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
1999
Nucleotide Analog Interference Mapping
Ryder S, Strobel S. Nucleotide Analog Interference Mapping. Methods 1999, 18: 38-50. PMID: 10208815, DOI: 10.1006/meth.1999.0755.Peer-Reviewed Original ResearchConceptsFunctional groupsActive moleculesGroup substitutionNucleotide analog interference mappingIncorporation propertiesIndividual analoguesMoleculesSeries 5AnaloguesSubstitution experimentsGel electrophoresisInterference mappingUnique biochemical signatureSubstitutionSynthesisNucleoside analog triphosphatesActivity assaysBiochemical informationReactionAnalog substitutionsAssayable functionChemogenetic approachRNA structureNucleotide analoguesIodine