2022
US-align: universal structure alignments of proteins, nucleic acids, and macromolecular complexes
Zhang C, Shine M, Pyle AM, Zhang Y. US-align: universal structure alignments of proteins, nucleic acids, and macromolecular complexes. Nature Methods 2022, 19: 1109-1115. PMID: 36038728, DOI: 10.1038/s41592-022-01585-1.Peer-Reviewed Original ResearchConceptsStructure comparisonStructural biology studiesStructure alignmentDNA dockingMacromolecular complexesBiology studiesMultiple structure alignmentNucleic acidsDifferent moleculesRNAProteinFundamental importanceDNAComplex structureDockingUniversal protocolAlignmentExtensive optimizationFunctionComplexes
2003
The Pathway for DNA Recognition and RNA Integration by a Group II Intron Retrotransposon
Aizawa Y, Xiang Q, Lambowitz AM, Pyle AM. The Pathway for DNA Recognition and RNA Integration by a Group II Intron Retrotransposon. Molecular Cell 2003, 11: 795-805. PMID: 12667460, DOI: 10.1016/s1097-2765(03)00069-8.Peer-Reviewed Original ResearchConceptsGroup II intron RNPsIntron-encoded proteinTarget site specificityMobile genetic elementsIntron invasionDNA recognitionDNA bindingGenetic elementsConformational changesDuplex DNADNA targetsSite specificityDNAStrand DNAComplex cascadeReverse transcriptionRNPInvasionRetrotransposonsSplicingTranscriptionProteinKinetic frameworkPathwayCascade
2002
The hepatitis C viral NS3 protein is a processive DNA helicase with cofactor enhanced RNA unwinding
Pang PS, Jankowsky E, Planet PJ, Pyle AM. The hepatitis C viral NS3 protein is a processive DNA helicase with cofactor enhanced RNA unwinding. The EMBO Journal 2002, 21: 1168-1176. PMID: 11867545, PMCID: PMC125889, DOI: 10.1093/emboj/21.5.1168.Peer-Reviewed Original ResearchConceptsRNA unwindingHelicase activityDNA helicase activityCytoplasmic RNA virusesProcessive DNA helicaseImportant drug targetsReplicative DNA intermediatesNS3 helicase activityViral NS3 proteinDNA helicaseDuplex unwindingPhylogenetic analysisReplicative roleProcessive helicaseDNA intermediatesHelicaseHost DNARNA virusesRNA activityRNA replicationDrug targetsNS3 proteinUnwindingCentral roleDNA