2024
Capturing membrane snapshots: A quantitative proteome-wide guide for high-throughput spatially resolved extraction of membrane proteins for structural/functional studies on native membranes
Brown C, Ghosh S, McAllister R, Coleman J, Sun E, Zheng H, Kumar S, Panda A, Rothman J, Bhattacharyya M, Gupta K. Capturing membrane snapshots: A quantitative proteome-wide guide for high-throughput spatially resolved extraction of membrane proteins for structural/functional studies on native membranes. Biophysical Journal 2024, 123: 68a-69a. DOI: 10.1016/j.bpj.2023.11.487.Peer-Reviewed Original Research
2023
Oligomeric organization of membrane proteins from native membranes at nanoscale spatial and single-molecule resolution
Walker G, Brown C, Ge X, Kumar S, Muzumdar M, Gupta K, Bhattacharyya M. Oligomeric organization of membrane proteins from native membranes at nanoscale spatial and single-molecule resolution. Nature Nanotechnology 2023, 19: 85-94. PMID: 38012273, PMCID: PMC10981947, DOI: 10.1038/s41565-023-01547-4.Peer-Reviewed Original ResearchMembrane proteinsNative membranesOligomeric organizationDiverse membrane proteinsMembrane protein biologyNative cell membranesTarget membrane proteinsNative membrane environmentSingle-molecule resolutionSingle-molecule platformReceptor tyrosine kinasesOligomeric distributionNative nanodiscsOligomerization statusProtein biologySmall GTPaseGrowth factor bindingMembrane environmentOligomeric assembliesTyrosine kinaseCritical regulatorOncogenic mutationsCell membraneProteinMembraneOligomeric distribution of membrane proteins in native-membrane environment at nanoscale spatial and single-molecule resolution
Walker G, Brown C, Ge X, Gupta K, Muzumdar M, Bhattacharyya M. Oligomeric distribution of membrane proteins in native-membrane environment at nanoscale spatial and single-molecule resolution. Biophysical Journal 2023, 122: 457a. DOI: 10.1016/j.bpj.2022.11.2457.Peer-Reviewed Original Research
2017
Deconstruction of the Ras switching cycle through saturation mutagenesis
Bandaru P, Shah NH, Bhattacharyya M, Barton JP, Kondo Y, Cofsky JC, Gee CL, Chakraborty AK, Kortemme T, Ranganathan R, Kuriyan J. Deconstruction of the Ras switching cycle through saturation mutagenesis. ELife 2017, 6: e27810. PMID: 28686159, PMCID: PMC5538825, DOI: 10.7554/elife.27810.Peer-Reviewed Original ResearchConceptsInactive stateNucleotide exchange factorsDeep mutational scanningVertebrate lineageSequence conservationRas proteinsEvolutionary analysisHigh conservationExchange factorMutational toleranceRas dynamicsMutational effectsSelection pressureMutational scanningGlobal selection pressureSaturation mutagenesisMutational dataRas sequencesProteinBiochemical analysisBiochemical networksMechanistic explanationRegulatorMutationsConservation
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
Recognition and Signaling in DNA Mismatch Repair: Interdomain Communication in T. Aquaticus Muts Proteins
Pieniazek S, Bhattacharyya M, Vishveshwara S, Hingorani M, Beveridge D. Recognition and Signaling in DNA Mismatch Repair: Interdomain Communication in T. Aquaticus Muts Proteins. Biophysical Journal 2010, 98: 568a-569a. DOI: 10.1016/j.bpj.2009.12.3084.Peer-Reviewed Original Research
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 changeFunctional 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