2020
Flexible linkers in CaMKII control the balance between activating and inhibitory autophosphorylation
Bhattacharyya M, Lee YK, Muratcioglu S, Qiu B, Nyayapati P, Schulman H, Groves JT, Kuriyan J. Flexible linkers in CaMKII control the balance between activating and inhibitory autophosphorylation. ELife 2020, 9: e53670. PMID: 32149607, PMCID: PMC7141811, DOI: 10.7554/elife.53670.Peer-Reviewed Original ResearchConceptsInhibitory autophosphorylationResidue linkerDependent protein kinase IISingle-molecule assaysMammalian cell expressionProtein kinase IICaMKII variantsShort linkerTransphosphorylation ratesKinase domainCaMKII holoenzymeKinase IIAutophosphorylationHoloenzymeFlexible linkerPrincipal isoformCalcium signalsRelative levelsIsoformsCaMKIIHuman CaCell expressionLinkerVariantsSequence
2014
Activation-triggered subunit exchange between CaMKII holoenzymes facilitates the spread of kinase activity
Stratton M, Lee IH, Bhattacharyya M, Christensen SM, Chao LH, Schulman H, Groves JT, Kuriyan J. Activation-triggered subunit exchange between CaMKII holoenzymes facilitates the spread of kinase activity. ELife 2014, 3: e01610. PMID: 24473075, PMCID: PMC3901001, DOI: 10.7554/elife.01610.Peer-Reviewed Original ResearchMeSH KeywordsAdenosine TriphosphateBinding SitesCalcium-Calmodulin-Dependent Protein Kinase Type 2CalmodulinCatalytic DomainEnzyme ActivationEnzyme StabilityHoloenzymesHumansKineticsMicroscopy, FluorescenceMolecular Docking SimulationMolecular Dynamics SimulationPhosphorylationProtein BindingProtein Structure, QuaternaryProtein SubunitsRecombinant ProteinsSignal TransductionThreonineConceptsExchange of subunitsActivation of CaMKIICalcium-independent phosphorylationRegulatory segmentNew subunitsCaMKII holoenzymeThr-305Subunit exchangeKinase activityHoloenzymeNeuronal signalingCentral hubCaMKIIPhosphorylationSubunitsMemory formationActivationMolecular dynamics simulationsUnactivated onesDodecamericSignalingCalmodulinInteractsResiduesMicroscopy techniques
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
2010
Elucidation of the conformational free energy landscape in H.pylori LuxS and its implications to catalysis
Bhattacharyya M, Vishveshwara S. Elucidation of the conformational free energy landscape in H.pylori LuxS and its implications to catalysis. BMC Molecular And Cell Biology 2010, 10: 27. PMID: 20704697, PMCID: PMC2929236, DOI: 10.1186/1472-6807-10-27.Peer-Reviewed Original ResearchConceptsFree energy landscapeConformational changesActive siteDifferent conformationsConformational free energy landscapeAutoinducer-2 productionStructure network analysisDynamics of waterBacterial quorum sensingMolecular dynamics simulationsDetailed molecular levelFree energy changeEnergy landscapeFree energy evaluationEnzyme catalysisQuorum sensingDimeric proteinSimulation trajectoriesDifferent ligandsDynamics simulationsMechanistic featuresLigandsMolecular levelInactive formMechanistic details
2009
Functional correlation of bacterial LuxS with their quaternary associations: interface analysis of the structure networks
Bhattacharyya M, Vishveshwara S. Functional correlation of bacterial LuxS with their quaternary associations: interface analysis of the structure networks. BMC Molecular And Cell Biology 2009, 9: 8. PMID: 19243584, PMCID: PMC2656534, DOI: 10.1186/1472-6807-9-8.Peer-Reviewed Original ResearchConceptsProtein structure networksSequence alignment studiesQuorum sensing moleculesDesign of inhibitorsHigh structural similarityCertain structural detailsGene homologuesStructure comparison methodsFlagellar motilityLux genesHomodimeric proteinDimer interfaceDimeric interfaceAI-2Protein interfacesVariety of functionsQuaternary associationMetabolic regulationSensing moleculesFunctional roleStructure networkProkaryotesX-ray crystallographyProteinToxin production