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
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 ResearchConceptsHuman 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