2020
Directional allosteric regulation of protein filament length
Jermyn AS, Cao W, Elam WA, De La Cruz EM, Lin MM. Directional allosteric regulation of protein filament length. Physical Review E 2020, 101: 032409. PMID: 32290018, PMCID: PMC7758089, DOI: 10.1103/physreve.101.032409.Peer-Reviewed Original Research
2013
Biophysics of actin filament severing by cofilin
Elam WA, Kang H, De La Cruz EM. Biophysics of actin filament severing by cofilin. FEBS Letters 2013, 587: 1215-1219. PMID: 23395798, PMCID: PMC4079045, DOI: 10.1016/j.febslet.2013.01.062.Peer-Reviewed Original Research
2012
Identification of cation-binding sites on actin that drive polymerization and modulate bending stiffness
Kang H, Bradley MJ, McCullough BR, Pierre A, Grintsevich EE, Reisler E, De La Cruz EM. Identification of cation-binding sites on actin that drive polymerization and modulate bending stiffness. Proceedings Of The National Academy Of Sciences Of The United States Of America 2012, 109: 16923-16927. PMID: 23027950, PMCID: PMC3479481, DOI: 10.1073/pnas.1211078109.Peer-Reviewed Original ResearchConceptsCation-binding sitesActin assemblyEukaryotic biologyLong-pitch helixActin functionSalt-dependent effectsCell divisionCell motilityActin polymerizationFilament assemblyAdjacent subunitsIntracellular transportActin filamentsPhysiological salt concentrationsActin monomersCellular shapeNonspecific ionic strength effectsDiscrete sitesATP Utilization and RNA Conformational Rearrangement by DEAD-Box Proteins
Henn A, Bradley MJ, De La Cruz EM. ATP Utilization and RNA Conformational Rearrangement by DEAD-Box Proteins. Annual Review Of Biophysics 2012, 41: 247-267. PMID: 22404686, PMCID: PMC7761782, DOI: 10.1146/annurev-biophys-050511-102243.Peer-Reviewed Original ResearchConceptsDEAD-box proteinsNucleotide-dependent interactionRegulatory partner proteinsMolecular motor proteinsMolecular motor functionPartner proteinsRNA helicasesHelicase coreRNA helicaseRNA metabolismVivo foldingATP bindingDBP functionMotor proteinsCellular RNARNA structureQuantitative mechanistic understandingConformational rearrangementsBiophysical investigationsEnzymatic adaptationLarge familyMechanistic understandingProteinRNAAuxiliary domainChapter 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 ResearchMeSH KeywordsAdenosine TriphosphateDEAD-box RNA HelicasesKineticsRNA StabilityTemperatureThermodynamicsConceptsDEAD-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
2011
Mechanism of Mss116 ATPase Reveals Functional Diversity of DEAD-Box Proteins
Cao W, Coman MM, Ding S, Henn A, Middleton ER, Bradley MJ, Rhoades E, Hackney DD, Pyle AM, De La Cruz EM. Mechanism of Mss116 ATPase Reveals Functional Diversity of DEAD-Box Proteins. Journal Of Molecular Biology 2011, 409: 399-414. PMID: 21501623, PMCID: PMC3125984, DOI: 10.1016/j.jmb.2011.04.004.Peer-Reviewed Original ResearchConceptsGroup II intronsWeak RNARNA bindingDEAD-box RNA helicase proteinATP hydrolysisBiochemical intermediatesDEAD-box proteinsRNA helicase proteinStrong RNA bindingStable RNA duplexAbsence of nucleotideATP utilizationStrong thermodynamic couplingFunctional diversityIntron splicingStrong RNAIntron foldingVivo splicingHelicase proteinMRNA translationMss116ATPase cyclingVivo functionBiological roleADP state
2010
Origin of Twist-Bend Coupling in Actin Filaments
De La Cruz EM, Roland J, McCullough BR, Blanchoin L, Martiel JL. Origin of Twist-Bend Coupling in Actin Filaments. Biophysical Journal 2010, 99: 1852-1860. PMID: 20858430, PMCID: PMC2941021, DOI: 10.1016/j.bpj.2010.07.009.Peer-Reviewed Original ResearchThe Kinetics of Cooperative Cofilin Binding Reveals Two States of the Cofilin-Actin Filament
De La Cruz EM, Sept D. The Kinetics of Cooperative Cofilin Binding Reveals Two States of the Cofilin-Actin Filament. Biophysical Journal 2010, 98: 1893-1901. PMID: 20441753, PMCID: PMC2862197, DOI: 10.1016/j.bpj.2010.01.023.Peer-Reviewed Original Research
2009
Kinetic Analysis of the Guanine Nucleotide Exchange Activity of TRAPP, a Multimeric Ypt1p Exchange Factor
Chin HF, Cai Y, Menon S, Ferro-Novick S, Reinisch KM, De La Cruz EM. Kinetic Analysis of the Guanine Nucleotide Exchange Activity of TRAPP, a Multimeric Ypt1p Exchange Factor. Journal Of Molecular Biology 2009, 389: 275-288. PMID: 19361519, PMCID: PMC2770256, DOI: 10.1016/j.jmb.2009.03.068.Peer-Reviewed Original ResearchConceptsMembrane trafficExchange factorGuanine nucleotide exchange activityRab GTPase Ypt1pLarge multimeric assembliesNucleotide exchange activityThermodynamic linkage analysisWeak thermodynamic couplingTRAPP complexesStable ternary complexTRAPP subunitsGEF activityYpt1pNucleotide bindingMultimeric assembliesNucleotide exchangeNucleotide dissociationNucleotide affinityLinkage analysisIndependent pathwaysGEF systemTernary complexExchange activityTRAPPOverall net changeChapter 6 Kinetic and Equilibrium Analysis of the Myosin ATPase
De La Cruz EM, Ostap EM. Chapter 6 Kinetic and Equilibrium Analysis of the Myosin ATPase. Methods In Enzymology 2009, 455: 157-192. PMID: 19289206, PMCID: PMC2921708, DOI: 10.1016/s0076-6879(08)04206-7.Peer-Reviewed Original Research
2008
Effects of Solution Crowding on Actin Polymerization Reveal the Energetic Basis for Nucleotide-Dependent Filament Stability
Frederick KB, Sept D, De La Cruz EM. Effects of Solution Crowding on Actin Polymerization Reveal the Energetic Basis for Nucleotide-Dependent Filament Stability. Journal Of Molecular Biology 2008, 378: 540-550. PMID: 18374941, PMCID: PMC2424216, DOI: 10.1016/j.jmb.2008.02.022.Peer-Reviewed Original ResearchMeSH KeywordsActin CytoskeletonAdenosine DiphosphateAdenosine TriphosphateHydrolysisSolutionsSurface PropertiesThermodynamicsConceptsADP-actin filamentsFilament stabilityCell structure maintenanceFundamental cellular processesADP-actinADP-F-actinSolution crowdingCellular processesAllosteric regulatorsMolecular basisRegulatory proteinsActin polymerizationATP hydrolysisActin activityNucleotide hydrolysisFilament subunitsEnergetic basisIntracellular conditionsStructure maintenanceSubunit dissociationStability of ATPATPConcentration-dependent mannerStructural differencesForce generation
2007
The ATPase Cycle Mechanism of the DEAD-box rRNA Helicase, DbpA
Henn A, Cao W, Hackney DD, De La Cruz EM. The ATPase Cycle Mechanism of the DEAD-box rRNA Helicase, DbpA. Journal Of Molecular Biology 2007, 377: 193-205. PMID: 18237742, PMCID: PMC2359651, DOI: 10.1016/j.jmb.2007.12.046.Peer-Reviewed Original ResearchContributions 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 ResearchMeSH KeywordsActinsAnimalsBinding SitesDrug StabilityKineticsModels, MolecularProtein ConformationRabbitsThermodynamicsThymosinConceptsProline residuesActin bindingWild-type complexHydrophobic contactsSite-directed mutagenesisStrong actin bindingHydrophobic residuesAlanine residuesCysteine 374Slow association rateRate of associationResiduesMutantsComplex variesTbeta4Association rateSulfo-1BindingCis-trans isomerizationKinetic basisComplexesPro27Pro29Lys19Mutagenesis
2006
Energetics and Kinetics of Cooperative Cofilin–Actin Filament Interactions
Cao W, Goodarzi JP, De La Cruz EM. Energetics and Kinetics of Cooperative Cofilin–Actin Filament Interactions. Journal Of Molecular Biology 2006, 361: 257-267. PMID: 16843490, DOI: 10.1016/j.jmb.2006.06.019.Peer-Reviewed Original Research
2005
Thermodynamics of Nucleotide Binding to Actomyosin V and VI: A Positive Heat Capacity Change Accompanies Strong ADP Binding †
Robblee JP, Cao W, Henn A, Hannemann DE, De La Cruz EM. Thermodynamics of Nucleotide Binding to Actomyosin V and VI: A Positive Heat Capacity Change Accompanies Strong ADP Binding †. Biochemistry 2005, 44: 10238-10249. PMID: 16042401, DOI: 10.1021/bi050232g.Peer-Reviewed Original Research
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
1996
Kinetics and Thermodynamics of Phalloidin Binding to Actin Filaments from Three Divergent Species †
De La Cruz E, Pollard T. Kinetics and Thermodynamics of Phalloidin Binding to Actin Filaments from Three Divergent Species †. Biochemistry 1996, 35: 14054-14061. PMID: 8916890, DOI: 10.1021/bi961047t.Peer-Reviewed Original Research