2021
Clusters of a Few Bound Cofilins Sever Actin Filaments
Bibeau JP, Gray S, De La Cruz EM. Clusters of a Few Bound Cofilins Sever Actin Filaments. Journal Of Molecular Biology 2021, 433: 166833. PMID: 33524412, PMCID: PMC8689643, DOI: 10.1016/j.jmb.2021.166833.Peer-Reviewed Original Research
2020
Thermal fracture kinetics of heterogeneous semiflexible polymers
Lorenzo AM, De La Cruz EM, Koslover EF. Thermal fracture kinetics of heterogeneous semiflexible polymers. Soft Matter 2020, 16: 2017-2024. PMID: 31996875, PMCID: PMC7047574, DOI: 10.1039/c9sm01637f.Peer-Reviewed Original Research
2019
Plastic Deformation and Fragmentation of Strained Actin Filaments
Schramm AC, Hocky GM, Voth GA, Martiel JL, De La Cruz EM. Plastic Deformation and Fragmentation of Strained Actin Filaments. Biophysical Journal 2019, 117: 453-463. PMID: 31301801, PMCID: PMC6697348, DOI: 10.1016/j.bpj.2019.06.018.Peer-Reviewed Original Research
2018
Insights into the Cooperative Nature of ATP Hydrolysis in Actin Filaments
Katkar HH, Davtyan A, Durumeric AEP, Hocky GM, Schramm AC, De La Cruz EM, Voth GA. Insights into the Cooperative Nature of ATP Hydrolysis in Actin Filaments. Biophysical Journal 2018, 115: 1589-1602. PMID: 30249402, PMCID: PMC6260209, DOI: 10.1016/j.bpj.2018.08.034.Peer-Reviewed Original Research
2015
Pi Release Limits the Intrinsic and RNA-Stimulated ATPase Cycles of DEAD-Box Protein 5 (Dbp5)
Wong EV, Cao W, Vörös J, Merchant M, Modis Y, Hackney DD, Montpetit B, De La Cruz EM. Pi Release Limits the Intrinsic and RNA-Stimulated ATPase Cycles of DEAD-Box Protein 5 (Dbp5). Journal Of Molecular Biology 2015, 428: 492-508. PMID: 26730886, PMCID: PMC4744555, DOI: 10.1016/j.jmb.2015.12.018.Peer-Reviewed Original Research
2013
Quantitative full time course analysis of nonlinear enzyme cycling kinetics
Cao W, De La Cruz EM. Quantitative full time course analysis of nonlinear enzyme cycling kinetics. Scientific Reports 2013, 3: 2658. PMID: 24029878, PMCID: PMC3772379, DOI: 10.1038/srep02658.Peer-Reviewed Original ResearchConceptsKinetic time coursesProduct inhibitionSteady-state enzyme kinetic parametersReaction schemeEnzymology approachReaction productsReversible bindingEnzyme kinetic parametersProduct releasePractical general methodKinetic parametersEnzyme inhibitionGeneral methodProductsEnzyme systemEnzymatic parametersAlteration in the cavity size adjacent to the active site of RB69 DNA polymerase changes its conformational dynamics
Xia S, Wood M, Bradley MJ, De La Cruz EM, Konigsberg WH. Alteration in the cavity size adjacent to the active site of RB69 DNA polymerase changes its conformational dynamics. Nucleic Acids Research 2013, 41: 9077-9089. PMID: 23921641, PMCID: PMC3799440, DOI: 10.1093/nar/gkt674.Peer-Reviewed Original ResearchConceptsRB69 DNA polymeraseFörster resonance energy transferDNA polymeraseHigh-resolution X-ray crystallographyResolution X-ray crystallographyHigh mutation rateB-family polConformational dynamicsExonuclease domainState kinetic parametersMutation rateG mutantResonance energy transferX-ray crystallographyM variantPolymerasePrimer terminusHydrophobic cavityActive siteBase selectivitySimilar substitutionSide chainsProfound effectDramatic effectInternal cavityTake advantage of time in your experiments: a guide to simple, informative kinetics assays
Pollard TD, De La Cruz EM. Take advantage of time in your experiments: a guide to simple, informative kinetics assays. Molecular Biology Of The Cell 2013, 24: 1103-1110. PMID: 23580192, PMCID: PMC3623632, DOI: 10.1091/mbc.e13-01-0030.Peer-Reviewed Original ResearchMeSH KeywordsAlgorithmsComputer SimulationCytological TechniquesKineticsModels, BiologicalResearch DesignBiophysics 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 ResearchMolecular Origins of Cofilin-Linked Changes in Actin Filament Mechanics
Fan J, Saunders MG, Haddadian EJ, Freed KF, De La Cruz EM, Voth GA. Molecular Origins of Cofilin-Linked Changes in Actin Filament Mechanics. Journal Of Molecular Biology 2013, 425: 1225-1240. PMID: 23352932, PMCID: PMC3740545, DOI: 10.1016/j.jmb.2013.01.020.Peer-Reviewed Original Research
2012
ATP 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 domainPlus‐end directed myosins accelerate actin filament sliding by single‐headed myosin VI
Ramamurthy B, Cao W, De La Cruz EM, Mooseker MS. Plus‐end directed myosins accelerate actin filament sliding by single‐headed myosin VI. Cytoskeleton 2012, 69: 59-69. PMID: 22213699, PMCID: PMC3327287, DOI: 10.1002/cm.21002.Peer-Reviewed Original ResearchChapter 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
Insights regarding guanine nucleotide exchange from the structure of a DENN-domain protein complexed with its Rab GTPase substrate
Wu X, Bradley MJ, Cai Y, Kümmel D, De La Cruz EM, Barr FA, Reinisch KM. Insights regarding guanine nucleotide exchange from the structure of a DENN-domain protein complexed with its Rab GTPase substrate. Proceedings Of The National Academy Of Sciences Of The United States Of America 2011, 108: 18672-18677. PMID: 22065758, PMCID: PMC3219131, DOI: 10.1073/pnas.1110415108.Peer-Reviewed Original ResearchMeSH KeywordsBinding SitesBiological TransportCrystallography, X-RayDeath Domain Receptor Signaling Adaptor ProteinsGuanineGuanine Nucleotide Exchange FactorsHumansKineticsNucleotidesProtein BindingProtein Structure, SecondaryProtein Structure, TertiaryRab GTP-Binding ProteinsRab1 GTP-Binding ProteinsConceptsGuanine nucleotide exchange factorsDENN domain proteinsMembrane traffic pathwaysNucleotide exchange factorsGDP-bound formGTP-bound formSwitch regions IHigher eukaryotesRab GTPasesGEF familyEukaryotic cellsTraffic pathwaysExchange factorSwitch INucleotide bindingKey regulatorConformational changesFirst structureNovel insightsRab35ProteinDENND1BEukaryotesRegion IGTPasesKinetic Analysis of Autotaxin Reveals Substrate-specific Catalytic Pathways and a Mechanism for Lysophosphatidic Acid Distribution*
Saunders LP, Cao W, Chang WC, Albright RA, Braddock DT, De La Cruz EM. Kinetic Analysis of Autotaxin Reveals Substrate-specific Catalytic Pathways and a Mechanism for Lysophosphatidic Acid Distribution*. Journal Of Biological Chemistry 2011, 286: 30130-30141. PMID: 21719699, PMCID: PMC3191052, DOI: 10.1074/jbc.m111.246884.Peer-Reviewed Original ResearchConceptsLysophosphatidic acidSecreted lysophospholipase DThr-210Synthase cycleVivo substrateSubstrate bindingQuantitative physiological modelsSignaling cascadesPosition 210LPA signalingCatalytic threonineFluorescent lipidLysophospholipase DCancer metastasisSlow catalysisCatalytic pathwayDiazol-4PathwayAutotaxinProduct releaseBindsLPA synthesisFS-3Acid distributionBioactive form
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 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
Myosin Isoform Determines the Conformational Dynamics and Cooperativity of Actin Filaments in the Strongly Bound Actomyosin Complex
Prochniewicz E, Chin HF, Henn A, Hannemann DE, Olivares AO, Thomas DD, De La Cruz EM. Myosin Isoform Determines the Conformational Dynamics and Cooperativity of Actin Filaments in the Strongly Bound Actomyosin Complex. Journal Of Molecular Biology 2009, 396: 501-509. PMID: 19962990, PMCID: PMC2834967, DOI: 10.1016/j.jmb.2009.11.063.Peer-Reviewed Original ResearchKinetic 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