcomparethesequenceconservationbetweenthe
1
25 distributionandoverallcontentofintrinsicdisorderinhistone disordered residues and the all residues in the histone proteins.
MB proteins were also analyzed by PONDRs VLXT,106 which Theconservationwasquantifiedusingrelativeentropy122based
C2 applies various compositional probabilities and hydrophobic ontheWeightedObservedPercentages(WOP)profilesgenerated
2039/ measuresofaminoacidastheinputfeaturestoartificialneural by PSI-Blast.123 PSI-Blast was run with default parameters
berta on 07 June 201ubs.rsc.org | doi:10.1 ncVsoeoefLnntWiwsXdtieeetoTninrvtaktei(lisfssftyrooaitnnhcutogtahsitoeepldnooplonotetecghrfnaefetoltrhirDcaemtoldhimsmieCstpoohomorlenedsocieptsumritreolaeednadrtahrciieclconstubdtiioderi1aarnu0ast9e.eecsstt)Ao.ipoinlHrntpehterdhmoneieudccotgepiotc,hritrfois,ttt.Peh1iiO0siten7c,Ni1ocas0hvDp8aevaRriebnarslslye.l trpaw(r3egraasoainsidfiitsnfieul-erslmetsatse.tetrimTmhoehednabersnrukaurs(enis(cid:2)ddneejagarotse3Pfag)XbFr,ieoaIlafnsLaonestTrid,v(wa1de20nho4e.diw0tnco0chtnor1rloPioelpeSema-ydIdvo--etaBcvodloleuaiqoellsuotnstaewdhgSni-rmdteceipofsneyhmno1octt5psolg,.dlneeW2xsn(0ei(cid:2)ee1trryv0dhaa)rit,stee0irwgo.We0ingho0a,Oin1cra)sPhds),
d by University of AlApril 2012 on http://p lilDwpneervvhvieseeeedCllns,iptcoiitrcgnnoeoadrcmtspoii,ocrp1nton0ait9ovrriainnebdsdstuetoatswtltoilhtimoteMwhdonorFfMueeomDsrFanbpaDcoecmarptunaorpdanarrnetdePeddiOsniidcsszNtieiegsvDtohoehrtfrRefdatuhesldlreioasVptnochroaLreedlnXdryetsireTrcinset.a,ecttTdiennpthdchtrelieeusddrodrieirseicsdnositdiegirdodruaeuneednesr- ttbmmahinioonoedndrtsifeipvanibarcngettioedstrdelihoecvstbageiitriyodcanuatalhelrloesrye,sfel1ecra2ceet5aclenetodptavnrlasaysetnreutdetirdicavcrysteas,i,sitostuiseounulstncg.sh1og.2s1fe7a2cs2soctTrasidelhtcsehiinsuartemitiscfite-fchbunaiirtstnltiyomhdneifenroaogiuslflunrunredsuestciraldlaepeuatopeedtdlssii,dc1btae2oy6--
Downloadehed on 12 scfuehgnamcrgteieon–nths(.yCdInDroaFpd)adtphiltoyiot,n(1C1t0Ho,11)D1piaslsCowto4en,1l,l10atwsaotnhdbeiirncacuormymudblaiisntoiavrtdeioedrnicskltanrisobswiufitneiorasns, AWnenoatnantiootnatoefdpposots-tttrraannsslalattioionnaallmmodoidfiicfiactaiotinosns (PTMs) using
blis CH–CDFanalysis,21,111,112wereused. the UniProt database.128,129 First, we mapped the histones
Pu WealsousedMoRFpred113topredictthedisorder-to-order
fromtheHistoneDatabaseintotheircorrespondingaccession
transition binding sites, also referred to as the Molecular
numberinUniProt.Someofthehistones,whichwereextracted
RecognitionFeatures(MoRF),whichmediatebindingevents
fromSWISS-PROT,hadtheaccessionnumber.Intheremaining
promotedbydisorderedregions.MoRFsareshortinteraction-
casesweusedtheidmappingtoolfromUniProt.Atotalof1859
prone regions of 5 to 25 amino acids located within long
(out of 2007) histones were successfully mapped. Next, we
disorderedregions(i.e.flankedbydisorderedregions).MoRFs
extractedPTMannotationsforthesechains.Wefoundanno-
undergo coupled folding and binding; i.e., disorder-to-order
tationsfor493chainsincluding37,145,139,109,and63from
transition induced by binding to specific partners.107,114,115
the H1/H5, H2A, H2B,H3, and H4 classes, respectively. We
MoRFs were found to be associated with signaling and
annotatedtwomaintypesofPTMs:modifiedandcross-linked
regulationfunctionsofintrinsicallydisorderedproteins,where
residues.Thecross-linkedaminoacidsweremostlyinvolvedin
highlyspecificbutweakinteractionsareneeded.11,107,114,115
covalent linkage(s) within and between proteins. We sub-
In addition to MoRFpred, potential binding sites in
divided the modified residues into three types: acetylation,
disordered regions of human histone proteins were searched
methylation, and phosphorylation. We did not find annota-
forusingtheANCHORalgorithm.116,117Thisapproachrelies
tionsforlipidationorglycosylationandtheothermodification
onthepairwiseenergyestimationapproachdevelopedforthe
had toofew annotations (73) to warranta statistically sound
general disorder prediction method IUPred,118–120 and is
analysis. Overall, we found a total of 3025 modified and 339
basedonthehypothesisthatlongregionsofdisordercontain
cross-linkedresidues(seeTable2).
localized potential binding sites that cannot form enough
favorable intrachain interactions to fold on their own, but
are likely to gain stabilizing energy by interacting with a Results and discussion
globular protein partner.116,117 We use the term ANCHOR-
Intrinsicdisorderinlinkerhistones:evidencefromtheNMR
indicatedbindingsite(AiBS)toidentifyaregionofaprotein
solutionstructure
suggested by the ANCHOR algorithm to have significant
potentialtobeabindingsiteforanappropriateandtypically In spite of intensive efforts of several research groups, the
unidentifiedpartnerprotein. crystal structure of the linker H1 histone from higher
Thisjournalis c TheRoyalSocietyofChemistry2012 Mol.BioSyst.,2012,8,1886–1901 1889
View Online
Table 2 The number of PTM annotations for the histone proteins
andspecifichistoneclasses.Themodifiedresiduesaresub-dividedinto
acetylated,methylated,andphosphorylatedaminoacids.Someamino
acids are annotated with several modifications and thus the total
numberofannotatedmodifiedresiduesdoesnotsumtothenumber
ofresiduesinthethreesub-types
All H1/H5 H2A H2B H3 H4
PTMtype histones class class class class class
#modifiedresidues 3035 149 439 669 1399 379
#acetylatedresidues 1694 56 279 493 609 257
#methylatedresidues 1636 3 36 130 1338 129
#phosphorylatedresidues 810 97 179 88 371 75
#cross-linkedresidues 339 6 104 213 0 16
G
2
0 eukaryotesisnotavailableasofyet.ThissuggeststhatH1/H5
1
5
2 histones are difficult crystallization targets, which indirectly
B
M indicatestheirpotentialintrinsicallydisorderednature.Fig.1A
2
9/C represents a solution NMR structure of the H1 globular
203 domain from Gallus gallus (PDB ID: 1GHC), which is a
11
on 07 June 20c.org | doi:10. 7Fmth3iaeg-tr.sieot1srniAudacultseuhfl-roleoexwnwisbgaitlshfitrdayate.gtmtTehrheimsnisitdnioseodmfainatnhinuethnp2eeo2xbs5psu-eerffcseetsseeriddscuosoeingb-tlnsoaeiinfirnvgciaanptngirto2onc1t,oe0insnmifn.o1Mc3re0-
versity of Alberta 2 on http://pubs.rs ulaNiqknaued2leeSyorOuht4sh,igash2ot4lui5tothiniomsincMsdstowrmNeitnhaagiHntloh2wPwcOoiilon4ln,dibicateinosdtnervse3.ne15ng30thmmT.MhoerreeNfdoair2seHo,rPidtOeir4se;dvie.erin.y,
Uni201 Intrinsicdisorderincorehistones:evidencefromthenucleosome Fig.2 StructuraldissectionoftheX.laevisnucleosomecoreparticle
d by April crystalstructure (PDBID:1AOI).(A)Completenucleosomecoreparticlewrappedin
Downloadehed on 12 bTpoahrtehticaHlne3alfayrnosidmsHoXf2.Bthlhaeeavcviresyrsrateanvldesoatlmreud-cctotuhirlaesteogthfmetehnNets-ntpeuracmslseiionnsagolbmteaetiwlcseoeornef DaCHf1N2tebArA)–trHh(edep2oBrDuesdbNeilnmeAtwerhrh,eiiwsmttehoo-enpvreiaenslak.sH((rC2CibA12baao()nngadr)n.adyC(B)(2C))a2nTHbdh)2esAHhn–2ouHBwcl2eh(Booissrtdoaoinmnmgeeees)rcHsoo.2rf(eACtph1(aseairltfivaiecrnsrldet)
s
Publi ttahielsghyarevseodfivtheregDenNtAstrsuucptuerrhese.l6ix2,ItwwhearseaalssothpeotiwnotedHo4uNt-ttheartmoinnalyl atentdramHe2rB. ((Dgr1eeann)doDf 2th)eHs3e–cHon4ddHim2eArs–.H(2DB1adiamnedr.D(D1b))(rHep3–reHse4n)2t
about one-third of the total length of the histone N- and histones H3 (blue) and H4 (red) of the first H3–H4 dimer, whereas
C-terminaltails,whichmakeupB28%ofthemassofthecore (D2a)and(D2b)showhistonesH3(yellow)andH4(tan)ofthesecond
histoneproteins,isseenintheelectrondensitymap,62suggesting H3–H4 dimer. All these structures were visualized using the VMD
that the remainders of tails are highly disordered. Fig. 1B software.157
illustratesthehighlydynamicstatusofbothtailsofcorehistones
fromX.laevisbyshowingtheirdramaticstructuraldivergence. Analysis of the H2A–H2B dimers (Fig. 2C1 and C2), the
Infact,althoughthecentralpartsofthecorehistonesarealmost (H3–H4) tetramer (Fig. 2D), and two H3–H4 dimers
2
indistinguishable structurally, the histone tails are structurally (Fig.2D1andD2)showsthattheseelementarysubcomplexes
diverseandthereforepliable.Ofspecialinterestisthefactthat, ofthenucleosomecoreparticlepossessglobularcoresandare
duetotheirstructuralplasticity,therelativelyshortN-terminal heavilydecoratedwithprotrusions,someofwhichareusedto
tailscanoccupylargevolumes,asshownbyasemi-transparent interactwithDNAandothersarenecessaryfortheformation
bluesphereattherightsideofFig.1B. of higher level complexes. Analysis of the individual histone
In the following parts of this paper we will show that proteins,H2A(Fig.2C1aandC2a),H2B(Fig.2C1bandC2a),
complex structure of the nucleosome core particle is heavily H3(Fig.2D1aandD2a),andH4(Fig.2D1bandD2b),clearly
dependent on (or is determined by) the intrinsic disorder of showstheirveryunusualshapesandanalmostcompletelackof
corehistones.Tothisend,Fig.2representstheresultsofthe globular structure. These peculiar shapes suggest that histones
step-by-step dissection of the nucleosome core particle. The formtheso-calledtwo-state(ordisordered)complexes,wherethe
major goal of this exercise is to show that the shapes of monomersunfoldupondimerseparation.Therefore,individual
individual histone proteins are highly unusual for foldable chainsinsuchcomplexesareverylikelyintrinsicallydisorderedin
globularproteins.Infact,evenbriefglanceatthenucleosome theirunboundformsandfoldatthecomplexformation,whichis
crystalstructurerevealsthathistonespossesslongdisordered different from the so-called three-state (or ordered) complexes,
regions, seen as extended tails protruding from the core individualchainsofwhichareindependentlyfoldedeveninthe
structure (see Fig. 2A). These extensions and protrusions unbound state.131,132 According to Gunasekaran et al.133 the
becomemoreevidentwhenDNAchainsaretakenout(Fig.2B). per-residuesurfaceareaversusper-residueinterfaceareaclearly
1890 Mol.BioSyst.,2012,8,1886–1901 Thisjournalis c TheRoyalSocietyofChemistry2012
View Online
distinguishesbetweenthetwoclassesofproteins,withmonomers
in the two-state complexes being characterized by extended
shapes and larger interface areas, and with monomers in the
three-statecomplexesbeingmoreglobularandcompact.
These observations suggest that the core histone proteins
are intrinsically disordered in their unbound state. This
hypothesis is in strong agreement with earlier experimental
studies which showed that individual core histones, H2A,
H2B, H3, and H4,79–87 and the mixture of the bovine core
histones,donotpossessorderedstructure,98whendissolvedin
waterwithnosaltadded.
Intrinsicdisorderinhistoneproteins:evidencefromtheamino
G
02 acidcomposition
51 Fig.3 Fractional difference in composition between the different
B2 The intrinsically disordered behavior of extended IDPs membersofthehistonefamily,H1/H5(gray),H2A(blue),H2B(cyan),
M
2 (also known as natively unfolded proteins) is determined by H3 (red), and H4 (pink), and a set of completely ordered proteins
C
9/ the unique composition of their amino acid sequences char- calculated for each amino acid residue (compositional profiles). The
3
1210 acterizedbyacombinationoflowmeanhydropathyandhigh fractionaldifferencewasevaluatedas(Cs(cid:2)Corder)/Corder,whereCsis
on 07 June 20c.org | doi:10. medIDlreeicvPatinsrnowgsnetefarotetircscchehroaefwrpognurel,stcoioosmnibn,epcesaaicngthdnioiigfinlhoc.4awnnAtehlttyyddtchrehoepaplremagtteeohdryleeinamddbeestuaanltiksloeydshsmytlreadovlrlneoelgr-, cCtthhooeermrDceposiponsoPstienrtnoidottinnodgfpatracaoobfignalietsveeeonniftsatsiymhnpoiincwtaohnleaifncoditrdaritcnaionssmiecataplaqloyrufisedorfiynsuolsl(rybedtle,aorcearkdnddebpraerCrodsot)re.dpienPrrsooitssfeirtiotinhvmsee.
ded by University of Alberta 2 April 2012 on http://pubs.rs pFoaLOeannshf,,nrdowaaHicbneNtfh,hioldcleVelrdadH(e,Iseso,)adiipt,ndLnhogwud,elldeaorhaisNrbins.choaud,TharnlahdaVndwrreede)ocsrp,ea-hukrpnaIdlonrdDdretoogepnwmPaeilnordsenoo,rtatemmawaimdnnseaagdrirlotneleiyracsordielsdfasaeshoomuircdor-iepmpiduwsnors,enoo:sstnsh,Rmaaetecmss,oousihTtdecilyb,lnohrydSegwerC,saoasiKcs,dpumoWu,hbAniQeosnt,stebo,aaIn(iE,nnWctaYt,dcocia,ai,ofdnGlYFrlCsdye,,., bwtashhoheataafhgervleslmmfreeheoaiceaasisfonnsttrottdcnr.hnloeieusesgFenopdasreioretgedinsv.lhtedoiewdar4nbvouBtcgaoeeoorsds(nrr3tieetshnm0emhseinodotiootwhrurnreeearsss.dbemteMsriofsiaocodvotohurueereranedse0sdienoc,.tr5osivhmn,neaacorwwstro,reehhecna9iiudb3ctcaehti%ohbsinvuohutmeitrnosddtefb7Aoeaahe5nrnAnl%ieetossdslstyw)o.athornOidenafe0intdss.hl2hoeayiip.inrstsdl0tcteoolTel.teu2nernahd%edeesis.desst,
Downloashed on 1 iaWnlsveoesiutnisgetahteaehtcyhodemrsoeppuchtooamtbiiopcno,asbilutitotosntoarlul,cbtCuiaorseme-sbproiensaikthiioinsntgoPnP.er8so,1.fi7T,l1e0hr0,i,1s1000t6o,1to3o4l iinndcliucadteeslonthgadtishoirsdtoerneedpsergomteeinnsts.are largely disordered and
ubli calculates a normalized composition of a given protein or
P Intrinsicdisorderinhistonesfromdifferentphyla
proteindatasetinthe(C (cid:2)C )/C form,whereC isthe
s order order s
content of a given residue in a query (histone) protein or Fig.5showsthathistonesinMetazoahavethelargestdisorder
dataset, and C is the corresponding value for the set of contentandthelargestfractionofchainswithlongdisordered
order
orderedproteinsfromPDBSelect25.101Fig.3showsthat,in segments.Fig.5AshowsthathistonesinFungiandAlveolata
comparisonwithtypicalorderedproteins,histonesaredepleted havelessdisorderthaninMetazoa,followedbyViridiplantae
inthemajororder-promotingaminoacids,W,F,Y(exceptfor and Euglenozoa. However, histones in Euglenozoa have the
H2BandH4),L,V,andN,andareenrichedinsomedisorder- largest number of disordered segments (most of them have 3
promoting residues, particularly R and E (except for H1/H5), disordered segments), and these segments are shorter than in
T, A, and K (except for H2A, H3, and H4). Furthermore, otherphyla(seeFig.5BandC).Fig.5Cshowsthathistonesin
H1/H5 histones are depleted in I and H, and contain the MetazoaandViridiplantaehavethelargestfractionofchains
increasedamountsofPandK,whereasH4ischaracterizedby withlongdisorderedsegments.
high G content. Clearly, the pronounced depletion in bulky
hydrophobic and aromatic amino acids and enrichment in Abundanceofintrinsicdisorderindifferenthistoneclasses
polar and charge residues may define the low propensity of
Fig. 6 shows substantial differences in the disorder profiles
histonesforautonomous(orpartner-independent)folding.
betweenthefivehistoneclasses.Accordingtothedatashown
inFig.6A,theH1/H5classincludeschainswithasubstantial
Disorderintheentirehistonefamily
amount of disorder; about 79% of them have over 60% of
Theconclusiononthehighprevalenceofintrinsicdisorderin disordered residues and the average disorder content is 0.67.
all the members of histone family was further supported by Histones from the H3 and H2B classes have the average
comprehensive computational analysis. Fig. 4 represents the disorder content of 0.6 and 0.53, respectively, while the H2A
resultsoftheintrinsicdisorderanalysisinnon-redundant2007 andH4classeshavealoweramountofdisorder,withcontents
histoneproteinsfromtheHistoneDatabase99bytheconsensus- of 0.48 and 0.41, respectively. Fig. 6B and C reveal that all
basedMFDpmethod.103Fig.4Ashowsthatallhistoneproteins classeshaveasignificantmajorityofproteinswithatleastone
include at least one disordered segment, and the majority of longdisorderedsegment.TheH2AandH2Bclasseshavemore
Thisjournalis c TheRoyalSocietyofChemistry2012 Mol.BioSyst.,2012,8,1886–1901 1891
View Online
G
2
0 Fig.4 DisorderintheentirefamilyofhistoneproteinsevaluatedbytheMFDpmethod.PanelAshowsthefractionofhistoneproteins(y-axis)
1
25 thathaveagivennumber(x-axis)ofdisorderedsegments(blackbars)andlongdisorderedsegments(Z30aminoacids)perchain.PanelBshows
B
M thefractionofchains(y-axis)withagivendisordercontent(x-axis).
2
C
9/
3
20
11
on 07 June 20c.org | doi:10.
erta bs.rs
bu
versity of Al2 on http://p
Uni201
d by April
de2
Downloahed on 1
s
bli
u
P
Fig.5 Disorderinhistonesfromdifferentphyla.PanelsAandBshowthefractionofhistoneproteins(y-axis)thathaveagivennumber(x-axis)
ofdisorderedsegmentsandlongdisorderedsegments(Z30aminoacids),respectively,perchain.PanelCshowsthefractionofchains(y-axis)
withagivendisordercontent(x-axis).
longdisorderedsegmentsperchaincomparedtootherclasses. evaluatedbyDisCon,whichprovidesmoreaccuratedisorder
Histones in the H1/H5 class usually have one (very) long content predictions when compared to MFDp and several
disorderedsegmentperchain,comparedtootherclassesthat other recent disorder predictors,109 and PONDRs VLXT,106
havemoredisorderedsegmentsthatareshorter. which is no longer the most accurate predictor, but is very
Itwasemphasizedthatthecombinedanalysisoftheintrinsic sensitive to the local compositional biases and is capable of
disorder propensity by several computational tools (especially identifying potential molecular interaction motifs.107,108
by tools that utilizes different attributes) provides additional Fig.7Ashowsthathistonescanbeclustered(bytheirintrinsic
advantages,135–138allowing,forexample,bettervisualizationof disorder content) into five clusters that correspond to five
the differences betweenthe variousprotein groups.139 Fig. 7A histonesubfamilies.HistonesH1/H5andH3arecharacterized
illustrates the power of this approach and represents a plot bythehighestdisordercontentevaluatedbybothcomputational
where disorder contents in histones from five groups were tools.Furthermore,allhistonesaremostlydisorderedproteins,
1892 Mol.BioSyst.,2012,8,1886–1901 Thisjournalis c TheRoyalSocietyofChemistry2012
View Online
G
2
0
1
5
2
B
M
2
C
9/
3
20
11
on 07 June 20c.org | doi:10.
erta bs.rs
bu
versity of Al2 on http://p
Uni201 Fig.6 Disorderindifferenthistoneclasses.PanelsAandBshowthefractionofhistoneproteins(y-axis)thathaveagivennumber(x-axis)of
d by April gdiivsoenrddeirseodrdseegrmcoennttsenatnd(xl-oanxgisd).isorderedsegments(Z30aminoacids),respectively,perchain.PanelCshowsthefractionofchains(y-axis)witha
de2
Downloahed on 1 ssicnocreestheexcveaesdtimngaj0o.r4i.tyTohfetihneseatntaolyFzeigd.s7eAqusehnocwesshtahvaetdhiissotorndeesr dpirsootredinesrw(ritahndcoommpaccotilsconafnodrmpartei-o‘n‘mso(‘l‘tmenoltgelnobgulolebsu’’l)e’’f-rloikme
blis canbesortedasH1/H5>H3>H2B>H4EH2Abytheir and rigid well-structured proteins). On the other hand,
Pu disorder content evaluated by DisCon, whereas PONDRs PONDR-basedCDFanalysismaydiscriminatealldisordered
VLXT is less discriminative and provides a slightly different conformations, including molten globules, from rigid well-
sort: H1/H5 > H3 E H2A E H4 > H2B. Interestingly, in folded proteins. Therefore, this discrepancy in the disorder
histone pairs known to form functional heterodimers (H3H4 prediction by CDF and CH-plot provides a computational
and H2AH2B), one chain is always predicted to be more tool to discriminate proteins with extended disorder from
disorderedthantheotherchainofthesamepair. ‘‘molten globules’’. Positive and negative y values in Fig. 7B
Fig. 7B represents the results of CH–CDF analysis of correspondtoproteinspredictedwithinCH-plotanalysistobe
histoneproteinsandprovidesfurthersupporttotheirmostly nativelyunfoldedorcompact,respectively.Ontheotherhand,
disordered nature, and clearly shows their disorder-based positive and negative x values are attributed to proteins
clustering.Inthisplot,thecoordinatesofeachspotarecalculated predicted within the CDF analysis to be ordered or intrinsi-
as a distance of the corresponding protein in the CH-plot callydisordered,respectively.Thus,theresultantquadrantsof
(charge–hydropathy plot) from the boundary (y-coordinate) CDF–CH phase space correspond to the following expecta-
and an average distance of the respective cumulative distri- tions:Q1,proteinspredictedtobedisorderedbyCH-plots,but
bution function (CDF) curve from the CDF boundary ordered by CDFs; Q2, ordered proteins; Q3, proteins pre-
(x-coordinate).21,111,112 The primary difference between these dicted to be disordered by CDFs, but compact by CH-plots
two binary predictors (i.e. predictors which evaluate the pre- (i.e. putative ‘‘molten globules’’); Q4, proteins predicted to
dispositionofagivenproteintobeorderedordisorderedasa be disordered by both methods (i.e. proteins with extended
whole)isthattheCH-plotisalinearclassifierthattakesinto disorder). Although these classifications could be question-
account only two parameters of the particular sequence able for large, multidomain proteins, they provide relatively
(chargeandhydropathy),whereasCDFanalysisisdependent unbiased description of histones, which are typically small
on the output of the PONDRs predictor, a nonlinear classi- proteins.
fier,whichwastrainedtodistinguishorderanddisorderbased Fig.7Bshowsthatthemajorityofhistonesarepredictedto
on a significantly larger feature space. According to these bedisorderedasawhole,withthevastmajorityofthembeing
methodological differences, CH-plot analysis is predisposed found in Q4, and are therefore expected to behave as native
todiscriminateproteinswithasubstantialamountofextended coils or native pre-molten globules in their unbound states.
Thisjournalis c TheRoyalSocietyofChemistry2012 Mol.BioSyst.,2012,8,1886–1901 1893
View Online
G
2
0
1
5
2
B
M
2
C
9/
3
20
11
on 07 June 20c.org | doi:10.
erta bs.rs
bu
versity of Al2 on http://p
Uni201
d by April
de2
Downloahed on 1
s
bli
u
P
Fig.7 Evaluationoftheabundanceofintrinsicdisorderinvariousmembersofthehistonefamily.Inallplots,dataforH1/H5,H2A,H2B,H3
andH4histonesareshownbygray,blue,cyan,redandpinksymbols,respectively.(A)DisCon–PONDRsVLXTplotrepresentingthecorrelation
between the disorder content evaluated by DisCon (y-axis)109 and fraction of intrinsically disordered regions evaluated by PONDRs VLXT
(x-axis).106InsetrepresentsthesameDisCon–PONDRsVLXTplotcontainingmeanvaluesaveragedoverallthedataforeachhistoneclass.
Errorbarscorrespondtothestandarddeviations.(B)CH–CDFplot.21,112InsetrepresentsthesimilarCH–CDFplotcontainingmeanvalues
averaged over all the data for each histone class. Error bars correspond to the standard deviations. (C) 3D CH–CDF–DisCon plot showing
correlationbetweentheDisCon-basedintrinsicdisordercontentinhistoneproteins,theirmeannetchargeandmeanhydropathy.
Furthermore,differenthistonesubfamiliesareclearlycharac- discriminated based on their spatial location within the
terized by the unique charge–hydropathy combinations, and CH–CDF–DisConspace.
theycanbesortedasH1/H5>H2B>H3EH4>H2Aby
theirdisorderpropensities.
Sequenceconservationinhistonefamily
Finally, Fig. 7C represents the 3D-disorder distribution
plot, where the DisCon outputs are added as a third dimen- Theconservationscoreswerecalculatedperchainusingrelative
sion to the CH–CDF plot. This representation clearly entropyevaluations.122Wecalculatedtheconservationperchain
shows that the members of the same histone subfamily are by averaging the conservation scores of the corresponding
clusteredtogether,andthatdifferenthistonesubfamiliescanbe residues;highervaluescorrespondedtostrongerconservation.
1894 Mol.BioSyst.,2012,8,1886–1901 Thisjournalis c TheRoyalSocietyofChemistry2012
View Online
G
2
0
1
5
2
B
M
2
C
9/
3
20
11
on 07 June 20c.org | doi:10.
erta bs.rs
bu
versity of Al2 on http://p
Uni201
d by April
de2
Downloahed on 1
s
bli
u
P
Fig.8 Conservationofhistonechainsanddisorderedresiduesinhistones.PanelAcomparesthefractionofhistoneproteins(y-axis)thathavea
givenrangeofconservationscores(x-axis)withthecorrespondingconservationofdisorderedresiduesinthesechains.PanelsBandCcomparethe
samefractionsforindividualclassesofhistones.
Fig. 8A compares the distributions of these values between differs substantiallybetweenthe histone classes.The histones
disorderedresidues(weaveragedconservationofthedisordered inH1/H5andH3classes(seeFig.8B)arecharacterizedbythe
residues) and all the residues in a given chain for the entire lowest and the highest conservation, respectively. Further-
histone dataset, while Fig. 8B and C show the distributions more, disordered and ordered residues in these two classes
for individual histone classes. Overall, over all histones, the have a similar degree of conservation. The similarity for the
conservationscorescovertheentirespectrumofvaluesandthe H1/H5classislikelyduetothefactthatthemajorityofamino
disorderedresidueshavesimilarconservationwhencompared acid residues in this class are disordered. The histones in the H4
withtheconservationofentirechains.However,theconservation class(seeFig.8B)arecharacterizedbyarelativelylowconservation,
Thisjournalis c TheRoyalSocietyofChemistry2012 Mol.BioSyst.,2012,8,1886–1901 1895