2024
A proteome-wide quantitative platform for nanoscale spatially resolved extraction of membrane proteins into native nanodiscs
Brown C, Ghosh S, McAllister R, Kumar M, Walker G, Sun E, Aman T, Panda A, Kumar S, Li W, Coleman J, Liu Y, Rothman J, Bhattacharyya M, Gupta K. A proteome-wide quantitative platform for nanoscale spatially resolved extraction of membrane proteins into native nanodiscs. Nature Methods 2024, 1-10. PMID: 39609567, DOI: 10.1038/s41592-024-02517-x.Peer-Reviewed Original ResearchTarget membrane proteinsMembrane proteinsMembrane contextSynaptic vesicle membrane proteinVesicle membrane proteinsMammalian membrane proteinsMembrane-active polymersExtraction of membrane proteinsNative nanodiscsOrganellar membranesNative membrane environmentMultiprotein complexesMolecular contextCellular membranesMembrane environmentQuantitative platformBioanalytical approachesExtraction efficiencyOpen-access databasesProteinMembraneExtraction conditionsNanodiscsTarget MPCapturing 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
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
2022
A tunable lipid bilayer native MS platform for direct determination of hierarchical organization of membrane proteins and lipids at the membrane
Panda A, Giska F, Brown C, Coleman J, Rothman J, Gupta K. A tunable lipid bilayer native MS platform for direct determination of hierarchical organization of membrane proteins and lipids at the membrane. Biophysical Journal 2022, 121: 312a-313a. DOI: 10.1016/j.bpj.2021.11.1192.Peer-Reviewed Original Research
2016
Phospholipase D activity couples plasma membrane endocytosis with retromer dependent recycling
Thakur R, Panda A, Coessens E, Raj N, Yadav S, Balakrishnan S, Zhang Q, Georgiev P, Basak B, Pasricha R, Wakelam M, Ktistakis N, Raghu P. Phospholipase D activity couples plasma membrane endocytosis with retromer dependent recycling. ELife 2016, 5: e18515. PMID: 27848911, PMCID: PMC5125754, DOI: 10.7554/elife.18515.Peer-Reviewed Original ResearchMeSH KeywordsADP-Ribosylation Factor 1AnimalsCell MembraneCytoplasmic VesiclesDrosophila melanogasterDrosophila ProteinsEndocytosisGene ExpressionGenetic Complementation TestGuanosine TriphosphateLightPhosphatidic AcidsPhospholipase DPhotic StimulationPhotoreceptor Cells, InvertebrateRab GTP-Binding ProteinsRab7 GTP-Binding ProteinsRhodopsinVision, OcularConceptsPlasma membranePLD activityRetromer-dependent recyclingWild-type photoreceptorsMembrane endocytosisDependent recyclingPhospholipase D activityPhosphatidic acidRhabdomere sizeRhodopsin proteinEndocytosisCell bodiesPhotoreceptorsReduced levelsActivity couplesD activityComplex functionsMembraneTurnoverRab7ProteinVesiclesPhenotypeConsequent changesActivity
2015
Transbilayer Lipid Interactions Mediate Nanoclustering of Lipid-Anchored Proteins
Raghupathy R, Anilkumar A, Polley A, Singh P, Yadav M, Johnson C, Suryawanshi S, Saikam V, Sawant S, Panda A, Guo Z, Vishwakarma R, Rao M, Mayor S. Transbilayer Lipid Interactions Mediate Nanoclustering of Lipid-Anchored Proteins. Cell 2015, 161: 581-594. PMID: 25910209, PMCID: PMC4651428, DOI: 10.1016/j.cell.2015.03.048.Peer-Reviewed Original ResearchConceptsLive cell membranesCell membraneDynamic actin filamentsInner leafletLiquid-ordered phaseAtom molecular dynamics simulationsActin filamentsLipid domainsGeneral mechanismTransbilayer couplingOpposite leafletLipid clustersAcyl chain lipidsProteinPhosphatidylserineLipidsMembraneMolecular dynamics simulationsLeafletsNanoclusteringCorresponding lipidsDomainGPIInteractionDynamics simulations