2025
Protein codes promote selective subcellular compartmentalization
Kilgore H, Chinn I, Mikhael P, Mitnikov I, Van Dongen C, Zylberberg G, Afeyan L, Banani S, Wilson-Hawken S, Lee T, Barzilay R, Young R. Protein codes promote selective subcellular compartmentalization. Science 2025, 387: 1095-1101. PMID: 39913643, PMCID: PMC12034300, DOI: 10.1126/science.adq2634.Peer-Reviewed Original ResearchConceptsProtein sequencesSubcellular compartmentsDiverse subcellular compartmentsProtein language modelsAmino acid sequenceProtein codingAcid sequenceSubcellular localizationDiverse proteinsHuman proteinsSubcellular compartmentalizationFolding codePathological mutationsCompartment localizationProteinSequenceCompartmentMutationsAminoNucleolusCompartmentalizationCells
2023
Diverse p120RasGAP interactions with doubly phosphorylated partners EphB4, p190RhoGAP, and Dok1
Vish K, Stiegler A, Boggon T. Diverse p120RasGAP interactions with doubly phosphorylated partners EphB4, p190RhoGAP, and Dok1. Journal Of Biological Chemistry 2023, 299: 105098. PMID: 37507023, PMCID: PMC10470053, DOI: 10.1016/j.jbc.2023.105098.Peer-Reviewed Original ResearchConceptsSH2 domainSpatial-temporal regulationDual SH2 domainsProper vascular developmentKey binding partnerProtein familySH2 interactionsBinding partnerHuman proteinsDistinct binding interactionsWeakened affinityVascular developmentRasGAPConformational differencesP190RhoGAPSmall-angle X-ray scatteringBindingBinding interactionsAffinity measurementsEphB4DomainGTPaseDok1X-ray scatteringProteinSyntaxin 11 Contributes to the Interferon-Inducible Restriction of Coxiella burnetii Intracellular Infection
Ganesan S, Alvarez N, Steiner S, Fowler K, Corona A, Roy C. Syntaxin 11 Contributes to the Interferon-Inducible Restriction of Coxiella burnetii Intracellular Infection. MBio 2023, 14: e03545-22. PMID: 36728431, PMCID: PMC9972978, DOI: 10.1128/mbio.03545-22.Peer-Reviewed Original ResearchConceptsC. burnetii replicationSNARE proteinsHost cellsSyntaxin-11Cell-autonomous responsesIntracellular pathogensMembrane fusion eventsLysosome-derived organellesDefense mechanismsModel bacterial pathogenMultiple cell typesEukaryotic cellsDefense pathwaysDelivery of cargoReplication of pathogensHuman proteinsFusion eventsDissemination of pathogensFusion pathwayHost proteinsIntrinsic defense mechanismsHost vesiclesHost restriction factorsStable expressionSubcellular organellesA basic phosphoproteomic-DIA workflow integrating precise quantification of phosphosites in systems biology
Di Y, Li W, Salovska B, Ba Q, Hu Z, Wang S, Liu Y. A basic phosphoproteomic-DIA workflow integrating precise quantification of phosphosites in systems biology. Biophysics Reports 2023, 9: 82-98. PMID: 37753060, PMCID: PMC10518521, DOI: 10.52601/bpr.2023.230007.Peer-Reviewed Original ResearchPost-translational modificationsData-independent acquisitionSystems biologySite-specific phosphorylation eventsImportant post-translational modificationMost human proteinsCritical protein functionsPhosphorylation eventsProtein functionPhosphoproteomic studiesPhosphoproteomic analysisBioinformatics AdvancesHuman proteinsMass spectrometry technologyBioinformatics analysisLarge-scale quantificationExperimental workflowHigh-resolution mass spectrometry technologySpectrometry technologyPhosphoproteomicsPhosphorylationBiologyProteinSystems medicineSingle experiment
2021
DMA-tudor interaction modules control the specificity of in vivo condensates
Courchaine EM, Barentine AES, Straube K, Lee DR, Bewersdorf J, Neugebauer KM. DMA-tudor interaction modules control the specificity of in vivo condensates. Cell 2021, 184: 3612-3625.e17. PMID: 34115980, PMCID: PMC8402948, DOI: 10.1016/j.cell.2021.05.008.Peer-Reviewed Original Research
2014
A repository of assays to quantify 10,000 human proteins by SWATH-MS
Rosenberger G, Koh CC, Guo T, Röst HL, Kouvonen P, Collins BC, Heusel M, Liu Y, Caron E, Vichalkovski A, Faini M, Schubert OT, Faridi P, Ebhardt HA, Matondo M, Lam H, Bader SL, Campbell DS, Deutsch EW, Moritz RL, Tate S, Aebersold R. A repository of assays to quantify 10,000 human proteins by SWATH-MS. Scientific Data 2014, 1: 140031. PMID: 25977788, PMCID: PMC4322573, DOI: 10.1038/sdata.2014.31.Peer-Reviewed Original ResearchPurification of Recombinant 2XMBP Tagged Human Proteins from Human Cells
Jensen R. Purification of Recombinant 2XMBP Tagged Human Proteins from Human Cells. Methods In Molecular Biology 2014, 1176: 209-217. PMID: 25030930, DOI: 10.1007/978-1-4939-0992-6_17.Peer-Reviewed Original Research
2013
Analysis of the Human Tissue-specific Expression by Genome-wide Integration of Transcriptomics and Antibody-based Proteomics*
Fagerberg L, Hallström B, Oksvold P, Kampf C, Djureinovic D, Odeberg J, Habuka M, Tahmasebpoor S, Danielsson A, Edlund K, Asplund A, Sjöstedt E, Lundberg E, Szigyarto C, Skogs M, Takanen J, Berling H, Tegel H, Mulder J, Nilsson P, Schwenk J, Lindskog C, Danielsson F, Mardinoglu A, Sivertsson Å, von Feilitzen K, Forsberg M, Zwahlen M, Olsson I, Navani S, Huss M, Nielsen J, Ponten F, Uhlén M. Analysis of the Human Tissue-specific Expression by Genome-wide Integration of Transcriptomics and Antibody-based Proteomics*. Molecular & Cellular Proteomics 2013, 13: 397-406. PMID: 24309898, PMCID: PMC3916642, DOI: 10.1074/mcp.m113.035600.Peer-Reviewed Original ResearchConceptsHuman protein-coding genesProtein-coding genesSpatial expression patternsTissue-specific expressionExpression patternsGenome-wide integrationIndividual gene levelAntibody-based profilingQuantitative transcriptomic analysisProtein expression dataHuman Protein AtlasMajor human organsTranscriptomic analysisHuman proteinsExpression mapProtein AtlasGene levelExpression dataHuman biologyProtein analysisGenesMolecular constituentsSame tissueRNAExpressionProNormz – An integrated approach for human proteins and protein kinases normalization
Subramani S, Raja K, Natarajan J. ProNormz – An integrated approach for human proteins and protein kinases normalization. Journal Of Biomedical Informatics 2013, 47: 131-138. PMID: 24144801, DOI: 10.1016/j.jbi.2013.10.003.Peer-Reviewed Original ResearchConceptsHuman protein kinasesHuman proteinsProtein kinaseHuman gene familiesProtein-protein interactionsGene normalization taskPathway reconstructionGene familyBiomedical literatureRegulatory mechanismsBiological processesProteinKinaseWeb toolHomo sapiensGenesDisambiguation moduleDisambiguation systemMining applicationsSemantic similarityNormalization implementationNormal tasksGN taskTest datasetMatching rulesRelated F-box proteins control cell death in Caenorhabditis elegans and human lymphoma
Chiorazzi M, Rui L, Yang Y, Ceribelli M, Tishbi N, Maurer CW, Ranuncolo SM, Zhao H, Xu W, Chan WC, Jaffe ES, Gascoyne RD, Campo E, Rosenwald A, Ott G, Delabie J, Rimsza LM, Shaham S, Staudt LM. Related F-box proteins control cell death in Caenorhabditis elegans and human lymphoma. Proceedings Of The National Academy Of Sciences Of The United States Of America 2013, 110: 3943-3948. PMID: 23431138, PMCID: PMC3593917, DOI: 10.1073/pnas.1217271110.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceAnimalsApoptosisBase SequenceCaenorhabditis elegansCaenorhabditis elegans ProteinsCaspasesCell Line, TumorEnzyme ActivationF-Box ProteinsHEK293 CellsHumansLymphomaLymphoma, Large B-Cell, DiffuseMolecular Sequence DataMutation, MissenseProto-Oncogene Proteins c-bcl-2Repressor ProteinsRNA, MessengerRNA, NeoplasmSequence Homology, Amino AcidConceptsCED-9Cell deathCaenorhabditis elegansDRE-1Caspase CED-3Control cell deathApoptotic cell deathRegulators of apoptosisEGL-1CED-3Cell fateHuman diffuse large B-cell lymphomaHuman proteinsCaspase activationFBXO10BCL2 proteinElegansProteinHuman malignanciesHuman lymphomasAlternative mechanismApoptosisActivationBH3RegulatorPPInterFinder—a mining tool for extracting causal relations on human proteins from literature
Raja K, Subramani S, Natarajan J. PPInterFinder—a mining tool for extracting causal relations on human proteins from literature. Database 2013, 2013: bas052. PMID: 23325628, PMCID: PMC3548331, DOI: 10.1093/database/bas052.Peer-Reviewed Original ResearchConceptsProtein-protein interactionsProtein-protein interaction pairsMine protein-protein interactionsHuman protein-protein interactionPredicting Protein-Protein InteractionsMEDLINE abstractsProtein namesHuman proteinsAIMed corpusBiological processesBiomedical text miningMining toolsProteinImpact of proteinsText mining toolsSpecific patternsKeyword co-occurrenceBiomedical literatureCo-occurrenceText miningExtract informationSyntactic naturePairs
2010
Identifying potential survival strategies of HIV-1 through virus-host protein interaction networks
van Dijk D, Ertaylan G, Boucher CA, Sloot PM. Identifying potential survival strategies of HIV-1 through virus-host protein interaction networks. BMC Systems Biology 2010, 4: 96. PMID: 20633292, PMCID: PMC2913931, DOI: 10.1186/1752-0509-4-96.Peer-Reviewed Original ResearchConceptsProtein interaction networksHuman protein interaction networkHuman proteinsInteraction networksCellular processesRNA polymerase II transcriptionVirus-host protein interaction networksPolymerase II transcriptionHuman Protein Interaction DatabaseSet of proteinsNetwork motifsPotential survival strategiesVirus-host dynamicsProtein interaction databasesCentral human proteinsVirus-host systemsTranscriptional machineryProteasomal proteinsMotif analysisImportant proteinsNetwork motif analysisInteraction databasesViral strategiesProteinSurvival strategies
2008
Identification of small-molecule inhibitors of autotaxin that inhibit melanoma cell migration and invasion
Saunders LP, Ouellette A, Bandle R, Chang WC, Zhou H, Misra RN, De La Cruz EM, Braddock DT. Identification of small-molecule inhibitors of autotaxin that inhibit melanoma cell migration and invasion. Molecular Cancer Therapeutics 2008, 7: 3352-3362. PMID: 18852138, PMCID: PMC7857123, DOI: 10.1158/1535-7163.mct-08-0463.Peer-Reviewed Original ResearchConceptsSmall molecule inhibitorsMelanoma cell migrationLysophosphatidic acidCell migrationRecombinant human proteinsChemical screenHuman proteinsATX levelsMalignant melanomaMigratory phenotypeMelanoma cell linesHuman melanoma cellsRole of autotaxinInvasion assaysLPA productionCell growthImmunohistochemistry of paraffinMolecular targetsCell linesATX inhibitorsAutotaxinMelanoma cellsHuman malignanciesEnzymatic productHuman tissuesRegulatory Polymorphisms and their Contribution to Interindividual Differences in the Expression of Enzymes Influencing Drug and Toxicant Disposition
Hines R, Koukouritaki S, Poch M, Stephens M. Regulatory Polymorphisms and their Contribution to Interindividual Differences in the Expression of Enzymes Influencing Drug and Toxicant Disposition. Drug Metabolism Reviews 2008, 40: 263-301. PMID: 18464046, DOI: 10.1080/03602530801952682.Peer-Reviewed Original ResearchConceptsRegulatory polymorphismsRegulatory sequencesHuman proteinsSelection pressureGene expressionCo-dominant traitEvolutionary perspectiveXenobiotic metabolismEnvironmental changesToxicant dispositionUnexpected paucityCurrent understandingHeterozygous stateTraitsPolymorphismSuch variationExpressionKnowledge gapsGenesProteinFitnessSequenceMetabolismVariationDrug disposition
2004
MitoP2, an integrated database on mitochondrial proteins in yeast and man
Andreoli C, Prokisch H, Hörtnagel K, Mueller JC, Münsterkötter M, Scharfe C, Meitinger T. MitoP2, an integrated database on mitochondrial proteins in yeast and man. Nucleic Acids Research 2004, 32: d459-d462. PMID: 14681457, PMCID: PMC308871, DOI: 10.1093/nar/gkh137.Peer-Reviewed Original ResearchConceptsMitochondrial proteinsProtein-protein interactionsMitochondrial proteomeHuman mitochondriopathiesMutant screeningHuman proteinsProteome mappingExpression profilingGenetic characterizationYeastProteinComputational predictionsSearch toolsMitoP2ProteomeReference setComprehensive listProfilingSequenceMitochondriopathy
2001
Phosphorylation of the Saccharomyces cerevisiae La protein does not appear to be required for its functions in tRNA maturation and nascent RNA stabilization.
Long K, Cedervall T, Walch-Solimena C, Noe D, Huddleston M, Annan R, Wolin S. Phosphorylation of the Saccharomyces cerevisiae La protein does not appear to be required for its functions in tRNA maturation and nascent RNA stabilization. RNA 2001, 7: 1589-602. PMID: 11720288, PMCID: PMC1370201.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceAutoantigensBinding SitesCell NucleolusCell NucleusFungal ProteinsMolecular Sequence DataPeptide MappingPhosphorylationProtein IsoformsRibonucleoproteinsRibonucleoproteins, Small NuclearRNARNA StabilityRNA, FungalRNA, TransferRNA-Binding ProteinsSaccharomyces cerevisiaeSaccharomyces cerevisiae ProteinsConceptsLa proteinAbundant nuclear phosphoproteinRNA polymerase III transcriptsS. cerevisiae proteinTwo-dimensional gel electrophoresisRole of phosphorylationPolymerase III transcriptsCerevisiae proteinsNascent RNANascent transcriptsS. pombeSchizosaccharomyces pombeLhp1pPhosphorylation sitesYeast SaccharomycesProtein functionMutant versionSubcellular locationFirst proteinHuman proteinsNuclear phosphoproteinExonucleolytic degradationSerine phosphorylationPhosphorylation statusRNA stabilization
2000
Human Upf Proteins Target an mRNA for Nonsense-Mediated Decay When Bound Downstream of a Termination Codon
Lykke-Andersen J, Shu M, Steitz J. Human Upf Proteins Target an mRNA for Nonsense-Mediated Decay When Bound Downstream of a Termination Codon. Cell 2000, 103: 1121-1131. PMID: 11163187, DOI: 10.1016/s0092-8674(00)00214-2.Peer-Reviewed Original ResearchConceptsNonsense-mediated decayExon-exon junctionsTermination codonMRNA exon-exon junctionsNovel human proteinTranslation termination siteHeLa cell extractsBeta-globin mRNAPremature termination codonUpf proteinsEukaryotic cellsAberrant mRNAsHuman proteinsTermination sitesIntact cellsCell extractsCodonHUpf2ProteinMRNAHUpf1CellsCytoplasmCytoplasmicTethering
1998
Maturation of Human Cyclin E Requires the Function of Eukaryotic Chaperonin CCT
Won K, Schumacher R, Farr G, Horwich A, Reed S. Maturation of Human Cyclin E Requires the Function of Eukaryotic Chaperonin CCT. Molecular And Cellular Biology 1998, 18: 7584-7589. PMID: 9819444, PMCID: PMC109339, DOI: 10.1128/mcb.18.12.7584.Peer-Reviewed Original ResearchConceptsHuman cyclin EChaperonin CCTCyclin EEukaryotic cytosolic chaperonin CCTCytosolic chaperonin CCTEukaryotic chaperonin CCTLarge oligomeric assembliesYeast-based screenG1/S phase transitionCyclin-dependent kinase CDK2ATP-dependent processS phase transitionCCT complexPresence of ATPProteasomal actionCCT functionHuman proteinsKinase CDK2Oligomeric assembliesHuman cellsNative stateCDK2ProteinMaturationBiogenesis
1997
Mpp10p, a U3 Small Nucleolar Ribonucleoprotein Component Required for Pre-18S rRNA Processing in Yeast
Dunbar D, Wormsley S, Agentis T, Baserga S. Mpp10p, a U3 Small Nucleolar Ribonucleoprotein Component Required for Pre-18S rRNA Processing in Yeast. Molecular And Cellular Biology 1997, 17: 5803-5812. PMID: 9315638, PMCID: PMC232428, DOI: 10.1128/mcb.17.10.5803.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceAnimalsAntibodiesCloning, MolecularEscherichia coliGenes, FungalHumansMiceMolecular Sequence DataMolecular WeightPhosphoproteinsRecombinant Fusion ProteinsRibonucleoproteinsRibonucleoproteins, Small NuclearRNA PrecursorsRNA Processing, Post-TranscriptionalRNA, RibosomalRNA, Ribosomal, 18SSaccharomyces cerevisiaeSaccharomyces cerevisiae ProteinsSequence Homology, Amino AcidSpores, FungalConceptsYeast proteinsU3 snoRNPProtein componentsU3 small nucleolar ribonucleoproteinNovel protein componentsPre-rRNA processingSmall nucleolar ribonucleoproteinS. cerevisiae cellsSpecific protein componentsPulse-chase analysisMitotic phosphorylationRibosome biogenesisEssential genesMpp10pYeast SaccharomycesNovel proteinU3 snoRNARRNA precursorNucleolar ribonucleoproteinSites A0Tetrad analysisHuman proteinsNull allelesCerevisiae cellsGenBank search
1996
A Yeast Protein Related to a Mammalian Ras-Binding Protein, Vps9p, Is Required for Localization of Vacuolar Proteins
Burd C, Mustol P, Schu P, Emr S. A Yeast Protein Related to a Mammalian Ras-Binding Protein, Vps9p, Is Required for Localization of Vacuolar Proteins. Molecular And Cellular Biology 1996, 16: 2369-2377. PMID: 8628304, PMCID: PMC231225, DOI: 10.1128/mcb.16.5.2369.Peer-Reviewed Original ResearchMeSH KeywordsAllelesAmino Acid SequenceAnimalsCarrier ProteinsCloning, MolecularFungal ProteinsGenes, FungalGenetic Complementation TestGuanine Nucleotide Exchange FactorsHumansMammalsMolecular Sequence DataMutagenesisPolymerase Chain ReactionRecombinant ProteinsSaccharomyces cerevisiaeSaccharomyces cerevisiae ProteinsSequence Homology, Amino AcidTemperatureVacuolesVesicular Transport ProteinsConceptsVacuolar protein sortingProtein sortingVacuolar proteinVPS pathwayVacuolar protein sorting (VPS) genesTemperature-sensitive growth defectTemperature-conditional alleleVacuolar protein precursorsFamily of proteinsSecretion of proteinsRab GTPaseRA-binding proteinsTransport vesiclesYeast proteinsHomology domainYeast SaccharomycesGrowth defectHuman proteinsVps9pDNA sequencesGene productsCytosolic proteinsNonpermissive temperatureCarboxypeptidase YIntracellular transport
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