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
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