Protein subcellular localization prediction - Wikipedia

Protein subcellular localization prediction involves the prediction of where a protein resides in a cell, its subcellular localization. Proteinsubcellularlocalizationprediction FromWikipedia,thefreeencyclopedia Jumptonavigation Jumptosearch Proteinsubcellularlocalizationprediction(orjustproteinlocalizationprediction)involvesthepredictionofwhereaproteinresidesinacell,itssubcellularlocalization. Ingeneral,predictiontoolstakeasinputinformationaboutaprotein,suchasaproteinsequenceofaminoacids,andproduceapredictedlocationwithinthecellasoutput,suchasthenucleus,Endoplasmicreticulum,Golgiapparatus,extracellularspace,orotherorganelles.Theaimistobuildtoolsthatcanaccuratelypredicttheoutcomeofproteintargetingincells. Predictionofproteinsubcellularlocalizationisanimportantcomponentofbioinformaticsbasedpredictionofproteinfunctionandgenomeannotation,anditcanaidtheidentificationofdrugtargets. Contents 1Background 2Tools 3Application 4Databases 5References 6Furtherreading Background[edit] Experimentallydeterminingthesubcellularlocalizationofaproteincanbealaboriousandtimeconsumingtask.Immunolabelingortagging(suchaswithagreenfluorescentprotein)toviewlocalizationusingfluorescencemicroscopeareoftenused.Ahighthroughputalternativeistouseprediction. Throughthedevelopmentofnewapproachesincomputerscience,coupledwithanincreaseddatasetofproteinsofknownlocalization,computationaltoolscannowprovidefastandaccuratelocalizationpredictionsformanyorganisms.Thishasresultedinsubcellularlocalizationpredictionbecomingoneofthechallengesbeingsuccessfullyaidedbybioinformatics,andmachinelearning. Manypredictionmethodsnowexceedtheaccuracyofsomehigh-throughputlaboratorymethodsfortheidentificationofproteinsubcellularlocalization.[1][2][3]Particularly,somepredictorshavebeendeveloped[4]thatcanbeusedtodealwithproteinsthatmaysimultaneouslyexist,ormovebetween,twoormoredifferentsubcellularlocations.Experimentalvalidationistypicallyrequiredtoconfirmthepredictedlocalizations. Tools[edit] Mainarticle:ListofProteinsubcellularlocalizationpredictiontools In1999PSORTwasthefirstpublishedprogramtopredictsubcellularlocalization.[5]Subsequenttoolsandwebsiteshavebeenreleasedusingtechniquessuchasartificialneuralnetworks,supportvectormachineandproteinmotifs.Predictorscanbespecializedforproteinsindifferentorganisms.Somearespecializedforeukaryoticproteins,[6]someforhumanproteins,[7]andsomeforplantproteins.[8]Methodsforthepredictionofbacteriallocalizationpredictors,andtheiraccuracy,havebeenreviewed.[9]In2021,SCLpred-MEM,amembraneproteinpredictiontoolpoweredbyartificial neuralnetworkswaspublished.[10]SCLpred-EMSisanothertoolpoweredbyArtificialneuralnetworksthatclassifyproteinsintoendomembranesystemandsecretorypathway(EMS)versusallothers.[11]Similarly,Light-Attentionusesmachinelearningmethodstopredicttendifferentcommonsubcellularlocations.[12] Thedevelopmentofproteinsubcellularlocationpredictionhasbeensummarizedintwocomprehensivereviewarticles.[13][14]RecenttoolsandanexperiencereportcanbefoundinarecentpaperbyMeinkenandMin(2012). Application[edit] Knowledgeofthesubcellularlocalizationofaproteincansignificantlyimprovetargetidentificationduringthedrugdiscoveryprocess.Forexample,secretedproteinsandplasmamembraneproteinsareeasilyaccessiblebydrugmoleculesduetotheirlocalizationintheextracellularspaceoronthecellsurface. Bacterialcellsurfaceandsecretedproteinsarealsoofinterestfortheirpotentialasvaccinecandidatesorasdiagnostictargets.Aberrantsubcellularlocalizationofproteinshasbeenobservedinthecellsofseveraldiseases,suchascancerandAlzheimer'sdisease.Secretedproteinsfromsomearchaeathatcansurviveinunusualenvironmentshaveindustriallyimportantapplications. Byusingpredictionahighnumberofproteinscanbeassessedinordertofindcandidatesthataretraffickedtothedesiredlocation. Databases[edit] Theresultsofsubcellularlocalizationpredictioncanbestoredindatabases.Examplesincludethemulti-speciesdatabaseCompartments,FunSecKB2,afungaldatabase;[15]PlantSecKB,aplantdatabase;[16]MetazSecKB,ananimalandhumandatabase;[17]andProtSecKB,aprotistdatabase.[18] References[edit] ^Kaleel,M;Zheng,Y;Chen,J;Feng,X;Simpson,JC;Pollastri,G;Mooney,C(6March2020)."SCLpred-EMS:subcellularlocalizationpredictionofendomembranesystemandsecretorypathwayproteinsbyDeepN-to-1ConvolutionalNeuralNetworks".Bioinformatics.36(11):3343–3349.doi:10.1093/bioinformatics/btaa156.hdl:10197/12182.PMID 32142105. ^ReyS,GardyJL,BrinkmanFS(2005)."Assessingtheprecisionofhigh-throughputcomputationalandlaboratoryapproachesforthegenome-wideidentificationofproteinsubcellularlocalizationinbacteria".BMCGenomics.6:162.doi:10.1186/1471-2164-6-162.PMC 1314894.PMID 16288665. ^Kaleel,Manaz;Ellinger,Liam;Lalor,Clodagh;Pollastri,Gianluca;Mooney,Catherine(2021)."SCLpred-MEM:SubcellularlocalizationpredictionofmembraneproteinsbydeepN-to-1convolutionalneuralnetworks".Proteins:Structure,Function,andBioinformatics.89(10):1233–1239.doi:10.1002/prot.26144.PMID 33983651.S2CID 234484678. ^ChouKC,ShenHB(2008)."Cell-PLoc:apackageofWebserversforpredictingsubcellularlocalizationofproteinsinvariousorganisms".NatureProtocols.3(2):153–62.doi:10.1038/nprot.2007.494.PMID 18274516.S2CID 226104. ^"ProteinSubcellularLocalizationPrediction".www.ncbi.nlm.nih.gov.Retrieved2016-12-31. ^ChouKC,WuZC,XiaoX(2011)."iLoc-Euk:amulti-labelclassifierforpredictingthesubcellularlocalizationofsingleplexandmultiplexeukaryoticproteins".PLOSONE.6(3):e18258.Bibcode:2011PLoSO...618258C.doi:10.1371/journal.pone.0018258.PMC 3068162.PMID 21483473. ^ShenHB,ChouKC(Nov2009)."Atop-downapproachtoenhancethepowerofpredictinghumanproteinsubcellularlocalization:Hum-mPLoc2.0".AnalyticalBiochemistry.394(2):269–74.doi:10.1016/j.ab.2009.07.046.PMID 19651102. ^ChouKC,ShenHB(2010)."Plant-mPLoc:atop-downstrategytoaugmentthepowerforpredictingplantproteinsubcellularlocalization".PLOSONE.5(6):e11335.Bibcode:2010PLoSO...511335C.doi:10.1371/journal.pone.0011335.PMC 2893129.PMID 20596258. ^GardyJL,BrinkmanFS(Oct2006)."Methodsforpredictingbacterialproteinsubcellularlocalization".NatureReviews.Microbiology.4(10):741–51.doi:10.1038/nrmicro1494.PMID 16964270.S2CID 62781755. ^Kaleel,Manaz;Ellinger,Liam;Lalor,Clodagh;Pollastri,Gianluca;Mooney,Catherine(2021)."SCLpred-MEM:SubcellularlocalizationpredictionofmembraneproteinsbydeepN-to-1convolutionalneuralnetworks".Proteins:Structure,Function,andBioinformatics.89(10):1233–1239.doi:10.1002/prot.26144.PMID 33983651.S2CID 234484678. ^Kaleel,Manaz;Zheng,Yandan;Chen,Jialiang;Feng,Xuanming;Simpson,JeremyC;Pollastri,Gianluca;Mooney,Catherine(1June2020)."SCLpred-EMS:subcellularlocalizationpredictionofendomembranesystemandsecretorypathwayproteinsbyDeepN-to-1ConvolutionalNeuralNetworks".Bioinformatics.36(11):3343–3349.doi:10.1093/bioinformatics/btaa156.hdl:10197/12182.PMID 32142105. ^Rost,Stark;Heinzinger,Dallago(26April2021)."LightAttentionPredictsProteinLocationfromtheLanguageofLife".Biorxiv.doi:10.1101/2021.04.25.441334.S2CID 233449747. ^Nakai,K.Proteinsortingsignalsandpredictionofsubcellularlocalization.Adv.ProteinChem.,2000,54,277-344. ^Chou,K.C.;Shen,H.B.Review:Recentprogressesinproteinsubcellularlocationprediction"Anal.Biochem2007,370,1-16. ^"FunSecKB2(TheFungalSecretomeandSubcellularProteomeKnowledgeBase2.1)".bioinformatics.ysu.edu.Archivedfromtheoriginalon2016-04-10.Retrieved2017-09-17. ^"PlantSecKB(ThePlantSecretomeandSubcellularProteomeKnowledgeBase)".bioinformatics.ysu.edu.Archivedfromtheoriginalon2016-04-06.Retrieved2017-09-17. ^"MetazSecKB(TheMetazoa(Human&Animal)ProteinSubcelluarLocation,SecretomeandSubcellularProteomeDatabase)".bioinformatics.ysu.edu.Archivedfromtheoriginalon2016-04-06.Retrieved2017-09-17. ^"ProtSecKB(TheProtistSecretomeandSubcellularProteomeKnowledgeBase)".proteomics.ysu.edu.Retrieved2017-09-17. Furtherreading[edit] BorkP,DandekarT,Diaz-LazcozY,EisenhaberF,HuynenM,YuanY(Nov1998)."Predictingfunction:fromgenestogenomesandback".JournalofMolecularBiology.283(4):707–25.doi:10.1006/jmbi.1998.2144.PMID 9790834. NakaiK(2000)."Proteinsortingsignalsandpredictionofsubcellularlocalization".AdvancesinProteinChemistry.54:277–344.doi:10.1016/s0065-3233(00)54009-1.ISBN 0120342545.PMID 10829231. EmanuelssonO(Dec2002)."Predictingproteinsubcellularlocalisationfromaminoacidsequenceinformation".BriefingsinBioinformatics.3(4):361–76.doi:10.1093/bib/3.4.361.PMID 12511065. SchneiderG,FechnerU(Jun2004)."Advancesinthepredictionofproteintargetingsignals".Proteomics.4(6):1571–80.doi:10.1002/pmic.200300786.PMID 15174127.S2CID 7217647. GardyJL,BrinkmanFS(Oct2006)."Methodsforpredictingbacterialproteinsubcellularlocalization".NatureReviews.Microbiology.4(10):741–51.doi:10.1038/nrmicro1494.PMID 16964270.S2CID 62781755. ChouKC,ShenHB(Nov2007)."Recentprogressinproteinsubcellularlocationprediction".AnalyticalBiochemistry.370(1):1–16.doi:10.1016/j.ab.2007.07.006.PMID 17698024. Retrievedfrom"https://en.wikipedia.org/w/index.php?title=Protein_subcellular_localization_prediction&oldid=1045340315" Categories:BiochemistrydetectionmethodsProteinmethodsCellbiologyComputationalscienceBioinformaticssoftwareProteintargeting Navigationmenu Personaltools NotloggedinTalkContributionsCreateaccountLogin Namespaces ArticleTalk English Views ReadEditViewhistory More Search Navigation MainpageContentsCurrenteventsRandomarticleAboutWikipediaContactusDonate Contribute HelpLearntoeditCommunityportalRecentchangesUploadfile Tools WhatlinkshereRelatedchangesUploadfileSpecialpagesPermanentlinkPageinformationCitethispageWikidataitem Print/export DownloadasPDFPrintableversion Languages العربيةDeutsch Editlinks