2024
Kinetic 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
Dynamic regulation of LINC complex composition and function across tissues and contexts
King M. Dynamic regulation of LINC complex composition and function across tissues and contexts. FEBS Letters 2023, 597: 2823-2832. PMID: 37846646, DOI: 10.1002/1873-3468.14757.Peer-Reviewed Original ResearchConceptsLINC complex componentsLINC complexLinker of nucleoskeletonProtein turnover mechanismsCytoplasmic intermediate filament networkIntermediate filament networkCytoskeleton (LINC) complexComplex componentsNuclear laminaCellular contextCytoplasmic cytoskeletonCell biologistsDynamic regulationNuclear envelopeRegulated expressionTurnover mechanismsFilament networkSplice variantsCell typesProtein configurationUnique functionCytoskeletonConcept of mechanotransductionComplexesNucleoskeletonThe Properties and Domain Requirements for Phase Separation of the Sup35 Prion Protein In Vivo
Grimes B, Jacob W, Liberman A, Kim N, Zhao X, Masison D, Greene L. The Properties and Domain Requirements for Phase Separation of the Sup35 Prion Protein In Vivo. Biomolecules 2023, 13: 1370. PMID: 37759770, PMCID: PMC10526957, DOI: 10.3390/biom13091370.Peer-Reviewed Original ResearchCoordinating nucleoporin condensation and nuclear pore complex assembly
Kuiper E, Prophet S, Schlieker C. Coordinating nucleoporin condensation and nuclear pore complex assembly. FEBS Letters 2023, 597: 2534-2545. PMID: 37620293, DOI: 10.1002/1873-3468.14725.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsNPC assemblyNuclear pore complexNuclear pore complex assemblyPore complex assemblyAberrant condensationNPC biogenesisAssembly machineryPore complexProtein complexesComplex assemblyRepeat nucleoporinsHuman disordersAmyotrophic lateral sclerosisAssemblyEukaryotesNucleoporinsBiogenesisRibosomesRecent progressProteasomeComplexesLateral sclerosisMachineryHomeostasisTherapeutic interventionsElectrocatalytic, Homogeneous Ammonia Oxidation in Water to Nitrate and Nitrite with a Copper Complex
Liu H, Lant H, Troiano J, Hu G, Mercado B, Crabtree R, Brudvig G. Electrocatalytic, Homogeneous Ammonia Oxidation in Water to Nitrate and Nitrite with a Copper Complex. ECS Meeting Abstracts 2023, MA2023-01: 2691-2691. DOI: 10.1149/ma2023-01552691mtgabs.Peer-Reviewed Original ResearchWater oxidationAmmonia oxidationO bond formationInitial mechanistic studiesMolecular catalystsCopper complexesMetal electrocatalystsFaradaic efficiencyAqueous mediaBond formationHigh selectivityOxidation processN2 productTitle reactionOxidationMechanistic studiesCatalysisComplexesRoom temperatureFriendly productionWaterElectrocatalystsElectrocatalyticNitrateCatalystMolecular Techniques and Gene Mutations in Myelodysplastic Syndromes
Mendoza H, Siddon A. Molecular Techniques and Gene Mutations in Myelodysplastic Syndromes. Clinics In Laboratory Medicine 2023, 43: 549-563. PMID: 37865502, DOI: 10.1016/j.cll.2023.06.002.Peer-Reviewed Original ResearchEvidence that OLE RNA is a component of a major stress‐responsive ribonucleoprotein particle in extremophilic bacteria
Breaker R, Harris K, Lyon S, Wencker F, Fernando C. Evidence that OLE RNA is a component of a major stress‐responsive ribonucleoprotein particle in extremophilic bacteria. Molecular Microbiology 2023, 120: 324-340. PMID: 37469248, DOI: 10.1111/mmi.15129.Peer-Reviewed Original ResearchConceptsOLE RNAPrecise biochemical functionFundamental cellular processesCell growthTOR complexesProtein partnersRibonucleoprotein complexesCellular processesRNP complexesBiochemical functionsGram-positive bacteriaNoncoding RNAsRibonucleoprotein particleExtremophilic bacteriaBacterial speciesGenetic disruptionStress conditionsDiverse pathwaysRNAMetabolic adaptationCell membraneExtreme environmentsCarbon sourceBacteriaComplexesDesign of Class I/IV Bromodomain-Targeting Degraders for Chromatin Remodeling Complexes
Zahid H, Costello J, Li Y, Kimbrough J, Actis M, Rankovic Z, Yan Q, Pomerantz W. Design of Class I/IV Bromodomain-Targeting Degraders for Chromatin Remodeling Complexes. ACS Chemical Biology 2023, 18: 1278-1293. PMID: 37260298, PMCID: PMC10698694, DOI: 10.1021/acschembio.2c00902.Peer-Reviewed Original ResearchConceptsChromatin Remodeling ComplexNon-BET bromodomainsRemodeling complexProtein degradationHeterobifunctional moleculesBET familyProtein targetsPyrimidine base analogsNumber of degradersDegradersOncogenic roleTernary complexExit vectorsWestern blottingProteinFirst exampleClass IChallenging targetComplexesCECR2ChromatinBromodomainsBPTFFamilyNanoBRETLigand Tuning in Cu(pyalk)2 Water Oxidation Electrocatalysis
Cody C, Caes Z, Capobianco M, Mercado B, Crabtree R, Brudvig G. Ligand Tuning in Cu(pyalk)2 Water Oxidation Electrocatalysis. Inorganics 2023, 11: 229. DOI: 10.3390/inorganics11060229.Peer-Reviewed Original ResearchWater oxidationWater oxidation electrocatalysisAnalogous copper complexesWater oxidation electrocatalystsArtificial photosynthetic systemsElectron-donating groupsSolar energy conversionPyalk ligandCatalyst tuningLigand tuningOxidation electrocatalystsCopper complexesFaradaic efficiencyLigand modificationCatalytic propertiesLigand formsAttractive scaffoldFirst-principles predictionPara positionGood activityMolecular systemsPhotosynthetic systemsEnergy conversionComplexesOxidationProteasomes: Isolation and Activity Assays
Li Y, Tomko R, Hochstrasser M. Proteasomes: Isolation and Activity Assays. Current Protocols 2023, 3: e717. PMID: 37026813, PMCID: PMC10337785, DOI: 10.1002/cpz1.717.Peer-Reviewed Original ResearchConceptsRegulatory particleOne-step purification schemeCore particlesMultisubunit protease complexUbiquitin-proteasome systemUbiquitin polypeptidesUnneeded proteinsYeast SaccharomycesProtein substratesProtease complexProteasomeGel filtration stepPurification schemeProteolytic activityEukaryotesSaccharomycesPolypeptideProteinSubstrateAssaysComplexesDetermining protein structures in cellular lamella at pseudo-atomic resolution by GisSPA
Cheng J, Liu T, You X, Zhang F, Sui S, Wan X, Zhang X. Determining protein structures in cellular lamella at pseudo-atomic resolution by GisSPA. Nature Communications 2023, 14: 1282. PMID: 36922493, PMCID: PMC10017804, DOI: 10.1038/s41467-023-36175-y.Peer-Reviewed Original ResearchConceptsProtein complexesCellular lamellaTarget protein complexesCryo-electron tomographyProtein structure determinationCryo-electron microscopy imagesHigh-throughput data collectionProtein structureAtomic resolutionStructure determinationComplexesPhycobilisomesComplex structureMajor toolLamellaeHigh-resolution reconstructionModeling HIV-1 nuclear entry with nucleoporin-gated DNA-origami channels
Shen Q, Feng Q, Wu C, Xiong Q, Tian T, Yuan S, Shi J, Bedwell G, Yang R, Aiken C, Engelman A, Lusk C, Lin C, Xiong Y. Modeling HIV-1 nuclear entry with nucleoporin-gated DNA-origami channels. Nature Structural & Molecular Biology 2023, 30: 425-435. PMID: 36807645, PMCID: PMC10121901, DOI: 10.1038/s41594-023-00925-9.Peer-Reviewed Original ResearchConceptsNuclear pore complexHIV-1 nuclear entryNuclear entryNuclear importNPC central channelPore complexHost nucleusCapsid dockingVirus genomeAffinity gradientNup153Central channelMechanistic insightsMolecular interactionsCapsidNucleoporinsNup358Nup62GenomeNucleusVirusDockingVirus-1 infectionImportComplexesRedox leveling of the Kok cycle of photosystem II established by water ligand binding to the oxygen evolving complex
Liu J, Yang K, Brudvig G, Batista V. Redox leveling of the Kok cycle of photosystem II established by water ligand binding to the oxygen evolving complex. Biophysical Journal 2023, 122: 199a-200a. DOI: 10.1016/j.bpj.2022.11.1210.Peer-Reviewed Original ResearchHPV is a cargo for the COPI sorting complex during virus entry
Harwood M, Woo T, Takeo Y, DiMaio D, Tsai B. HPV is a cargo for the COPI sorting complex during virus entry. Science Advances 2023, 9: eadc9830. PMID: 36662862, PMCID: PMC9858521, DOI: 10.1126/sciadv.adc9830.Peer-Reviewed Original ResearchConceptsCoat protein complex ITrans-Golgi networkProtein complex IGene knockdown strategyVirus entryCOPI complexProtein complexesCellular fractionationUnbiased proteomicsRetrograde traffickingCytoplasmic segmentGolgi stacksCellular cargoL2 mutantKnockdown strategyGolgi apparatusComplex IIncoming virusCell surfaceGolgiHost factorsCargoComplexesMutantsEndosomes
2022
The Get1/2 insertase forms a channel to mediate the insertion of tail-anchored proteins into the ER
Heo P, Culver J, Miao J, Pincet F, Mariappan M. The Get1/2 insertase forms a channel to mediate the insertion of tail-anchored proteins into the ER. Cell Reports 2022, 42: 111921. PMID: 36640319, PMCID: PMC9932932, DOI: 10.1016/j.celrep.2022.111921.Peer-Reviewed Original ResearchConceptsTransmembrane domainTA proteinsSingle C-terminal transmembrane domainC-terminal transmembrane domainTail-anchored (TA) proteinsTail-anchored proteinsEndoplasmic reticulum membraneGet3Reticulum membraneChannel functionInsertaseBulk fluorescenceAqueous channelsProteinChannel activityMutation analysisMembraneMicrofluidic assayTranslocaseYeastComplexesInsertionTranslocationHydrophilic segmentsBindingPM-IRRAS and DFT investigation of the surface orientation of new Ir piano-stool complexes attached to Au(111)
Miller C, Brunner F, Kelly H, Cheung P, Torquato N, Gembicky M, Okuno S, Chan T, Batista V, Kubiak C. PM-IRRAS and DFT investigation of the surface orientation of new Ir piano-stool complexes attached to Au(111). Dalton Transactions 2022, 51: 17688-17699. PMID: 36345597, DOI: 10.1039/d2dt02730e.Peer-Reviewed Original ResearchPiano-stool complexesPhenylpyridine ligandsPM-IRRASPolarization modulation infrared reflection absorption spectroscopyInfrared reflection absorption spectroscopySelf-assembled monolayersNew catalytic systemReflection absorption spectroscopyMinimum energy orientationMolecular catalystsOrganometallic catalystsCatalytic systemDFT calculationsSurface immobilizationDFT investigationAbsorption spectroscopyCatalystSurface mechanismBipyridineLigandsHeterogenous surfaceComplexesEnergy orientationSuch hybrid systemsSurface orientationDeconvolution of in vivo protein-RNA contacts using fractionated eCLIP-seq
Biancon G, Busarello E, Joshi P, Lesch B, Halene S, Tebaldi T. Deconvolution of in vivo protein-RNA contacts using fractionated eCLIP-seq. STAR Protocols 2022, 3: 101823. PMID: 36595959, PMCID: PMC9676202, DOI: 10.1016/j.xpro.2022.101823.Peer-Reviewed Original ResearchConceptsProtein-RNA interactionsIndividual RNA-binding proteinsTranscriptome-wide analysisThousands of RNAsProtein-RNA contactsRNA-binding proteinSingle nucleotide levelComputational analysis pipelineRNA processingMulticomponent complexesRNA immunoprecipitationRead countsComplete detailsAnalysis pipelineAdditional levelProteinImmunoprecipitationRNAInteractionComplexesStructures of a mobile intron retroelement poised to attack its structured DNA target
Chung K, Xu L, Chai P, Peng J, Devarkar S, Pyle A. Structures of a mobile intron retroelement poised to attack its structured DNA target. Science 2022, 378: 627-634. PMID: 36356138, PMCID: PMC10190682, DOI: 10.1126/science.abq2844.Peer-Reviewed Original ResearchConceptsGroup II intronsCryo-electron microscopy structureDNA targetsStem-loop motifMicroscopy structureGenetic diversificationDNA substratesForward splicingRetroelementsAncient elementsDNA targetingIntronsTertiary complexRibozymeRetrotransposonsGenomeRetrotranspositionSplicingComplexesRNPDNAMotifTargetDiversificationTargetingStructural Insights into Binding of Remdesivir Triphosphate within the Replication–Transcription Complex of SARS-CoV‑2
Wang J, Shi Y, Reiss K, Maschietto F, Lolis E, Konigsberg WH, Lisi GP, Batista VS. Structural Insights into Binding of Remdesivir Triphosphate within the Replication–Transcription Complex of SARS-CoV‑2. Biochemistry 2022, 61: 1966-1973. PMID: 36044776, PMCID: PMC9469760, DOI: 10.1021/acs.biochem.2c00341.Peer-Reviewed Original ResearchConceptsReplication-transcription complexStructural basisCryo-EM structureAdenosine monophosphateRemdesivir triphosphateStructural insightsDuplex productsPrimer extensionNucleotide selectivityBase pairsNucleotide incorporationIncoming substrateRibosyl moietyActive complexSARS-CoV-2 inhibitorsNew detailed informationTriphosphateComplexesMolecular dynamics simulationsAdenosine triphosphateUS-align: universal structure alignments of proteins, nucleic acids, and macromolecular complexes
Zhang C, Shine M, Pyle AM, Zhang Y. US-align: universal structure alignments of proteins, nucleic acids, and macromolecular complexes. Nature Methods 2022, 19: 1109-1115. PMID: 36038728, DOI: 10.1038/s41592-022-01585-1.Peer-Reviewed Original ResearchConceptsStructure comparisonStructural biology studiesStructure alignmentDNA dockingMacromolecular complexesBiology studiesMultiple structure alignmentNucleic acidsDifferent moleculesRNAProteinFundamental importanceDNAComplex structureDockingUniversal protocolAlignmentExtensive optimizationFunctionComplexes
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