2025
Neuronal potassium channel activity triggers initiation of mRNA translation through binding of translation regulators
Malone T, Wu J, Zhang Y, Licznerski P, Chen R, Nahiyan S, Pedram M, Jonas E, Kaczmarek L. Neuronal potassium channel activity triggers initiation of mRNA translation through binding of translation regulators. Science Advances 2025, 11: eadv3140. PMID: 40435242, PMCID: PMC12118559, DOI: 10.1126/sciadv.adv3140.Peer-Reviewed Original ResearchConceptsMRNA translationTranslational regulationInitiation of mRNA translationInitiation of translationSevere intellectual disabilityRegulation of translationMRNA translation regulationNeurites of cortical neuronsB-actinChannel activityIntellectual disabilityPotassium channel activityNeuronal activityMolecular mechanismsInhibit initiationMutationsCell linesPharmacological stimulationCortical neuronsMRNABindingRegulationTranslationEIF4ECYFIP1ETS emerges to heat up adipose
Rodeheffer M. ETS emerges to heat up adipose. Genes & Development 2025 PMID: 40389324, DOI: 10.1101/gad.352966.125.Peer-Reviewed Original ResearchTranscription factor bindingE26 transformation-specific (ETS) transcription factorsPromoter chromatin accessibilityChromatin accessibilityFactor bindingTranscription factorsHistone acetylationAdipose biologyGene expressionETV4HistoneTranscriptionGenesUCP1AcetylationE26AdipogenesisBindingBiologyThermogenesisExpressionAdiposeA triple-action inhibitory mechanism of allosteric TYK2-specific inhibitors
Wang J, Lomakin I, Batista V, Bunick C. A triple-action inhibitory mechanism of allosteric TYK2-specific inhibitors. Journal Of Investigative Dermatology 2025 PMID: 40378946, DOI: 10.1016/j.jid.2025.04.025.Peer-Reviewed Original ResearchJak-signal transducer and activatorAutoinhibited statePseudokinase domainIFN-induced gene expressionAtomic resolution structuresPhosphorylation of downstream proteinsAdenosine triphosphate bindingTyk2 kinaseTriphosphate bindingKinase domainActive stateResolution structureKinase activityTyk2Gene expressionStructural basisDownstream proteinsAllosteric drugsSteric clashesAllosteric inhibitorsInhibition mechanismMechanistic hypothesesKinaseBindingProteinLithium fine tunes lipid membranes through phospholipid binding
Bunel L, Adrien V, Coleman J, Heo P, Pincet F. Lithium fine tunes lipid membranes through phospholipid binding. Scientific Reports 2025, 15: 13366. PMID: 40246965, PMCID: PMC12006515, DOI: 10.1038/s41598-025-97828-0.Peer-Reviewed Original ResearchConceptsUnrelated pathwaysBipolar disorderIntracellular traffickingPhospholipid bindingMembrane protein activityMembrane reorganizationProtein activityMolecular mechanismsLithium effectsModel membrane systemsLipid bilayerBindingDiverse effectsEffects of lithiumMembraneLipid membranesMembrane systemPhospholipid headgroupsOrganellesTANGO2 is an acyl-CoA binding protein
Lujan A, Foresti O, Wojnacki J, Bigliani G, Brouwers N, Pena M, Androulaki S, Hashidate-Yoshida T, Kalyukina M, Novoselov S, Shindou H, Malhotra V. TANGO2 is an acyl-CoA binding protein. Journal Of Cell Biology 2025, 224: e202410001. PMID: 40015245, PMCID: PMC11867700, DOI: 10.1083/jcb.202410001.Peer-Reviewed Original ResearchConceptsAcyl-CoA binding proteinPeriphery of lipid dropletsAcyl-coenzyme A binding proteinA-binding proteinsAcyl-coenzyme AMitochondrial lumenHeme transportBinding proteinTANGO2Cellular localizationLipid dropletsStructural regionsLipid metabolismHeightened energy demandsMutationsProteinResiduesNrdEMetabolic crisisBindingMetabolismHemeSevere cardiomyopathyLipidStructural basis of promiscuous inhibition of Listeria virulence activator PrfA by oligopeptides
Hainzl T, Scortti M, Lindgren C, Grundström C, Krypotou E, Vázquez-Boland J, Sauer-Eriksson A. Structural basis of promiscuous inhibition of Listeria virulence activator PrfA by oligopeptides. Cell Reports 2025, 44: 115290. PMID: 39970044, DOI: 10.1016/j.celrep.2025.115290.Peer-Reviewed Original ResearchConceptsDNA-binding helix-turn-helix motifInhibit virulence gene expressionVirulence gene expressionPathogen Listeria monocytogenesPrfA activityVirulence factorsPrfAMaster regulatorsHydrophobic residuesInhibitory bindingGene expressionStructural basisBinding promiscuityPeptide bindingBinding sitesConformational changesPeptide residuesOligopeptidesPeptideInhibitory peptidesBindingPeptide backboneResiduesPromiscuous inhibitionExpressionDSP-1, the major fibronectin type-II protein of donkey seminal plasma is a small heat-shock protein and exhibits chaperone-like activity against thermal and oxidative stress
Alim S, Cheppali S, Pawar S, Swamy M. DSP-1, the major fibronectin type-II protein of donkey seminal plasma is a small heat-shock protein and exhibits chaperone-like activity against thermal and oxidative stress. Biochimica Et Biophysica Acta (BBA) - Proteins And Proteomics 2025, 1873: 141064. PMID: 39956303, DOI: 10.1016/j.bbapap.2025.141064.Peer-Reviewed Original ResearchConceptsChaperone-like activitySeminal plasmaFibronectin type IITetramer to monomersSperm capacitationSurface hydrophobicityMolecular chaperonesClient proteinsHeat shock proteinsBiophysical studiesAlcohol dehydrogenaseOxidative stressPhysiological ligandsShock proteinsProteinHead group moietySHspsBinding of phosphorylcholineCholine phospholipidsBindingFibronectinDehydrogenaseChaperoneSpermMammals
2024
Enhancing RBP Binding Site Prediction on Long RNA Sequences through Large Language Models
Guo J, Yang Y. Enhancing RBP Binding Site Prediction on Long RNA Sequences through Large Language Models. 2024, 00: 6998-7004. DOI: 10.1109/bibm62325.2024.10822773.Peer-Reviewed Original ResearchRNA-binding proteinsBinding site predictionRNA sequencingSite predictionRNA-binding protein binding sitesLong RNA sequencesRNA structureGene regulationSequence informationBase pairsSequence integrityBinding proteinBiological processesRNABinding sitesSequenceProteinProtein bindingSequence predictionLong sequencesGenesEnformerSitesBindingBiologyFertilization and evolution: AI-powered search finds a missing link in sperm–egg interaction
Huang X, Chung J. Fertilization and evolution: AI-powered search finds a missing link in sperm–egg interaction. Current Biology 2024, 34: r1169-r1172. PMID: 39626626, DOI: 10.1016/j.cub.2024.10.051.Peer-Reviewed Original ResearchCross-regulations of two connected domains form a mechanical circuit for steady force transmission during clathrin-mediated endocytosis
Ren Y, Yang J, Fujita B, Zhang Y, Berro J. Cross-regulations of two connected domains form a mechanical circuit for steady force transmission during clathrin-mediated endocytosis. Cell Reports 2024, 43: 114725. PMID: 39276354, PMCID: PMC11476202, DOI: 10.1016/j.celrep.2024.114725.Peer-Reviewed Original ResearchClathrin-mediated endocytosisF-actinActin cytoskeletonFission yeast Schizosaccharomyces pombeYeast Schizosaccharomyces pombeCell adhesion complexAdhesion complexesMembrane localizationPN forcesStable bindingEnd4pCross-regulationCytoskeletonActinEndocytosisMembraneBindingMechanical forcesTalinTransmission of forcesThatchForce transmissionDomainCellsFissionEndoplasmic reticulum exit sites are segregated for secretion based on cargo size
Saxena S, Foresti O, Liu A, Androulaki S, Pena Rodriguez M, Raote I, Aridor M, Cui B, Malhotra V. Endoplasmic reticulum exit sites are segregated for secretion based on cargo size. Developmental Cell 2024, 59: 2593-2608.e6. PMID: 38991587, PMCID: PMC11813558, DOI: 10.1016/j.devcel.2024.06.009.Peer-Reviewed Original ResearchEndoplasmic reticulum exit sitesProline-rich domainC-terminal proline-rich domainCOPII assemblyExit siteER membraneCargo exportJuxtanuclear regionU2OS cellsCargo moleculesBulky cargoSEC23AOptimal secretionCollagen VIIHuman osteosarcomaProlonged bindingComplex organismsCargoCargo sizeBindingCollagen ICTAGE5TANGO1COPIIERGIC53Identification of the potassium-binding site in serotonin transporter
Hellsberg E, Boytsov D, Chen Q, Niello M, Freissmuth M, Rudnick G, Zhang Y, Sandtner W, Forrest L. Identification of the potassium-binding site in serotonin transporter. Proceedings Of The National Academy Of Sciences Of The United States Of America 2024, 121: e2319384121. PMID: 38652746, PMCID: PMC11067047, DOI: 10.1073/pnas.2319384121.Peer-Reviewed Original ResearchConceptsSerotonin transporterSite-directed mutagenesis of residuesMutagenesis of residuesSite-directed mutagenesisHeterologous expression systemStudy of vesiclesNa2 siteClearance of serotoninPatch-clamp recordingsExpression systemBinding residuesSequential bindingMolecular dynamics simulationsBinding sitesPotassium binding siteSubstrate accumulationClamp recordingsVesiclesResiduesTurnover rateBindingStructural studiesChemical gradientsBinding configurationsSynaptic cleftCrystallographic and Computational Insights into Isoform-Selective Dynamics in Nitric Oxide Synthase
Li H, Hardy C, Reidl C, Jing Q, Xue F, Cinelli M, Silverman R, Poulos T. Crystallographic and Computational Insights into Isoform-Selective Dynamics in Nitric Oxide Synthase. Biochemistry 2024, 63: 788-796. PMID: 38417024, PMCID: PMC10956423, DOI: 10.1021/acs.biochem.3c00601.Peer-Reviewed Original ResearchConceptsHydrogen bondsHeme propionatesDimer interfaceInhibitor bindingCombination of crystallographyInhibitor binding siteDevelopment of isoform-selective inhibitorsIsoform-selective inhibitorsStructural basisComputational insightsStructural changesInhibitor moleculesChanges conformationBinding sitesConformational changesBondsSite inhibitorsPterin cofactorBindingHydrogenSynthaseDimerStructural differencesTyrosineInhibitorsDimeric Tubulin Modifies Mechanical Properties of Lipid Bilayer, as Probed Using Gramicidin A Channel
Rostovtseva T, Weinrich M, Jacobs D, Rosencrans W, Bezrukov S. Dimeric Tubulin Modifies Mechanical Properties of Lipid Bilayer, as Probed Using Gramicidin A Channel. International Journal Of Molecular Sciences 2024, 25: 2204. PMID: 38396879, PMCID: PMC10889239, DOI: 10.3390/ijms25042204.Peer-Reviewed Original ResearchConceptsRegulation of protein-protein interactionsProtein-protein interactionsNon-lamellar lipidsMembrane hydrophobic coreMembrane remodelingMechanical properties of lipid bilayersMembrane bindingProperties of lipid bilayersRegulatory functionsTubulin bindingTubulinHydrophobic regionLipid headgroupsHydrophobic coreCell proliferationLipid bilayerPlanar lipid membranesMembrane mechanical propertiesMembraneMolecular probesLipid packingLipidLipid membranesGramicidin A channelBindingHead-to-head comparison of [18F]-Flortaucipir, [18F]-MK-6240 and [18F]-PI-2620 postmortem binding across the spectrum of neurodegenerative diseases
Aguero C, Dhaynaut M, Amaral A, Moon S, Neelamegam R, Scapellato M, Carazo-Casas C, Kumar S, El Fakhri G, Johnson K, Frosch M, Normandin M, Gómez-Isla T. Head-to-head comparison of [18F]-Flortaucipir, [18F]-MK-6240 and [18F]-PI-2620 postmortem binding across the spectrum of neurodegenerative diseases. Acta Neuropathologica 2024, 147: 25. PMID: 38280071, PMCID: PMC10822013, DOI: 10.1007/s00401-023-02672-z.Peer-Reviewed Original ResearchConceptsNon-AD tauopathiesTau aggregationTau PET tracersDNA-binding proteinsBinds to neurofibrillary tanglesSecond-generation tau tracersTransactive response DNA-binding proteinSpectrum of neurodegenerative diseasesNeurofibrillary tanglesTau lesionsMelanin-containing cellsTDP-43Binding signalTauopathiesBinding targetsCerebral amyloid angiopathyOff-target bindingB-amyloidBinding patternsNeurodegenerative diseasesTau tracersTauBinding to areasBinding profilesBinding
2023
Nuclear envelope assembly relies on CHMP-7 in the absence of BAF–LEM-mediated hole closure
Barger S, Penfield L, Bahmanyar S. Nuclear envelope assembly relies on CHMP-7 in the absence of BAF–LEM-mediated hole closure. Journal Of Cell Science 2023, 136: jcs261385. PMID: 37795681, PMCID: PMC10668030, DOI: 10.1242/jcs.261385.Peer-Reviewed Original ResearchConceptsNuclear envelope assemblySpindle microtubulesNE assemblyEnvelope assemblyC. elegans oocytesLEM-2C. elegansHelix domainBAF-1Family proteinsNucleoplasmic poolNE formationDistinct rolesMicrotubulesAdditional roleNE stabilityPermeability barrierRedundant mechanismsBAFProteinEmbryo survivalBindingAssemblyElegansAutointegrationThe release of inhibition model reproduces kinetics and plasticity of neurotransmitter release in central synapses
Norman C, Krishnakumar S, Timofeeva Y, Volynski K. The release of inhibition model reproduces kinetics and plasticity of neurotransmitter release in central synapses. Communications Biology 2023, 6: 1091. PMID: 37891212, PMCID: PMC10611806, DOI: 10.1038/s42003-023-05445-2.Peer-Reviewed Original ResearchConceptsFusion clampSV exocytosisSynaptic vesiclesNeurotransmitter releaseSNARE complexSNARE proteinsSV fusionPhysiological timescalesSynaptotagmin-1Synergistic regulationMolecular biochemistryComplete assemblyPresynaptic proteinsSynaptotagmin-7Molecular architectureCalcium bindingExocytosisDual bindingProteinCentral synapsesBindingPlasticitySynaptotagminSnareVesiclesUnannotated microprotein EMBOW regulates the interactome and chromatin and mitotic functions of WDR5
Chen Y, Su H, Zhao J, Na Z, Jiang K, Bacchiocchi A, Loh K, Halaban R, Wang Z, Cao X, Slavoff S. Unannotated microprotein EMBOW regulates the interactome and chromatin and mitotic functions of WDR5. Cell Reports 2023, 42: 113145. PMID: 37725512, PMCID: PMC10629662, DOI: 10.1016/j.celrep.2023.113145.Peer-Reviewed Original ResearchConceptsG2/M phaseWD40-repeat protein WDR5Mitotic spindle lengthMultiple interaction partnersM phaseOff-target genesLate G1 phaseWDR5 interactionMitotic functionsH3K4me3 levelsWDR5Interaction partnersMultiple proteinsExpression maximaCell cycleSpindle lengthG1 phaseGenesCell proliferationOff-target bindingBindingInteractomeChromatinTranscriptionKIF2A.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 scatteringProteinMicrotubule-binding-induced allostery triggers LIS1 dissociation from dynein prior to cargo transport
Ton W, Wang Y, Chai P, Beauchamp-Perez C, Flint N, Lammers L, Xiong H, Zhang K, Markus S. Microtubule-binding-induced allostery triggers LIS1 dissociation from dynein prior to cargo transport. Nature Structural & Molecular Biology 2023, 30: 1365-1379. PMID: 37322240, PMCID: PMC10590275, DOI: 10.1038/s41594-023-01010-x.Peer-Reviewed Original ResearchConceptsCryo-EM structureCargo transportProtein Lis1Human dyneinDynein mutantsCytoplasmic dyneinStructural insightsDynein activityIntracellular localizationCritical regulatorDynein activationLIS1Conformational changesDyneinMotor domainMutantsBindingHigh affinityAffinityYeastMicrotubulesRegulatorRegulationTransportActivation
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