2020
Breakage of the Oligomeric CaMKII Hub by the Regulatory Segment of the Kinase
Karandur D, Bhattacharyya M, Xia Z, Lee YK, Muratcioglu S, McAffee D, McSpadden E, Qiu B, Groves JT, Williams ER, Kuriyan J. Breakage of the Oligomeric CaMKII Hub by the Regulatory Segment of the Kinase. ELife 2020, 9: e57784. PMID: 32902386, PMCID: PMC7538161, DOI: 10.7554/elife.57784.Peer-Reviewed Original ResearchMeSH KeywordsCalcium-Calmodulin-Dependent Protein Kinase Type 2Escherichia coliHEK293 CellsHoloenzymesHumansMolecular Dynamics SimulationPhosphorylationProteinsSignal TransductionConceptsRegulatory segmentDependent protein kinase IIExchange of subunitsProtein kinase IIMammalian cellsFluorescence intensity analysisKinase IIOligomeric enzymesHoloenzymePhosphorylated peptidesNeuronal signalingSmall oligomersActive stateSubunitsCaMKIIActivationCrucial roleMolecular dynamics simulationsMass spectrometryKinasePhosphorylationSignalingHub structureBindsEnzyme
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
2013
An automated approach to network features of protein structure ensembles
Bhattacharyya M, Bhat CR, Vishveshwara S. An automated approach to network features of protein structure ensembles. Protein Science 2013, 22: 1399-1416. PMID: 23934896, PMCID: PMC3795498, DOI: 10.1002/pro.2333.Peer-Reviewed Original ResearchMeSH KeywordsBacterial ProteinsComputational BiologyCrystallography, X-RayMethanocaldococcusModels, MolecularMolecular Dynamics SimulationNuclear Magnetic Resonance, BiomolecularProtein ConformationProteinsReceptors, Adrenergic, beta-2RNA, TransferSaccharomyces cerevisiaeSaccharomyces cerevisiae ProteinsSoftwareTyrosine-tRNA LigaseConceptsStructural ensemblesX-ray structureSide-chain interactionsNMR studiesSingle static structureChemical knowledgeMD trajectoriesLong-range allosteric communicationInteraction energyMultiple X-ray structuresDevelopment/applicationGeneral biological communityStructural dataStructure ensemblesProtein structureProgram packageStructureBiological relevanceProtein structure ensemblesAllosteric communicationAmino acidsTRNA complexHereinComplexesEasy access
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 simulationsPylRSQuantum clustering and network analysis of MD simulation trajectories to probe the conformational ensembles of protein – ligand interactions
Bhattacharyya M, Vishveshwara S. Quantum clustering and network analysis of MD simulation trajectories to probe the conformational ensembles of protein – ligand interactions. Molecular Omics 2011, 7: 2320-2330. PMID: 21617814, DOI: 10.1039/c1mb05038a.Peer-Reviewed Original ResearchConceptsConformational ensemblesPyrrolysyl-tRNA synthetaseProtein conformational ensemblesImportant biological phenomenaRNA/DNA complexesProtein-ligand interactionsProtein foldingLigand induced variationsConformational populationsDifferent ligandsMD simulation trajectoriesDNA complexesAmino acidsBiological phenomenaSuch subtle changesD. hafnienseSimulation trajectoriesEnzyme catalysisBackbone levelProteinAtomistic detailsNetwork analysisMD snapshotsMolecular dynamics simulationsObjective clustering
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
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 ResearchMeSH KeywordsAllosteric SiteComputational BiologyHumansModels, MolecularMolecular Dynamics SimulationProtein ConformationThermodynamicsTryptophan-tRNA LigaseConceptsHuman 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