2025
The pathways of secretory cargo export at the endoplasmic reticulum
Malhotra V. The pathways of secretory cargo export at the endoplasmic reticulum. Nature Communications 2025, 16: 2138. PMID: 40032897, PMCID: PMC11876584, DOI: 10.1038/s41467-025-57408-2.Peer-Reviewed Original ResearchMolecular Components of Vesicle Cycling at the Rod Photoreceptor Ribbon Synapse
Hanke-Gogokhia C, Zapadka T, Finkelstein S, Arshavsky V, Demb J. Molecular Components of Vesicle Cycling at the Rod Photoreceptor Ribbon Synapse. Advances In Experimental Medicine And Biology 2025, 1468: 325-330. PMID: 39930217, DOI: 10.1007/978-3-031-76550-6_54.Peer-Reviewed Original ResearchConceptsSynaptic vesicle exocytosisSynaptic vesicle recyclingPhotoreceptor ribbon synapseVesicle exocytosisVesicle recyclingVesicle cycleVesicle releaseRibbon synapseProtein synthesisProperties of synaptic transmissionMolecular componentsMouse rodsSynaptic terminalsRod cellsProteinVesiclesRod photoreceptorsDim lightSynaptic transmissionInner segmentsCellsExocytosisEndocytosisOuter segmentsEnergy productionA quantitative ultrastructural timeline of nuclear autophagy reveals a role for dynamin-like protein 1 at the nuclear envelope
Mannino P, Perun A, Surovtsev I, Ader N, Shao L, Rodriguez E, Melia T, King M, Lusk C. A quantitative ultrastructural timeline of nuclear autophagy reveals a role for dynamin-like protein 1 at the nuclear envelope. Nature Cell Biology 2025, 27: 464-476. PMID: 39920277, PMCID: PMC11908896, DOI: 10.1038/s41556-025-01612-1.Peer-Reviewed Original ResearchConceptsInner nuclear membraneDynamin-like protein 1Membrane fissionNuclear envelopeMembrane fission stepNon-canonical rolesDouble-membrane vesiclesProtein 1Nuclear envelope remodelingLattice light-sheet microscopyFission stepDnm1Nuclear autophagyIntact nucleiPerinuclear spaceNuclear membraneAutophagic mechanismsNucleophagyCorrelative lightLight-sheet microscopyFissionElectron tomographyVesiclesVacuolesAtg11
2024
Minimal presynaptic protein machinery governing diverse kinetics of calcium-evoked neurotransmitter release
Bose D, Bera M, Norman C, Timofeeva Y, Volynski K, Krishnakumar S. Minimal presynaptic protein machinery governing diverse kinetics of calcium-evoked neurotransmitter release. Nature Communications 2024, 15: 10741. PMID: 39738049, PMCID: PMC11685451, DOI: 10.1038/s41467-024-54960-1.Peer-Reviewed Original ResearchConceptsSynaptotagmin-7Synaptotagmin-1Protein machinerySNARE complex assemblyFusion clampExocytosis processVesicle fusionVesicular fusionComplex assemblySynaptic vesiclesFusion assayMolecular basisPhysiologically relevant conditionsPresynaptic calcium influxNeurotransmitter releaseVesiclesSNAREProteinMachineryCompetitive bindingFusion dynamicsComplexinExocytosisFusionCalcium influxQuantitative single-molecule analysis of assembly and Ca2+-dependent disassembly of synaptotagmin oligomers on lipid bilayers
Li F, Coleman J, Redondo-Morata L, Kalyana Sundaram R, Stroeva E, Rothman J, Pincet F. Quantitative single-molecule analysis of assembly and Ca2+-dependent disassembly of synaptotagmin oligomers on lipid bilayers. Communications Biology 2024, 7: 1608. PMID: 39627539, PMCID: PMC11615320, DOI: 10.1038/s42003-024-07317-9.Peer-Reviewed Original ResearchConceptsSyt-1Lipid bilayerRing-like oligomersCa2+-evoked releaseSynaptotagmin-1Single-molecule imaging methodsSynaptic vesiclesBiochemical evidencePhysiological requirementsOligomerizationAnalysis of assembliesBilayerOligomersCa2+LipidAssemblyCa2Classes of oligomersMutationsVesiclesDisassemblyEvoked releaseSubstrate geometry and topography induce F-actin reorganization and chiral alignment in an adherent model cortex
Sakamoto R, Murrell M. Substrate geometry and topography induce F-actin reorganization and chiral alignment in an adherent model cortex. Cell Reports Physical Science 2024, 5: 102338. DOI: 10.1016/j.xcrp.2024.102338.Peer-Reviewed Original ResearchF-actin organizationF-actin networkF-actinF-actin reorganizationSubstrate featuresActin cortexCytoskeletal organizationGiant unilamellar vesiclesIntracellular signalingCell adhesionGeometry sensingLiposome shapeCell membraneMembrane deformationUnilamellar vesiclesAdherent liposomeCellsActinOrganizationVesiclesAdhesionLiposomesAbsence of ATG9A and synaptophysin demixing on Rab5 mutation-induced giant endosomes
Choi J, Wu Y, Park D. Absence of ATG9A and synaptophysin demixing on Rab5 mutation-induced giant endosomes. Molecular Brain 2024, 17: 63. PMID: 39223639, PMCID: PMC11367939, DOI: 10.1186/s13041-024-01132-3.Peer-Reviewed Original ResearchConceptsGiant endosomesFormation of enlarged endosomesAutophagy-related (ATG) proteinsPool of vesiclesIntegral membrane proteinsRab5 mutantsEnlarged endosomesCore autophagy-related (ATG) proteinsEndosomal localizationIntracellular sortingMembrane proteinsEndocytic originEndosomesATG9ARab5ProteinVesiclesMutantsSegregation mechanismSynapsinCo-assemblyNerve terminalsSynaptophysinFibroblastsCellsPhotosensitive Nanoprobes for Rapid High Purity Isolation and Size‐Specific Enrichment of Synthetic and Extracellular Vesicle Subpopulations (Adv. Funct. Mater. 34/2024)
Weerakkody J, Tseng T, Topper M, Thoduvayil S, Radhakrishnan A, Pincet F, Kyriakides T, Gunasekara R, Ramakrishnan S. Photosensitive Nanoprobes for Rapid High Purity Isolation and Size‐Specific Enrichment of Synthetic and Extracellular Vesicle Subpopulations (Adv. Funct. Mater. 34/2024). Advanced Functional Materials 2024, 34 DOI: 10.1002/adfm.202470191.Peer-Reviewed Original ResearchVesicle biogenesisExtracellular vesicle subpopulationsLipid nanoprobesVesicle subpopulationsNative extracellular vesiclesVesicle populationsSeparate vesiclesPurity isolationExtracellular vesiclesVesiclesCellular originHydrophobic interactionsBiogenesisSize variabilitySubpopulationsIsolatesExtracellularLipocoacervate, a tunable vesicle for protein delivery
Yeh C, Wright N, Loh C, Chu N, Wang Y. Lipocoacervate, a tunable vesicle for protein delivery. Nano Research 2024, 17: 9135-9140. DOI: 10.1007/s12274-024-6889-6.Peer-Reviewed Original ResearchProtein delivery vehiclesDelivery of proteinsCells in vitroGrowth factorVesiclesProteinMembrane functionControlled delivery of growth factorsTreated cells in vitroProtein deliveryControlled deliveryControlled delivery of proteinsDelivery of therapeuticsSalt concentrationDelivery of growth factorsMembraneVesicle sizeControlled delivery of therapeuticsProtocol for isolating and identifying small extracellular vesicles derived from human umbilical cord mesenchymal stem cells
Chen Y, Qian H, Mak M, Tao Z. Protocol for isolating and identifying small extracellular vesicles derived from human umbilical cord mesenchymal stem cells. STAR Protocols 2024, 5: 103197. PMID: 39028618, PMCID: PMC11315167, DOI: 10.1016/j.xpro.2024.103197.Peer-Reviewed Original ResearchSmall extracellular vesiclesUmbilical cord mesenchymal stem cellsHuman umbilical cord mesenchymal stem cellsIsolation of small extracellular vesiclesLipid bilayer-enclosed particlesExtracellular vesiclesMesenchymal stem cellsNanoparticle tracking analysisAtomic force microscopeStem cellsMolecular markersLiving cellsTransmission electron microscopyWestern blottingIsolatesVesiclesCellsForce microscopeComposite branched and linear F-actin maximize myosin-induced membrane shape changes in a biomimetic cell model
Sakamoto R, Murrell M. Composite branched and linear F-actin maximize myosin-induced membrane shape changes in a biomimetic cell model. Communications Biology 2024, 7: 840. PMID: 38987288, PMCID: PMC11236970, DOI: 10.1038/s42003-024-06528-4.Peer-Reviewed Original ResearchConceptsF-actin networkF-actinF-actin architectureMembrane shape changesCell shape changesActivity of myosinInduce membrane deformationActomyosin contractilityShape changesActin cortexActomyosin cortexGiant unilamellar vesiclesActinMembrane deformationUnilamellar vesiclesCell modelNo-slip boundariesForce generationActomyosinMyosinVesiclesForce transmissionOverlapping role of synaptophysin and synaptogyrin family proteins in determining the small size of synaptic vesicles
Park D, Fujise K, Wu Y, Luján R, Del Olmo-Cabrera S, Wesseling J, De Camilli P. Overlapping role of synaptophysin and synaptogyrin family proteins in determining the small size of synaptic vesicles. Proceedings Of The National Academy Of Sciences Of The United States Of America 2024, 121: e2409605121. PMID: 38985768, PMCID: PMC11260120, DOI: 10.1073/pnas.2409605121.Peer-Reviewed Original ResearchConceptsSynaptic vesiclesFamily proteinsBiogenesis of synaptic vesiclesClusters of small vesiclesSize of synaptic vesiclesSynaptogyrin familySynaptogyrin-1Vesicle proteinsSynaptogyrinTransmembrane domainOrganismal levelSmall vesiclesProteinMild defectsVesiclesFamily membersBiogenesisSmall sizeFamilyMiceSynapsinCoexpressionAbundanceSynaptoporinMembersBiology of Exfoliation of Plasma Membrane-Derived Vesicles and the Radiation Response: Historical Background, Applications in Biodosimetry and Cell-Free Therapeutics, and Quantal Mechanisms for Their Release and Function with Implications for Space Travel
Dainiak N. Biology of Exfoliation of Plasma Membrane-Derived Vesicles and the Radiation Response: Historical Background, Applications in Biodosimetry and Cell-Free Therapeutics, and Quantal Mechanisms for Their Release and Function with Implications for Space Travel. Radiation Research 2024, 202: 328-354. PMID: 38981604, DOI: 10.1667/rade-24-00078.1.Peer-Reviewed Original ResearchCell-free therapeuticsPlasma membrane-derived vesiclesExtracellular vesiclesExposure to ionizing radiationIndividual radiation dosesMembrane-derived vesiclesExposure to radiationProperties of extracellular vesiclesPathogenesis of diseaseSpace travelDeep spaceRadiation doseInhibitory moleculesSignal traffickingHuman cellsClinical disordersQuantal mechanismRadiation responseMembrane turnoverVesiclesNucleic acidsVesicle surfaceBiophysical propertiesCell-freeRadiationTailored assemblies of COPII proteins in secretion
Malhotra V. Tailored assemblies of COPII proteins in secretion. Journal Of Cell Biology 2024, 223: e202404013. PMID: 38958655, PMCID: PMC11222725, DOI: 10.1083/jcb.202404013.Peer-Reviewed Original ResearchDual-Ring SNAREpin Machinery Tuning for Fast Synaptic Vesicle Fusion
Caruel M, Pincet F. Dual-Ring SNAREpin Machinery Tuning for Fast Synaptic Vesicle Fusion. Biomolecules 2024, 14: 600. PMID: 38786007, PMCID: PMC11117985, DOI: 10.3390/biom14050600.Peer-Reviewed Original ResearchIdentification 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 cleftPhotosensitive Nanoprobes for Rapid High Purity Isolation and Size‐Specific Enrichment of Synthetic and Extracellular Vesicle Subpopulations
Weerakkody J, Tseng T, Topper M, Thoduvayil S, Radhakrishnan A, Pincet F, Kyriakides T, Gunasekara R, Ramakrishnan S. Photosensitive Nanoprobes for Rapid High Purity Isolation and Size‐Specific Enrichment of Synthetic and Extracellular Vesicle Subpopulations. Advanced Functional Materials 2024, 34 PMID: 39372670, PMCID: PMC11452007, DOI: 10.1002/adfm.202400390.Peer-Reviewed Original ResearchExtracellular vesicle subpopulationsVesicle subpopulationsIsolation of vesiclesPurity extracellular vesiclesRelease of vesiclesAnalysis of nucleic acidsNear-native formLarge-scale isolationLipid nanoprobesDownstream analysisPurity isolationEfficient isolationVesiclesSynthetic vesiclesNucleic acidsExtracellular vesiclesIsolation methodIsolatesBiomarker discoveryExposure to lightSubpopulationsEnrichmentProteinComplex biological mediaCleavage
2023
Sorting secretory proteins
Parchure A, von Blume J. Sorting secretory proteins. ELife 2023, 12: e93490. PMID: 37997893, PMCID: PMC10672786, DOI: 10.7554/elife.93490.Peer-Reviewed Original ResearchSynaptophysin chaperones the assembly of 12 SNAREpins under each ready-release vesicle
Bera M, Radhakrishnan A, Coleman J, Sundaram R, Ramakrishnan S, Pincet F, Rothman J. Synaptophysin chaperones the assembly of 12 SNAREpins under each ready-release vesicle. Proceedings Of The National Academy Of Sciences Of The United States Of America 2023, 120: e2311484120. PMID: 37903271, PMCID: PMC10636311, DOI: 10.1073/pnas.2311484120.Peer-Reviewed Original ResearchConceptsSpecific molecular functionsSynaptic vesicle protein synaptophysinTarget membrane bilayerSensor synaptotagminSNARE proteinsMolecular functionsMembrane proteinsSNAREpinsReceptor vesiclesSingle-molecule measurementsGene knockoutMembrane bilayerLipid bilayersProtein synaptophysinVesiclesDetergent extractsHexamer structureSYPMechanism of actionProteinAssemblyChaperonesSynaptotagminExocytosisBilayersThe 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 synapsesBindingPlasticitySynaptotagminSnareVesicles
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