2012
Chapter Two Analyzing ATP Utilization by DEAD-Box RNA Helicases Using Kinetic and Equilibrium Methods
Bradley MJ, De La Cruz EM. Chapter Two Analyzing ATP Utilization by DEAD-Box RNA Helicases Using Kinetic and Equilibrium Methods. Methods In Enzymology 2012, 511: 29-63. PMID: 22713314, PMCID: PMC7768905, DOI: 10.1016/b978-0-12-396546-2.00002-4.Peer-Reviewed Original ResearchConceptsDEAD-box RNA helicasesProduct release rate constantsEscherichia coli DbpAATP utilizationSteady-state ATPase activityRNA unwindingRNA helicasesATP bindingPreferred kinetic pathwayDsRNA unwindingConformational rearrangementsATPase activityRNAUnwindingCombination of equilibriumMss116HelicasesDbpAChapter TwoSubstrate propertiesSolution conditionsPathwayBindingKinetic pathwaysRearrangement
2005
Hydrodynamic Characterization of the DEAD-box RNA Helicase DbpA
Talavera MA, Matthews EE, Eliason WK, Sagi I, Wang J, Henn A, De La Cruz EM. Hydrodynamic Characterization of the DEAD-box RNA Helicase DbpA. Journal Of Molecular Biology 2005, 355: 697-707. PMID: 16325852, DOI: 10.1016/j.jmb.2005.10.058.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid MotifsChromatography, GelComputersCross-Linking ReagentsDEAD-box RNA HelicasesElectrophoretic Mobility Shift AssayEscherichia coliEscherichia coli ProteinsModels, BiologicalModels, MolecularProtein Structure, TertiaryRNARNA HelicasesRNA-Binding ProteinsStructural Homology, ProteinConceptsHelicase core domainNucleic acid helicasesCarboxyl-terminal domainAb initio structure prediction methodNucleic acid unwindingHelicase activityRNA metabolismHydrodynamic bead modelingDistinct RNARNA substratesHairpin 92ATP hydrolysisStructural homologyStructure prediction methodsCore domainOligomeric formsAnalytical ultracentrifugationDbpAProtein AMulti-angle laserBead modelingRNASize exclusion chromatographyKey roleFunctional properties
2004
Equilibrium and Kinetic Analysis of Nucleotide Binding to the DEAD-Box RNA Helicase DbpA †
Talavera MA, De La Cruz EM. Equilibrium and Kinetic Analysis of Nucleotide Binding to the DEAD-Box RNA Helicase DbpA †. Biochemistry 2004, 44: 959-970. PMID: 15654752, DOI: 10.1021/bi048253i.Peer-Reviewed Original ResearchConceptsFluorescence resonance energy transferAbsence of RNARNA helicaseATP bindingNucleotide bindingConformational rearrangementsResonance energy transferConformational flexibilityDbpADependent conformationStructural rearrangementsDbpA.Protein AUnfavorable entropic contributionNucleotidesPhysiological temperatureBindingAssociation rate constantsADP