2008
An Uncharged Amine in the Transition State of the Ribosomal Peptidyl Transfer Reaction
Kingery DA, Pfund E, Voorhees RM, Okuda K, Wohlgemuth I, Kitchen DE, Rodnina MV, Strobel SA. An Uncharged Amine in the Transition State of the Ribosomal Peptidyl Transfer Reaction. Cell Chemical Biology 2008, 15: 493-500. PMID: 18482701, PMCID: PMC2851197, DOI: 10.1016/j.chembiol.2008.04.005.Peer-Reviewed Original ResearchConceptsTransition stateAminolysis reactionBond formationNitrogen-carbon bond formationLinear free energy relationshipSubstantial positive chargeChemical transition stateFree energy relationshipsPeptidyl transfer reactionTransfer reactionsActive sitePositive chargeUncharged amineReactionNucleophilesPuromycin derivativesDeprotonationChemistryDetailed understandingAminesFormationDerivativesChargeSolutionA relaxed active site after exon ligation by the group I intron
Lipchock SV, Strobel SA. A relaxed active site after exon ligation by the group I intron. Proceedings Of The National Academy Of Sciences Of The United States Of America 2008, 105: 5699-5704. PMID: 18408159, PMCID: PMC2311373, DOI: 10.1073/pnas.0712016105.Peer-Reviewed Original ResearchConceptsActive siteMetal ionsRelaxed active siteActive site metal ionScissile phosphateDirect metal coordinationHydrogen bonding contactsMetal coordinationBonding contactsTransition stateCrystal structureThermodynamic measurementsIonsGround stateStructureCoordinationStructural observationsTertiary interactionsIntron releaseExon ligationGroup I intronPhosphateComplexesReactionSecond step
2006
Structural Investigation of the GlmS Ribozyme Bound to Its Catalytic Cofactor
Cochrane JC, Lipchock SV, Strobel SA. Structural Investigation of the GlmS Ribozyme Bound to Its Catalytic Cofactor. Cell Chemical Biology 2006, 14: 97-105. PMID: 17196404, PMCID: PMC1847778, DOI: 10.1016/j.chembiol.2006.12.005.Peer-Reviewed Original Research
1999
An important base triple anchors the substrate helix recognition surface within the Tetrahymena ribozyme active site
Szewczak A, Ortoleva-Donnelly L, Zivarts M, Oyelere A, Kazantsev A, Strobel S. An important base triple anchors the substrate helix recognition surface within the Tetrahymena ribozyme active site. Proceedings Of The National Academy Of Sciences Of The United States Of America 1999, 96: 11183-11188. PMID: 10500151, PMCID: PMC18008, DOI: 10.1073/pnas.96.20.11183.Peer-Reviewed Original ResearchConceptsHelix dockingBase triplesRecognition surfaceGroup I intronActive siteNetwork of interactionsTetrahymena group IP3 helixStructural biologySubstrate bindingI intronCatalytic RNAProduct bindingSuppression analysisFunctional importanceRNA foldingRNA constructsSubstrate helixBiochemical evidenceMutant ribozymesRibozyme active siteSubstantial rearrangementHelixCrystallographic modelRibozymeA hydrogen-bonding triad stabilizes the chemical transition state of a group I ribozyme
Strobel S, Ortoleva-Donnelly L. A hydrogen-bonding triad stabilizes the chemical transition state of a group I ribozyme. Cell Chemical Biology 1999, 6: 153-165. PMID: 10074469, DOI: 10.1016/s1074-5521(99)89007-3.Peer-Reviewed Original Research
1997
RNA seeing double: Close-packing of helices in RNA tertiary structure
Strobel S, Doudna J. RNA seeing double: Close-packing of helices in RNA tertiary structure. Trends In Biochemical Sciences 1997, 22: 262-266. PMID: 9255068, DOI: 10.1016/s0968-0004(97)01056-6.Peer-Reviewed Original ResearchConceptsHigher-order structure formationPacking of helicesChromosome maintenanceNoncanonical base pairsRNA processingDouble-helical segmentsRNA tertiary structureProtein biosynthesisRecognition motifRNA moleculesTertiary structureBase pairsHelical packingRNAEssential roleProteinActive siteBiosynthesisComplex architectureFoldingMotifHelixAssemblyDifferent strategies
1988
Triticone A: A novel bioactive lactam with potential as a molecular probe
Kenfield D, Strobel S, Sugawara F, Berglund D, Strobel G. Triticone A: A novel bioactive lactam with potential as a molecular probe. Biochemical And Biophysical Research Communications 1988, 157: 174-182. PMID: 3196330, DOI: 10.1016/s0006-291x(88)80029-9.Peer-Reviewed Original ResearchConceptsPlant pathogenic fungiMolecular probesProtoplast assaysSH functional groupsCO2 fixation reactionWheat cellsPathogenic fungiPhysiological functionsSpirocyclic lactamsFunctional groupsActive siteEnantiomeric mixturesNovel compoundsFluorescein diacetateBiological activityFixation reactionBiological systemsAccurate quantitationLactamsPhotosynthesisProtoplastsChlorosisFungiPlantsWheat