2024
Tetrameric PilZ protein stabilizes stator ring in complex flagellar motor and is required for motility in Campylobacter jejuni
Chen Y, Tachiyama S, Li Y, Feng X, Zhao H, Wu Y, Guo Y, Lara-Tejero M, Hua C, Liu J, Gao B. Tetrameric PilZ protein stabilizes stator ring in complex flagellar motor and is required for motility in Campylobacter jejuni. Proceedings Of The National Academy Of Sciences Of The United States Of America 2024, 122: e2412594121. PMID: 39793078, PMCID: PMC11725899, DOI: 10.1073/pnas.2412594121.Peer-Reviewed Original ResearchConceptsFlagellar motorPilZ domain-containing proteinsBound cyclic di-GMPCyclic di-GMPC-di-GMPDomain-containing proteinsStator unitsDi-GMPFamily proteinsSuperfamily proteinsBacterial flagellaRing assemblyCellular pathwaysCampylobacter jejuniCryoelectron tomographyCampylobacter jejuni</i>.Subtomogram averagingPilZProteinFlagellaPhylumAncestorMotilityJejuniStructural components
2023
A CUG-initiated CATSPERθ functions in the CatSper channel assembly and serves as a checkpoint for flagellar trafficking
Huang X, Miyata H, Wang H, Mori G, Iida-Norita R, Ikawa M, Percudani R, Chung J. A CUG-initiated CATSPERθ functions in the CatSper channel assembly and serves as a checkpoint for flagellar trafficking. Proceedings Of The National Academy Of Sciences Of The United States Of America 2023, 120: e2304409120. PMID: 37725640, PMCID: PMC10523455, DOI: 10.1073/pnas.2304409120.Peer-Reviewed Original ResearchConceptsChannel assemblySperm flagellaTransmembrane domain-containing proteinsSperm tail formationDomain-containing proteinsCatSper channel complexMale fertilityFlagellar traffickingMacromolecular complexesTail formationPhysiological roleSuccessful fertilizationCalcium signalingCatSper channelsFlagellaGenetic abrogationChannel complexNormal expressionDimer formationSpermatid cellsProteinCheckpointHyperactivated motilityAssemblyPotential roleBiomolecular Condensation of SH2 Domain-Containing Proteins on Membranes
Zeng L, Su X. Biomolecular Condensation of SH2 Domain-Containing Proteins on Membranes. Methods In Molecular Biology 2023, 2705: 371-379. PMID: 37668985, DOI: 10.1007/978-1-0716-3393-9_20.Peer-Reviewed Original ResearchConceptsSH2 domainSH2 domain-containing proteinsDomain-containing proteinsT cell receptorReceptors/adaptorsReceptor pathwayContext of membraneEndomembrane systemMembrane receptor pathwaysSignal transductionBiomolecular condensationSpecific tyrosinePlasma membraneReconstitution systemGolgi apparatusEndoplasmic reticulumLiquid-liquid phase separationMultivalent interactionsCondensate formationProteinMembranePathwayPhosphotyrosineAssaysTransductionArabidopsis Tubby domain‐containing F‐box proteins positively regulate immunity by modulating PI4Kβ protein levels
Devendrakumar K, Copeland C, Adamchek C, Zhong X, Huang X, Gendron J, Li X. Arabidopsis Tubby domain‐containing F‐box proteins positively regulate immunity by modulating PI4Kβ protein levels. New Phytologist 2023, 240: 354-371. PMID: 37571862, PMCID: PMC11114105, DOI: 10.1111/nph.19187.Peer-Reviewed Original ResearchConceptsTubby-like proteinsN-terminal F-box domainF-box E3 ligase complexesImmunoprecipitation-mass spectrometry analysisArabidopsis Immune ResponsesPlant immune responsesProtein levelsDomain-containing proteinsF-box domainF-box proteinsE3 ligase complexProteasome-dependent mannerRedundant homologsOverexpression linesTubby domainUbiquitination substratesSkp1-CullinTLP functionsLigase complexTubby proteinBiosynthesis enzymesDouble mutantMass spectrometry analysisProtein 6Novel mechanism
2022
UBXN3B Controls Immunopathogenesis of Arthritogenic Alphaviruses by Maintaining Hematopoietic Homeostasis
Geng T, Yang D, Lin T, Cahoon J, Wang P. UBXN3B Controls Immunopathogenesis of Arthritogenic Alphaviruses by Maintaining Hematopoietic Homeostasis. MBio 2022, 13: e02687-22. PMID: 36377866, PMCID: PMC9765034, DOI: 10.1128/mbio.02687-22.Peer-Reviewed Original ResearchConceptsUbiquitin regulatory X domain-containing proteinDomain-containing proteinsDiverse cellular processesCell-intrinsic mannerCellular processesHematopoietic homeostasisPhysiological functionsRNA virus replicationEssential roleControl of infectionChikungunya virusHuman genomeArthritogenic alphavirusesImmune responseCHIKV replicationDNA virusesRNA virusesInnate immune responseVirus-specific immunoglobulin GO'nyong'nyong virusLong-term neurological disordersSignificant public health problemSerum cytokine levelsSpecific antiviral drugsHigh viral load
2021
UBX Domain Protein 6 Positively Regulates JAK-STAT1/2 Signaling.
Ketkar H, Harrison A, Graziano V, Geng T, Yang L, Vella A, Wang P. UBX Domain Protein 6 Positively Regulates JAK-STAT1/2 Signaling. The Journal Of Immunology 2021, 206: 2682-2691. PMID: 34021047, PMCID: PMC8164993, DOI: 10.4049/jimmunol.1901337.Peer-Reviewed Original ResearchConceptsTyrosine kinase 2Domain-containing proteinsExpression of hundredsComplex cellular regulationRNA viral replicationJAK/STATCellular regulationType I/III IFNsKinase 2JAK/Type I/III IFNProtein 6IFN expressionGenesViral infectionSignalingExpressionViral replicationExpression of IFNCellsType IProteinSTATOverexpressionDeletion
2020
Absence of Sac2/INPP5F enhances the phenotype of a Parkinson’s disease mutation of synaptojanin 1
Cao M, Park D, Wu Y, De Camilli P. Absence of Sac2/INPP5F enhances the phenotype of a Parkinson’s disease mutation of synaptojanin 1. Proceedings Of The National Academy Of Sciences Of The United States Of America 2020, 117: 12428-12434. PMID: 32424101, PMCID: PMC7275725, DOI: 10.1073/pnas.2004335117.Peer-Reviewed Original ResearchConceptsSynaptojanin 1Sac domain-containing proteinsDisease mutationsDomain-containing proteinsGenome-wide association studiesPD risk lociSynaptic vesicle recyclingEndocytic factorsPD risk genesPhosphatase domainPhosphoinositide phosphataseParkinson's diseaseNumerous genesParkinson’s disease mutationsVesicle recyclingRisk lociAssociation studiesRisk genesInactivating mutationStriatal dopaminergic nerve terminalsGenesOccasional survivorsMutationsDopaminergic nerve terminalsSJ1
2019
Modeling cell line-specific recruitment of signaling proteins to the insulin-like growth factor 1 receptor
Erickson KE, Rukhlenko OS, Shahinuzzaman M, Slavkova KP, Lin YT, Suderman R, Stites EC, Anghel M, Posner RG, Barua D, Kholodenko BN, Hlavacek WS. Modeling cell line-specific recruitment of signaling proteins to the insulin-like growth factor 1 receptor. PLOS Computational Biology 2019, 15: e1006706. PMID: 30653502, PMCID: PMC6353226, DOI: 10.1371/journal.pcbi.1006706.Peer-Reviewed Original ResearchConceptsReceptor tyrosine kinasesSrc homology 2Autophosphorylation sitesInsulin-like growth factor 1 receptorGrowth factor 1 receptorFactor 1 receptorPTB domain-containing proteinsCopy numberDomain-containing proteinsPhosphotyrosine-binding (PTB) domainProtein copy numbersMultiple autophosphorylation sitesProtein abundance profilesMultiple signaling proteinsShort linear motifsOutcome of competitionCell line-specific modelsHomology 2Cytoplasmic domainSignaling proteinsLinear motifsTyrosine kinaseEffects of competitionRule-based modeling approachRelative abundance
2018
UBXN3B positively regulates STING-mediated antiviral immune responses
Yang L, Wang L, Ketkar H, Ma J, Yang G, Cui S, Geng T, Mordue DG, Fujimoto T, Cheng G, You F, Lin R, Fikrig E, Wang P. UBXN3B positively regulates STING-mediated antiviral immune responses. Nature Communications 2018, 9: 2329. PMID: 29899553, PMCID: PMC5998066, DOI: 10.1038/s41467-018-04759-8.Peer-Reviewed Original ResearchConceptsUbiquitin regulatory X domain-containing proteinAntiviral immune responseImmune responseDeficient immune responseDomain-containing proteinsInterferon genes (STING) signalingVesicular stomatitis virus infectionDiverse biological processesStomatitis virus infectionPhosphorylation of TBK1Physiological evidenceHerpes simplex virus 1Cre-loxP approachSimplex virus 1Virus infectionAdult miceGene signalingHSV-1Biological processesPhysiological functionsVirus 1MicePrimary cellsConsequent recruitmentResponseMembrane shape-mediated wave propagation of cortical protein dynamics
Wu Z, Su M, Tong C, Wu M, Liu J. Membrane shape-mediated wave propagation of cortical protein dynamics. Nature Communications 2018, 9: 136. PMID: 29321558, PMCID: PMC5762918, DOI: 10.1038/s41467-017-02469-1.Peer-Reviewed Original ResearchConceptsMembrane shape changesF-BAR proteinsDomain-containing proteinsPeripheral membrane proteinsProtein lateral diffusionActin machineryProtein recruitmentMembrane proteinsProtein dynamicsCortical proteinsShape changesProtein waveActin wavesUnderappreciated roleProteinMembrane undulationsLateral diffusionSpatial gradientsMachineryCytoplasmImmune cellsRecruitmentAssemblyCells
2013
Tdrkh is essential for spermatogenesis and participates in primary piRNA biogenesis in the germline
Saxe JP, Chen M, Zhao H, Lin H. Tdrkh is essential for spermatogenesis and participates in primary piRNA biogenesis in the germline. The EMBO Journal 2013, 32: 1869-1885. PMID: 23714778, PMCID: PMC3981179, DOI: 10.1038/emboj.2013.121.Peer-Reviewed Original ResearchConceptsPrimary piRNA biogenesisPiRNA biogenesisKH domain-containing proteinPiRNA biogenesis pathwayPing-pong cycleDomain-containing proteinsMature piRNAsPIWI proteinsBiogenesis pathwayMitochondrial proteinsEpigenetic programmingNuclear localizationCytoplasmic localizationZygotene stageBiogenesisTDRKHArginine residuesMeiotic arrestMIWI2MIWIDistinct populationsProteinMutantsGermlineRNA
2012
Zasp regulates integrin activation
Bouaouina M, Jani K, Long JY, Czerniecki S, Morse EM, Ellis SJ, Tanentzapf G, Schöck F, Calderwood DA. Zasp regulates integrin activation. Journal Of Cell Science 2012, 125: 5647-5657. PMID: 22992465, PMCID: PMC3575701, DOI: 10.1242/jcs.103291.Peer-Reviewed Original ResearchConceptsIntegrin activationDomain-containing proteinsExtracellular matrixHeterodimeric adhesion receptorsPDZ motif-containing proteinΑ5β1 integrinMammalian tissue cultureScaffold proteinCytoplasmic tailFirst proteinECM ligandsMuscle contractile machineryΒ-integrinExtracellular domainAdhesion receptorsIntegrin heterodimersTalinConformational changesHigh-affinity bindingEssential processProteinIntegrinsHuman cardiomyopathyZASPTissue culture
2011
Structural basis for dimethylarginine recognition by the Tudor domains of human SMN and SPF30 proteins
Tripsianes K, Madl T, Machyna M, Fessas D, Englbrecht C, Fischer U, Neugebauer KM, Sattler M. Structural basis for dimethylarginine recognition by the Tudor domains of human SMN and SPF30 proteins. Nature Structural & Molecular Biology 2011, 18: 1414-1420. PMID: 22101937, DOI: 10.1038/nsmb.2185.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceArginineBinding SitesHumansModels, MolecularMolecular Sequence DataNuclear Magnetic Resonance, BiomolecularProtein Structure, TertiaryRibonucleoproteins, Small NuclearRNA Splicing FactorsSequence AlignmentSMN Complex ProteinsSurvival of Motor Neuron 1 ProteinThermodynamics
2010
Chapter 136 Pleckstrin Homology (PH) Domains
Lemmon M. Chapter 136 Pleckstrin Homology (PH) Domains. 2010, 1093-1101. DOI: 10.1016/b978-0-12-374145-5.00136-4.Peer-Reviewed Original ResearchPleckstrin homology domainPH domainHomology domainPH domain-containing proteinsDifferent PH domainsDomain-containing proteinsReceptor-mediated endocytosisParticular phosphoinositidesMembrane traffickingMembrane associationProtein functionSequence similarityCommon foldCellular signalingCytoskeletal organizationFunctional relatednessProtein targetsPhosphoinositidePhysiological rolePhysiological relevancePromiscuous bindingX-ray crystallographyPhospholipid modificationStructural similarityProtein
2008
A PDZ‐Binding Motif Controls Basolateral Targeting of Syndecan‐1 Along the Biosynthetic Pathway in Polarized Epithelial Cells
Maday S, Anderson E, Chang HC, Shorter J, Satoh A, Sfakianos J, Fölsch H, Anderson JM, Walther Z, Mellman I. A PDZ‐Binding Motif Controls Basolateral Targeting of Syndecan‐1 Along the Biosynthetic Pathway in Polarized Epithelial Cells. Traffic 2008, 9: 1915-1924. PMID: 18764819, PMCID: PMC2820280, DOI: 10.1111/j.1600-0854.2008.00805.x.Peer-Reviewed Original ResearchConceptsPolarized epithelial cellsBiosynthetic pathwayPDZ domain-containing proteinsType II PDZDomain-containing proteinsPDZ-binding motifSyndecan-1Cell surface proteoglycansEpithelial cellsBasolateral targetingNormal epithelial morphologyBasolateral domainMotif leadPlasma membranePDZBasolateral localizationSurface proteoglycansBasolateral surfaceApical surfaceEpithelial morphologyMotifPotential rolePathwayCellsMislocalization
2007
The structural basis of cyclic diguanylate signal transduction by PilZ domains
Benach J, Swaminathan SS, Tamayo R, Handelman SK, Folta‐Stogniew E, Ramos JE, Forouhar F, Neely H, Seetharaman J, Camilli A, Hunt JF. The structural basis of cyclic diguanylate signal transduction by PilZ domains. The EMBO Journal 2007, 26: 5153-5166. PMID: 18034161, PMCID: PMC2140105, DOI: 10.1038/sj.emboj.7601918.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceAnimalsBacterial ProteinsBinding SitesCrystallography, X-RayCyclic GMPHumansMiceModels, MolecularMolecular ConformationMolecular Sequence DataPhylogenyProtein BindingProtein Structure, QuaternaryProtein Structure, SecondaryProtein Structure, TertiarySequence AlignmentSequence Homology, Amino AcidSignal TransductionVibrio choleraeConceptsPilZ domain-containing proteinsPilZ domainDomain-containing proteinsN-terminal domainConformational switchSecond messenger cyclic diguanylateBeta-barrel foldN-terminal loopEvolutionary diversificationCyclic diguanylateSignal transductionBioinformatics analysisStructural basisInteraction surfaceSessile growthEffector pathwaysVibrio choleraeProteinV. choleraeGMPCholeraeDomainClose appositionDiguanylateEubacteriaTraffic to the Malaria Parasite Food Vacuole A NOVEL PATHWAY INVOLVING A PHOSPHATIDYLINOSITOL 3-PHOSPHATE-BINDING PROTEIN *
McIntosh M, Vaid A, Hosgood H, Vijay J, Bhattacharya A, Sahani M, Baevova P, Joiner K, Sharma P. Traffic to the Malaria Parasite Food Vacuole A NOVEL PATHWAY INVOLVING A PHOSPHATIDYLINOSITOL 3-PHOSPHATE-BINDING PROTEIN *. Journal Of Biological Chemistry 2007, 282: 11499-11508. PMID: 17289673, DOI: 10.1074/jbc.m610974200.Peer-Reviewed Original ResearchConceptsFYVE proteinFood vacuolesFYVE domain-containing proteinsDomain-containing proteinsZinc finger motifsParasite food vacuoleHigher eukaryotesEndosomal proteinFinger motifSecretory pathwayParasite cytosolDeletion mutantsDomain familyEndocytic organellesRegulatory proteinsKey residuesMutagenesis studiesPeptide domainBinding proteinLysosomal compartmentNovel pathwayFunctional roleProteinKey ligandPathway
2004
Actin/α-Actinin-Dependent Transport of AMPA Receptors in Dendritic Spines: Role of the PDZ-LIM Protein RIL
Schulz TW, Nakagawa T, Licznerski P, Pawlak V, Kolleker A, Rozov A, Kim J, Dittgen T, Köhr G, Sheng M, Seeburg PH, Osten P. Actin/α-Actinin-Dependent Transport of AMPA Receptors in Dendritic Spines: Role of the PDZ-LIM Protein RIL. Journal Of Neuroscience 2004, 24: 8584-8594. PMID: 15456832, PMCID: PMC6729893, DOI: 10.1523/jneurosci.2100-04.2004.Peer-Reviewed Original ResearchConceptsAMPA receptorsDendritic spinesLIM domain-containing proteinsDomain-containing proteinsActin-dependent mannerCultured neuronsPostsynaptic density fractionSynaptic AMPA receptorsLIM domainsPDZ domainProtein complexesActin cytoskeletonC-terminal peptideNovel regulationHeterologous cellsReceptor transportRILsExcitatory transmissionForebrain synaptosomesMiniature EPSCsSynaptic accumulationRat forebrainSynaptic sitesSynaptic surfaceReceptorsThe Novel Cdc42 Guanine Nucleotide Exchange Factor, Zizimin1, Dimerizes via the Cdc42-binding CZH2 Domain*
Meller N, Irani-Tehrani M, Ratnikov BI, Paschal BM, Schwartz MA. The Novel Cdc42 Guanine Nucleotide Exchange Factor, Zizimin1, Dimerizes via the Cdc42-binding CZH2 Domain*. Journal Of Biological Chemistry 2004, 279: 37470-37476. PMID: 15247287, DOI: 10.1074/jbc.m404535200.Peer-Reviewed Original ResearchConceptsExchange factorCdc42 Guanine Nucleotide Exchange FactorGuanine nucleotide exchange factorsRho family small GTPasesDomain-containing proteinsNucleotide exchange factorsMultiple cellular processesCDM proteinsCZH proteinsSmall GTPasesRho proteinsCellular processesCdc42 activationRho-GEFsCdc42Acid regionHomology analysisCritical regulatorZizimin1ProteinPositive cooperativityMutation analysisDimerizationDock180GTPases
2003
Integrin β cytoplasmic domain interactions with phosphotyrosine-binding domains: A structural prototype for diversity in integrin signaling
Calderwood DA, Fujioka Y, de Pereda JM, García-Alvarez B, Nakamoto T, Margolis B, McGlade CJ, Liddington RC, Ginsberg MH. Integrin β cytoplasmic domain interactions with phosphotyrosine-binding domains: A structural prototype for diversity in integrin signaling. Proceedings Of The National Academy Of Sciences Of The United States Of America 2003, 100: 2272-2277. PMID: 12606711, PMCID: PMC151330, DOI: 10.1073/pnas.262791999.Peer-Reviewed Original ResearchMeSH KeywordsAlanineAmino Acid SequenceAnimalsCHO CellsCricetinaeCytoplasmDatabases as TopicDNADose-Response Relationship, DrugElectrophoresis, Polyacrylamide GelGlutathione TransferaseHumansIntegrin beta ChainsIntegrinsMiceModels, MolecularMolecular Sequence DataMutagenesis, Site-DirectedMutationPhosphorylationPhosphotyrosinePrecipitin TestsProtein BindingProtein ConformationProtein Structure, TertiaryRecombinant Fusion ProteinsRecombinant ProteinsSequence Homology, Amino AcidSignal TransductionTransfectionTyrosineConceptsIntegrin beta tailsBeta tailsPTB domainIntegrin tailsDok-1Heterodimeric integrin adhesion receptorsBiological functionsDomain interactionsPTB domain-containing proteinsDomain-containing proteinsDomain-ligand interactionsPhosphotyrosine-binding (PTB) domainPhosphotyrosine-binding domainCytoplasmic domain interactionsIntegrin-binding proteinsIntegrin adhesion receptorsIntegrin alpha IIbNPXY motifProtein modulesCytoplasmic domainCytoplasmic proteinsAlpha IIbCytoskeletal proteinsCanonical recognition sequenceInteracting residues
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