dbPTM3.0(蛋白质翻译数据库)

Publishedonline27November2012

NucleicAcidsResearch,2013,Vol.41,DatabaseissueD295–D305

doi:10.1093/nar/gks1229

dbPTM3.0:aninformativeresourceforinvestigatingsubstratesitespecificityandfunctionalassociationofproteinpost-translationalmodifications

Cheng-TsungLu1,Kai-YaoHuang1,Min-GangSu1,Tzong-YiLee1,2,*,

NeilArvinBretan

a1,Wen-ChiChang3,Yi-JuChen4,Yu-JuChen4andHsien-DaHuang5,6,*

1

DepartmentofComputerScienceandEngineering,YuanZeUniversity,2GradulatePrograminBiomedicalInformatics,YuanZeUniversity,Chung-Li320,3InstituteofTropicalPlantSciences,NationalChengKungUniversity,Tainan701,4InstituteofChemistry,AcademiaSinica,Taipei115,5InstituteofBioinformaticsandSystemsBiologyand6DepartmentofBiologicalScienceandTechnology,NationalChiaoTungUniversity,Hsin-Chu300,Taiwan

ReceivedSeptember18,2012;RevisedOctober26,2012;AcceptedOctober31,2012

ABSTRACT

locatedinprotein-interactingdomains.Additionally,Proteinmodificationisanextremelyimportanttheinformationofstructuraltopologiesontrans-post-translationalregulationthatadjuststhemembrane(TM)proteinsisintegratedindbPTMinphysicalandchemicalproperties,conformation,ordertodelineatethestructuralcorrelationbetweenstabilityandactivityofaprotein;thusalteringthereportedPTMsitesandTMtopologies.Tofacili-proteinfunction.DuetothehighthroughputoftatetheinvestigationofPTMsonTMproteins,themassspectrometry(MS)-basedmethodsinidentify-PTMsubstratesitesandthestructuraltopologyareingsite-specificpost-translationalmodificationsgraphicallyrepresented.Also,literatureinformation(PTMs),dbPTM(http://dbPTM.mbc.nctu.edu.tw/)isrelatedtoPTMs,orthologousconservationsandupdatedtointegrateexperimentalPTMsobtainedsubstratemotifsofPTMsarealsoprovidedinthefrompublicresourcesaswellasmanuallycuratedresource.Finally,thisversionfeaturesanimprovedMS/MSpeptidesassociatedwithPTMsfromwebinterfacetofacilitateconvenientaccesstotheresearcharticles.Version3.0ofdbPTMaimstoberesource.

aninformativeresourceforinvestigatingthesub-stratespecificityofPTMsitesandfunctionalasso-ciationofPTMsbetweensubstratesandtheirINTRODUCTION

interactingproteins.Inordertoinvestigatethesub-Proteinpost-translationalmodi cation(PTM)playsanstratespecificityformodificationsites,anewlyde-essentialroleinvariouscellularprocessesthatadjustsvelopedstatisticalmethodhasbeenappliedtothephysicalandchemicalproperties,folding,conform-identifythesignificantsubstratemotifsforeachation,stabilityandactivityofproteins;thusalteringtypeofPTMscontainingsufficientexperimentalproteinfunction(1).Morethan200differenttypesofdata.AccordingtothedatastatisticsindbPTM,PTMshavebeenidenti edbymassspectrometry(MS)->60%ofPTMsitesarelocatedinthefunctionalbasedproteomics(2).Thebiologicalfunctionsofthisdomainsofproteins.ItisknownthatmostPTMsubiquitousregulatorymechanismsincludephosphoryl-cancreatebindingsitesforspecificprotein-ationforsignaltransduction,attachmentoffattyacidsinteractiondomainsthatworktogetherforcellularformembraneanchoringandassociation,glycosylationfunction.Thus,thisupdateintegratesprotein–forchangingproteinhalf-life,targetingsubstrates,promo-tionofcell–cellandcell–matrixinteractions,acetylationproteininteractionanddomain–domaininteractionandmethylationofhistoneforgeneregulationandtodeterminethefunctionalassociationofPTMsites

ubiquitylationforproteindegradation(3).Withthe

*Towhomcorrespondenceshouldbeaddressed.Tel:+88634638800(ext.3007);Fax:+88634638850;Email:francis@saturn.yzu.edu.tw

CorrespondencemayalsobeaddressedtoHsien-DaHuang.Tel:+88635712121(ext.56952);Fax:+88635739320;Email:bryan@mail.nctu.edu.twTheauthorswishittobeknownthat,intheiropinion,the rstthreeauthorsshouldberegardedasjointFirstAuthors.

ßTheAuthor(s)2012.PublishedbyOxfordUniversityPress.

ThisisanOpenAccessarticledistributedunderthetermsoftheCreativeCommonsAttributionLicense(/licenses/by-nc/3.0/),whichpermitsnon-commercialreuse,distribution,andreproductioninanymedium,providedtheoriginalworkisproperlycited.Forcommercialre-use,pleasecontactjournals.permissions@.

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D296NucleicAcidsResearch,2013,Vol.41,Databaseissuehigh-throughputMSorMS/MS-basedmethodsinprote-omics,severaldatabasesassociatedwithaspeci cmodi -cationtypehavebeenestablished.Phospho.ELM(4),PhosphorylationSiteDatabase(5),PhosphoSitePlus(6),PHOSIDA(7)andPhosPhAt(8)weredevelopedforaccumulatingexperimentallyveri worKIN(9)andRegPhos(10)designedaninte-grativemethodtoidentifythekinase-substratephosphor-ylationnetworks.O-GLYCBASE(11)anddbOGAP(12)arethedatabasesofglycoproteins,mostofwhichincludeexperimentallyveri edO-linkedglycosylationsites.UbiProt(13)storesexperimentalubiquitylatedproteinsandubiquitylationsites,whichareimplicatedinproteindegradationthroughanintracellularATP-dependentpro-teolyticsystem.PupDB(14)isaprokaryoticubiquitin-likeprotein(Pup)databasewhichstoresacollectionofexperi-mentallyidenti edpupylatedproteinsandpupylationsitesfrompublishedarticles.Italsointegratestheinfor-mationofpupylatedproteinswithcorrespondingstruc-turesandfunctionalannotations.AnincreasingnumberofproteomicstudieshavesuggestedthatproteinS-nitrosylationplaysimportantroleinthenitricoxide(NO)-relatedredoxpathway.Withthis,anewdatabasenameddbSNO(15)wasestablishedbymanuallycuratingS-nitrosylationpeptidesfromresearcharticles.

WithregardtopublicresourcesofmultiplePTMtypescurrentlyavailable,UniProtKB/Swiss-Prot(2,16)includesasmuchinformationofPTMsasisavailablewithfunc-tionalandstructuralannotations.SysPTM(17)hasdesignedasystematicplatformformulti-typePTMresearchanddatamining.Additionally,HumanProteinReferenceDatabase(HPRD)(18)containsawealthofinformationrelevanttothefunctionofhumanproteinsinhealthanddisease,aswellastheannotationofPTMs.Withtheimportanceofproteinmodi cationsinbiologicalprocesses,wehavepreviouslyproposeddbPTM(19)whichintegratespublisheddatabasesinordertoobtainexperimentallyvalidatedproteinmodi cations,aswellasputativePTMsubstratesitespredictedbyaseriesofaccuratecomputationaltools(20–22).Version2.0ofdbPTMwasextendedtoaknowledgebasecomprisingthemodi edsites,solventaccessibilityofsubstrate,proteinsecondaryandtertiarystructures,proteindomainsandproteinvariations(23).

DuetothehighthroughputofMS/MS-basedmethodsinidentifyingsite-speci cPTMs,thisversion(dbPTM3.0)notonlyintegratesexperimentalPTMsfrompublicre-sourcesbutalsomanuallycuratesMS/MSpeptidesassociatedwithPTMsfromresearcharticlesusingatextminingapproach.ThedbPTM3.0aimstobeaninform-ativeresourceforinvestigatingthesubstratespeci cityofPTMsitesandfunctionalassociationofPTMsbetweensubstratesandtheirinteractingproteins.Inordertoinves-tigatethesubstratespeci cityformodi cationsites,anewlydevelopedmethod,MDDLogo(24),hasbeenappliedtoidentifythesigni cantsubstratemotifsforeachtypeofPTMs.AccordingtothedatastatisticsindbPTM,>60%ofPTMsitesarelocatedinproteinfunc-tionaldomains.ManyPTMscancreatebindingsitesforspeci cprotein-interactiondomainsthatworktogetherforcellularfunctionandreadthestateofproteometo

cellularorganization(25).Thus,thisupdateintegratesbothprotein–proteininteraction(PPI)anddomain–domaininteractioninformationtodeterminethefunctionalassociationofPTMsiteslocatedinprotein-interactingdomains.Additionally,inordertodelineatethestructuralcorrelationbetweenthereportedPTMsitesandtransmembrane(TM)topologies,theinforma-tionofstructuraltopologiesonTMproteinsisintegratedindbPTM3.0.TofacilitatetheinvestigationofPTMsonTMproteins,PTMsitesaswellasthestructuraltopologyofTMproteinsaregraphicallyrepresented.Furthermore,thewebinterfaceisenhancedtofacilitateaccesstotheresourceandisnowfreelyaccessibleathttp://dbPTM.mbc.nctu.edu.tw/.IMPROVEMENTS

ThehighlightedimprovementsandadvancesindbPTM3.0arepresentedinFigure1includingdataintegrationfrompublicPTMresourcesandresearcharticles,investi-gationofPTMsubstratesitespeci city,investigationofPTM-associatedproteininteractions,aswellastheinves-tigationoftheeffectsofPTMonTMproteins.Tofacili-tatethestudyofPTMsandtheirfunctions,thewebinterfaceisredesignedandenhanced.PublishedliteratureinformationrelatedtoPTMs,orthologousconservationsandsubstratemotifsofPTMsitesarealsoprovidedinthisonlineresource.Thedetailsofeachimprovedprocessaredepictedasfollows.

DataintegrationfrompublicPTMresourcesandresearcharticles

SupplementaryFigureS1showsthedetailedsystem owoftheconstructionofdbPTM3.0.Duetotheinaccess-ibilityofdatabasecontentsinseveralonlinePTMresources,atotal11biologicaldatabasesrelatedtoPTMsareintegratedindbPTM,includingUniProtKB/Swiss-Prot(2),version9.0ofPhospho.ELM(4),PhosphoSitePlus(6),PHOSIDA(26),version6.0ofO-GLYCBASE(11),dbOGAP(12),dbSNO(15),version1.0ofUbiProt(13),PupDB(14),version1.1ofSysPTM(17)andrelease9.0ofHPRD(27).Abriefde-scriptionandthedatastatisticsoftheintegrateddatabasesaregiveninSupplementaryTableS1.Tosolvethehetero-geneityamongthedatacollectedfromdifferentsources,thereportedmodi cationsitesaremappedtotheUniProtKBproteinentriesusingsequencecomparison.WiththehighthroughputofMS-basedmethodsinpost-translationalproteomics,thisupdatealsoincludesmanuallycuratedMS/MS-identi edpeptidesassociatedwithPTMsfromresearcharticlesthroughaliteraturesurvey.First,atablelistofPTM-relatedkeywordsiscon-structedbyreferringtotheUniProtKB/SwissProtPTMlist(/docs/ptmlist.txt)andthean-notationsofRESID(28).Then,all eldsinthePubMeddatabasearesearchedbasedonthekeywordsofthecon-structedtablelist.Thisisthenfollowedbydownloadingthefulltextoftheresearcharticles.Forthevariousexperimentsofproteomicidenti cation,atext-miningsystemisdevelopedtosurveyfull-textliteraturethat

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Figure1.ThehighlightedimprovementsandadvancesindbPTM3.0.

potentiallydescribesthesite-speci cidenti cationofChi-squaredtest 2ðAmodi edsites.Approximately800originalandreviewi,AjÞtoevaluatethedependenceofaminoacidoccurrencebetweentwopositionsAarticlesassociatedwithMS/MSproteomicsandproteiniandAthatsurroundthePTMsubstratesites.MDDLogohasjmodi cationsareretrievedfromPubMed(July2012).demonstrateditseffectivenessinidentifyingsubstrateNext,thefull-lengtharticlesaremanuallyreviewedformotifsofplantandvirusphosphorylation(29,30),preciselyextractingtheMS/MSpeptidesalongwiththeaswellasthemouseS-nitrosylation(31).Inordertomodi edsites.Furthermore,inordertodeterminethelo-extractthemotifsthathaveconservedbiochemicalcationsofPTMsonafull-lengthproteinsequence,thepropertyofaminoacidswhendoingMDD,itcategorizesexperimentallyveri edMS/MSpeptidesarethenthe20typesofaminoacidsinto vegroupssuchasmappedtoUniProtKBproteinentriesbasedonitsaliphatic,polaranduncharged,acid,basicandaromaticdatabaseidenti er(ID)andsequenceidentity.Inthegroups,asshowninSupplementaryFigureS2.Anprocessofdatamapping,MS/MSpeptidesthatcannotexampleofMDDclusteringonS-nitrosylationdataalignexactlytoaproteinsequencearediscarded.showsthatpositionÀ7hasthemaximaldepend-Finally,eachmappedPTMsiteisattributedwithacor-encewiththeoccurrenceofbasicaminoacids,includingrespondingliterature(PubMedID).lysine(k),arginine(r)andhistidine(H).Subsequently,alldatacanbedividedintotwosubgroups:onehasDetectionofPTMsubstratesitespeci cities

theoccurrenceofbasicaminoacidsinpositionÀ7Duetothedif cultyofdetectingtheconservedmotifsforandtheotherdoesnothavetheoccurrenceofbasicaspeci cPTMwithalargedatasize,MDDLogo(24)wasaminoacidsinpositionÀ7.TheMDDclusteringisare-usedtoidentifythesubstratemotifsforeachtypeofcursiveprocesstodividethedatasetsintotree-likePTMscontaining>500modi edpeptides.MDDLogosubgroups.

exploitsmaximaldependencedecomposition(MDD)inordertodiscoverconservedmotifsfromagroupofIntegrationofproteindomains,domain–domainalignedsignalsequences.MDDgroupsasetofalignedinteractionsandPPIs

signalsequencesintosubgroupsthatcapturethemostsig-Protein-interactiondomainsusuallyrecognizeshortni cantdependenciesbetweenpositions.MDDadopts

peptidemotifsofatargetproteinbutdonotbind

stably

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D298NucleicAcidsResearch,2013,Vol.41,DatabaseissueuntilthepeptideshavetheappropriatePTMs;thiscancreatebindingsitesforspeci cprotein-interactiondomainsthatworktogetherforcellularfunctionandreadthestateofproteometocellularorganization(25).Forinstance,theSH2domaincanbindtophospho-tyrosine(pTyr)-associatedpeptidesinamannerthatdependsonligandphosphorylationandthemotifofthe ankingaminoacids(32,33).Thus,thisupdateintegratestheinformationofproteinfunctionaldomainsandPPIstoinferthePTM-dependentproteininteractions.Toinvesti-gatethepreferenceoffunctionaldomainsforPTM,thisstudyreferstothedomainannotationsinInterPro(34).InterProisanintegratedresource,whichwasdevelopedinitiallyasameansofrationalizingthecomplementaryeffortsofthePROSITE(35),PRINTS(36),Pfam(37)andProDom(38)databases,forprovidingprotein‘signa-tures’suchasproteinfamilies,domainsandfunctionalsites.Fortheinformationofexperimentallyveri edPPIs, vedatabasesincludingDIP(39),MINT(40),IntAct(41),HPRD(18)andSTRING(42)areintegratedindbPTM(seeSupplementaryTableS2).Additionally,thedomain–domaininteractionsofInterDom(43)arealsointegratedtodeterminethefunctionalassociationforthePTMsiteswhichlocateinprotein-interactingdomains.

IntegrationofTMproteinswithstructuraltopologyTMproteinsplaycrucialrolesinvariouscellularprocesses(44).Agenome-widestudyhasdiscoveredthat$20–30%oftheproteinsencodedbyatypicalgenomeareTMproteins(45).However,duetotheexperimentaldif cultiesinobtaininghigh-qualitystructures,TMproteinsarenotablyunder-representedinProteinDataBank(46).ThebiologicalrolesofPTMsplayingonTMproteinsincludephosphorylationforsignaltransductionandiontransport,acetylationforstructurestability,at-tachmentoffattyacidsformembraneanchoringandas-sociation,aswellastheglycosylationforreceptorstargeting,cell–cellinteractionsandvirusinfection(44,47).WiththeimportanceofPTMsfunctioningonTMproteins,theexperimentallycuratedinformationofmembranetopologiesiscollectedfromTMPad(48),TOPDB(49),PDB_TM(50)andOPM(51).InordertoprovideacomprehensiveinvestigationofTMproteins,apotentialsetofTMproteinsisextractedfromUniProtKB(52)bychoosingproteinentrieswhichcontainthekeyword‘TRANSMEM’infeature(‘FT’)line,thelocal-izationof‘membrane’andtheinformationofTMtopology.ThepotentialTMproteinsarefurther lteredusingaTMpredictionprogramMEMSAT(53)todeter-mineitsmembranetopologies.AsshowninSupplementaryTableS3,the lteringprocessresultedin2216experimentaland43142potentialTMproteinswithmembranetopologies.TofacilitatetheinvestigationofPTMsonTMproteins,thestructuraltopologyofTMproteinsisgraphicallyrepresentedusingPHPGDlibrary,aswellasthePTMsubstratesites.Moreover,thetertiarystructuresofTMproteinsandPTMsitesarevisualizedusingtheJmolprogram(54).

Integrationofexternalbiologicaldatabases

Foragivenprotein,thebasicbiologicalfunctionscanbeobtainedfromtheannotationsofUniProtKB.Toprovidemoreinformationaboutproteinfunctionalandstructuralannotationsrelevanttothemodi edproteinsandthePTMsubstratesites,thedatacontentsofGeneOntology(GO)(55),ProteinDataBank(PDB)(46)andClustersofOrthologousGroups(COGs)(56)havebeenintegratedindbPTM.Inthisstudy,theinformationre-gardingthemolecularfunction,cellularcomponentsandbiologicalprocessforamodi edproteincanbeaccessedbyacrosslinkthatreferstothecorrespondingentryfromQuickGO(57)viaaUniProtKBaccessionnumber.Inordertofacilitatetheinvestigationofstructuralcharacter-isticssurroundingthePTMsubstratesites,proteintertiarystructureobtainedfromPDBwasgraphicallypresentedbyJmolprogram.Forproteinswithtertiarystructures(5%ofUniProtKB/Swiss-Protproteins),theproteinstructuralproperties,suchassolventaccessibilityandsec-ondarystructureofresidues,werecalculatedbyDSSP(58).WithrespecttothepreviousstudiesinvestigatingthestructuralcharacteristicsofPTMs(59–61)inproteinswithoutknowntertiarystructures,twoeffectivetools,RVP-net(62)andPSIPRED(63),areusedtopredictthesolventaccessibilityandsecondarystructure,respectively.InordertoobservewhetheraPTMsiteslocatedintheconservedregionsamongorthologousproteinsequences,theCOGsofproteinswereintegratedandtheClustalW(64)programwasadoptedtoimplementthealignmentofmultipleproteinsequencesineachCOGcluster.

DATACONTENTANDUTILITYDatastatisticsoftheintegratedPTMsites

InordertoprovidethemostcomprehensivedataofPTMs,thisupdatenotonlyintegratesexperimentalPTMsfrom11externalPTM-relatedresourcesbutalsomanuallycuratesMS/MSpeptidesassociatedwithPTMsfrom$800researcharticles.Afterremovingtheredun-dancydataamongtheseheterogeneousresources,therearetotally208521experimentalPTMsitesindbPTM3.0.AlltheexperimentalPTMsitesarefurthercategorizedbyPTMtypesandthenumberofnon-redundantPTMsitesiscalculated.AsthedatastatisticsofrepresentativePTMtypesshowninTable1,proteinphosphorylationcontainsthemostabundantdataofexperimentallyveri edsubstratesites.DuetothehighthroughputofMs/MS-basedproteomicsinthesite-speci cidenti cationofmodi edpeptides,severalPTMshaveasigni cantlyincreasingnumberofexperimentaldata,includingproteinubiquitylation,acetylation,methylation,N-linkedandO-linkedglycosylation,aswellastheemergingS-nitrosylation.InadditiontotheexperimentalPTMsites,UniProtKB/Swiss-ProtprovidesputativePTMsitesbyusingsequencesimilarityorevolutionarypoten-tial,whichareannotatedas‘bysimilarity’,‘potential’or‘probable’inthe‘MOD_RES’ elds.Atotalof226122putativesitesforallPTMtypesareintegratedindbPTM.

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Table1.DatastatisticsofexperimentalandputativePTMsitesindbPTMPTMtypes

NumberofexperimentalNumberofputativeNumberof

substratesitessubstratesitesfromHMM-predictedsitesUniProtKB/Swiss-ProtPhoshorylation142446741741414879

Ubiquitylation

2364717028865N-linkedglycosylation1524287529418253Acetylation

9683199811156O-linkedglycosylation35083695373758Amidation25331445114034Hydroxylation162912749743Methylation

1585547922332Pyrrolidonecarboxylicacid82974212322Sumoylation

72580013042Gamma-carboxyglutamicacid4488141942Palmitoylation312525233830Sulfation

20780070005Myristoylation

1781275988C-linkedglycosylation156993923Prenylation13013276741Nitration80931432Deamidation521652022

S-nitrosylation3096170–Oxidation

333180–ADP-ribosylation140164–N6-succinyllysine8869–Formylation56125–GPIanchoring34849–Bromination

3356–N6-malonyllysine33167–Citrullination32110–N6-carboxylysine301566–Glutathionylation1932–FAD19163–Others121815825–

Total

208521

226122

2509267

Moreover,aKinasePhos-likemethod(19–22)hasbeensubstratesites.Accordingtothemultiplesequencealign-adoptedtoconstructthepro lehiddenMarkovmodelsmentresultoforthologousproteins,userscaninvestigate(HMMs)for18typesofPTM.Especiallyinproteinphos-whetheraPTMsitelocatedinevolutionaryconservedphorylation,>70kinase-speci cpredictionmodelsareregions,whichindicatesthattheorthologoussitesinconstructedandusedtoidentifytheputativephosphoryl-otherspeciescouldbeinvolvedinthesamemodi cation.ationsiteswiththeirkinases.ThesemodelswereappliedAdditionally,thisupdateincorporatestheproteinfunc-tosearchthepotentialPTMsitesagainstUniProtKB/tionaldomainsanddomain–domaininteractionstoinferSwiss-Protproteinsequences.AsgiveninTable1,totally2509267putativesitesforallPTMtypesarethePTM-dependentproteininteractions.Moreover,thedetectedbyHMMswith90%predictivespeci city.AllliteraturesassociatedwithPTMsarecategorizedbythetheexperimentalPTMsitesandputativePTMsitesaremodi cationtype.

availableanddownloadableinthewebinterface.Inadditiontothedatabasequerybytheproteinname,genename,UniProtKBIDoraccession,theproteinEnhancedwebinterface

sequenceisallowedforhomologysearchagainstUniProtKBproteinsequencedatabaseusingBlast(65)TofacilitatetheuseofthedbPTMresource,thewebinter-program.ForbrowsefunctionofdbPTMwebsite,afacehasbeenredesignedandenhancedtoallowef cientsummarytableofPTMtypesandtheirmodi edaccesstotheproteinofinterest.SupplementaryFigureS3residuesisprovidedforuserstoef cientlyaccesstheshowsthecontentofatypicaldbPTMquery:(i)quicknumberofdatainaspeci cmodi edaminoacidofasearchbyIDsandkeywords,(ii)basicinformation,PTMtype.TheannotationsofPTMtypesarereferred(iii)graphicalvisualizationofPTMsiteswithstructuraltotheUniProtKB/Swiss-ProtPTMlist(http://www.characteristicsandfunctionaldomains,(iv)/docs/ptmlist.txt).AsdepictedinSupplemen-experimentalPTMsiteswithreportedliterature,taryFigureS4,theacetylationoflysine(K)ischosento(v)orthologousconservationofPTMsubstratesites,obtainmoredetailedinformationsuchasthelocationof(vi)PPIsanddomain–domaininteractionsand(vii)litera-themodi cationinproteinsequence,themodi edturerelatedtoPTMs.ThecombinedvisualizationofPTMchemicalformula,themassdifferenceandthesubstratesitesandfunctiondomainsforaproteinsequencecanhelpsitespeci city,whichisthepreferenceofaminoacidsuserstounderstandthefunctionalassociationsofPTMsurroundingthemodi cationsites.Thestructural

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D300NucleicAcidsResearch,2013,Vol.41,Databaseissuecharacteristics,suchassolventaccessibilityandsecondaryfurthercategorizedinto>200kinasegroups.AsgiveninstructuresurroundingthePTMsubstratesites,arealsoSupplementaryFigureS5,mostofthekinase-speci csub-provided.Additionally,thesubstratesitespeci cityofstratemotifshaveconservedaminoacidssurroundingthetheacetylatedlysinesisinvestigatedindetailwithrefer-phosphorylationsites.ForthePTMsotherthanphos-encetothesubcellularlocalizationsofacetylatedproteins.phorylation,therearenoannotationsofcatalyticPreviousworkhasdemonstratedthattheco-localizationofacetyltransferasesandsubstrateproteinscouldbeaenzymesortransferasesduetotheexperimentaldif cultypromisingmethodtoinvestigatethesubstratesiteinidentifyingthecatalyticenzymesforaspeci cPTM.speci citiesandcouldbeadoptedtoimprovethecompu-Basedonthebasicconceptofsequenceconservation,atationalidenti cationofproteinacetylationsites(66).sequencelogocoulddisplaythesubstratemotifforeachPTMtypewithagroupofalignedsequences.However,itInvestigationofPTMsubstratesitespeci cities

isdif culttoexploreconservedmotifsforlarge-scalesequencedata;forinstance,asequencelogoforallphos-Givenawindowlength,n,thefragmentof2n+1residuesphorylationdatainvolvedwithvariouscatalytickinasescenteringonPTMsite(position0)isextractedandthefailstoobviouslypresentthekinase-speci csubstratespe-positionalfrequenciesofaminoacidsarecalculatedandci city.Thus,forthePTMcontainingsuf cientdataofpresentedassequencelogosbyWebLogo(67).experimentalsubstratesites,MDDLogowasperformedtoSupplementaryFigureS5showsthesubstratemotifandclusteragroupofalignedsubstratesequencesintosub-structuralcharacteristicsofexperimentalphosphorylationgroupscontainingstatisticallysigni cantmotifs.Asthesites.Accordingtothekinaseclassi cationextractedfromexampleofproteinS-nitrosylationpresentedinFigure2,KinBase(/)andRegPhos(10),thesub-10sequencelogos,whichwereidenti edfrom3095stratesitespeci cityofproteinphosphorylationcouldbe

S-nitrosylatedpeptideswitha13-merwindow

length,

Figure2.TheMDDLogo-identi edsubstratemotifsofproteinS-nitrosylationsites.

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containaconservedmotifofpositivelychargedaminocovers47S-nitrosylationsites.Anotherpreferredfunc-acids(K,RandH)surroundingtheS-nitrosocysteine.tionaldomainisthe‘RNArecognitionmotif,RNP-1’Interestingly,the rstandsixthgroupscontainthedomainwithInterProID:IPR000504whichcovers46conservedmotifsofnegativelychargedaminoacids(DS-nitrosylationsites.ThisinvestigationindicatesthatandE)accompaniedbypositivelychargedaminoacidstheseS-nitrosylationsitesmayplayimportantrolesinattwospeci cpositions.Consistentwithpreviousstudies(68–73),theS-nitrosylatedcysteinesmaybethedomainsofproteinsinvolvinginDNAorRNAlocatedwithinanacid-basemotif ankedbyacidicandbinding(74).Inaddition,SupplementaryTableS5basicaminoacids.

showsthedistributionoffunctionaldomainscoveringsubstratesitesforseveralrepresentativePTMs,includingInvestigationofPTM-associateddomainsandproteinacetylation,methylation,hydroxylation,N-linkedandinteractions

O-linkedglycosylation,phosphorylationandubiquitylation.

AccordingtothedatastatisticsindbPTM,>60%ofex-ManyPTMsprovidebindingsitesforspeci cprotein-perimentallyveri edPTMsiteslocateinthefunctionalinteractiondomains,whichoftencontainaconserveddomainsofproteins.Suchstatisticscouldbeanalyzedinstructureforthemodi edsiteandamore exibledetailforeachtypeofPTMs.Forinstanceofproteinsurfaceforthe ankingaminoacids,synergizetoS-nitrosylation,whichisanemergingPTMplayingregulatecellularprocesses(75–78).InordertoinvestigatecrucialroleintheregulationofNO-relatedcellularthePTM-associatedproteininteractions,theinformationprocesses,thestatisticsshowsthat$70%ofthereportedofdomain–domaininteractionscollectedfromInterDomS-nitrosylationsiteslocatewithinthefunctionaldomains.isadoptedinthisstudy.Asthecasestudyof‘HistoneH3’Furthermore,thedetaileddistributionoffunctional(UniProtKBID:H31_HUMAN)presentedinFigure3,domainscoveringS-nitrosylationsitesisgivenin‘Heterochromatinprotein1homologalpha’(‘HP1’,SupplementaryTableS4.ItisobservedthatthemostUniProtKBID:CBX5_HUMAN)and‘WDrepeat-preferredfunctionaldomainisthe‘nucleotide-bindingcontainingprotein5’(‘WDR5’,UniProtKBID:alpha–betaplait’withInterProID:IPR012677which

WDR5_HUMAN)interactwith‘HistoneH3’.

When

Figure3.Acasestudyofdomain–domaininteractionsandPTM-associatedproteininteractionsonHistoneH3(UniProtKBID:H31_HUMAN).

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D302NucleicAcidsResearch,2013,Vol.41,Databaseissueinvestigatingtheproteininteractionbetween‘HP1’andcategorizedintofourtypes:extracellular,cytoplasmic,‘HistoneH3’indetail,thereisadomain–domaininter-TMandunknownregions.SupplementaryTableS6pro-actionbetween‘Chromodomain’(InterProID:videsthestructuraldistributionofPTMscontaining>10IPR000953)and‘HistoneH3’(InterProID:IPR000164).substratesitesonexperimentalTMproteins.Interestingly,AmongthePTMslocatedinthedomainof‘HistoneH3’,withouttheconsiderationofsubstratesiteslocatedinapreviousstudyhasdemonstratedthatthe‘HP1unknownregion,alloftheN-linked(GlcNAc...)glycosy-chromodomain’canbindtothe‘HistoneH3’methylatedlationsitesarelocatedintheextracellularregion,aswellatlysine10(79).AnotherproteininteractionshowsthatastheO-linkedandC-linkedglycosylationsites.Thisin-thereisadomain–domaininteractionbetweenthe‘WD40vestigationisreasonabletounderstandthebiologicalRepeat’(InterProID:IPR001680)and‘HistoneCore’effectofglycosylationfunctioningonTMproteinsfor(InterProID:IPR007125).Ithasbeenproposedthatthereceptortargetingandcell–cellinteractions(47).structuralmotifforthespeci crecognitionofmethylatedOtherwise,thephosphorylationsitesaremainlylocated‘HistoneH3’lysine5by‘WD40Repeat’of‘WDR5’isincytoplasmicregions,whichinducesignaltransductionessentialtovertebratedevelopment(80,81).Thisinvesti-andiontransport.ThestructuraldistributionofPTMgationindicatesthattheotherPTMsitescouldbethesitescouldbethemeanstoinferthepotentialrolesofpotentialbindingsitesforprotein-interactiondomains.PTMsfunctioningonTMproteins.Actually,apreviousworkhasdemonstratedthattheincorporationofInvestigationofPTMsitesonTMproteins

membranetopologycouldimprovetheperformanceofpredictingO-linkedglycosylationsitesonTMproteinsAccordingtothedatastatisticsofPTMsitesandTM(82).SupplementaryFigureS6showsagraphicalproteinsindbPTM,atotalof9644and68775PTMsub-visualizationofthePTMsandmembranetopologyonstratesiteslocateonthe2088experimentaland33747humanBeta-2adrenergicreceptor(ADRB2).Further-potentialTMproteins,respectively.Inordertoinvestigatemore,twomodi cationsitesTyr141(pTyr)andCys341thestructuraldistributionofPTMsitesonTMproteins,(S-palmitoylcysteine)arefurtherhighlightedinredonthethestructuraltopologiesofaTMproteinaremainly

tertiarystructure(PDBID:2R4R)usingJmolviewer,

Table2.Advancesandimprovementsinthisupdate(dbPTM3.0)FeaturesdbPTM1.0

dbPTM2.0

dbPTM3.0

ProteinentryUniProtKB/Swiss-ProtUniProtKB/Swiss-Prot(releaseUniProtKBrelease2012-04

(release46)

55)

ExperimentalPTMUniProtKB/Swiss-Prot,UniProtKB/Swiss-Prot,

UniProtKB/Swiss-Prot,HPRD,SysPTM,

resource

Phospho.ELMandPhospho.ELM,PHOSIDA,Phospho.ELM,PhosphoSitePlus,PHOSIDA,O-GLYCBASEHPRD,O-GLYCBASEandO-GLYCBASE,dbOGAP,dbSNO,UbiProtUbiProtandPupDB

LiteraturesurveyofPTMs––>5000modi edpeptidesextractedfrom$800articles

Literaturesrelatedto–

Yes

Yes(categorizedbyPTMtypes)PTMS

ComputationallypredictedPhosphorylation,20typesofPTM

18typesofPTM

PTMs

glycosylationandsulfation

ProteintertiarystructureProteinDataBank(PDB)ProteinDataBank(PDB)ProteinDataBank(PDB)

StructuralpropertiesofAminoacidfrequencyAminoacidfrequency,solventAminoacidfrequency,solventaccessibility,sec-PTMsitesaccessibilityandsecondaryondarystructureandintrinsicdisorderregionstructure

PTMannotation

RESID(373PTMRESID(431PTMannotations)RESID(431PTMannotations)

annotations)Kinasefamilyannotation–

KinBaseKinBaseandRegPhosProteinfunctionaldomainInterProInterProInterProandInterProScan

Protein–proteininteraction––DIP,MINT,IntAct,HPRDandSTRINGDomain–domain––InterDom

interaction

Functionalassociationof––PTM-associateddomainsandPTM-dependentPTM

proteininteractions

PTMsubstratemotif

–WebLogoWebLogoandMDDLogoEvolutionaryconservation–

ClustalW

ClustalWandCOG

ofPTMsites

Transmembranetopology–

–

TMPad,PDBTM,TOPDBandOPM

Graphicalvisualization

PTM,solventaccessibility,PTM,solventaccessibility,sec-PTM,solventaccessibility,secondarystructure,proteinvariationandondarystructure,proteinvari-proteinvariation,proteindomain,tertiarystruc-proteindomain

ation,proteindomain,tertiaryture,orthologousconservation,sequencelogo,structure,orthologousconser-PTMsubstratemotifs,domain–domaininter-vationandsequencelogo

action,protein–proteininteraction,transmem-branetopologyandtertiarystructureofPTMs

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whichindicatesthesolventaccessibilityanddistancebetweenthem.CONCLUSION

TheexpansionofthedbPTMdatabaseincreasesitsuse-fulnessforresearchersinvestigatingtheimpactofPTMsonproteinfunctionandcellularprocesses.Additionally,theenhancedwebinterfaceenablesbothwet-labbiologistsandbioinformaticsresearcherstoef cientlyexplorethefurtherinformationaboutproteinPTMs.Table2sum-marizestheadvancementsandnewfeaturessupportedindbPTM3.0.Inthefuture,weexpectdbPTMtocontinuetogrowwiththeincreasingavailabilityofdatainre-sourcessuchasPhospho.ELM,PhosphoSitePlusandUniProtKB.OneareathatwecanenvisiondbPTMim-provinggreatlyinprospectiveworksisimplementingamoreaccuratemethodforthediscoveryofPTMsubstratemotifs.Also,enhancementsonthetextminingalgorithmwillenablethesystemtoselectMS/MSpeptidesfromresearcharticlesassociatedwithproteinmodi cationswithahighercon dencerate.InordertoprovidemoreadequateinformationforPTMfunction,thedescriptionsassociatedwiththebiologicalfunctionofPTMswillbeextractedfromresearcharticlesusinganinformationre-trievalsystem.Moreover,thethermodynamicparametersforproteins(83),PPIs(84)andprotein–nucleicacidinter-actions(85)couldbeintegratedfortheinvestigationofPTM-associatedproteinstability.AVAILABILITY

ThedatacontentofdbPTMwillberegularlymaintainedandsemiannuallyupdated.Theresourceisnowavailableathttp://dbPTM.mbc.nctu.edu.tw/.SUPPLEMENTARYDATA

SupplementaryDataareavailableatNAROnline:Sup-plementaryTables1–6andSupplementaryFigures1–6.FUNDING

NationalScienceCounciloftheRepublicofChina nan-cialsupport,[contractno.101-2628-E-155-002-MY2,NSC101-2311-B-009-003-MY3,NSC100-2627-B-009-002,NSC101-2911-I-009-101andNSC101-2319-B-400-001].Fundingforopenaccesscharge:NationalScienceCouncilofTaiwan.

Con ictofintereststatement.Nonedeclared.REFERENCES

1.Mann,M.andJensen,O.N.(2003)Proteomicanalysisof

post-translationalmodi cations.Nat.Biotechnol.,21,255–261.2.Farriol-Mathis,N.,Garavelli,J.S.,Boeckmann,B.,Duvaud,S.,Gasteiger,E.,Gateau,A.,Veuthey,A.L.andBairoch,A.(2004)Annotationofpost-translationalmodi cationsintheSwiss-Protknowledgebase.Proteomics,4,1537–1550.

NucleicAcidsResearch,2013,Vol.41,Databaseissue

D303

3.Seo,J.andLee,K.J.(2004)Post-translationalmodi cationsandtheirbiologicalfunctions:proteomicanalysisandsystematicapproaches.J.Biochem.Mol.Biol.,37,35–44.

4.Dinkel,H.,Chica,C.,Via,A.,Gould,C.M.,Jensen,L.J.,Gibson,T.J.andDiella,F.(2011)Phospho.ELM:adatabaseofphosphorylationsites—update2011.NucleicAcidsRes.,39,D261–D267.

5.Wurgler-Murphy,S.M.,King,D.M.andKennelly,P.J.(2004)ThePhosphorylationSiteDatabase:aguidetotheserine-,threonine-,and/ortyrosine-phosphorylatedproteinsinprokaryoticorganisms.Proteomics,4,1562–1570.

6.Hornbeck,P.V.,Kornhauser,J.M.,Tkachev,S.,Zhang,B.,Skrzypek,E.,Murray,B.,Latham,V.andSullivan,M.(2012)

PhosphoSitePlus:acomprehensiveresourceforinvestigatingthestructureandfunctionofexperimentallydetermined

post-translationalmodi cationsinmanandmouse.NucleicAcidsRes.,40,D261–D270.

7.Gnad,F.,Ren,S.,Cox,J.,Olsen,J.V.,Macek,B.,Oroshi,M.andMann,M.(2007)PHOSIDA(phosphorylationsitedatabase):management,structuralandevolutionaryinvestigation,andpredictionofphosphosites.GenomeBiol.,8,R250.

8.Heazlewood,J.L.,Durek,P.,Hummel,J.,Selbig,J.,Weckwerth,W.,Walther,D.andSchulze,W.X.(2008)PhosPhAt:adatabaseofphosphorylationsitesinArabidopsisthalianaandaplant-speci cphosphorylationsitepredictor.NucleicAcidsRes.,36,D1015–D1021.

9.Linding,R.,Jensen,L.J.,Pasculescu,A.,Olhovsky,M.,Colwill,K.,Bork,P.,Yaffe,M.B.andPawson,T.(2008)NetworKIN:a

resourceforexploringcellularphosphorylationnetworks.NucleicAcidsRes.,36,D695–D699.

10.Lee,T.Y.,Bo-KaiHsu,J.,Chang,W.C.andHuang,H.D.(2011)

RegPhos:asystemtoexploretheproteinkinase-substratephosphorylationnetworkinhumans.NucleicAcidsRes.,39,D777–D787.

11.Gupta,R.,Birch,H.,Rapacki,K.,Brunak,S.andHansen,J.E.

(1999)O-GLYCBASEversion4.0:areviseddatabaseofO-glycosylatedproteins.NucleicAcidsRes.,27,370–372.12.Wang,J.,Torii,M.,Liu,H.,Hart,G.W.andHu,Z.Z.(2011)

dbOGAP—anintegratedbioinformaticsresourceforproteinO-GlcNAcylation.BMCBioinformatics,12,91.

13.Chernorudskiy,A.L.,Garcia,A.,Eremin,E.V.,Shorina,A.S.,

Kondratieva,E.V.andGainullin,M.R.(2007)UbiProt:adatabaseofubiquitylatedproteins.BMCBioinformatics,8,126.

14.Tung,C.W.(2012)PupDB:adatabaseofpupylatedproteins.

BMCBioinformatics,13,40.

15.Lee,T.Y.,Chen,Y.J.,Lu,C.T.,Ching,W.C.,Teng,Y.C.and

Huang,H.D.(2012)dbSNO:adatabaseofcysteineS-nitrosylation.Bioinformatics,28,2293–2295.

16.Apweiler,R.,Bairoch,A.,Wu,C.H.,Barker,W.C.,Boeckmann,B.,

Ferro,S.,Gasteiger,E.,Huang,H.,Lopez,R.,Magrane,M.etal.(2004)UniProt:theUniversalProteinknowledgebase.NucleicAcidsRes.,32,D115–D119.

17.Li,H.,Xing,X.,Ding,G.,Li,Q.,Wang,C.,Xie,L.,Zeng,R.and

Li,Y.(2009)SysPTM:asystematicresourceforproteomic

researchonpost-translationalmodi cations.Mol.CellProteomics,8,1839–1849.

18.KeshavaPrasad,T.S.,Goel,R.,Kandasamy,K.,Keerthikumar,S.,

Kumar,S.,Mathivanan,S.,Telikicherla,D.,Raju,R.,Shafreen,B.,Venugopal,A.etal.(2009)HumanProteinReferenceDatabase—2009update.NucleicAcidsRes.,37,D767–D772.

19.Lee,T.Y.,Huang,H.D.,Hung,J.H.,Huang,H.Y.,Yang,Y.S.and

Wang,T.H.(2006)dbPTM:aninformationrepositoryofproteinpost-translationalmodi cation.NucleicAcidsRes.,34,D622–D627.

20.Huang,H.D.,Lee,T.Y.,Tzeng,S.W.,Wu,L.C.,Horng,J.T.,

Tsou,A.P.andHuang,K.T.(2005)IncorporatinghiddenMarkovmodelsforidentifyingproteinkinase-speci put.Chem.,26,1032–1041.

21.Huang,H.D.,Lee,T.Y.,Tzeng,S.W.andHorng,J.T.(2005)

KinasePhos:awebtoolforidentifyingproteinkinase-speci cphosphorylationsites.NucleicAcidsRes.,33,W226–W229.22.Wong,Y.H.,Lee,T.Y.,Liang,H.K.,Huang,C.M.,Wang,T.Y.,

Yang,Y.H.,Chu,C.H.,Huang,H.D.,Ko,M.T.andHwang,J.K.(2007)KinasePhos2.0:awebserverforidentifyingprotein

Downloaded from / at Da Lian Science and Technology University on March 25, 2013

D304NucleicAcidsResearch,2013,Vol.41,Databaseissue

kinase-speci cphosphorylationsitesbasedonsequencesandcouplingpatterns.NucleicAcidsRes.,35,W588–W594.23.Lee,T.Y.,Hsu,J.B.,Chang,W.C.,Wang,T.Y.,Hsu,P.C.and

Huang,H.D.(2009)Acomprehensiveresourceforintegratinganddisplayingproteinpost-translationalmodi cations.BMCRes.Notes,2,111.

24.Lee,T.Y.,Lin,Z.Q.,Hsieh,S.J.,Bretana,N.A.andLu,C.T.(2011)

Exploitingmaximaldependencedecompositiontoidentifyconservedmotifsfromagroupofalignedsignalsequences.Bioinformatics,27,1780–1787.

25.Seet,B.T.,Dikic,I.,Zhou,M.M.andPawson,T.(2006)Reading

proteinmodi cationswithinteractiondomains.Nat.Rev.Mol.CellBiol.,7,473–483.

26.Gnad,F.,Gunawardena,J.andMann,M.(2011)PHOSIDA2011:

theposttranslationalmodi cationdatabase.NucleicAcidsRes.,39,D253–D260.

27.Mishra,G.R.,Suresh,M.,Kumaran,K.,Kannabiran,N.,Suresh,S.,

Bala,P.,Shivakumar,K.,Anuradha,N.,Reddy,R.,Raghavan,T.M.etal.(2006)Humanproteinreferencedatabase—2006update.NucleicAcidsRes.,34,D411–D414.

28.Garavelli,J.S.(2004)TheRESIDDatabaseofProtein

Modi cationsasaresourceandannotationtool.Proteomics,4,1527–1533.

29.Lee,T.Y.,Bretana,N.A.andLu,C.T.(2011)PlantPhos:using

maximaldependencedecompositiontoidentifyplant

phosphorylationsiteswithsubstratesitespeci city.BMCBioinformatics,12,261.

30.Bretana,N.A.,Lu,C.T.,Chiang,C.Y.,Su,M.G.,Huang,K.Y.,

Lee,T.Y.andWeng,S.L.(2012)Identifyingprotein

phosphorylationsiteswithkinasesubstratespeci cityonhumanviruses.PLoSOne,7,e40694.

31.Lee,T.Y.,Chen,Y.J.,Lu,T.C.andHuang,H.D.(2011)SNOSite:

exploitingmaximaldependencedecompositiontoidentifycysteineS-nitrosylationwithsubstratesitespeci city.PLoSOne,6,e21849.

32.Bradshaw,J.M.andWaksman,G.(2002)Molecularrecognitionby

SH2domains.Adv.ProteinChem.,61,161–210.

33.Verkhivker,G.M.,Bouzida,D.,Gehlhaar,D.K.,Rejto,P.A.,

Schaffer,L.,Arthurs,S.,Colson,A.B.,Freer,S.T.,Larson,V.,Luty,B.A.etal.(2001)Hierarchyofsimulationmodelsin

predictingmolecularrecognitionmechanismsfromthebindingenergylandscapes:structuralanalysisofthepeptidecomplexeswithSH2domains.Proteins,45,456–470.

34.Hunter,S.,Apweiler,R.,Attwood,T.K.,Bairoch,A.,Bateman,A.,

Binns,D.,Bork,P.,Das,U.,Daugherty,L.,Duquenne,L.etal.

(2009)InterPro:theintegrativeproteinsignaturedatabase.NucleicAcidsRes.,37,D211–D215.

35.Bairoch,A.(1991)PROSITE:adictionaryofsitesandpatternsin

proteins.NucleicAcidsRes.,19(Suppl.),2241–2245.

36.Attwood,T.K.,Beck,M.E.,Bleasby,A.J.andParry-Smith,D.J.

(1994)PRINTS—adatabaseofproteinmotif ngerprints.NucleicAcidsRes.,22,3590–3596.

37.Sonnhammer,E.L.,Eddy,S.R.andDurbin,R.(1997)Pfam:a

comprehensivedatabaseofproteindomainfamiliesbasedonseedalignments.Proteins,28,405–420.

38.Corpet,F.,Gouzy,J.andKahn,D.(1998)TheProDom

databaseofproteindomainfamilies.NucleicAcidsRes.,26,323–326.

39.Xenarios,I.,Salwinski,L.,Duan,X.J.,Higney,P.,Kim,S.M.and

Eisenberg,D.(2002)DIP,theDatabaseofInteractingProteins:aresearchtoolforstudyingcellularnetworksofproteininteractions.NucleicAcidsRes.,30,303–305.

40.Chatr-Aryamontri,A.,Ceol,A.,Palazzi,L.M.,Nardelli,G.,

Schneider,M.V.,Castagnoli,L.andCesareni,G.(2006)MINT:theMolecularINTeractiondatabase.NucleicAcidsRes.,35,D572–D574.

41.Kerrien,S.,Alam-Faruque,Y.,Aranda,B.,Bancarz,I.,Bridge,A.,

Derow,C.,Dimmer,E.,Feuermann,M.,Friedrichsen,A.,Huntley,R.etal.(2007)IntAct—opensourceresourcefor

molecularinteractiondata.NucleicAcidsRes.,35,D561–D565.42.vonMering,C.,Jensen,L.J.,Kuhn,M.,Chaffron,S.,Doerks,T.,

Kruger,B.,Snel,B.andBork,P.(2007)STRING7—recentdevelopmentsintheintegrationandpredictionofproteininteractions.NucleicAcidsRes.,35,D358–D362.

43.Ng,S.K.,Zhang,Z.,Tan,S.H.andLin,K.(2003)InterDom:a

databaseofputativeinteractingproteindomainsforvalidatingpredictedproteininteractionsandcomplexes.NucleicAcidsRes.,31,251–254.

44.Vinothkumar,K.R.andHenderson,R.(2010)Structuresof

membraneproteins.Q.Rev.Biophys.,43,65–158.

45.Wallin,E.andvonHeijne,G.(1998)Genome-wideanalysisof

integralmembraneproteinsfromeubacterial,archaean,andeukaryoticorganisms.ProteinSci.,7,1029–1038.

46.Rose,P.W.,Beran,B.,Bi,C.,Bluhm,W.F.,Dimitropoulos,D.,

Goodsell,D.S.,Prlic,A.,Quesada,M.,Quinn,G.B.,Westbrook,J.D.etal.(2011)TheRCSBProteinDataBank:redesignedwebsiteandwebservices.NucleicAcidsRes.,39,D392–D401.

47.Ackers,G.K.andSmith,F.R.(1985)Effectsofsite-speci camino

acidmodi cationonproteininteractionsandbiologicalfunction.Annu.Rev.Biochem.,54,597–629.

48.Lo,A.,Cheng,C.W.,Chiu,Y.Y.,Sung,T.Y.andHsu,W.L.(2011)

TMPad:anintegratedstructuraldatabaseforhelix-packingfoldsintransmembraneproteins.NucleicAcidsRes.,39,D347–D355.49.Tusnady,G.E.,Kalmar,L.andSimon,I.(2008)TOPDB:topology

databankoftransmembraneproteins.NucleicAcidsRes.,36,D234–D239.

50.Tusnady,G.E.,Dosztanyi,Z.andSimon,I.(2005)PDB_TM:

selectionandmembranelocalizationoftransmembraneproteinsintheproteindatabank.NucleicAcidsRes.,33,D275–D278.51.Lomize,M.A.,Lomize,A.L.,Pogozheva,I.D.andMosberg,H.I.

(2006)OPM:orientationsofproteinsinmembranesdatabase.Bioinformatics,22,623–625.

52.Bairoch,A.,Apweiler,R.,Wu,C.H.,Barker,W.C.,Boeckmann,B.,

Ferro,S.,Gasteiger,E.,Huang,H.,Lopez,R.,Magrane,M.etal.(2005)TheUniversalProteinResource(UniProt).NucleicAcidsRes.,33,D154–D159.

53.Nugent,T.andJones,D.T.(2009)Transmembraneprotein

topologypredictionusingsupportvectormachines.BMCBioinformatics,10,159.

54.Herraez,A.(2006)Biomoleculesinthecomputer:Jmoltothe

rescue.Biochem.Mol.Biol.Educ.,34,255–261.

55.Consortium,T.G.O.(2011)TheGeneOntology:enhancementsfor

2011.NucleicAcidsRes.,40,D559–D564.

56.Tatusov,R.L.,Fedorova,N.D.,Jackson,J.D.,Jacobs,A.R.,

Kiryutin,B.,Koonin,E.V.,Krylov,D.M.,Mazumder,R.,Mekhedov,S.L.,Nikolskaya,A.N.etal.(2003)TheCOGdatabase:anupdatedversionincludeseukaryotes.BMCBioinformatics,4,41.

57.Binns,D.,Dimmer,E.,Huntley,R.,Barrell,D.,O’Donovan,C.and

Apweiler,R.(2009)QuickGO:aweb-basedtoolforGeneOntologysearching.Bioinformatics,25,3045–3046.

58.Kabsch,W.andSander,C.(1983)Dictionaryofproteinsecondary

structure:patternrecognitionofhydrogen-bondedandgeometricalfeatures.Biopolymers,22,2577–2637.

59.Shien,D.M.,Lee,T.Y.,Chang,W.C.,Hsu,J.B.,Horng,J.T.,

Hsu,P.C.,Wang,T.Y.andHuang,H.D.(2009)Incorporatingstructuralcharacteristicsforidenti put.Chem.,30,1532–1543.

60.Lu,C.T.,Chen,S.A.,Bretana,N.A.,Cheng,T.H.andLee,T.Y.

Carboxylator:put.AidedMol.Des.,25,987–995.

61.Lee,T.Y.,Hsu,J.B.,Lin,F.M.,Chang,W.C.,Hsu,P.C.and

Huang,H.D.N-Ace:usingsolventaccessibilityand

put.Chem.,31,2759–2771.

62.Ahmad,S.,Gromiha,M.M.andSarai,A.(2003)RVP-net:online

predictionofrealvaluedaccessiblesurfaceareaofproteinsfromsinglesequences.Bioinformatics,19,1849–1851.

63.McGuf n,L.J.,Bryson,K.andJones,D.T.(2000)ThePSIPRED

proteinstructurepredictionserver.Bioinformatics,16,404–405.64.Thompson,J.D.,Higgins,D.G.andGibson,T.J.(1994)CLUSTAL

W:improvingthesensitivityofprogressivemultiplesequencealignmentthroughsequenceweighting,position-speci cgappenaltiesandweightmatrixchoice.NucleicAcidsRes.,22,4673–4680.

65.Altschul,S.F.,Madden,T.L.,Schaffer,A.A.,Zhang,J.,Zhang,Z.,

Miller,W.andLipman,D.J.(1997)GappedBLASTand

Downloaded from / at Da Lian Science and Technology University on March 25, 2013

PSI-BLAST:anewgenerationofproteindatabasesearchprograms.NucleicAcidsRes.,25,3389–3402.

66.Lee,T.Y.,Hsu,J.B.,Lin,F.M.,Chang,W.C.,Hsu,P.C.and

Huang,H.D.(2010)N-Ace:usingsolventaccessibilityand

put.Chem.,31,2759–2771.

67.Crooks,G.E.,Hon,G.,Chandonia,J.M.andBrenner,S.E.(2004)

WebLogo:asequencelogogenerator.GenomeRes.,14,1188–1190.

68.Hao,G.,Derakhshan,B.,Shi,L.,Campagne,F.andGross,S.S.

(2006)SNOSID,aproteomicmethodforidenti A,103,1012–1017.

69.Greco,T.M.,Hodara,R.,Parastatidis,I.,Heijnen,H.F.,

Dennehy,M.K.,Liebler,D.C.andIschiropoulos,H.(2006)

Identi cationofS-nitrosylationmotifsbysite-speci A,103,7420–7425.

ne,P.,Hao,G.andGross,S.S.(2001)S-nitrosylationisemerging

asaspeci candfundamentalposttranslationalprotein

modi cation:head-to-headcomparisonwithO-phosphorylation.SciSTKE,2001,re1.

71.Stamler,J.S.,Toone,E.J.,Lipton,S.A.andSucher,N.J.(1997)

(S)NOsignals:translocation,regulation,andaconsensusmotif.Neuron,18,691–696.

72.Greco,T.M.,Hodara,R.,Parastatidis,I.,Heijnen,H.G.,

Dennehy,M.K.,Liebler,D.C.andIschiropoulos,H.(2006)

Identi cationofS-nitrosylationmotifsbysite-speci A,103,7420–7425.

73.Chen,Y.-J.,Ku,W.-C.,Lin,P.-Y.,Chou,H.-C.,Khoo,K.-H.and

Chen,Y.-J.(2010)S-alkylatinglabelingstrategyforsite-speci cidenti cationofthes-nitrosoproteome.J.ProteomeRes.,9,6417–6439.

74.delaTorre,A.,Schroeder,R.A.,Bartlett,S.T.andKuo,P.C.(1998)

Differentialeffectsofnitricoxide-mediatedS-nitrosylationonp50andc-junDNAbinding.Surgery,124,137–141;discussion141–132.

75.Su,D.,Hu,Q.,Li,Q.,Thompson,J.R.,Cui,G.,Fazly,A.,

Davies,B.A.,Botuyan,M.V.,Zhang,Z.andMer,G.(2012)StructuralbasisforrecognitionofH3K56-acetylatedhistoneH3-H4bythechaperoneRtt106.Nature,483,104–107.

NucleicAcidsResearch,2013,Vol.41,Databaseissue

D305

76.Umehara,T.,Nakamura,Y.,Jang,M.K.,Nakano,K.,Tanaka,A.,

Ozato,K.,Padmanabhan,B.andYokoyama,S.(2010)StructuralbasisforacetylatedhistoneH4recognitionbythehumanBRD2bromodomain.J.Biol.Chem.,285,7610–7618.

77.Owen,D.J.,Ornaghi,P.,Yang,J.C.,Lowe,N.,Evans,P.R.,

Ballario,P.,Neuhaus,D.,Filetici,P.andTravers,A.A.(2000)ThestructuralbasisfortherecognitionofacetylatedhistoneH4bythebromodomainofhistoneacetyltransferasegcn5p.EMBOJ.,19,6141–6149.

78.Durocher,D.,Taylor,I.A.,Sarbassova,D.,Haire,L.F.,

Westcott,S.L.,Jackson,S.P.,Smerdon,S.J.andYaffe,M.B.(2000)ThemolecularbasisofFHAdomain:phosphopeptidebindingspeci cityandimplicationsforphospho-dependentsignalingmechanisms.Mol.Cell,6,1169–1182.

79.Nielsen,P.R.,Nietlispach,D.,Mott,H.R.,Callaghan,J.,

Bannister,A.,Kouzarides,T.,Murzin,A.G.,Murzina,N.V.andLaue,E.D.(2002)StructureoftheHP1chromodomainboundtohistoneH3methylatedatlysine9.Nature,416,103–107.80.Wysocka,J.,Swigut,T.,Milne,T.A.,Dou,Y.,Zhang,X.,

Burlingame,A.L.,Roeder,R.G.,Brivanlou,A.H.andAllis,C.D.(2005)WDR5associateswithhistoneH3methylatedatK4andisessentialforH3K4methylationandvertebratedevelopment.Cell,121,859–872.

81.Han,Z.,Guo,L.,Wang,H.,Shen,Y.,Deng,X.W.andChai,J.

(2006)Structuralbasisforthespeci crecognitionofmethylatedhistoneH3lysine4bytheWD-40proteinWDR5.Mol.Cell,22,137–144.

82.Chen,S.A.,Lee,T.Y.andOu,Y.Y.(2010)Incorporatingsigni cant

aminoacidpairstoidentifyO-linkedglycosylationsiteson

transmembraneproteinsandnon-transmembraneproteins.BMCBioinformatics,11,536.

83.Gromiha,M.M.,An,J.,Kono,H.,Oobatake,M.,Uedaira,H.and

Sarai,A.(1999)ProTherm:ThermodynamicDatabaseforProteinsandMutants.NucleicAcidsRes.,27,286–288.

84.Kumar,M.D.andGromiha,M.M.(2006)PINT:protein-protein

InteractionsThermodynamicDatabase.NucleicAcidsRes.,34,D195–D198.

85.Prabakaran,P.,An,J.,Gromiha,M.M.,Selvaraj,S.,Uedaira,H.,

Kono,H.andSarai,A.(2001)Thermodynamicdatabaseforprotein-nucleicacidinteractions(ProNIT).Bioinformatics,17,1027–1034.

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