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 simulationsPylRS
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