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 ResearchConceptsRegulatory segmentDependent protein kinase IIExchange of subunitsProtein kinase IIMammalian cellsFluorescence intensity analysisKinase IIOligomeric enzymesHoloenzymePhosphorylated peptidesNeuronal signalingSmall oligomersActive stateSubunitsCaMKIIActivationCrucial roleMolecular dynamics simulationsMass spectrometryKinasePhosphorylationSignalingHub structureBindsEnzyme
2016
Protein Structure and Function: Looking through the Network of Side-Chain Interactions.
Bhattacharyya M, Ghosh S, Vishveshwara S. Protein Structure and Function: Looking through the Network of Side-Chain Interactions. Current Protein And Peptide Science 2016, 17: 4-25. PMID: 26412788, DOI: 10.2174/1389203716666150923105727.Peer-Reviewed Original ResearchConceptsNetwork theoryImportant problemComplex biological problemsProtein structure networksBipartite networksStructure networkEquilibrium structureModel validationDifferent schemesBiological problemsProblemNetwork approachTheoryNetwork metricsGeneral applicationComplex phenomenonGeneral featuresFormalismNetworkLarge numberProtein structureGeometrySpecific featuresBiological dataEnsemble
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 accessRapid mass spectrometric determination of disulfide connectivity in peptides and proteins
Bhattacharyya M, Gupta K, Gowd KH, Balaram P. Rapid mass spectrometric determination of disulfide connectivity in peptides and proteins. Molecular Omics 2013, 9: 1340-1350. PMID: 23467691, DOI: 10.1039/c3mb25534d.Peer-Reviewed Original ResearchConceptsMass spectrometric fragmentationDisulfide connectivityRapid mass spectrometric determinationPeptide toxinsNatural peptide toxinsMass spectrometric determinationCID fragmentationSpectrometric determinationNatural peptidesProteolytic nickProteolytic peptidesDirect fragmentationUnambiguous characterisationDisulfide linkagesSubsequent determinationSynthetic analoguesRapid screeningMS profilesDisulfide crosslinksStraightforward approachNative disulfidesDeterminationPeptidesFoldamersIntact polypeptide
2012
Interaction Signatures Stabilizing the NAD(P)-Binding Rossmann Fold: A Structure Network Approach
Bhattacharyya M, Upadhyay R, Vishveshwara S. Interaction Signatures Stabilizing the NAD(P)-Binding Rossmann Fold: A Structure Network Approach. PLOS ONE 2012, 7: e51676. PMID: 23284738, PMCID: PMC3524241, DOI: 10.1371/journal.pone.0051676.Peer-Reviewed Original Research