2025
Crystal structure of Isthmin-1 and reassessment of its functional role in pre-adipocyte signaling
Li T, Stayrook S, Li W, Wang Y, Li H, Zhang J, Liu Y, Klein D. Crystal structure of Isthmin-1 and reassessment of its functional role in pre-adipocyte signaling. Nature Communications 2025, 16: 3580. PMID: 40234450, PMCID: PMC12000326, DOI: 10.1038/s41467-025-58828-w.Peer-Reviewed Original ResearchConceptsThrombospondin type I repeatsIsthmin-1Pre-adipocytesType I repeatsBacterial streptavidinSurface helicesI repeatsMolecular detailsDiverse functionsFunctional studiesAkt phosphorylationFunctional roleStructural plasticityInsulin-like propertiesCrystal structureAMOPGrowth factorDomainPhosphorylationApoptosisLiver steatosisProteinHelixAktStreptavidin
2024
Structure and mechanism of the human CTDNEP1–NEP1R1 membrane protein phosphatase complex necessary to maintain ER membrane morphology
Gao S, Rodríguez J, Bahmanyar S, Airola M. Structure and mechanism of the human CTDNEP1–NEP1R1 membrane protein phosphatase complex necessary to maintain ER membrane morphology. Proceedings Of The National Academy Of Sciences Of The United States Of America 2024, 121: e2321167121. PMID: 38776370, PMCID: PMC11145253, DOI: 10.1073/pnas.2321167121.Peer-Reviewed Original ResearchConceptsProtein phosphatase complexPhosphatase complexER membrane biogenesisHigh-resolution crystal structuresProtein serine/threonine phosphatasesCancer-associated mutationsDevelopment of medulloblastomaMembrane biogenesisSubstrate recognitionER expansionActive siteRegulatory subunitSubstrate peptideMammalian cellsSerine/threonine phosphataseIdentical phenotypesArg residuesMolecular detailsSubunit 1Phosphatase 1Inactivating mutationsPeptide sequencesAggressive childhood cancerMutationsPhosphatase activity
2023
Structure Determination of SH2–Phosphopeptide Complexes by X-Ray Crystallography: The Example of p120RasGAP
Stiegler A, Boggon T. Structure Determination of SH2–Phosphopeptide Complexes by X-Ray Crystallography: The Example of p120RasGAP. Methods In Molecular Biology 2023, 2705: 77-89. PMID: 37668970, PMCID: PMC11059313, DOI: 10.1007/978-1-0716-3393-9_5.Peer-Reviewed Original ResearchConceptsSrc homology 2SH2 domain bindsSH2 domainDomain bindsNew molecular-level insightsSH2 domain proteinsMolecular-level insightsX-ray crystallographyX-ray diffraction studiesDomain proteinsPartner proteinsHomology 2Three-dimensional structureMolecular detailsStructure determinationSuitable crystalsCanonical interactionsVapour-diffusion methodCareful structural analysisDrop vapor diffusion methodCrystallographic studiesCrystallography studiesSH2-phosphopeptide complexesDiffraction studiesP120RasGAPStructural basis for activation of CB1 by an endocannabinoid analog
Krishna Kumar K, Robertson M, Thadhani E, Wang H, Suomivuori C, Powers A, Ji L, Nikas S, Dror R, Inoue A, Makriyannis A, Skiniotis G, Kobilka B. Structural basis for activation of CB1 by an endocannabinoid analog. Nature Communications 2023, 14: 2672. PMID: 37160876, PMCID: PMC10169858, DOI: 10.1038/s41467-023-37864-4.Peer-Reviewed Original ResearchConceptsCannabinoid receptor 1Activation of cannabinoid receptor 1Molecular dynamics simulationsLigand-binding pocketDesigning effective drugsECB anandamideDynamics simulationsBinding pocketAllosteric modulatorsLigand interactionsEndocannabinoidFunctional consequencesLigandEndogenous ligandActivate G proteinsECBG protein-coupled receptorsSignaling ComplexMolecular detailsStructural basisAnandamideCannabinoidSignaling assaysG-proteinReceptor 1
2022
Molecular determinants of complexin clamping and activation function
Bera M, Ramakrishnan S, Coleman J, Krishnakumar SS, Rothman JE. Molecular determinants of complexin clamping and activation function. ELife 2022, 11: e71938. PMID: 35442188, PMCID: PMC9020821, DOI: 10.7554/elife.71938.Peer-Reviewed Original ResearchConceptsSynaptotagmin-1Single-vesicle fusionAccessory helixFusion clampHelical domainMolecular detailsComplexinMutational analysisVesicle releaseFusion kineticsMolecular determinantsSpecific interactionsInhibitory functionProbability of fusionRapid CaSNAREpinsAssembly processFusionClamping functionDomainHelixVesiclesFunctionMembraneInteraction
2021
Mitofusin-2 regulates leukocyte adhesion and β2 integrin activation
Liu W, Hsu AY, Wang Y, Lin T, Sun H, Pachter JS, Groisman A, Imperioli M, Yungher FW, Hu L, Wang P, Deng Q, Fan Z. Mitofusin-2 regulates leukocyte adhesion and β2 integrin activation. Journal Of Leukocyte Biology 2021, 111: 771-791. PMID: 34494308, PMCID: PMC8901796, DOI: 10.1002/jlb.1a0720-471r.Peer-Reviewed Original ResearchConceptsΒ2 integrin activationIntegrin activationMitofusin 2Mfn2 deficiencyConformation-specific monoclonal antibodiesMFN2 knockdownHL60 cellsNeutrophil-like HL60 cellsMolecular detailsActin polymerizationCell spreadingAdhesion defectsReduced expressionInnate immunityKnockdownNew insightsActivationCellsLeukocyte adhesionAdhesionCell rollingCrucial stepMonoclonal antibodiesDifferentiationVascular endothelium
2020
Sequence-dependent dynamics of synthetic and endogenous RSSs in V(D)J recombination
Hirokawa S, Chure G, Belliveau NM, Lovely GA, Anaya M, Schatz DG, Baltimore D, Phillips R. Sequence-dependent dynamics of synthetic and endogenous RSSs in V(D)J recombination. Nucleic Acids Research 2020, 48: gkaa418-. PMID: 32449932, PMCID: PMC7337519, DOI: 10.1093/nar/gkaa418.Peer-Reviewed Original Research
2015
Tissue-based map of the human proteome
Uhlén M, Fagerberg L, Hallström B, Lindskog C, Oksvold P, Mardinoglu A, Sivertsson Å, Kampf C, Sjöstedt E, Asplund A, Olsson I, Edlund K, Lundberg E, Navani S, Szigyarto C, Odeberg J, Djureinovic D, Takanen J, Hober S, Alm T, Edqvist P, Berling H, Tegel H, Mulder J, Rockberg J, Nilsson P, Schwenk J, Hamsten M, von Feilitzen K, Forsberg M, Persson L, Johansson F, Zwahlen M, von Heijne G, Nielsen J, Pontén F. Tissue-based map of the human proteome. Science 2015, 347: 1260419. PMID: 25613900, DOI: 10.1126/science.1260419.Peer-Reviewed Original ResearchConceptsPutative protein-coding genesHuman tissue proteomesProtein-coding genesInteractive web-based databaseIntegrated omics approachDifferent tissuesGlobal expression patternsSingle-cell levelMembrane proteomeProteome variationDruggable proteomeOmics approachesHuman proteomeHuman secretomeMolecular detailsIndividual proteinsQuantitative transcriptomicsCancer proteomeTissue proteomeProteomeExpression patternsHuman biologyMetabolic functionsTissue microarray-based immunohistochemistryMajor tissues
2014
Role of the Vector in Arbovirus Transmission
Conway MJ, Colpitts TM, Fikrig E. Role of the Vector in Arbovirus Transmission. Annual Review Of Virology 2014, 1: 71-88. PMID: 26958715, PMCID: PMC7809425, DOI: 10.1146/annurev-virology-031413-085513.Peer-Reviewed Original ResearchDisease vectorsDominant lethal geneArbovirus transmissionTransmission of arbovirusesLethal genesMolecular detailsTransgenic mosquitoesHost-seeking behaviorMosquito populationsArboviral diseasesGenomicsProteomicsPrevalence of diseaseNovel strategyGenesArbovirusesMicrobesImmunological controlGrowthVectorDiseaseSignificant diseasePathogensHostRoleC-terminal motif within Sec7 domain regulates guanine nucleotide exchange activity via tuning protein conformation
Qiu B, Zhang K, Wang S, Sun F. C-terminal motif within Sec7 domain regulates guanine nucleotide exchange activity via tuning protein conformation. Biochemical And Biophysical Research Communications 2014, 446: 380-386. PMID: 24613384, DOI: 10.1016/j.bbrc.2014.02.125.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid MotifsAmino Acid SequenceBinding SitesConserved SequenceCrystallography, X-RayGuanine Nucleotide Exchange FactorsModels, MolecularMolecular Sequence DataMutagenesis, Site-DirectedNuclear Magnetic Resonance, BiomolecularProtein ConformationProtein StabilityProtein Structure, SecondaryRecombinant ProteinsSaccharomyces cerevisiaeSaccharomyces cerevisiae ProteinsSequence Homology, Amino AcidStatic ElectricityStructural Homology, ProteinConceptsGuanine exchange factorSec7 domainARF-GEFCatalytic domainActivity regulationGolgi network membranesNucleotide exchange activityC-terminal motifGEF catalytic activityADP-ribosylation factorCatalytic activity regulationExchange activityActivation of ARFARF-GEFsMembrane trafficExchange factorHelix JOrganelle structureMolecular detailsMutagenesis studiesProtein conformationLoop regionMotifRegulationKey role
2013
The lipoprotein La7 contributes to Borrelia burgdorferi persistence in ticks and their transmission to naïve hosts
Yang X, Hegde S, Shroder DY, Smith AA, Promnares K, Neelakanta G, Anderson JF, Fikrig E, Pal U. The lipoprotein La7 contributes to Borrelia burgdorferi persistence in ticks and their transmission to naïve hosts. Microbes And Infection 2013, 15: 729-737. PMID: 23774694, PMCID: PMC3769513, DOI: 10.1016/j.micinf.2013.06.001.Peer-Reviewed Original ResearchConceptsComplex enzootic cycleInner membrane proteinB. burgdorferi persistenceProtein-protein interactionsOuter membrane lipoproteinNaïve hostsSpirochete life cycleCo-immunoprecipitation studiesMammalian infectivityMembrane proteinsRedundant rolesMolecular detailsMammalian hostsMembrane lipoproteinGene expressionWild typeInfection cycleLiquid chromatography-mass spectrometry analysisPathogen survivalBiological significanceHost transmissionEnzootic cyclePathogen transmissionSpectrometry analysisLA7
2012
Structural Basis for Paxillin Binding and Focal Adhesion Targeting of β-Parvin*
Stiegler AL, Draheim KM, Li X, Chayen NE, Calderwood DA, Boggon TJ. Structural Basis for Paxillin Binding and Focal Adhesion Targeting of β-Parvin*. Journal Of Biological Chemistry 2012, 287: 32566-32577. PMID: 22869380, PMCID: PMC3463362, DOI: 10.1074/jbc.m112.367342.Peer-Reviewed Original ResearchConceptsΒ-parvinFocal adhesionsPaxillin bindingΑ-parvinFocal adhesion targetingN-terminal α-helixPaxillin LD1 motifCalponin homology domainFirst molecular detailsHigh sequence similarityCytoplasmic adaptor proteinIntegrin-linked kinasePaxillin LD1Co-crystal structureLD4 motifSignificant conformational flexibilityHomology domainAdaptor proteinCellular functionsSequence similarityRepeat motifsProper localizationMolecular detailsPaxillinStructural basis
2011
Emerging roles of TET proteins and 5-hydroxymethylcytosines in active DNA demethylation and beyond
Guo J, Su Y, Zhong C, Ming G, Song H. Emerging roles of TET proteins and 5-hydroxymethylcytosines in active DNA demethylation and beyond. Cell Cycle 2011, 10: 2662-2668. PMID: 21811096, PMCID: PMC3219536, DOI: 10.4161/cc.10.16.17093.Peer-Reviewed Original Research
2007
Input–output robustness in simple bacterial signaling systems
Shinar G, Milo R, Martínez M, Alon U. Input–output robustness in simple bacterial signaling systems. Proceedings Of The National Academy Of Sciences Of The United States Of America 2007, 104: 19931-19935. PMID: 18077424, PMCID: PMC2148400, DOI: 10.1073/pnas.0706792104.Peer-Reviewed Original ResearchReceptor Activator of Nuclear Factor-κB Ligand-Induced Nuclear Factor of Activated T Cells (C1) Autoregulates Its Own Expression in Osteoclasts and Mediates the Up-Regulation of Tartrate-Resistant Acid Phosphatase
Fretz JA, Shevde NK, Singh S, Darnay BG, Pike JW. Receptor Activator of Nuclear Factor-κB Ligand-Induced Nuclear Factor of Activated T Cells (C1) Autoregulates Its Own Expression in Osteoclasts and Mediates the Up-Regulation of Tartrate-Resistant Acid Phosphatase. Endocrinology 2007, 22: 737-750. PMID: 18063694, PMCID: PMC2262172, DOI: 10.1210/me.2007-0333.Peer-Reviewed Original ResearchMeSH KeywordsAcid PhosphataseAnimalsBlotting, WesternBone and BonesCell LineChromatin ImmunoprecipitationHomeostasisIsoenzymesMiceMice, Inbred C57BLNFATC Transcription FactorsOsteoclastsPromoter Regions, GeneticRANK LigandReverse Transcriptase Polymerase Chain ReactionRNA, MessengerTartrate-Resistant Acid PhosphataseTranscription, GeneticUp-RegulationConceptsNFAT membersRNA polymerase IIDNA-binding proteinsSpecific transcription factorsChromatin immunoprecipitation analysisSignal transduction pathwaysAdditional molecular detailsNuclear factorActivated T cells cytoplasmic 1Polymerase IIAcp5 promotersTranscription factorsTransduction pathwaysMolecular detailsTarget genesOwn expressionImmunoprecipitation analysisP1 promoterBone-resorbing cellsReceptor activatorHematopoietic precursorsGenesNuclear factor-κB ligandCytoplasmic 1Time-dependent accumulationA Proteomics Study of Brassinosteroid Response in Arabidopsis *
Deng Z, Zhang X, Tang W, Oses-Prieto JA, Suzuki N, Gendron JM, Chen H, Guan S, Chalkley RJ, Peterman TK, Burlingame AL, Wang ZY. A Proteomics Study of Brassinosteroid Response in Arabidopsis *. Molecular & Cellular Proteomics 2007, 6: 2058-2071. PMID: 17848588, PMCID: PMC2966871, DOI: 10.1074/mcp.m700123-mcp200.Peer-Reviewed Original ResearchConceptsTwo-dimensional DIGEProteomic studiesBiosynthesis of hormonesSpecific cellular processesPrevious microarray studyBri1-116Bzr1-1DBrassinosteroid responsesBR regulationBR actionVesicle traffickingBR responsesCellular processesRT-PCR analysisPosttranslational modificationsBrassinosteroidsCytoskeleton rearrangementMolecular detailsProtein responseBR treatmentPlant steroidsBR mutantsMolecular networksDiverse processesPhysiological processes
2004
Staggered AID‐dependent DNA double strand breaks are the predominant DNA lesions targeted to Sµ in Ig class switch recombination
Rush JS, Fugmann SD, Schatz DG. Staggered AID‐dependent DNA double strand breaks are the predominant DNA lesions targeted to Sµ in Ig class switch recombination. International Immunology 2004, 16: 549-557. PMID: 15039385, DOI: 10.1093/intimm/dxh057.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsAntibodies, MonoclonalB-LymphocytesBlotting, SouthernCell DivisionCytidine DeaminaseDeoxyribonucleases, Type II Site-SpecificDNADNA DamageDNA PrimersFlow CytometryGene ExpressionImmunoglobulin Class SwitchingImmunoglobulin DImmunoglobulin GImmunoglobulin Switch RegionInterleukin-4LipopolysaccharidesMiceMice, Inbred C57BLMice, KnockoutPlasmidsPolymerase Chain ReactionRecombination, GeneticConceptsClass switch recombinationDNA double-strand breaksPredominant DNA lesionsDouble-strand breaksActivation-induced cytidine deaminaseDNA lesionsSwitch recombinationAID-dependent DNA double-strand breaksStrand breaksIg class switch recombinationLigation-mediated PCRS mu regionCellular regulationKinetics of inductionMolecular detailsMurine B cellsDNA DSBsStaggered breaksCytidine deaminaseDSBsMu regionMinor speciesB cellsS muEffector properties
2001
Ion Channels, Membrane Ion Currents, and the Action Potential
B.Levitan I, Kaczmarek L. Ion Channels, Membrane Ion Currents, and the Action Potential. 2001, 113-138. DOI: 10.1093/oso/9780195145236.003.0006.Peer-Reviewed Original ResearchIon channelsPotassium channel proteinIon currentDetailed mechanistic understandingMembrane proteinsMolecular detailsActive ion channelsChannel proteinsBiological membranesMechanistic understandingSingle-channel recordingsProteinMembrane ion currentsVoltage-clamp measurementsMembraneChannel recordingsCellsMacroscopic currentsClamp measurementsCurrentElectrical phenomenaVoltage clampCurrent chapterMacroscopic membranesPotassium current
2000
Accessory factors in clathrin-dependent synaptic vesicle endocytosis
Slepnev V, De Camilli P. Accessory factors in clathrin-dependent synaptic vesicle endocytosis. Nature Reviews Neuroscience 2000, 1: 161-172. PMID: 11257904, DOI: 10.1038/35044540.Peer-Reviewed Original ResearchConceptsAccessory factorsNumerous accessory proteinsSynaptic vesicle endocytosisClathrin-mediated endocytosisRecent structural studiesPlasma membrane componentsSynaptic vesicle recyclingInternalization of receptorsVesicle endocytosisCoat assemblyExtracellular ligandsClathrin coatMolecular detailsVesicle recyclingAccessory proteinsGenetic studiesEndocytosisMembrane componentsSurface proteinsClathrinStructural studiesProteinVesiclesInternalizationNew aspects
1999
Molecular analysis of protein interactions mediating the function of the cell surface protein CD8
Devine L, Kavathas P. Molecular analysis of protein interactions mediating the function of the cell surface protein CD8. Immunologic Research 1999, 19: 201-210. PMID: 10493174, DOI: 10.1007/bf02786488.Peer-Reviewed Original ResearchConceptsProtein interactionsForms of CD8Such protein interactionsTyrosine kinase p56lckDisulfide-linked homodimerCell surface glycoproteinMolecular detailsKinase p56lckMutational analysisMolecular analysisFunctional differencesCoreceptor CD8ProteinHistocompatibility complex class IAffinity measurementsMajor histocompatibility complex class IComplex class ICellsP56lckHomodimerHeterodimersCrystal structureClass IGlycoproteinInteraction
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