2023
Turning up the heat mimics allosteric signaling in imidazole-glycerol phosphate synthase
Maschietto F, Morzan U, Tofoleanu F, Gheeraert A, Chaudhuri A, Kyro G, Nekrasov P, Brooks B, Loria J, Rivalta I, Batista V. Turning up the heat mimics allosteric signaling in imidazole-glycerol phosphate synthase. Nature Communications 2023, 14: 2239. PMID: 37076500, PMCID: PMC10115891, DOI: 10.1038/s41467-023-37956-1.Peer-Reviewed Original ResearchConceptsEffector bindingImidazole Glycerol Phosphate SynthaseLocal amino acidsAmino acid dynamicsImidazole glycerolAllosteric drugsAllosteric activationAllosteric responsePhosphate synthaseAllosteric mechanismMode of activationEnzyme functionAmino acidsAllosteryDrug discoverySynthaseNuclear magnetic resonance spectroscopyBindingMolecular dynamics simulationsActivationAllostericCascadeDynamics simulations
2019
ATP-Triggered, Allosteric Self-Assembly of DNA Nanostructures
Li Q, Liu L, Mao D, Yu Y, Li W, Zhao X, Mao C. ATP-Triggered, Allosteric Self-Assembly of DNA Nanostructures. Journal Of The American Chemical Society 2019, 142: 665-668. PMID: 31877040, DOI: 10.1021/jacs.9b10272.Peer-Reviewed Original ResearchConceptsDNA nanostructuresVersatile molecular platformAptamer-ligand bindingResponsive assembliesSelf-AssemblyResponsive DNADrug deliveryResponsive behaviorATP aptamerMolecular machinesMolecular platformNanostructuresBiological systemsAllosteric mechanismBiosensingAssemblyAptamerGreat challengeConformationHerein
2015
Inhibition of ErbB3 by a monoclonal antibody that locks the extracellular domain in an inactive configuration
Lee S, Greenlee EB, Amick JR, Ligon GF, Lillquist JS, Natoli EJ, Hadari Y, Alvarado D, Schlessinger J. Inhibition of ErbB3 by a monoclonal antibody that locks the extracellular domain in an inactive configuration. Proceedings Of The National Academy Of Sciences Of The United States Of America 2015, 112: 13225-13230. PMID: 26460020, PMCID: PMC4629334, DOI: 10.1073/pnas.1518361112.Peer-Reviewed Original ResearchConceptsAllosteric mechanismExtracellular domainUnique allosteric mechanismFormation of heterodimersReceptor tyrosine kinasesEGF receptor familyTyrosine kinase domainStructure-based designPseudo-kinaseKinase domainLigand-dependent mechanismInactive conformationTyrosine kinaseInactive configurationReceptor familyFamily activationErbB3 activationErbB3KinaseErbB2ErbB4Family membersDomainActivationHeterodimerization
2014
Kill HIV by Starvation–Mechanism of Allosteric Activation of SAMHD1
Ji X, Wu Y, Yan J, Mehrens J, DeLucia M, Hao C, Gronenborn A, Skowronski J, Anh J, Xiong Y. Kill HIV by Starvation–Mechanism of Allosteric Activation of SAMHD1. Acta Crystallographica Section A: Foundations And Advances 2014, 70: c121-c121. DOI: 10.1107/s2053273314098787.Peer-Reviewed Original ResearchCellular dNTP poolsCellular dNTP levelsDNTP poolsDNTP levelsDeoxyribonucleoside triphosphate triphosphohydrolaseActive tetrameric formMammalian cellsAllosteric activationSAMHD1 functionAllosteric mechanismMajor regulatorAllosteric siteInactive dimerAllosteric bindingTetrameric formAicardi-Goutières syndromeTetrameric complexMechanistic understandingCongenital viral infectionViral reverse transcriptionMonomers/dimersSAMHD1Reverse transcriptionHIV restrictionClinical manifestations
2013
Transmitting the allosteric signal in methylglyoxal synthase
Falahati H, Pazhang M, Zareian S, Ghaemi N, Rofougaran R, Hofer A, Rezaie AR, Khajeh K. Transmitting the allosteric signal in methylglyoxal synthase. Protein Engineering Design And Selection 2013, 26: 445-452. PMID: 23592737, DOI: 10.1093/protein/gzt014.Peer-Reviewed Original ResearchConceptsAllosteric signalMethylglyoxal synthaseEnzyme methylglyoxal synthaseSite of phosphateActive site amino acidsSite-directed mutagenesisSite amino acidsAllosteric networkDynamic proteinsTerminal tailNew salt bridgesSer-55Gly-56Allosteric mechanismActive siteAsp-10Val-101Arg-97AllosteryThermus spAmino acidsPhosphoryl groupHomotropic allosterySalt bridgeModel system
2012
Allosteric pathways in imidazole glycerol phosphate synthase
Rivalta I, Sultan MM, Lee NS, Manley GA, Loria JP, Batista VS. Allosteric pathways in imidazole glycerol phosphate synthase. Proceedings Of The National Academy Of Sciences Of The United States Of America 2012, 109: e1428-e1436. PMID: 22586084, PMCID: PMC3365145, DOI: 10.1073/pnas.1120536109.Peer-Reviewed Original ResearchMeSH KeywordsAlgorithmsAllosteric RegulationAllosteric SiteAminohydrolasesBacterial ProteinsBinding SitesBiocatalysisCrystallography, X-RayImidazolesKineticsModels, MolecularMolecular Dynamics SimulationProtein BindingProtein ConformationProtein MultimerizationProtein Structure, TertiaryProtein SubunitsRibonucleotidesSignal TransductionThermotoga maritimaConceptsAllosteric pathwayImidazole glycerolNucleotide biosynthetic pathwayGlutaminase active siteProtein-protein interfacesGlutamine-binding siteNew allosteric drugsImportant branch pointSolution NMR techniquesAllosteric drugsBiosynthetic pathwayAllosteric mechanismCommunity analysisCorrelated protein motionsInactive enzymeProtein motionsPRFARAlternative herbicidesPotential therapeutic targetPathwayTherapeutic targetActive siteNMR techniquesBranch pointsFundamental insights
2011
Probing the Allosteric Mechanism in Pyrrolysyl-tRNA Synthetase Using Energy-Weighted Network Formalism
Bhattacharyya M, Vishveshwara S. Probing the Allosteric Mechanism in Pyrrolysyl-tRNA Synthetase Using Energy-Weighted Network Formalism. Biochemistry 2011, 50: 6225-6236. PMID: 21650159, DOI: 10.1021/bi200306u.Peer-Reviewed Original ResearchConceptsPyrrolysyl-tRNA synthetaseDimeric proteinFunctioning of proteinsSequence/structureAllosteric regulationAllosteric communicationAnticodon recognitionTRNA synthetasesImportant residuesAllosteric mechanismKey residuesSubtle rearrangementsProteinKey playersPyrrolysineFunctional aspectsSynthetaseResiduesAtypical enzymeGlobal perturbationsComprehensive viewComplexesStructure networkMolecular dynamics simulationsPylRS
2009
Allostery and conformational free energy changes in human tryptophanyl‐tRNA synthetase from essential dynamics and structure networks
Bhattacharyya M, Ghosh A, Hansia P, Vishveshwara S. Allostery and conformational free energy changes in human tryptophanyl‐tRNA synthetase from essential dynamics and structure networks. Proteins Structure Function And Bioinformatics 2009, 78: 506-517. PMID: 19768679, DOI: 10.1002/prot.22573.Peer-Reviewed Original ResearchConceptsHuman tryptophanyl-tRNA synthetaseTryptophanyl-tRNA synthetaseConcept of allosteryProtein structure networksProtein complexesMultidomain proteinsAllosteric communicationFunctional insightsProtein biosynthesisCognate tRNAAllosteric mechanismAllosteryConformational free energy changesEnzymatic catalysisConformational mobilityFlexible regionsMolecular levelAmino acidsProteinStructure networkMolecular-level understandingFree energy landscapePopulation shiftsMolecular dynamics simulationsFree energy change
1997
The crystal structure of the asymmetric GroEL–GroES–(ADP)7 chaperonin complex
Xu Z, Horwich A, Sigler P. The crystal structure of the asymmetric GroEL–GroES–(ADP)7 chaperonin complex. Nature 1997, 388: 741-750. PMID: 9285585, DOI: 10.1038/41944.Peer-Reviewed Original ResearchConceptsGroEL-GroESApical domainCis ringMulti-subunit protein assembliesCo-chaperonin GroESRings of subunitsPeptide-binding residuesChaperonin complexConsumption of ATPProtein foldingGroEL subunitProtein assembliesTrans ringAllosteric mechanismGroESEquatorial domainBloc movementDouble toroidSecond GroESEscherichia coliOutward tiltAsymmetric intermediatesCentral cavitySubunitsInward tilt
1996
Ligand-gated calcium channels inside and out
Striggow F, Ehrlich B. Ligand-gated calcium channels inside and out. Current Opinion In Cell Biology 1996, 8: 490-495. PMID: 8791458, DOI: 10.1016/s0955-0674(96)80025-1.Peer-Reviewed Original ResearchConceptsLigand-gated calcium channelsStore-operated channelsCalcium-permeable channelsIntracellular membranesFunctional characterizationPlasma membraneAllosteric mechanismAssociated proteinsTrisphosphate receptorCalcium releaseRyanodine receptorIntracellular storesIntracellular calciumCalcium channelsMembraneReceptorsProteinTypes of channelsInositolRelease
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