2022
Sub-Nanometer Mapping of the Interfacial Electric Field Profile Using a Vibrational Stark Shift Ruler
Bhattacharyya D, Videla P, Palasz J, Tangen I, Meng J, Kubiak C, Batista V, Lian T. Sub-Nanometer Mapping of the Interfacial Electric Field Profile Using a Vibrational Stark Shift Ruler. Journal Of The American Chemical Society 2022, 144: 14330-14338. PMID: 35905473, DOI: 10.1021/jacs.2c05563.Peer-Reviewed Original ResearchConceptsSelf-assembled monolayersElectrode surfaceElectrode/electrolyte interfaceDensity functional theory simulationsDouble layerStern layer thicknessElectrical double layerInterfacial electric fieldElectric double layerMolecular electrocatalystsGold surfaceElectrolyte interfaceIsocyanide groupElectric field profileElectrochemical conditionsElectrochemical processesVibrational reporterElectrolyte penetrationElectrode interfaceElectrolyte environmentSpectroscopic methodsElectric field strengthReaction mechanismW centerCatalytic rate
1999
Allosteric selection of ribozymes that respond to the second messengers cGMP and cAMP
Koizumi M, Soukup G, Kerr J, Breaker R. Allosteric selection of ribozymes that respond to the second messengers cGMP and cAMP. Nature Structural & Molecular Biology 1999, 6: 1062-1071. PMID: 10542100, DOI: 10.1038/14947.Peer-Reviewed Original ResearchConceptsRNA molecular switchGenetic control elementsMolecular recognition characteristicsEmergence of ribozymesSecond messenger cGMPRNAs exhibitAllosteric ribozymesRNA transcriptsCellular RNASelective sensorCAMP additionMolecular switchFold activationCatalytic rateRecognition characteristicsRibozymeControl elementsEffector compoundsHammerhead ribozymeChemical agentsCompoundsStructural characteristicsSpecific nucleosideNew combinatorial strategyCombinatorial strategiesThe CDK-activating Kinase (Cak1p) from Budding Yeast Has an Unusual ATP-binding Pocket*
Enke D, Kaldis P, Holmes J, Solomon M. The CDK-activating Kinase (Cak1p) from Budding Yeast Has an Unusual ATP-binding Pocket*. Journal Of Biological Chemistry 1999, 274: 1949-1956. PMID: 9890950, DOI: 10.1074/jbc.274.4.1949.Peer-Reviewed Original ResearchConceptsProtein kinaseInvariant lysineMajor cyclin-dependent kinaseLoop regionEssential protein kinaseMost protein kinasesAmino acidsATP-binding pocketCyclin-dependent kinasesBudding YeastCak1pMutagenic analysisATP phosphatesSequence differencesLoop motifKinaseCovalent modificationCore sequenceATP analogYeastCatalytic rateInhibitory drugsLysineMutationsATP
1997
Examination of the catalytic fitness of the hammerhead ribozyme by in vitro selection.
Tang J, Breaker R. Examination of the catalytic fitness of the hammerhead ribozyme by in vitro selection. RNA 1997, 3: 914-25. PMID: 9257650, PMCID: PMC1369536.Peer-Reviewed Original ResearchConceptsConsensus sequenceATP-binding RNA aptamerCatalytic fitnessHammerhead ribozymeAbsence of ATPRNA poolAllosteric ribozymesVitro SelectionRNA aptamersCatalytic functionSequence variantsAllosteric interactionsCombinatorial poolsRibozymeTranscriptionATPRNACatalytic rateSequenceHammerhead domainRibozyme constructsFitnessAllosteric delayPoolSimilar strategiesPre-Steady-State Kinetic Analysis of the Trichodiene Synthase Reaction Pathway †
Cane D, Chiu H, Liang P, Anderson K. Pre-Steady-State Kinetic Analysis of the Trichodiene Synthase Reaction Pathway †. Biochemistry 1997, 36: 8332-8339. PMID: 9204880, DOI: 10.1021/bi963018o.Peer-Reviewed Original ResearchConceptsChemical catalysisReaction pathwaysRapid chemical quench methodsActive siteSteady-state catalytic rateSingle turnover reactionsRate constant kcatEnzyme active siteNerolidyl diphosphateDeuterium isotope effectSingle-turnover experimentsSingle turnover rateState kinetic analysisTurnover reactionsDetection limitCatalytic rateOverall reactionSteady-state releaseIsotope effectRate-limiting stepState kineticsCatalysisReactionQuench methodSynthase reactionRational design of allosteric ribozymes
Tang J, Breaker R. Rational design of allosteric ribozymes. Cell Chemical Biology 1997, 4: 453-459. PMID: 9224568, DOI: 10.1016/s1074-5521(97)90197-6.Peer-Reviewed Original ResearchConceptsAllosteric regulationAllosteric ribozymesEffector moleculesProtein enzymesActive siteCatalytic ratePresence of dATPSelf-cleaving ribozymesSmall effector moleculesPresence of ATPSmall molecule receptorRational design strategyCellular processesEnzyme active siteAptamer domainAllosteric controlAllosteric enzymeCatalytic RNARNA aptamersConformational changesLigand moleculesMetabolic pathwaysCatalytic activityAllosteric hammerheadCatalytic features
1994
A DNA enzyme that cleaves RNA
Breaker R, Joyce G. A DNA enzyme that cleaves RNA. Cell Chemical Biology 1994, 1: 223-229. PMID: 9383394, DOI: 10.1016/1074-5521(94)90014-0.Peer-Reviewed Original ResearchConceptsDNA enzymeRNA enzymeDependent cleavageSimilarity of DNATypes of RNACatalytic domainDNA sequencesRandom nucleotidesRapid turnoverRNASuccessive roundsEnzymeDNACatalytic rateSelective amplificationBiological systemsTurnover rateSequenceCleavageIntermolecular contextNucleotidesPopulationTurnoverPhosphoesters
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