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
2010
A Myosin V Inhibitor Based on Privileged Chemical Scaffolds
Islam K, Chin HF, Olivares AO, Saunders LP, De La Cruz EM, Kapoor TM. A Myosin V Inhibitor Based on Privileged Chemical Scaffolds. Angewandte Chemie International Edition 2010, 49: 8484-8488. PMID: 20878825, PMCID: PMC3063097, DOI: 10.1002/anie.201004026.Peer-Reviewed Original ResearchActin filament remodeling by actin depolymerization factor/cofilin
Pfaendtner J, De La Cruz EM, Voth GA. Actin filament remodeling by actin depolymerization factor/cofilin. Proceedings Of The National Academy Of Sciences Of The United States Of America 2010, 107: 7299-7304. PMID: 20368459, PMCID: PMC2867716, DOI: 10.1073/pnas.0911675107.Peer-Reviewed Original ResearchConceptsActin depolymerization factorSubunit interactionsCofilin bindingActin filamentsADF/cofilinFactor/cofilinLong-pitch helixHelix monomersNeighboring subunitMolecular basisSevering proteinHydrophobic loopConformational dynamicsSubdomain 1Subdomain 2Loop movesTriggers reorganizationCofilinFilament flexibilityFilamentsNative filamentsDNaseFilament contactsAtom simulationsBinding
2007
Contributions from All Over
AU JK, DE LA CRUZ EM, SAFER D. Contributions from All Over. Annals Of The New York Academy Of Sciences 2007, 1112: 38-44. PMID: 17468230, DOI: 10.1196/annals.1415.015.Peer-Reviewed Original ResearchConceptsProline residuesActin bindingWild-type complexHydrophobic contactsSite-directed mutagenesisStrong actin bindingHydrophobic residuesAlanine residuesCysteine 374Slow association rateRate of associationResiduesMutantsComplex variesTbeta4Association rateSulfo-1BindingCis-trans isomerizationKinetic basisComplexesPro27Pro29Lys19Mutagenesis
2004
Cofilin Binding to Muscle and Non-muscle Actin Filaments: Isoform-dependent Cooperative Interactions
De La Cruz EM. Cofilin Binding to Muscle and Non-muscle Actin Filaments: Isoform-dependent Cooperative Interactions. Journal Of Molecular Biology 2004, 346: 557-564. PMID: 15670604, DOI: 10.1016/j.jmb.2004.11.065.Peer-Reviewed Original ResearchConceptsActin filamentsConcentration of cofilinActin isoformsFilament severingRegulatory proteinsCooperative free energyActin fluorescencePyrene-actin fluorescenceCofilinFilament bindingHuman cofilinEquilibrium bindingCooperative interactionsIntrinsic affinitySkeletal muscleIsoformsBindingFilamentsSeveringMuscle actinHill coefficientCooperativity modelFilament latticeIsolated siteProteinEquilibrium 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
2000
Thymosin-β4 Changes the Conformation and Dynamics of Actin Monomers
De La Cruz E, Ostap E, Brundage R, Reddy K, Sweeney H, Safer D. Thymosin-β4 Changes the Conformation and Dynamics of Actin Monomers. Biophysical Journal 2000, 78: 2516-2527. PMID: 10777749, PMCID: PMC1300842, DOI: 10.1016/s0006-3495(00)76797-x.Peer-Reviewed Original ResearchMeSH KeywordsActinsAnimalsBinding SitesBiophysical PhenomenaBiophysicsCircular DichroismCross-Linking ReagentsFluorescent DyesHumansIn Vitro TechniquesKineticsMacromolecular SubstancesModels, MolecularMuscle, SkeletalMutagenesis, Site-DirectedNaphthalenesulfonatesOsmotic PressureProtein BindingProtein ConformationRabbitsRecombinant ProteinsThermodynamicsThymosinTritiumViscosityConceptsActin monomersActin monomer poolMgATP-actinMetazoan cellsNucleotide exchangeC-terminusSubdomain 2Conformational changesMonomer poolN-iodoacetyl-N'Cleavage siteActinThymosin β4Rate of dissociationAmide protonsSulfo-1Unique abilityBindingStructural dynamicsConformationTerminusNucleotidesProteolysisDifferent stabilitiesDegrees C