2023
Studying Membrane Protein–Lipid Specificity through Direct Native Mass Spectrometric Analysis from Tunable Proteoliposomes
Panda A, Brown C, Gupta K. Studying Membrane Protein–Lipid Specificity through Direct Native Mass Spectrometric Analysis from Tunable Proteoliposomes. Journal Of The American Society For Mass Spectrometry 2023, 34: 1917-1927. PMID: 37432128, PMCID: PMC10932607, DOI: 10.1021/jasms.3c00110.Peer-Reviewed Original ResearchConceptsIntegral membrane proteinsMembrane proteinsNative mass spectrometryTrafficking pathwaysPlasma membraneEukaryotic integral membrane proteinsEndoplasmic reticulumBiophysical propertiesMembrane protein assemblySynaptic vesiclesCellular trafficking pathwaysOrganellar membranesLipid specificityTransmembrane proteinProtein assembliesMembrane contextMass spectrometric analysisProteinNative mass spectrometric analysesVAMP2Lipid compositionExogenous ligandsLipid membranesIndividual lipidsMembraneDirect determination of oligomeric organization of integral membrane proteins and lipids from intact customizable bilayer
Panda A, Giska F, Duncan A, Welch A, Brown C, McAllister R, Hariharan P, Goder J, Coleman J, Ramakrishnan S, Pincet F, Guan L, Krishnakumar S, Rothman J, Gupta K. Direct determination of oligomeric organization of integral membrane proteins and lipids from intact customizable bilayer. Nature Methods 2023, 20: 891-897. PMID: 37106230, PMCID: PMC10932606, DOI: 10.1038/s41592-023-01864-5.Peer-Reviewed Original ResearchConceptsIntegral membrane proteinsMembrane proteinsOligomeric organizationOligomeric stateNative mass spectrometry analysisFunctional oligomeric stateKey membrane componentMass spectrometry analysisNMS analysisTarget membraneLipid bindingMembrane componentsProteolipid vesiclesMembrane compositionLipid compositionSpectrometry analysisLipid membranesNeurotransmitter releaseProteinMembraneLipidsMembrane propertiesDirect determinationBilayersTransporters
2018
Identifying key membrane protein lipid interactions using mass spectrometry
Gupta K, Li J, Liko I, Gault J, Bechara C, Wu D, Hopper JTS, Giles K, Benesch JLP, Robinson CV. Identifying key membrane protein lipid interactions using mass spectrometry. Nature Protocols 2018, 13: 1106-1120. PMID: 29700483, PMCID: PMC6049616, DOI: 10.1038/nprot.2018.014.Peer-Reviewed Original Research
2017
The role of interfacial lipids in stabilizing membrane protein oligomers
Gupta K, Donlan JAC, Hopper JTS, Uzdavinys P, Landreh M, Struwe WB, Drew D, Baldwin AJ, Stansfeld PJ, Robinson CV. The role of interfacial lipids in stabilizing membrane protein oligomers. Nature 2017, 541: 421-424. PMID: 28077870, PMCID: PMC5501331, DOI: 10.1038/nature20820.Peer-Reviewed Original ResearchMeSH KeywordsBacterial ProteinsBinding SitesCardiolipinsCell MembraneEscherichia coliEscherichia coli ProteinsLigandsLipidsMass SpectrometryMembrane ProteinsModels, MolecularMolecular Dynamics SimulationMoritellaProtein MultimerizationProtein StabilityReceptors, G-Protein-CoupledSodium-Hydrogen ExchangersThermodynamicsThermus thermophilusIntegrating mass spectrometry with MD simulations reveals the role of lipids in Na+/H+ antiporters
Landreh M, Marklund EG, Uzdavinys P, Degiacomi MT, Coincon M, Gault J, Gupta K, Liko I, Benesch JL, Drew D, Robinson CV. Integrating mass spectrometry with MD simulations reveals the role of lipids in Na+/H+ antiporters. Nature Communications 2017, 8: 13993. PMID: 28071645, PMCID: PMC5234078, DOI: 10.1038/ncomms13993.Peer-Reviewed Original ResearchConceptsIon mobility mass spectrometryGas phaseMass spectrometryMobility mass spectrometryMolecular dynamics simulationsCatalysis rateMD simulationsLipid-binding propertiesDynamics simulationsConformational stabilityStable dimerLarge-scale conformational changesSecondary active transportersConformational changesSpectrometryAntiporter NhaAKingdoms of lifeAnnular lipidsNative foldProtein segmentsInter-domain contactsRole of lipidsThermus thermophilusMembrane lipidsNHA2
2016
Mass spectrometric analysis of dimer-disrupting mutations in Plasmodium triosephosphate isomerase
Bandyopadhyay D, Prakash S, Gupta K, Balaram P. Mass spectrometric analysis of dimer-disrupting mutations in Plasmodium triosephosphate isomerase. Analytical Biochemistry 2016, 500: 45-50. PMID: 26919806, DOI: 10.1016/j.ab.2016.02.011.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsDimerizationHydrogen BondingMass SpectrometryMutationPlasmodiumTriose-Phosphate IsomeraseHigh-resolution mass spectrometry of small molecules bound to membrane proteins
Gault J, Donlan JA, Liko I, Hopper JT, Gupta K, Housden NG, Struwe WB, Marty MT, Mize T, Bechara C, Zhu Y, Wu B, Kleanthous C, Belov M, Damoc E, Makarov A, Robinson CV. High-resolution mass spectrometry of small molecules bound to membrane proteins. Nature Methods 2016, 13: 333-336. PMID: 26901650, PMCID: PMC4856209, DOI: 10.1038/nmeth.3771.Peer-Reviewed Original ResearchMeSH KeywordsHumansLipidsMass SpectrometryMembrane ProteinsModels, MolecularPeptide FragmentsProtein BindingSmall Molecule Libraries
2013
Cyclic AMP-dependent Protein Lysine Acylation in Mycobacteria Regulates Fatty Acid and Propionate Metabolism*
Nambi S, Gupta K, Bhattacharyya M, Ramakrishnan P, Ravikumar V, Siddiqui N, Thomas AT, Visweswariah SS. Cyclic AMP-dependent Protein Lysine Acylation in Mycobacteria Regulates Fatty Acid and Propionate Metabolism*. Journal Of Biological Chemistry 2013, 288: 14114-14124. PMID: 23553634, PMCID: PMC3656268, DOI: 10.1074/jbc.m113.463992.Peer-Reviewed Original ResearchMeSH KeywordsAcetylesteraseAmino Acid SequenceBacterial ProteinsCoenzyme A LigasesCyclic AMPFatty AcidsGene DeletionGene Expression Regulation, BacterialLysineMass SpectrometryMolecular Sequence DataMutagenesisMycobacterium bovisMycobacterium tuberculosisPropionatesSequence Homology, Amino AcidSignal TransductionConceptsCAMP-dependent mannerAcyl-CoA synthetaseLysine residuesProtein Lysine AcylationLysine acetyltransferaseLysine acylationPosttranslational modificationsImportant lysine residuesFatty acidsBiological processesIntracellular cAMP levelsFADDMultiple substratesCoA synthetasePropionyl-CoAAcetylationBiological organismsRegulatory cycleCritical roleCAMP levelsResiduesBovis bacillus Calmette-GuérinPropionate metabolismMetabolismEukaryotesRapid 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 ResearchMeSH KeywordsCystineDisulfidesLactalbuminMass SpectrometryNatriuretic PeptidesNeurotoxinsPeptide FragmentsProteinsRecombinant ProteinsConceptsMass 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
Distinct Disulfide Isomers of μ‑Conotoxins KIIIA and KIIIB Block Voltage-Gated Sodium Channels
Khoo KK, Gupta K, Green BR, Zhang MM, Watkins M, Olivera BM, Balaram P, Yoshikami D, Bulaj G, Norton RS. Distinct Disulfide Isomers of μ‑Conotoxins KIIIA and KIIIB Block Voltage-Gated Sodium Channels. Biochemistry 2012, 51: 9826-9835. PMID: 23167564, PMCID: PMC4131687, DOI: 10.1021/bi301256s.Peer-Reviewed Original ResearchConceptsΜ-Conotoxin KIIIADisulfide connectivityCollision-induced dissociation fragmentationDisulfide isomersNuclear magnetic resonance dataNative disulfide connectivityDisulfide patternVenom-derived peptidesDisulfide bond connectivitySame disulfide connectivityOxidative foldingDissociation fragmentationMagnetic resonance dataBond connectivityMultiple disulfide bondsMinor productsMajor isomerSolution structureActive peptidesIsomersΜ-conotoxinsResonance dataKIIIAVenom of ConusDisulfide bondsLipopeptides from the Banyan Endophyte, Bacillus subtilis K1: Mass Spectrometric Characterization of a Library of Fengycins
Pathak KV, Keharia H, Gupta K, Thakur SS, Balaram P. Lipopeptides from the Banyan Endophyte, Bacillus subtilis K1: Mass Spectrometric Characterization of a Library of Fengycins. Journal Of The American Society For Mass Spectrometry 2012, 23: 1716-1728. PMID: 22847390, DOI: 10.1007/s13361-012-0437-4.Peer-Reviewed Original ResearchMeSH KeywordsBacillus subtilisBacterial ProteinsChromatography, High Pressure LiquidLipopeptidesMass SpectrometryPeptides, CyclicConceptsHigh-performance liquid chromatographyMass spectrometryIonization mass spectrometric studyHigh-resolution mass spectrometryDiagnostic fragment ionsResolution mass spectrometryMass spectrometric characterizationMass spectrometric studyChain length variationReversed-phase high-performance liquid chromatographyMS/MS analysisLaser desorption ionizationMass spectrometric analysisLinear precursorsFragment ionsMacrocyclic ringFatty acid chainsPerformance liquid chromatographySpectrometric characterizationGlu replacementSpectrometric studyAcid moietyComplex mixturesDesorption ionizationFatty acid moieties
2011
Combined Electron Transfer Dissociation–Collision-Induced Dissociation Fragmentation in the Mass Spectrometric Distinction of Leucine, Isoleucine, and Hydroxyproline Residues in Peptide Natural Products
Gupta K, Kumar M, Chandrashekara K, Krishnan KS, Balaram P. Combined Electron Transfer Dissociation–Collision-Induced Dissociation Fragmentation in the Mass Spectrometric Distinction of Leucine, Isoleucine, and Hydroxyproline Residues in Peptide Natural Products. Journal Of Proteome Research 2011, 11: 515-522. PMID: 22111579, DOI: 10.1021/pr200091v.Peer-Reviewed Original ResearchConceptsIsobaric residuesMass spectrometric peptide sequencingNatural peptide librariesPeptide natural productsCrude peptide mixturesTandem mass spectrometric methodMass spectrometric distinctionMass spectrometric methodRadical ionsIsobaric leucineElectron transferCollisional activationDissociation fragmentationPeptide mixturesNatural productsNominal massSpectrometric methodLiquid chromatographyPeptide sequencingPresence of hydroxyprolineIonsPeptide libraryDifferent peptidesDissociation approachHydroxyproline residues