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 ResearchMeSH KeywordsAmino Acid SequenceCell CompartmentationCell NucleolusHumansMutationProtein FoldingProteinsConceptsProtein sequencesSubcellular compartmentsDiverse subcellular compartmentsProtein language modelsAmino acid sequenceProtein codingAcid sequenceSubcellular localizationDiverse proteinsHuman proteinsSubcellular compartmentalizationFolding codePathological mutationsCompartment localizationProteinSequenceCompartmentMutationsAminoNucleolusCompartmentalizationCellsThe C2 domain augments Ras GTPase-activating protein catalytic activity
Paul M, Chen D, Vish K, Lartey N, Hughes E, Freeman Z, Saunders T, Stiegler A, King P, Boggon T. The C2 domain augments Ras GTPase-activating protein catalytic activity. Proceedings Of The National Academy Of Sciences Of The United States Of America 2025, 122: e2418433122. PMID: 39899710, PMCID: PMC11831179, DOI: 10.1073/pnas.2418433122.Peer-Reviewed Original ResearchConceptsGTPase-activating proteinC2 domainActivity of GTPase-activating proteinGTPase-activating protein domainProtein catalytic activityDomain in vitroAllosteric lobeRas GTPasesSequence conservationGTPase activityAlphaFold modelsRasGAPSignaling defectsRasMutationsCatalytic activityConstitutive disruptionCatalytic advantageGTPaseAlphaFoldDomainGenesSynGAPProteinSequenceDeep mutational scanning of the Trypanosoma brucei developmental regulator RBP6 reveals an essential disordered region influenced by positive residues
Rojas-Sánchez S, Kolev N, Tschudi C. Deep mutational scanning of the Trypanosoma brucei developmental regulator RBP6 reveals an essential disordered region influenced by positive residues. Nature Communications 2025, 16: 1168. PMID: 39885181, PMCID: PMC11782513, DOI: 10.1038/s41467-025-56553-y.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceAnimalsMutationProtozoan ProteinsRNA-Binding ProteinsTrypanosoma brucei bruceiTrypanosomiasis, AfricanTsetse FliesConceptsN-terminal intrinsically disordered regionRNA binding protein 6RNA recognition motifDeep mutational scanningMutational scanningDisordered regionsProtein-RNA interactionsIntrinsically disordered regionsComplex developmental programPositively charged residuesSingle-point variantsProtein-RNARNA recognitionDeleterious mutationsMutational constraintsProcyclic formsAnimal African trypanosomiasisTrypanosoma bruceiCharged residuesPrimary structureRegained infectivityDevelopmental programRegulatory roleProtein 6Positive residues
2024
Bioinformatics analysis of myelin-microbe interactions suggests multiple types of molecular mimicry in the pathogenesis of multiple sclerosis
Bigdeli A, Ghaderi-Zefrehei M, Lesch B, Behmanesh M, Arab S. Bioinformatics analysis of myelin-microbe interactions suggests multiple types of molecular mimicry in the pathogenesis of multiple sclerosis. PLOS ONE 2024, 19: e0308817. PMID: 39775333, PMCID: PMC11684644, DOI: 10.1371/journal.pone.0308817.Peer-Reviewed Original ResearchConceptsBile salt hydrolaseMyelin oligodendrocyte glycoproteinBioinformatics approachProtein structureMyelin basic proteinIn silico bioinformatics approachesAmino acidsIdentical amino acidsAmino acid sequenceCapsid protein structureCentral nervous systemAspergillus speciesAcid sequenceBacterial proteinsMultiple sclerosisMyelin sheath componentsBiological insightsGut flora metabolitesBioinformatics analysisMOG proteinPathogenesis of multiple sclerosisCNS diseaseWzyBacteriaProteinPTMoreR-enabled cross-species PTM mapping and comparative phosphoproteomics across mammals
Wang S, Di Y, Yang Y, Salovska B, Li W, Hu L, Yin J, Shao W, Zhou D, Cheng J, Liu D, Yang H, Liu Y. PTMoreR-enabled cross-species PTM mapping and comparative phosphoproteomics across mammals. Cell Reports Methods 2024, 4: 100859. PMID: 39255793, PMCID: PMC11440062, DOI: 10.1016/j.crmeth.2024.100859.Peer-Reviewed Original ResearchConceptsP-siteSurrounding amino acid sequenceKinase-substrate networkQuantitative phosphoproteomic analysisFunctional enrichment analysisPhosphoproteomic resultsKinase motifsComparative phosphoproteomicsPTM sitesPhosphorylation eventsPhosphoproteomic analysisProteomic analysisEnrichment analysisMammalian speciesSpeciesEvolutionary anglePhosphoproteomeMotifEnvironmental factorsNon-human speciesPTMProteomicsKinaseMammalsProtein
2023
Scaling up robust immunopeptidomics technologies for a global T cell surveillance digital network
Kapoor S, Maréchal L, Sirois I, Caron É. Scaling up robust immunopeptidomics technologies for a global T cell surveillance digital network. Journal Of Experimental Medicine 2023, 221: e20231739. PMID: 38032361, PMCID: PMC10689202, DOI: 10.1084/jem.20231739.Commentaries, Editorials and LettersProteome-wide screening for mitogen-activated protein kinase docking motifs and interactors
Shi G, Song C, Torres Robles J, Salichos L, Lou H, Lam T, Gerstein M, Turk B. Proteome-wide screening for mitogen-activated protein kinase docking motifs and interactors. Science Signaling 2023, 16: eabm5518. PMID: 36626580, PMCID: PMC9995140, DOI: 10.1126/scisignal.abm5518.Peer-Reviewed Original ResearchConceptsMitogen-activated protein kinaseDocking motifSequence motifsDocking sequenceShort linear sequence motifsLinear sequence motifsSubstrate recruitmentHuman proteomeProtein kinaseCatalytic cleftExchange mutantsEssential functionsCultured cellsScreening pipelineWide screeningInteractorsMotifSequenceLimited repertoireSelective bindingInteractomeCombinatorial librariesMKK6ProteomeMKK7
2022
Molecular basis for integrin adhesion receptor binding to p21-activated kinase 4 (PAK4)
Ha B, Yigit S, Natarajan N, Morse E, Calderwood D, Boggon T. Molecular basis for integrin adhesion receptor binding to p21-activated kinase 4 (PAK4). Communications Biology 2022, 5: 1257. PMID: 36385162, PMCID: PMC9669019, DOI: 10.1038/s42003-022-04157-3.Peer-Reviewed Original ResearchConceptsP21-activated kinase 4Integrin adhesion receptorsMolecular basisAdhesion receptorsIntegrin β5Potential cellular rolesIntegrin β tailsKinase 4Membrane-proximal halfSubstrate-binding grooveSubstrate-binding siteSite-directed mutagenesisCellular rolesPhosphoacceptor sitesΒ tailExtracellular ligandsCytoplasmic signalingCytoplasmic tailKinase domainMultiple kinasesIntegrin complexΒ5 integrinsΒ5TailMutagenesisTousled-like kinase 2 targets ASF1 histone chaperones through client mimicry
Simon B, Lou HJ, Huet-Calderwood C, Shi G, Boggon TJ, Turk BE, Calderwood DA. Tousled-like kinase 2 targets ASF1 histone chaperones through client mimicry. Nature Communications 2022, 13: 749. PMID: 35136069, PMCID: PMC8826447, DOI: 10.1038/s41467-022-28427-0.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid MotifsAmino Acid SequenceCatalytic DomainCell Cycle ProteinsConserved SequenceCrystallography, X-RayHistonesHumansMolecular ChaperonesMolecular Docking SimulationMolecular MimicryMutagenesisPeptide LibraryPhosphorylationProtein KinasesRecombinant ProteinsSubstrate SpecificityConceptsTousled-like kinaseDNA replication-coupled nucleosome assemblyNuclear serine-threonine kinaseReplication-coupled nucleosome assemblyHistone chaperone proteinsGlobular N-terminal domainProper cell divisionPhosphorylation site motifsSerine-threonine kinaseShort sequence motifsAsf1 histone chaperonesC-terminal tailN-terminal domainHistone chaperonesGenome maintenanceNucleosome assemblySequence motifsChaperone proteinsNon-catalytic interactionsCatalytic domainCell divisionSite motifN-terminusStringent selectivityCell growthHigh-affinity, neutralizing antibodies to SARS-CoV-2 can be made without T follicular helper cells
Chen JS, Chow RD, Song E, Mao T, Israelow B, Kamath K, Bozekowski J, Haynes WA, Filler RB, Menasche BL, Wei J, Alfajaro MM, Song W, Peng L, Carter L, Weinstein JS, Gowthaman U, Chen S, Craft J, Shon JC, Iwasaki A, Wilen CB, Eisenbarth SC. High-affinity, neutralizing antibodies to SARS-CoV-2 can be made without T follicular helper cells. Science Immunology 2022, 7: eabl5652. PMID: 34914544, PMCID: PMC8977051, DOI: 10.1126/sciimmunol.abl5652.Peer-Reviewed Original ResearchConceptsSARS-CoV-2 infectionSARS-CoV-2Follicular helper cellsB cell responsesHelper cellsAntibody productionCell responsesSARS-CoV-2 vaccinationB-cell receptor sequencingSevere COVID-19Cell receptor sequencingIndependent antibodiesT cell-B cell interactionsViral inflammationAntiviral antibodiesImmunoglobulin class switchingVirus infectionGerminal centersViral infectionClonal repertoireInfectionAntibodiesClass switchingCOVID-19PatientsKidney-Targeted Renalase Agonist Prevents Cisplatin-Induced Chronic Kidney Disease by Inhibiting Regulated Necrosis and Inflammation
Guo X, Xu L, Velazquez H, Chen TM, Williams RM, Heller DA, Burtness B, Safirstein R, Desir GV. Kidney-Targeted Renalase Agonist Prevents Cisplatin-Induced Chronic Kidney Disease by Inhibiting Regulated Necrosis and Inflammation. Journal Of The American Society Of Nephrology 2022, 33: 342-356. PMID: 34921111, PMCID: PMC8819981, DOI: 10.1681/asn.2021040439.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceAnimalsAntineoplastic AgentsCell LineCisplatinCreatinineDisease Models, AnimalGene ExpressionGlomerular Filtration RateHepatitis A Virus Cellular Receptor 1HumansKidneyMiceMice, Inbred C57BLMice, KnockoutMonoamine OxidaseNanocapsulesPeptidesRenal Insufficiency, ChronicConceptsRenal proximal tubulesSingle-cell RNA sequencing analysisMesoscale nanoparticlesFirst doseCisplatin chemotherapyProximal tubulesAgonist peptideInduced Chronic Kidney DiseaseGenetic deletionNeck squamous cell carcinomaRNA sequencing analysisCisplatin-induced AKIKidney-targeted deliveryChronic kidney diseaseDevelopment of CKDSquamous cell carcinomaAdministration of cisplatinPlasma renalaseAdvanced headCell carcinomaInflammatory cytokinesKidney diseasePlasma creatinineSystemic administrationRegulated necrosisThe flagellar motor protein FliL forms a scaffold of circumferentially positioned rings required for stator activation
Tachiyama S, Chan KL, Liu X, Hathroubi S, Li W, Peterson B, Khan M, Ottemann K, Liu J, Roujeinikova A. The flagellar motor protein FliL forms a scaffold of circumferentially positioned rings required for stator activation. Proceedings Of The National Academy Of Sciences Of The United States Of America 2022, 119: e2118401119. PMID: 35046042, PMCID: PMC8794807, DOI: 10.1073/pnas.2118401119.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceBacterial Physiological PhenomenaBacterial ProteinsFlagellaHelicobacter pyloriMembrane ProteinsModels, MolecularMolecular Motor ProteinsMultiprotein ComplexesProtein BindingProtein ConformationProtein Interaction Domains and MotifsProtein TransportStructure-Activity RelationshipConceptsStator unitsStomatin/prohibitin/flotillin/HflK/C (SPFH) domainWild-type cellsSignificant structural similarityPeriplasmic domainAssembly factorsFlagellar motorAccessory proteinsFliLLinker regionActive conformationFlagellar baseC-domainMotBStructural similarityStator assemblyProteinPutative mechanismsElectron tomography reconstructionsIntact motorCellsActivationDomainMotAHelixHigh cell surface expression and peptide binding affinity of HLA-DQA1*05:03, a susceptible allele of neuromyelitis optica spectrum disorders (NMOSD)
Beppu S, Kinoshita M, Wilamowski J, Suenaga T, Yasumizu Y, Ogawa K, Ishikura T, Tada S, Koda T, Murata H, Shiraishi N, Sugiyama Y, Kihara K, Sugimoto T, Arase H, Standley D, Okuno T, Mochizuki H. High cell surface expression and peptide binding affinity of HLA-DQA1*05:03, a susceptible allele of neuromyelitis optica spectrum disorders (NMOSD). Scientific Reports 2022, 12: 106. PMID: 34997058, PMCID: PMC8742014, DOI: 10.1038/s41598-021-04074-1.Peer-Reviewed Original ResearchConceptsNeuromyelitis optica spectrum disorderPeptide major histocompatibility complexDevelopment of neuromyelitis optica spectrum disorderAnti-aquaporin-4HLA-DQA1Associated with neuromyelitis optica spectrum disordersHigh cell surface expressionJapanese patient cohortPresence of pathogenic autoantibodiesCell surface expression levelsRelapsing autoimmune diseaseHLA-DQA1 allelesCell surface expressionSurface expression levelsAQP4 peptidesMajor histocompatibility complexAnti-aquaporinPathogenic autoantibodiesHLA-DQPatient cohortAutoimmune diseasesPathogenic roleSurface expressionIn silico 3D structure modelingHistocompatibility complex
2021
A Mosquito AgTRIO Monoclonal Antibody Reduces Early Plasmodium Infection of Mice
Chuang YM, Tang XD, Fikrig E. A Mosquito AgTRIO Monoclonal Antibody Reduces Early Plasmodium Infection of Mice. Infection And Immunity 2021, 90: e00359-21. PMID: 34724388, PMCID: PMC8788779, DOI: 10.1128/iai.00359-21.Peer-Reviewed Original ResearchConceptsMonoclonal antibodiesFuture malaria vaccinesInfection of miceIsotype monoclonal antibodyVector antigensProtective immunityPassive immunizationMalaria vaccinePlasmodium infectionPassive transferProtein monoclonal antibodySignificant protectionSynergistic protectionMiceInfectionAntibodiesFc regionAntiserumVertebrate hostsProtein TrioImmunizationVaccineMalariaAntigenImmunityImmunogenic amino acid motifs and linear epitopes of COVID-19 mRNA vaccines
Wisnewski AV, Redlich CA, Liu J, Kamath K, Abad QA, Smith RF, Fazen L, Santiago R, Luna J, Martinez B, Baum-Jones E, Waitz R, Haynes WA, Shon JC. Immunogenic amino acid motifs and linear epitopes of COVID-19 mRNA vaccines. PLOS ONE 2021, 16: e0252849. PMID: 34499652, PMCID: PMC8428655, DOI: 10.1371/journal.pone.0252849.Peer-Reviewed Original ResearchConceptsCOVID-19 mRNA vaccine recipientsLinear epitopesSARS-CoV-2 neutralizationCOVID-19 mRNA vaccinesVaccine-induced IgGMRNA vaccine recipientsSARS-CoV-2 spike proteinDominant linear epitopeElicit IgGVaccine recipientsVaccine effectivenessMRNA vaccinesVaccination samplesImmune escapeHuman coronavirusesHealthy adultsSARS-CoVVaccine epitopesCritical epitopesAdverse responsesReverse vaccinologySpike proteinNatural infectionS2 subunitIgGInsights into the structure and RNA-binding specificity of Caenorhabditis elegans Dicer-related helicase 3 (DRH-3)
Li K, Zheng J, Wirawan M, Trinh NM, Fedorova O, Griffin PR, Pyle AM, Luo D. Insights into the structure and RNA-binding specificity of Caenorhabditis elegans Dicer-related helicase 3 (DRH-3). Nucleic Acids Research 2021, 49: 9978-9991. PMID: 34403472, PMCID: PMC8464030, DOI: 10.1093/nar/gkab712.Peer-Reviewed Original ResearchConceptsC-terminal domainN-terminal domainDRH-3RNA interferenceTandem caspase activationSimilar domain architectureEndogenous RNAi pathwaysRNA helicase familyDouble-stranded RNACARDs of RIGUnique structural dynamicsGermline developmentEvolutionary divergenceChromosome segregationRNAi pathwayCaenorhabditis elegansDomain architectureHelicase familyCaspase activationDistinct foldsRecruitment domainMolecular understandingRLR familyRNA duplexesRNAA structurally preserved allosteric site in the MIF superfamily affects enzymatic activity and CD74 activation in D-dopachrome tautomerase
Chen E, Reiss K, Shah D, Manjula R, Allen B, Murphy EL, Murphy JW, Batista VS, Bhandari V, Lolis EJ, Lisi GP. A structurally preserved allosteric site in the MIF superfamily affects enzymatic activity and CD74 activation in D-dopachrome tautomerase. Journal Of Biological Chemistry 2021, 297: 101061. PMID: 34384784, PMCID: PMC8405996, DOI: 10.1016/j.jbc.2021.101061.Peer-Reviewed Original ResearchMeSH KeywordsAllosteric SiteAmino Acid SequenceAntigens, Differentiation, B-LymphocyteBinding SitesCatalytic DomainCrystallography, X-RayCytokinesHistocompatibility Antigens Class IIHumansIntramolecular OxidoreductasesMacrophage Migration-Inhibitory FactorsProtein BindingStructure-Activity RelationshipConceptsAllosteric siteDopachrome tautomeraseDynamic regulatory networksEnzymatic activityLow sequence identityLigand-binding siteMultiple ligand-binding sitesNonoverlapping functionsRegulatory networksAllosteric couplingMacrophage migration inhibitory factor (MIF) familyFactor familySequence identityHomolog DStructural basisPrimary sequenceCD74 activationFunctional similarityConformational changesSolution NMRMIF-2X-ray crystallographyCatalytic siteStructural consequencesSolvent channelsSmart-RRBS for single-cell methylome and transcriptome analysis
Gu H, Raman AT, Wang X, Gaiti F, Chaligne R, Mohammad AW, Arczewska A, Smith ZD, Landau DA, Aryee MJ, Meissner A, Gnirke A. Smart-RRBS for single-cell methylome and transcriptome analysis. Nature Protocols 2021, 16: 4004-4030. PMID: 34244697, PMCID: PMC8672372, DOI: 10.1038/s41596-021-00571-9.Peer-Reviewed Original ResearchConceptsSingle cellsProtein-coding genesSingle-cell methylomesSame single cellMulti-omics approachRare cell populationsSmart-seq2Transcriptional statesDNA methylomeTranscriptome analysisImportant mechanistic insightsEpigenetic modificationsDNA methylationDissected tissue samplesGenomic DNAHundreds of cellsCellular heterogeneityFlow sortingRegulatory consequencesMethylomeEpigenetic promoterMechanistic insightsCell populationsCellsTypical single cellPhosphorylated WNK kinase networks in recoded bacteria recapitulate physiological function
Schiapparelli P, Pirman NL, Mohler K, Miranda-Herrera PA, Zarco N, Kilic O, Miller C, Shah SR, Rogulina S, Hungerford W, Abriola L, Hoyer D, Turk BE, Guerrero-Cázares H, Isaacs FJ, Quiñones-Hinojosa A, Levchenko A, Rinehart J. Phosphorylated WNK kinase networks in recoded bacteria recapitulate physiological function. Cell Reports 2021, 36: 109416. PMID: 34289367, PMCID: PMC8379681, DOI: 10.1016/j.celrep.2021.109416.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceAnimalsCell Line, TumorCell MovementCell ProliferationEscherichia coliFemaleGlioblastomaHEK293 CellsHumansMaleMice, NudeMiddle AgedPhosphorylationPhosphoserineProtein Serine-Threonine KinasesRecombinant ProteinsSignal TransductionSmall Molecule LibrariesSubstrate SpecificityWNK Lysine-Deficient Protein Kinase 1ConceptsKinase networkAuthentic post-translational modificationsGenetic code expansionPost-translational modificationsProduction of proteinsSmall molecule kinase inhibitorsKinase inhibitorsGenetic codePhosphorylated proteinsCode expansionKinase proteinWNK kinasesPhysiological functionsWNK4 kinaseBiochemical propertiesGlioblastoma cellsKinaseBacterial strainsProteinDistinct sitesPhosphoserineSPAKBacteriaCellular systemsCellsAn epilepsy-causing mutation leads to co-translational misfolding of the Kv7.2 channel
Urrutia J, Aguado A, Gomis-Perez C, Muguruza-Montero A, Ballesteros OR, Zhang J, Nuñez E, Malo C, Chung HJ, Leonardo A, Bergara A, Villarroel A. An epilepsy-causing mutation leads to co-translational misfolding of the Kv7.2 channel. BMC Biology 2021, 19: 109. PMID: 34020651, PMCID: PMC8138981, DOI: 10.1186/s12915-021-01040-1.Peer-Reviewed Original ResearchConceptsKv7.2 channelsChannel functionSequences of proteinsNon-native configurationsNascent chainsProper foldingEpilepsy-causing mutationsIQ motifResponsive domainHuman diseasesHelix ANative conformationFolding routeIon channelsKCNQ2 geneMutationsNeuronal compartmentsFoldingMisfoldingProteinKey pathogenic mechanismsPathogenic variantsSilico studiesPathogenic mechanismsSide chains
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