Kallol Gupta, PhD
Associate Professor of Cell BiologyCards
Appointments
Additional Titles
Co-Directors of Graduate Admission- BBS MCGD Track , Department of Cell Biology
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Appointments
Additional Titles
Co-Directors of Graduate Admission- BBS MCGD Track , Department of Cell Biology
Contact Info
Appointments
Additional Titles
Co-Directors of Graduate Admission- BBS MCGD Track , Department of Cell Biology
Contact Info
About
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Titles
Associate Professor of Cell Biology
Co-Directors of Graduate Admission- BBS MCGD Track , Department of Cell Biology
Biography
Trained as a chemist, I was introduced to the world of biology through the aquatic route, where my goal was to uncover the molecular diversity present in the venoms of marine cone snails and understand how it impairs the functions of key ion channels and transporters. This introduced me to the world of membrane proteins and fascinated me.
I subsequently moved to the University of Oxford as a Fellow of the 1851 Royal Commission. My research led to a transformative advancement that enabled top-down mass spectrometric (MS) analysis of membrane protein-lipid complexes. The application of this approach yielded an atomistic understanding of how lipids act as key signaling molecules that regulate the structural and functional organization of membrane proteins.
In the Fall of 2018, I crossed the pond to start my own lab at Yale. Combining native mass spectrometry with an array of orthogonal chemical biology and experimental and computational approaches, our lab is focused on developing platforms that enable quantitative analysis of macromolecular protein complexes directly from the cellular environment. Applying this, the lab aims to understand how the spatiotemporal organization of membrane proteins and lipids regulates cellular physiology. For more, check out https://www.theguptalab.com/
Appointments
Cell Biology
Associate Professor TenurePrimary
Other Departments & Organizations
Education & Training
- Non Degree Program
- University of Oxford, Department of Chemistry (2018)
- Fellow of the 1851 Royal Commission
- Oxford University (2018)
- PhD
- Indian Institute of Science, Molecular Biophysics Unit (2013)
- BSc
- Presidency College, Chemistry (2005)
Research
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Overview
Medical Research Interests
ORCID
0000-0002-3557-3242- View Lab Website
Gupta Lab
Research at a Glance
Yale Co-Authors
Publications Timeline
Research Interests
Jeff Coleman, PhD
Moitrayee Bhattacharyya, PhD
Nikhil S. Malvankar
Pietro De Camilli, MD
Sathish Ramakrishnan, PhD
Shyam Krishnakumar, PhD
Mass Spectrometry
Cell Membrane Permeability
Publications
2026
Lipofuscin accumulation in aging and CLN1 is associated with deficient de-S-acylation, lyso-mitochondrial dysfunction, and lipid dyshomeostasis
Tieze S, Esqueda A, McAllister R, Lagator M, Yücel B, Sun E, Henke K, Lam T, Lockyer N, Gupta K, Chandra S. Lipofuscin accumulation in aging and CLN1 is associated with deficient de-S-acylation, lyso-mitochondrial dysfunction, and lipid dyshomeostasis. Acta Neuropathologica 2026, 151: 52. PMID: 42070169, DOI: 10.1007/s00401-026-03012-7.Peer-Reviewed Original ResearchAltmetricMeSH Keywords and ConceptsConceptsOrganellar originS-acylationNeuronal ceroid lipofuscinosisProtein S-acylationLysosomal-mitochondrial axisLipid-modified proteinsEnzyme activityLipid compositionResident proteinsCLN1Lipid homeostasisLipid dyshomeostasisLysosomal storage disorderNeurodegenerative diseasesMolecular pathwaysProteinPPT1Ceroid lipofuscinosisLong-Chain Polyunsaturated Fatty AcidsAged tissuesBis(monoacylglycerol)phosphatePolyunsaturated fatty acidsUltrastructural analysisFatty acidsOxidized phosphatidylethanolamine
2025
Structure and function of the human apoptotic scramblase Xkr4
Chakraborty S, Feng Z, Lee S, Alvarenga O, Panda A, Zhang S, Bruni R, Khelashvili G, Gupta K, Accardi A. Structure and function of the human apoptotic scramblase Xkr4. Nature Communications 2025, 16: 7317. PMID: 40781244, PMCID: PMC12334663, DOI: 10.1038/s41467-025-62739-1.Peer-Reviewed Original ResearchCitationsAltmetricMeSH Keywords and ConceptsConceptsCombination of biochemical approachesMolecular mechanismsNegative electrostatic surfaceSurface of dying cellsCaspase cleavagePhosphatidylserine externalizationBiochemical approachesAcid residuesNovel conformationActivated scramblasesXKR4Electrostatic surfaceLigand bindingScramblaseMolecular dynamics simulationsCryoEM imagesMembrane thinningMembraneDynamics simulationsCaspaseCryoEMPhosphatidylserineConformationResiduesCleavageTriglycerides are an important fuel reserve for synapse function in the brain
Kumar M, Wu Y, Knapp J, Pontius C, Park D, Witte R, McAllister R, Gupta K, Rajagopalan K, De Camilli P, Ryan T. Triglycerides are an important fuel reserve for synapse function in the brain. Nature Metabolism 2025, 7: 1392-1403. PMID: 40595405, PMCID: PMC12286841, DOI: 10.1038/s42255-025-01321-x.Peer-Reviewed Original ResearchThis study investigates how brain neurons utilize triglycerides as an energy source during synaptic activity, revealing their essential role in maintaining cognitive and physiological functions.Native Top–Down Analysis of Membrane Protein Complexes Directly From In Vitro and Native Membranes
Jung W, Panda A, Lee J, Ghosh S, Shaw J, Gupta K. Native Top–Down Analysis of Membrane Protein Complexes Directly From In Vitro and Native Membranes. Molecular & Cellular Proteomics 2025, 24: 100993. PMID: 40378922, PMCID: PMC12305242, DOI: 10.1016/j.mcpro.2025.100993.Peer-Reviewed Original ResearchCitationsAltmetricConceptsNative mass spectrometryProtein complexesMembrane proteinsBAM complexTop-down MS/MSAnalysis of membrane protein complexesMembrane-associated protein complexesTarget membrane proteinsNative membranesIntegral membrane proteinsTop-down identificationMembrane protein complexesCell-derived membrane vesiclesMass spectrometryMembrane vesiclesOrganization of proteinsDestabilize lipid bilayersAntibiotic targetsProtein-lipid complexesHeteromeric natureSynthetic liposomesCellular membranesCo-factorNative membrane vesiclesTotal membranesA widespread and ancient bacterial machinery assembles cytochrome OmcS nanowires essential for extracellular electron transfer
Shen C, Salazar-Morales A, Jung W, Erwin J, Gu Y, Coelho A, Gupta K, Yalcin S, Samatey F, Malvankar N. A widespread and ancient bacterial machinery assembles cytochrome OmcS nanowires essential for extracellular electron transfer. Cell Chemical Biology 2025, 32: 239-254.e7. PMID: 39818215, PMCID: PMC11845295, DOI: 10.1016/j.chembiol.2024.12.013.Peer-Reviewed Original ResearchCitationsAltmetricMeSH Keywords and ConceptsConceptsExtracellular electron transferPhylogenetically diverse speciesATP-dependent mannerMicrobial extracellular electron transferBacterial machineryDiverse prokaryotesDiverse speciesBiotechnological applicationsGeobacter sulfurreducensCell growthSurface-displayedMorphology maintenanceBiophysical methodsMulti-heme cytochromesCytochromeElectron transferOsCHSProkaryotesPhylogeneticallySulfurreducensGeobacterOverexpressionSpeciesMachinery
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, 22: 412-421. PMID: 39609567, PMCID: PMC11810782, DOI: 10.1038/s41592-024-02517-x.Peer-Reviewed Original ResearchCitationsAltmetricConceptsTarget 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 MPAuthor Correction: Structure of Geobacter cytochrome OmcZ identifies mechanism of nanowire assembly and conductivity
Gu Y, Guberman-Pfeffer M, Srikanth V, Shen C, Giska F, Gupta K, Londer Y, Samatey F, Batista V, Malvankar N. Author Correction: Structure of Geobacter cytochrome OmcZ identifies mechanism of nanowire assembly and conductivity. Nature Microbiology 2024, 9: 2759-2759. PMID: 38684912, DOI: 10.1038/s41564-024-01702-0.Commentaries, Editorials and LettersAltmetricConceptsA 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 JE, Bhattacharyya M, Gupta K. A proteome-wide quantitative platform for nanoscale spatially resolved extraction of membrane proteins into native nanodiscs. BioRxiv 2024 PMID: 38405833, DOI: 10.1101/2024.02.10.579775.Peer-Reviewed Original Research In Press
2023
Isolation and Lipidomic Profiling of Neuronal Lipid Droplets: Unveiling the Lipid Landscape for insights into Neurodegenerative Disorders.
Kumar M, Knapp JA, Gupta K, Ryan TA. Isolation and Lipidomic Profiling of Neuronal Lipid Droplets: Unveiling the Lipid Landscape for insights into Neurodegenerative Disorders. BioRxiv 2023 PMID: 38168251, DOI: 10.1101/2023.12.13.571527.Peer-Reviewed Original ResearchOligomeric 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 ResearchCitationsAltmetricConceptsMembrane 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 membraneProteinMembrane
Academic Achievements & Community Involvement
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Activities
activity American Society for Mass Spectrometry
2019 - PresentProfessional OrganizationsMemberactivity Biophysical Society
2021 - PresentProfessional OrganizationsMemberactivity Protein Society
2023 - PresentProfessional OrganizationsMemberactivity Journal of the American Chemical Society
2026 - PresentJournal ServiceRevieweractivity American Society for Cell Biology
2025 - PresentProfessional OrganizationsMember
Honors
honor Emerging Investigator
06/01/2023International AwardAmerican Society for Mass SpectrometryDetailsUnited Stateshonor Junior Research Fellow in Mathematical Physical and Life Sciences
01/01/2015International AwardUniversity of OxfordDetailsUnited Kingdomhonor Research Fellow of the 1851 Royal Commission
11/01/2013International AwardUniversity of OxfordDetailsUnited Kingdom
Teaching & Mentoring
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Teaching
Didactic MCDB/CBIO630b: Biochemical and Biophysical Approaches in Molecular and Cellular Biology
LecturerLecture SettingDetails4/1/2021 - PresentForGraduate8 Average Instructional Hours Per YearIn this course, we provide an overall of various biochemical and biophysical approaches used in modern research in molecular and cellular biology, ranging from spectroscopic tools, microscopy, to X-ray crystallography. The goal of the course is to make students familiar with these techniques so that they can find relevant materials in their future research. Does not count for graduate course credit for BQBS graduate students.
Didactic MCDB/CBIO901b: Research Skills and Ethics
LecturerLecture SettingDetails3/1/2022 - PresentForGraduate2 Average Instructional Hours Per YearThis course consists of a weekly seminar that covers ethics, writing, and research methods in cellular and molecular biology as well as student presentations (“rotation talks”) of work completed in the third laboratory rotation.
Mentoring
Chiara Mancinelli
Postdoc2025 - PresentSouvik Roy
Postgrad associate2025 - PresentMeera Chari
Summer Student2024 - 2024Samantha Shepherd
Postdoc2024 - Present
Willing and Available to Mentor
- Postdoctoral Researchers
- Students
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Locations
221 C
Lab
West Campus Integrative Science & Technology Center
850 West Campus Drive
West Haven, CT 06516