2025
Catalyst-Controlled Regiodivergent Oxidation of Unsymmetrical Diols
Zacate S, Rein J, Rozema S, Annor R, Miller S, Lin S. Catalyst-Controlled Regiodivergent Oxidation of Unsymmetrical Diols. Journal Of The American Chemical Society 2025, 147: 8118-8124. PMID: 40019207, PMCID: PMC11918261, DOI: 10.1021/jacs.5c00330.Peer-Reviewed Original Research
2023
KDM5 Lysine Demethylases in Pathogenesis, from Basic Science Discovery to the Clinic
Zhang S, Cao J, Yan Q. KDM5 Lysine Demethylases in Pathogenesis, from Basic Science Discovery to the Clinic. Advances In Experimental Medicine And Biology 2023, 1433: 113-137. PMID: 37751138, DOI: 10.1007/978-3-031-38176-8_6.ChaptersConceptsPlant homeodomainFamily proteinsKey epigenetic markCell fate determinationHistone methylation marksCancer type-dependent mannerKetoglutarate-dependent dioxygenasesSelective KDM5 inhibitorsTumor suppressive functionType-dependent mannerEpigenetic marksTumor suppressive roleFate determinationJumonji CLysine 4Active chromatinMethylation marksHistone H3Lysine demethylasesCatalytic coreKDM5 inhibitorsDrug targetsKDM5Cancer metastasisSuppressive role
2018
The life of U6 small nuclear RNA, from cradle to grave
Didychuk A, Butcher S, Brow D. The life of U6 small nuclear RNA, from cradle to grave. RNA 2018, 24: 437-460. PMID: 29367453, PMCID: PMC5855946, DOI: 10.1261/rna.065136.117.Peer-Reviewed Original ResearchConceptsU6 small nuclear RNASmall nuclear RNAPre-mRNANuclear RNAProcess of RNA splicingCatalyzes intron removalEukaryotic gene expressionPre-mRNA substrateUridine-rich small nuclear RNAsRemoval of intronsPrecursor messenger RNACryo-EM structureSplicing cycleNoncoding transcriptsCatalytic coreProtein partnersRNA splicingIntron removalSplice siteGenetic dataMacromolecular machinesSpliceosomeGene expressionSplicingConformational changes
2004
Cytoplasmic localization of calcium/calmodulin‐dependent protein kinase I‐α depends on a nuclear export signal in its regulatory domain
Stedman DR, Uboha NV, Stedman TT, Nairn AC, Picciotto MR. Cytoplasmic localization of calcium/calmodulin‐dependent protein kinase I‐α depends on a nuclear export signal in its regulatory domain. FEBS Letters 2004, 566: 275-280. PMID: 15147908, DOI: 10.1016/j.febslet.2004.04.042.Peer-Reviewed Original ResearchMeSH KeywordsActive Transport, Cell NucleusAnimalsCalcium-Calmodulin-Dependent Protein Kinase Type 1Calcium-Calmodulin-Dependent Protein KinasesConsensus SequenceCytoplasmEnzyme ActivationKaryopherinsMicroscopy, FluorescenceNuclear Localization SignalsPC12 CellsProtein Structure, TertiaryRatsReceptors, Cytoplasmic and NuclearRecombinant Fusion ProteinsSubcellular FractionsTransfectionConceptsNuclear export signalExport signalRegulatory domainCytoplasmic localizationCalmodulin-dependent protein kinase ICalcium/calmodulin-dependent protein kinase IRev-like nuclear export signalProtein kinase IUbiquitous cytosolic enzymeCalcium/calmodulinTranscriptional regulationNuclear exportKinase INuclear proteinsNuclear entryCatalytic coreCytosolic enzymeI alphaSequenceCRM1VitroMutantsLocalizationCalmodulinDomain
2001
Characterization of a DNA-Cleaving deoxyribozyme
Carmi N, Breaker R. Characterization of a DNA-Cleaving deoxyribozyme. Bioorganic & Medicinal Chemistry 2001, 9: 2589-2600. PMID: 11557347, DOI: 10.1016/s0968-0896(01)00035-9.Peer-Reviewed Original ResearchMeSH KeywordsBase SequenceCatalysisCopperDeoxyadenosinesDeoxyribonucleotidesDNADNA, CatalyticDNA, Single-StrandedElectrophoresis, Gel, Two-DimensionalModels, MolecularMolecular StructureNucleic Acid ConformationOxidation-ReductionSequence Analysis, DNAStructure-Activity RelationshipSubstrate SpecificityCrystal Structure of the Atypical Protein Kinase Domain of a TRP Channel with Phosphotransferase Activity
Yamaguchi H, Matsushita M, Nairn A, Kuriyan J. Crystal Structure of the Atypical Protein Kinase Domain of a TRP Channel with Phosphotransferase Activity. Molecular Cell 2001, 7: 1047-1057. PMID: 11389851, DOI: 10.1016/s1097-2765(01)00256-8.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid MotifsAmino Acid SequenceAnimalsBinding SitesCalcium ChannelsCrystallography, X-RayCyclic AMP-Dependent Protein KinasesEvolution, MolecularMiceModels, MolecularMolecular Sequence DataNucleotidesPhosphotransferasesProtein Structure, SecondaryProtein Structure, TertiarySequence AlignmentTRPC Cation ChannelsZincConceptsEukaryotic protein kinasesProtein kinaseTransient receptor potential channelsCatalytic domainKinase domainProtein kinase domainKinase catalytic domainDetectable sequence similarityATP-grasp domainEukaryotic cellsThreonine residuesSequence similarityChannel kinaseSequence comparisonCatalytic corePotential channelsMetabolic enzymesPhosphotransferase activityKinaseChannel functionTRP channelsExternal signalsUnexpected similaritiesWide distributionProtein
2000
[10] Using DNAzylnes to cut, process, and map RNA molecules for structural studies or modification
Pyle AM, Chu VT, Jankowsky E, Boudvillain M. [10] Using DNAzylnes to cut, process, and map RNA molecules for structural studies or modification. Methods In Enzymology 2000, 317: 140-146. PMID: 10829278, DOI: 10.1016/s0076-6879(00)17012-0.Peer-Reviewed Original ResearchConceptsStructural studiesTypes of DNAzymeTemplate-directed ligationDNAzyme reactionDNAzyme moleculesSimple DNA moleculesDNAzymeDivalent ionsAnalytical scaleMoleculesDNA moleculesAddition of Mg2Crystallographic applicationsRNA targetsRNA moleculesCatalytic coreIonsLong RNAsReactionModificationDifferent applicationsInexpensive wayRNA fragmentsMg2Incorporation
1998
A minor groove RNA triple helix within the catalytic core of a group I intron
Szewczak A, Ortoleva-Donnelly L, Ryder S, Moncoeur E, Strobel S. A minor groove RNA triple helix within the catalytic core of a group I intron. Nature Structural & Molecular Biology 1998, 5: 1037-1042. PMID: 9846872, DOI: 10.1038/4146.Peer-Reviewed Original ResearchCharacterization of the Mechanism of Regulation of Ca2+/ Calmodulin-dependent Protein Kinase I by Calmodulin and by Ca2+/Calmodulin-dependent Protein Kinase Kinase*
Matsushita M, Nairn A. Characterization of the Mechanism of Regulation of Ca2+/ Calmodulin-dependent Protein Kinase I by Calmodulin and by Ca2+/Calmodulin-dependent Protein Kinase Kinase*. Journal Of Biological Chemistry 1998, 273: 21473-21481. PMID: 9705275, DOI: 10.1074/jbc.273.34.21473.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceAnimalsCalcium-Calmodulin-Dependent Protein Kinase KinaseCalcium-Calmodulin-Dependent Protein Kinase Type 1Calcium-Calmodulin-Dependent Protein Kinase Type 4Calcium-Calmodulin-Dependent Protein KinasesCalmodulinCloning, MolecularEnzyme ActivationKineticsMolecular Sequence DataPhosphorylationProtein Serine-Threonine KinasesRatsConceptsProtein kinase IAbsence of CaMKinase ICalmodulin-dependent protein kinase IDetailed structure-function analysisDependent protein kinase IDependent protein kinase kinaseProtein kinase kinaseStructure-function analysisMechanism of regulationSpecific amino acidsEnzyme activityKinase kinaseAutoinhibited stateRegulatory domainCatalytic coreCaMKIMutant formsBasal enzyme activitySecond enzymeCaMKKAmino acidsAdditional mutationsMutationsActive formRibozyme chemogenetics
Strobel S. Ribozyme chemogenetics. Biopolymers 1998, 48: 65-81. PMID: 9846125, DOI: 10.1002/(sici)1097-0282(1998)48:1<65::aid-bip7>3.0.co;2-d.Peer-Reviewed Original ResearchConceptsHelix-helix packing interactionsDNA-protein interactionsLarge catalytic RNAsSingle-site substitutionsRibozyme catalytic coreTetrahymena group ICatalytic coreTertiary hydrogen bondsCatalytic RNAGenetic revertantsReceptor motifRibozyme functionPacking interactionsChemogenetic approachChemical correlatesReview ISuppressorGenetic analogyRevertantsTriple helixChemical basisNucleotide analoguesModification experimentsMutagenesisRNA
1996
Structural Basis for the Autoinhibition of Calcium/Calmodulin-Dependent Protein Kinase I
Goldberg J, Nairn A, Kuriyan J. Structural Basis for the Autoinhibition of Calcium/Calmodulin-Dependent Protein Kinase I. Cell 1996, 84: 875-887. PMID: 8601311, DOI: 10.1016/s0092-8674(00)81066-1.Peer-Reviewed Original ResearchMeSH KeywordsAdenosine TriphosphateAnimalsBinding SitesCalcium-Calmodulin-Dependent Protein Kinase Type 1Calcium-Calmodulin-Dependent Protein KinasesCrystallographyImage Processing, Computer-AssistedMolecular Sequence DataPhosphorylationProtein ConformationProtein KinasesRatsSequence Homology, Amino AcidSubstrate SpecificityConceptsCalmodulin-dependent protein kinase ICalcium/calmodulin-dependent protein kinase IProtein kinase IKinase IRegulatory regionsATP-binding domainTerminal regulatory regionCatalytic domainCatalytic coreSecond helixStructural basisAlpha-helixCalmodulin targetsConformational changesPeptide substratesHelix segmentsCalmodulinHelixSubstantial structural changesRecognition elementInitial interactionInhibitory interactionsDomainAutoinhibitionCrystal structure
1993
Selection of a ‘minimal’ glutaminyl‐tRNA synthetase and the evolution of class I synthetases.
Schwob E, Söll D. Selection of a ‘minimal’ glutaminyl‐tRNA synthetase and the evolution of class I synthetases. The EMBO Journal 1993, 12: 5201-5208. PMID: 7505222, PMCID: PMC413784, DOI: 10.1002/j.1460-2075.1993.tb06215.x.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acyl-tRNA SynthetasesBacterial ProteinsBase SequenceBinding SitesBiological EvolutionEscherichia coliModels, MolecularMolecular Sequence DataMutagenesis, Site-DirectedProtein Structure, TertiaryRNA, BacterialRNA, Transfer, GlnRNA, Transfer, SerStructure-Activity RelationshipTransfer RNA AminoacylationConceptsGlutaminyl-tRNA synthetaseAminoacyl-tRNA synthetasesEscherichia coli glutaminyl-tRNA synthetaseClass I aminoacyl-tRNA synthetasesNew recognition specificitiesNon-catalytic domainSubstrate recognition propertiesNon-cognate tRNAsRecognition of tRNACommon ancestorSequence motifsAmber suppressorGenetic codeTRNA substratesCatalytic coreGlnRTRNARecognition specificityDistinct domainsEnzymatic activityElaborate relationshipSynthetasesSpecific roleClass ISynthetase
1992
Group II introns deleted for multiple substructures retain self-splicing activity.
Koch J, Boulanger S, Dib-Hajj S, Hebbar S, Perlman P. Group II introns deleted for multiple substructures retain self-splicing activity. Molecular And Cellular Biology 1992, 12: 1950-1958. PMID: 1569932, PMCID: PMC364365, DOI: 10.1128/mcb.12.5.1950.Peer-Reviewed Original ResearchConceptsGroup II intronsSplice site selectionSelf-splicing activitySplice junctionsDomain 2Domain 5Domain 1Essential catalytic coreYeast mitochondrial DNASecondary structure elementsCoxI geneSelf-splicing reactionMitochondrial DNAPrecursor RNAMutant intronsCatalytic coreIntron domainsTriple deletionIntronsTrans assaySingle deletionSecondary structureDomain 6DeletionStructure elementsGroup II Introns Deleted for Multiple Substructures Retain Self-Splicing Activity
Koch J, Boulanger S, Dib-Hajj S, Hebbar S, Perlman P. Group II Introns Deleted for Multiple Substructures Retain Self-Splicing Activity. Molecular And Cellular Biology 1992, 12: 1950-1958. DOI: 10.1128/mcb.12.5.1950-1958.1992.Peer-Reviewed Original ResearchGroup II intronsSplice site selectionSplice junctionsDomain 2Domain 5Domain 1Essential catalytic coreYeast mitochondrial DNASelf-splicing activitySecondary structure elementsCoxI geneSelf-splicing reactionMitochondrial DNAPrecursor RNAMutant intronsCatalytic coreIntron domainsTriple deletionTrans assayIntronsSingle deletionSecondary structureDomain 6DeletionStructure elements
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