2022
CSSR: assignment of secondary structure to coarse‐grained RNA tertiary structures
Zhang C, Pyle AM. CSSR: assignment of secondary structure to coarse‐grained RNA tertiary structures. Acta Crystallographica Section D, Structural Biology 2022, 78: 466-471. PMID: 35362469, PMCID: PMC8972804, DOI: 10.1107/s2059798322001292.Peer-Reviewed Original Research
2015
HOTAIR Forms an Intricate and Modular Secondary Structure
Somarowthu S, Legiewicz M, Chillón I, Marcia M, Liu F, Pyle AM. HOTAIR Forms an Intricate and Modular Secondary Structure. Molecular Cell 2015, 58: 353-361. PMID: 25866246, PMCID: PMC4406478, DOI: 10.1016/j.molcel.2015.03.006.Peer-Reviewed Original ResearchMeSH KeywordsBase SequenceConserved SequenceHumansIn Vitro TechniquesModels, MolecularNucleic Acid ConformationPhylogenyRNA, Long NoncodingConceptsFunctional secondary structureFundamental cellular processesSecondary structureProtein-binding motifsProtein-binding domainsGroup II intronsMetastasis suppressor geneSecondary structure elementsCellular processesPhylogenetic analysisLncRNA moleculesEpidermal developmentChemical probingMolecular mechanismsSuppressor geneCancer progressionStructural organizationKey playersLncRNA HOTAIRHOTAIRStructure elementsRNAHomogenous formReceptor activatorIntrons
2014
Principles of ion recognition in RNA: insights from the group II intron structures
Marcia M, Pyle AM. Principles of ion recognition in RNA: insights from the group II intron structures. RNA 2014, 20: 516-527. PMID: 24570483, PMCID: PMC3964913, DOI: 10.1261/rna.043414.113.Peer-Reviewed Original ResearchConceptsActive siteSite-bound ionsIon recognitionMetal ionsOrganic ionsLatter ionIon-binding sitesCatalytic ionsCrystal structureGU wobble pairsMonovalent ionsLarge RNA moleculesIonsStructural ionsBiophysical methodsGroup II intron structureGA mismatchesLong-range tertiary contactsRNA structureRNA foldingTertiary contactsWobble pairStructureCatalysisHeteronuclear
2004
The identification of novel RNA structural motifs using COMPADRES: an automated approach to structural discovery
Wadley LM, Pyle AM. The identification of novel RNA structural motifs using COMPADRES: an automated approach to structural discovery. Nucleic Acids Research 2004, 32: 6650-6659. PMID: 15608296, PMCID: PMC545444, DOI: 10.1093/nar/gkh1002.Peer-Reviewed Original ResearchPrediction of functional tertiary interactions and intermolecular interfaces from primary sequence data
Pang PS, Jankowsky E, Wadley LM, Pyle AM. Prediction of functional tertiary interactions and intermolecular interfaces from primary sequence data. Journal Of Experimental Zoology Part B Molecular And Developmental Evolution 2004, 304B: 50-63. PMID: 15595717, DOI: 10.1002/jez.b.21024.Peer-Reviewed Original ResearchMeSH KeywordsAlgorithmsAnimalsBiopolymersDatabases, ProteinModels, MolecularMolecular Sequence DataProtein Interaction MappingConceptsRNA-protein complexesPattern of conservationProtein-protein interactionsPrimary sequence dataRNA-proteinDifferent organismsSequence dataSequence informationIntermolecular interfaceEnergetic couplingTertiary interactionsMacromolecular interactionsRNAsGenesImportant intramolecular interactionsProteinSequenceIntramolecular interactionsRNAOrganismsSpeciesInteractionMutationsNumber of predictionsConservationSolution structure of domain 5 of a group II intron ribozyme reveals a new RNA motif
Sigel RK, Sashital DG, Abramovitz DL, Palmer AG, Butcher SE, Pyle AM. Solution structure of domain 5 of a group II intron ribozyme reveals a new RNA motif. Nature Structural & Molecular Biology 2004, 11: 187-192. PMID: 14745440, DOI: 10.1038/nsmb717.Peer-Reviewed Original ResearchConceptsGroup II intron ribozymeMetal ion titrationsSolution structureMetal ion bindingDivalent metal ionsMetal ion-binding sitesRibozyme active siteBackbone substituentsMetal ionsMajor groove faceIon-binding sitesIon titrationActive siteIon bindingSyn conformationIntron ribozymesMinor groove sideAGC triadNew RNA motifMajor grooveGroove faceStrong Mg2Catalytic triadGroove sideCentral core
2003
A Group II Intron Inserted into a Bacterial Heat-Shock Operon Shows Autocatalytic Activity and Unusual Thermostability †
Adamidi C, Fedorova O, Pyle AM. A Group II Intron Inserted into a Bacterial Heat-Shock Operon Shows Autocatalytic Activity and Unusual Thermostability †. Biochemistry 2003, 42: 3409-3418. PMID: 12653544, DOI: 10.1021/bi027330b.Peer-Reviewed Original Research
2002
Productive folding to the native state by a group II intron ribozyme11Edited by D. Draper
Swisher JF, Su LJ, Brenowitz M, Anderson VE, Pyle AM. Productive folding to the native state by a group II intron ribozyme11Edited by D. Draper. Journal Of Molecular Biology 2002, 315: 297-310. PMID: 11786013, DOI: 10.1006/jmbi.2001.5233.Peer-Reviewed Original Research
1996
Role of metal ions in ribozymes.
Pyle AM. Role of metal ions in ribozymes. 1996, 32: 479-520. PMID: 8640529.Peer-Reviewed Original Research