三種分析蛋白結(jié)構(gòu)域(Domains)的方法

1、三種分析蛋白結(jié)構(gòu)域(Domains)的方法三種分析蛋白結(jié)構(gòu)域(Domains)的方法1,SMARAH,蛋白結(jié)構(gòu)和功能分析SMARTSSMART(aSimpleModularArchitectureResearchTool)allowstheidentificationandannotationofgeneticallymobiledomainsandtheanalysisofdomainarchitectures.Morethan500domainfamiliesfoundinsignalling,extracellularandchromatin-associatedproteinsared

2、etectable.Thesedomainsareextensivelyannotatedwithrespecttophyleticdistributions,functionalclass,tertiarystructuresandfunctionallyimportantresidues.Eachdomainfoundinanon-redundantproteindatabaseaswellassearchparametersandtaxonomicinformationarestoredinarelationaldatabasesystem.Userinterfacestothisdat

3、abaseallowsearchesforproteinscontainingspecificcombinationsofdomainsindefinedtaxa.Forallthedetails,pleaserefertothepublicationsonSMART.SMARTttp:smart.embl-heidelberg.de/),可以說是蛋白結(jié)構(gòu)預(yù)測(cè)和功能分析的工具集合。簡(jiǎn)單點(diǎn)說，就是集合了一些工具，可以預(yù)測(cè)蛋白的一些二級(jí)結(jié)構(gòu)。如跨膜區(qū)(Transmembranesegments)，復(fù)合螺旋區(qū)(coiledcoilregions),信號(hào)肽(Signalpeptides),蛋白結(jié)構(gòu)域(

4、PFAMdomains 等。SMART?該知道的1,SMAR 有兩種不同的模式：normal 或 genomic主要是用的數(shù)據(jù)庫不一樣。 NormalSMART,用的數(shù)據(jù)庫 Swiss-Prot,SP-TrEMBL 和stableEnsemblproteomes。GenomicSMART,用全基因組序列。詳細(xì)列表：http:smart.embl-heidelberg.de/smart/listgenomes.pl2,一些名詞解釋http:smart.embl-heidelberg.de/help/smartglossary.shtmlSMAR 進(jìn)行時(shí)可以直接用各個(gè)數(shù)據(jù)庫蛋白的ID。 如Unip

5、rot/EnsemblID/Accessionnumber(ACC)?；蚴侵苯拥鞍仔蛄?。運(yùn)行 SMAR 也可選擇 signalpeptides、PFAMdomains 等的預(yù)測(cè)，勾上就是。看下圖SequenceanalysisYoumayuseeitheraUnjprutXEnsemtilsequenceidentifier(ID)/accessionnumberCACC)orsequenceitselftorequestttieSMARTsemceSequenceIDorACC(Q8N9N1SequencelUGJJrrTVGLAVCJTPHEVCTmSSFLNSQGRLNSCHFSTmGI

6、QMFQALNVKPRELLRHGRCPPTSLIRCHmYFRHDLFI,KPVFLLTFLTFSULHLCLLL3APSQIYISVfHLFSLPlCRFCLGlIDYIYLGLLKTLPTFPSVRSFPSVmiVFIKKTHKTmL1VPST1mFLCFTLQ 工 TQKSYLYFLQFl5Y5PLMAL5HPURF555TIISMI?ksiyS5TF5P51T1SequenceSMARTIResetHMMERsearchesoftheSMARTdatabaseoccurbydefault.YoumayalsafindSMARGESctuH!用3l.(1QQe)PfW!.的拉恥我.Sa

7、i.廿狷95.陽舁不部4Letuniaet.值口值)岫c相 E 刖熠住s.ctai:10.1093/t*arflgknfipeMESETUPFAQABOUTGLOSSARYWHAFSHEWFEEDSACKutlierhomologiesandhomologuesofknownstructurePFAMdomainssignalpeptidesinternalrepeatsMriq迎p(rt 日indisorderSMARTS運(yùn)行后的結(jié)果用圖表表示。其實(shí)運(yùn)行后的結(jié)果都有明確的解釋詳細(xì)請(qǐng)看下Mouseoverdomainundefinedregionformoreinfo;clickanittog

8、otodetainedarinatation;TransmemtiranesegmentsaspredictedbytheWWW2program(I).colledcoilregionsderpeptidesdeterminedbytheprogram().Introrpc-sitiorsareindicatedwithvertical不同結(jié)構(gòu)的預(yù)測(cè)由不同的工具完成。如果你想了解更多，可訪問去該工具的網(wǎng)站?？缒^(qū)(Transmembranesegments),TMHMM2ogram。(用表示)復(fù)合螺旋區(qū)(coiledcoilregions),Coils2program0(用表示)信號(hào)肽(Sig

9、nalpeptides),SignalPprogram。()蛋白結(jié)構(gòu)域(PFAM,PFAM等等。不止這幾個(gè)的。其它不一一列舉。因?yàn)槎际窃敿?xì)的說明。點(diǎn)擊圖標(biāo)鏈接，就能看到該區(qū)域的序列，或是一些詳細(xì)的描述。如上圖的跨膜區(qū)，點(diǎn)擊進(jìn)去就是該跨膜區(qū)從開始到結(jié)束的序列。面。SMARMGST1_HUMAN(P1ISshutEet司I,(ISaajPnciG.刖.凡初.SQtwsa95.5637-5364Leitunicetsi.WjtctefccsWs,田 m,doi：!10二!1。4內(nèi)krSSHOMESETLIPFAQABOUTOLOSARYWHATStJEWFEEDBACKtransferase1Dom

10、ainswithinHomosapiensproteinNDUA6HUMAN(P5lpeptidesdeterminedbythe3ra/Fprogram().Hitsonlyfoundby日LASTareIndicated網(wǎng).DisorderedregionsdetectedbyDisEtdBL().另外，不一定所有預(yù)測(cè)的區(qū)域都會(huì)用在圖示里看到。一般 SMART 勺顯示順序是SMARTPFAMPROSPEROrepeatsSignalpeptideTransmembraneCoiledcoilUnstructuredregionsLowcomplexity。另夕卜其它不用圖解顯示的區(qū)域，在底

11、下的表格也有詳細(xì)說明。2,Sanger 的 Pfam 數(shù)據(jù)庫網(wǎng)址：http:/pfam.sanger.ac.uk/目前的版本：Pfam23.0(July2008,10340families)ThePfamdatabaseisalargecollectionofproteinfamilies,eachrepresentedbymultiplesequencealignmentsandhiddenMarkovmodels(HMMs).SMARcovered時(shí)domainsreindicatedbyHOMESETUPFAQABOUTGLOSSARYUVHATSNEWFEEDBACKSehuitset

12、al,口gq盯Fee用禮AcMSa5szi35.我口.科 gbfturicet3l.pOOGJM除田間?武號(hào)fifey34,如MouseoverdomainJundefinedr&gionformoreirtfo;clickonittogotodetailedannotation;TramsmembranesegmentsaspredictedbtheTAfK/WM?program:!),tailedcoilregionsdePfam23,0(July2008,10340families)ThePfamdatabaseisalrgscollectioncfproteinfamilies

13、jeachrepresentedalignmentsandhiddenMarkovmodels(HMMs),PdDreANALYZEYOURPROTEINSEQUENCEIP5steyourprateinsecjuenceheretnfinBL&USK1V&CtFSftpsDtmELCKSLreiTIIinSKESITTSKUirRlHklEETEEIETCITSEnnEntEDFIFEPDQ三resultspage.jrsearchsequence(7siqnificaritsnd9insiqnifitrit),Voudidnotehoosetoicethatyousubmi

14、tted,Pfamdomainsonanawsequence.VIEWAGLAMVIEWASEQUENCEVIEWASTRUCTUREKEYWORDSEARCHJUMPTOSLQATSEnnmiKLTTLIJIJnjvuipmlorumnsiLS?THfPmSFT?H?BLTDLFllPTSDIIT?FlilLTKLBr?CE?FFLCSTSLPEF?VRUnQtELTIT?KI?V?ETII?TTKD1wrwcmrTHTII-TeuwTHUUU PiiTLimnThissearchwillu*且且bothglobalandlocalmode1.0.You匚匚君君nsetyour口口 件件se

15、archp自自r4mEtEirm宿宿searcheshere-QUICKLINKS3,NCBI 的 CDD(ConservedDomainDatabase)數(shù)據(jù)庫網(wǎng)址：/Structure/cdd/wrpsb.cgiProteinsoftencontainseveralmodulesordomains,eachwithadistinctevolutionaryoriginandfunction.NCBIsConservedDomainDatabaseisacollectionofmultiplesequencealignmentsforanc

16、ientdomainsandfull-lengthproteins.Conserveddomainsoni胴生良心掘我%112x21LocdlquerysequiGraphicalsummary)12505H113li1i111I1i11Queryse?,3i.b3,hdih卜 Kj.七 it-eQplwbictinFcoredorainphosphotQinebindingpodketAiL.tkRhdrphob:bIndiri-gpockdkphffffph-fftryrflffMTBbindingFochsSearchforsimilardomainarListofdomainhitsQ

17、Defi|rtiQn+cjQDIy,FLCMFhosEM迎即跑Migdomain,Phosphoinositide-specificiphospholi+gd00275,C22,Proteinkirase|consepedregion2,subgroup.Ca2+45lndingmotii+lcd01246,PH_PLC,PhospholipaseC(PLC)pleckstrlnhomology(PH)domair,Thereare-+HQ248aPLCF,Phcspholipase%catalyticdGm9in,Phosphoiricsitide-specificphohaliFHcdOOI73,SH2,Srcfiomology2domains;Signaltransdudian,invclvedinrecognitiun3豺+cd00173,8H21Srchomology2domains;Signalinnsducti