2016
Molecular mechanism of activation-triggered subunit exchange in Ca2+/calmodulin-dependent protein kinase II
Bhattacharyya M, Stratton MM, Going CC, McSpadden ED, Huang Y, Susa AC, Elleman A, Cao YM, Pappireddi N, Burkhardt P, Gee CL, Barros T, Schulman H, Williams ER, Kuriyan J. Molecular mechanism of activation-triggered subunit exchange in Ca2+/calmodulin-dependent protein kinase II. ELife 2016, 5: e13405. PMID: 26949248, PMCID: PMC4859805, DOI: 10.7554/elife.13405.Peer-Reviewed Original ResearchMeSH KeywordsCalcium-Calmodulin-Dependent Protein Kinase Type 2HumansModels, BiologicalModels, MolecularMolecular ConformationProtein MultimerizationProtein SubunitsConceptsDependent protein kinase IIProtein kinase IICaMKII holoenzymeKinase IIExchange of subunitsKinase domainSubunit exchangeIntersubunit interfaceMolecular mechanismsOligomeric enzymesHoloenzymeHub interfaceCalmodulinCaMKIIThree-way competitionUnactivated onesDimersDodecamericSubunitsOrganismsEnzymeHubMechanismSpiral formActivation
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
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