2024
Global screening of base excision repair in nucleosome core particles
Sutton T, Sawyer D, Naila T, Sweasy J, Tomkinson A, Delaney S. Global screening of base excision repair in nucleosome core particles. DNA Repair 2024, 144: 103777. PMID: 39476546, PMCID: PMC11611610, DOI: 10.1016/j.dnarep.2024.103777.Peer-Reviewed Original ResearchBase excision repairUracil-DNA glycosylaseAP endonuclease 1Nucleosome core particleBase excision repair enzymesAbsence of chromatin remodelingExcision repairDNA polymerase BGenome wide mappingContext of chromatinEukaryotic genomic DNADNA damageCore particlesPolymerase BChromatin remodelingActivities of BER enzymesNick siteGenomic DNAProtein interactionsMutational hotspotsNucleosomal DNADNA glycosylaseGenomic instabilityCellular factorsEntry/exit regionVersatility of 14-3-3 proteins and their roles in bone and joint-related diseases
Zhou R, Hu W, Ma P, Liu C. Versatility of 14-3-3 proteins and their roles in bone and joint-related diseases. Bone Research 2024, 12: 58. PMID: 39406741, PMCID: PMC11480210, DOI: 10.1038/s41413-024-00370-4.Peer-Reviewed Original ResearchDNA-Based Molecular Clamp for Probing Protein Interactions and Structure under Force
Chung M, Zhou K, Powell J, Lin C, Schwartz M. DNA-Based Molecular Clamp for Probing Protein Interactions and Structure under Force. ACS Nano 2024, 18: 27590-27596. PMID: 39344156, PMCID: PMC11518680, DOI: 10.1021/acsnano.4c08663.Peer-Reviewed Original ResearchConceptsTalin rod domainNegative-stain electron microscopyDouble-stranded DNADNA clampProtein functionRod domainCryptic sitesProtein interactionsMolecular clampCellular mechanotransductionStudy proteinsBiochemical studiesCell biologyAdult physiologyProtein conformationTalinProteinBiochemical scaleMultiple diseasesDNAARPC5LVinculinStructural analysisEmbryogenesisDNA-based devicesStructural insights into PPP2R5A degradation by HIV-1 Vif
Hu Y, Delviks-Frankenberry K, Wu C, Arizaga F, Pathak V, Xiong Y. Structural insights into PPP2R5A degradation by HIV-1 Vif. Nature Structural & Molecular Biology 2024, 31: 1492-1501. PMID: 38789685, DOI: 10.1038/s41594-024-01314-6.Peer-Reviewed Original ResearchHost-virus protein interactionsCullin RING E3 ubiquitin ligasesInduced G2/M cell cycle arrestSets of proteinsG2/M cell cycle arrestSubstrate-binding siteCryogenic-electron microscopy structuresProtein phosphatase 2ADegradation-independent mechanismCell cycle arrestUbiquitin ligaseProtein interactionsPhosphatase 2AAntiviral proteinCycle arrestDegradation-dependentA-resolutionHIV-1 VifPPP2R5AStructural insightsDiverse interactionsProteinCellular studiesPhosphatase activityPotential targetKinetic study of membrane protein interactions: from three to two dimensions
Adrien V, Reffay M, Taulier N, Verchère A, Monlezun L, Picard M, Ducruix A, Broutin I, Pincet F, Urbach W. Kinetic study of membrane protein interactions: from three to two dimensions. Scientific Reports 2024, 14: 882. PMID: 38195620, PMCID: PMC10776792, DOI: 10.1038/s41598-023-50827-5.Peer-Reviewed Original ResearchConceptsMembrane proteinsMembrane protein interactionsProtein-protein interactionsProtein complexesProtein interactionsMembrane environmentOpposite membranesBacterial efflux pumpsProtein behaviorProtein systemsMolecular interactionsEfflux pumpsProteinExploration distanceMembraneFluorescence recovery experimentsInteractionBinding rateBinding constantsComplexes
2023
Site-specific crosslinking reveals Phosphofructokinase-L inhibition drives self-assembly and attenuation of protein interactions
Sivadas A, McDonald E, Shuster S, Davis C, Plate L. Site-specific crosslinking reveals Phosphofructokinase-L inhibition drives self-assembly and attenuation of protein interactions. Advances In Biological Regulation 2023, 90: 100987. PMID: 37806136, PMCID: PMC11108229, DOI: 10.1016/j.jbior.2023.100987.Peer-Reviewed Original ResearchConceptsProtein interactionsProtein-protein interactionsSite-specific crosslinkingSite-specific incorporationMetabolic proteinsRegulated stepProtein assembliesCentral enzymePuncta formationMetabolic fluxHuman cellsInterface 2Amino acidsCytoskeletonLiver isoformCentral roleCompartmentalizationGlycolysisActive siteInteractorsInhibitionInterface 1IsoformsProteinCitrate inhibitionUncovering biology by single-cell proteomics
Mansuri M, Williams K, Nairn A. Uncovering biology by single-cell proteomics. Communications Biology 2023, 6: 381. PMID: 37031277, PMCID: PMC10082756, DOI: 10.1038/s42003-023-04635-2.Peer-Reviewed Original Research
2022
SEMA7AR148W mutation promotes lipid accumulation and NAFLD progression via increased localization on the hepatocyte surface
Zhao N, Zhang X, Ding J, Pan Q, Zheng MH, Liu WY, Luo G, Qu J, Li M, Li L, Cheng Y, Peng Y, Xie Q, Wei Q, Li Q, Zou L, Ouyang X, Cai SY, Boyer JL, Chai J. SEMA7AR148W mutation promotes lipid accumulation and NAFLD progression via increased localization on the hepatocyte surface. JCI Insight 2022, 7: e154113. PMID: 35938531, PMCID: PMC9462498, DOI: 10.1172/jci.insight.154113.Peer-Reviewed Original ResearchConceptsIntegrin β1Lipid accumulationPrimary mouse hepatocytesProtein interactionsLipid droplet accumulationMouse liverFatty acid oxidationHeterozygous mutationsIntegrin β1 proteinPKC-α phosphorylationFA uptakeGenetic determinantsMouse peritoneal macrophagesCell membraneStrong genetic determinantsMutationsMouse hepatocytesDroplet accumulationΒ1 proteinCD36 expressionAcid oxidationPKCTriglyceride synthesisGenetic polymorphismsAccumulationChromatin profiling in human neurons reveals aberrant roles for histone acetylation and BET family proteins in schizophrenia
Farrelly L, Zheng S, Schrode N, Topol A, Bhanu N, Bastle R, Ramakrishnan A, Chan J, Cetin B, Flaherty E, Shen L, Gleason K, Tamminga C, Garcia B, Li H, Brennand K, Maze I. Chromatin profiling in human neurons reveals aberrant roles for histone acetylation and BET family proteins in schizophrenia. Nature Communications 2022, 13: 2195. PMID: 35459277, PMCID: PMC9033776, DOI: 10.1038/s41467-022-29922-0.Peer-Reviewed Original ResearchConceptsHistone posttranslational modificationsPosttranslational modificationsUnbiased proteomic approachPluripotent stem cellsPatient-derived neuronsH2A.Z acetylationChromatin profilingHyperacetylated histonesFamily proteinsProteomic approachProtein interactionsHistone acetylationTranscriptional abnormalitiesEpigenetic factorsExtraterminal (BET) proteinsSZ casesRisk variantsHuman neuronsStem cellsAberrant roleProtein inhibitionBona fideTreatment of schizophreniaPostmortem human brainCritical role
2021
MAL2 mediates the formation of stable HER2 signaling complexes within lipid raft-rich membrane protrusions in breast cancer cells
Jeong J, Shin JH, Li W, Hong JY, Lim J, Hwang JY, Chung JJ, Yan Q, Liu Y, Choi J, Wysolmerski J. MAL2 mediates the formation of stable HER2 signaling complexes within lipid raft-rich membrane protrusions in breast cancer cells. Cell Reports 2021, 37: 110160. PMID: 34965434, PMCID: PMC8762588, DOI: 10.1016/j.celrep.2021.110160.Peer-Reviewed Original ResearchMeSH KeywordsAntineoplastic Agents, ImmunologicalBreast NeoplasmsCell ProliferationCytoskeletal ProteinsDrug Resistance, NeoplasmEndocytosisFemaleHumansMembrane MicrodomainsMyelin and Lymphocyte-Associated Proteolipid ProteinsPhosphoproteinsPlasma Membrane Calcium-Transporting ATPasesReceptor, ErbB-2Sodium-Hydrogen ExchangersTrastuzumabTumor Cells, CulturedConceptsLipid raft formationBreast cancer cellsLipid raftsLipid raft resident proteinsCancer cellsRaft formationRaft-resident proteinsProximity ligation assayProtein complexesMembrane protrusionsProtein interactionsPlasma membraneLigation assayMAL2Membrane stabilityStructural organizationPotential therapeutic targetPhysical interactionMembrane retentionProteinRaftsTherapeutic targetCellsIntracellular calcium concentrationLow intracellular calcium concentrationCross-Species and Human Inter-Tissue Network Analysis of Genes Implicated in Longevity and Aging Reveal Strong Support for Nutrient Sensing
Podder A, Raju A, Schork N. Cross-Species and Human Inter-Tissue Network Analysis of Genes Implicated in Longevity and Aging Reveal Strong Support for Nutrient Sensing. Frontiers In Genetics 2021, 12: 719713. PMID: 34512728, PMCID: PMC8430347, DOI: 10.3389/fgene.2021.719713.Peer-Reviewed Original ResearchProtein-protein interaction networkMechanistic target of rapamycinMechanistic target of rapamycin signalingHuman protein-protein interaction networkNetwork analysis of genesSignaling pathwayCross-species orthologsLongevity-associated genesHigh-throughput dataAnalysis of genesCurated gene listsInteractions of proteinsProtein databaseGene listsSpecies genesProtein interactionsNutrient sensingInteraction networkNon-human speciesTarget of rapamycinTarget proteinsCross-speciesBiological pathwaysBiological processesGenesDiscovery and functional interrogation of SARS-CoV-2 RNA-host protein interactions
Flynn RA, Belk JA, Qi Y, Yasumoto Y, Wei J, Alfajaro MM, Shi Q, Mumbach MR, Limaye A, DeWeirdt PC, Schmitz CO, Parker KR, Woo E, Chang HY, Horvath TL, Carette JE, Bertozzi CR, Wilen CB, Satpathy AT. Discovery and functional interrogation of SARS-CoV-2 RNA-host protein interactions. Cell 2021, 184: 2394-2411.e16. PMID: 33743211, PMCID: PMC7951565, DOI: 10.1016/j.cell.2021.03.012.Peer-Reviewed Original ResearchConceptsSARS-CoV-2 RNASARS-CoV-2Virus-induced cell deathHost protein interactionsRNA-binding proteinActive infectionRNA virusesHost-virus interfaceGlobal mortalityTherapeutic benefitCRISPR screensAntiviral factorsProtein interactionsAntiviral activityViral specificityHost pathwaysFunctional RNA-binding proteinsFunctional connectionsRNA-centric approachesCell deathHost proteinsVirusFunctional interrogationRNAComprehensive catalogLimited Proteolysis-Coupled Mass Spectrometry Identifies Phosphatidylinositol 4,5-Bisphosphate Effectors in Human Nuclear Proteome
Sztacho M, Šalovská B, Červenka J, Balaban C, Hoboth P, Hozák P. Limited Proteolysis-Coupled Mass Spectrometry Identifies Phosphatidylinositol 4,5-Bisphosphate Effectors in Human Nuclear Proteome. Cells 2021, 10: 68. PMID: 33406800, PMCID: PMC7824793, DOI: 10.3390/cells10010068.Peer-Reviewed Original ResearchConceptsGene expressionHuman nuclear proteomeLimited proteolysisLabel-free quantitative mass spectrometryNuclear pore complexGene ontology analysisCell cycle regulationQuantitative mass spectrometryNuclear proteomeProtein effectorsPore complexPol IIRNA splicingOntology analysisMRNA splicingCycle regulationPIP2 bindingProtein interactionsDNA repairBioinformatics analysisNuclear envelopeFunctional domainsMass spectrometry identifiesSpecific proteinsCell cycle
2020
Actin flow-dependent and -independent force transmission through integrins
Driscoll TP, Ahn SJ, Huang B, Kumar A, Schwartz MA. Actin flow-dependent and -independent force transmission through integrins. Proceedings Of The National Academy Of Sciences Of The United States Of America 2020, 117: 32413-32422. PMID: 33262280, PMCID: PMC7768777, DOI: 10.1073/pnas.2010292117.Peer-Reviewed Original ResearchConceptsActin binding siteProtein interactionsDistinct protein interactionsDynamic protein interactionsIntegrin-dependent adhesionBinding sitesSubstrate stiffnessActin flowActin filamentsStiff substratesExtracellular matrixTalinVinculinIntegrinsReciprocal exchangeClutchesForce transmissionAdhesionFlow-independent mechanismsLarge adhesionABS3Cell edgeABS2SitesInteractionA reference map of the human binary protein interactome
Luck K, Kim D, Lambourne L, Spirohn K, Begg B, Bian W, Brignall R, Cafarelli T, Campos-Laborie F, Charloteaux B, Choi D, Coté A, Daley M, Deimling S, Desbuleux A, Dricot A, Gebbia M, Hardy M, Kishore N, Knapp J, Kovács I, Lemmens I, Mee M, Mellor J, Pollis C, Pons C, Richardson A, Schlabach S, Teeking B, Yadav A, Babor M, Balcha D, Basha O, Bowman-Colin C, Chin S, Choi S, Colabella C, Coppin G, D’Amata C, De Ridder D, De Rouck S, Duran-Frigola M, Ennajdaoui H, Goebels F, Goehring L, Gopal A, Haddad G, Hatchi E, Helmy M, Jacob Y, Kassa Y, Landini S, Li R, van Lieshout N, MacWilliams A, Markey D, Paulson J, Rangarajan S, Rasla J, Rayhan A, Rolland T, San-Miguel A, Shen Y, Sheykhkarimli D, Sheynkman G, Simonovsky E, Taşan M, Tejeda A, Tropepe V, Twizere J, Wang Y, Weatheritt R, Weile J, Xia Y, Yang X, Yeger-Lotem E, Zhong Q, Aloy P, Bader G, De Las Rivas J, Gaudet S, Hao T, Rak J, Tavernier J, Hill D, Vidal M, Roth F, Calderwood M. A reference map of the human binary protein interactome. Nature 2020, 580: 402-408. PMID: 32296183, PMCID: PMC7169983, DOI: 10.1038/s41586-020-2188-x.Peer-Reviewed Original ResearchConceptsProtein-protein interactionsBinary protein interactionsTissue-specific networksContext-specific functionsTissue-specific phenotypesSubcellular rolesGenome functionProtein interactomeInteractome networkMendelian diseasesInteractome mapCurated interactionsProtein interactionsCellular contextCellular functionsPhenotypic outcomesCellular organizationMolecular mechanismsInteractomeReference mapGlobal insightGenomeHuriComprehensive understandingInteractionAn in vitro mimic of in‐cell solvation for protein folding studies
Davis CM, Deutsch J, Gruebele M. An in vitro mimic of in‐cell solvation for protein folding studies. Protein Science 2020, 29: 1046-1054. PMID: 31994240, PMCID: PMC7096716, DOI: 10.1002/pro.3833.Peer-Reviewed Original ResearchConceptsPhosphoglycerate kinaseLysis bufferCytoplasmic protein interactionsSignificant nonadditive effectsVariety of proteinsProtein folding studiesEukaryotic cellsProtein foldingProtein interactionsCellular crowdingProtein-like sequencesEffect of FicollFolding studiesHydrophobic patchVariable major protein-like sequenceNonadditive effectsCellular effectsProteinCell environmentInert macromoleculesBiomolecular interactionsCellsTest tubeSmall crowdersMimics
2018
Noncoding RNA Ginir functions as an oncogene by associating with centrosomal proteins
Panda S, Setia M, Kaur N, Shepal V, Arora V, Singh D, Mondal A, Teli A, Tathode M, Gajula R, Padhy L, Shiras A. Noncoding RNA Ginir functions as an oncogene by associating with centrosomal proteins. PLOS Biology 2018, 16: e2004204. PMID: 30296263, PMCID: PMC6193740, DOI: 10.1371/journal.pbio.2004204.Peer-Reviewed Original ResearchConceptsGenomic stabilityNoncoding RNAsMouse cellsBreast cancer type 1 susceptibility proteinLong intergenic noncoding RNAsIntergenic noncoding RNAsGrowth regulatory signalsLong noncoding RNAHitherto unknown mechanismEukaryotic transcriptomesMitotic regulationCellular homeostasisTranscript pairsCentrosomal proteinsRNA functionMitotic fidelityAntisense transcriptsSusceptibility proteinProtein interactionsEmbryonic developmentFunctional characterisationIndividual transcriptsBRCA1 proteinRegulatory signalsAdult tissuesTalin as a mechanosensitive signaling hub
Goult BT, Yan J, Schwartz MA. Talin as a mechanosensitive signaling hub. Journal Of Cell Biology 2018, 217: 3776-3784. PMID: 30254032, PMCID: PMC6219721, DOI: 10.1083/jcb.201808061.Peer-Reviewed Original ResearchConceptsSignaling hubsExtracellular matrixRod domainTalin rod domainIntegrin β subunitsDifferent protein interactionsLong rod domainSwitch-like behaviorActin cytoskeletonCytoplasmic domainCytoplasmic proteinsProtein interactionsHelical bundleGlobular head domainTalin functionTransmembrane receptorsHelix bundleΒ-subunitHead domainIntegrin familyTalinCell adhesionIndividual domainsRecent evidenceDomain
2017
Precise Temporal Profiling of Signaling Complexes in Primary Cells Using SWATH Mass Spectrometry
Caron E, Roncagalli R, Hase T, Wolski W, Choi M, Menoita M, Durand S, García-Blesa A, Fierro-Monti I, Sajic T, Heusel M, Weiss T, Malissen M, Schlapbach R, Collins B, Ghosh S, Kitano H, Aebersold R, Malissen B, Gstaiger M. Precise Temporal Profiling of Signaling Complexes in Primary Cells Using SWATH Mass Spectrometry. Cell Reports 2017, 18: 3219-3226. PMID: 28355572, PMCID: PMC5382234, DOI: 10.1016/j.celrep.2017.03.019.Peer-Reviewed Original ResearchConceptsSWATH mass spectrometryProtein interactionsProtein interaction dynamicsPrimary cellsTissue-specific contextDifferential protein expressionCell-signaling eventsInteraction proteomeProtein Grb2Cellular functionsMouse geneticsCell signalingAffinity purificationMammalian tissuesDevelopmental stagesTemporal profilingSpatiotemporal organizationMass spectrometryFundamental processesProtein expressionCell populationsRobust workflowCellsInteraction dynamicsGrb2
2016
A novel mosquito ubiquitin targets viral envelope protein for degradation and reduces virion production during dengue virus infection
Troupin A, Londono-Renteria B, Conway MJ, Cloherty E, Jameson S, Higgs S, Vanlandingham DL, Fikrig E, Colpitts TM. A novel mosquito ubiquitin targets viral envelope protein for degradation and reduces virion production during dengue virus infection. Biochimica Et Biophysica Acta 2016, 1860: 1898-1909. PMID: 27241849, PMCID: PMC4949077, DOI: 10.1016/j.bbagen.2016.05.033.Peer-Reviewed Original ResearchConceptsProtein degradationUbiquitin proteinGene expressionProtein expression constructsSite-directed mutagenesisViral protein degradationInnate immune signalingDengue virusProteasomal degradationProtein interactionsExpression constructsMosquito cellsSignificant human diseaseMicroarray analysisImmune signalingViral envelope proteinsVirus infectionHuman diseasesBlood feedingAmino acidsProteinMultiple functionsQRT-PCRVirion productionAntiviral function
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