Research papers

2024

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. Nature Methods (Accepted) bioRxiv [Preprint] doi: 10.1101/2024.02.10.579775. PMID: 38405833; PMCID: PMC10888908.

2023

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 [Preprint]. 2023 Dec 14:2023.12.13.571527. doi: 10.1101/2023.12.13.571527. PMID: 38168251; PMCID: PMC10760103.

Walker G, Brown C, Ge X, Kumar S, Muzumdar MD, Gupta K, Bhattacharyya M. Oligomeric organization of membrane proteins from native membranes at nanoscale spatial and single-molecule resolution. Nature
Nanotechnol. 2024 Jan;19(1):85-94. doi: 10.1038/s41565-023-01547-4. Epub 2023 Nov 27. PMID: 38012273; PMCID:PMC10981947.

Kalyana Sundaram RV, Chatterjee A, Bera M, Grushin K, Panda A, Li F, Coleman J, Lee S, Ramakrishnan S, Ernst AM, Gupta K, Rothman JE, Krishnakumar SS. Roles for diacylglycerol in synaptic vesicle priming and release revealed by complete reconstitution of core protein machinery. Proc Natl Acad Sci U S A. 2023 Aug
22;120(34):e2309516120. doi: 10.1073/pnas.2309516120. Epub 2023 Aug 17. PMID: 37590407; PMCID: PMC10450444.

Panda A, Brown C, Gupta K. Studying Membrane Protein-Lipid Specificity through Direct Native Mass Spectrometric Analysis from Tunable Proteoliposomes. J Am Soc Mass Spectrom. 2023 Sep 6;34(9):1917-1927. doi: 10.1021/jasms.3c00110. Epub 2023 Jul 11. PMID: 37432128; PMCID: PMC10932607.

Panda, A., Giska, F., Duncan, A. L., Welch, A. J., Brown, C., McAllister, R., Parameswaran, H., Goder, J. N. D., Coleman, J., Ramakrishnan, S., Pincet, F., Guan, L., Krishnakumar, S., Rothman, J. E., Gupta K. (2023) Direct determination of oligomeric organization of integral membrane proteins and lipids from intact customizable bilayer. Nature Methods, 20(6):891-897. doi: 10.1038/s41592-023-01864-5 (*Cover Article)

Olivas, T. J., Wu, Y., Yu, S., Luan, L., Choi, P., Guinn, E. D., Nag, S., De Camilli, P. V., Gupta, K., Melia, T. J. (2023) ATG9 vesicles comprise the seed membrane of mammalian autophagosomes. The Journal of Cell Biology, 222(7): e202208088. doi: 10.1083/jcb.202208088

Gu, Y., Guberman-Pfeffer, M. J., Srikanth, V., Shen C., Giska, F., Gupta, K., Londer, Y., Samatey, F. A., Batista, V. S., Malvankar, N. S. (2023) Structure of Geobacter cytochrome OmcZ identifies mechanism of nanowire assembly and conductivity. Nature Microbiology,8(2):284-298. doi: 10.1038/s41564-022-01315-5

2022

Hong, Z., Adlakha, J., Wan, N., Guinn, E., Giska, F., Gupta, K., Melia, T., Reinisch, K. M. (2022). Mitoguardin-2-mediated lipid transfer preserves mitochondrial morphology and lipid droplet formation. The Journal of Cell Biology, 221(12)e202207022. doi:10.1083/jcb.202207022

Giska, F., Mariappan, M., Bhattacharyya, M. and Gupta, K. (2022). Deciphering the molecular organization of GET pathway chaperones through native mass spectrometry. Biophysical Journal, 121(7), 1289–1298. doi:10.1016/j.bpj.2022.02.026

2021

Arranz-Gibert, P., Vanderschuren, K., Haimovich, A., Halder, A., Gupta, K., Rinehart, J. and Isaacs, F. J. (2022). Chemoselective restoration of para-azido-phenylalanine at multiple sites in proteins. Cell Chemical Biology, 29(6), 1046-1052.e4. doi:10.1016/j.chembiol.2021.12.002

Gaudet RG, Zhu S, Halder A, Kim BH, Bradfield CJ, Huang S, Xu D, Mamiñska A, Nguyen TN, Lazarou M, Karatekin E, Gupta K, MacMicking JD. A human apolipoprotein L with detergent-like activity kills intracellular pathogens. Science. 2021 Jul 16;373(6552):eabf8113. doi: 10.1126/science.abf8113.PMID: 34437126

2018

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. Nat Protoc. 2018 May; 2018 Apr 26. PMID: 29700483

2017

Ambrose S, Housden NG, Gupta K, Fan J, White P, Yen HY, Marcoux J, Kleanthous C, Hopper JTS, Robinson CV: Native Desorption Electrospray Ionization Liberates Soluble and Membrane Protein Complexes from Surfaces. Angew Chem Int Ed Engl. 2017 Nov 13; 2017 Sep 18. PMID: 28884954

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 Jan 19; 2017 Jan 11. PMID: 28077870

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. Nat Commun. 2017 Jan 10; 2017 Jan 10. PMID: 28071645

2016

Kumar S, Prakash S, Gupta K, Dongre A, Balaram P, Balaram H: Unexpected functional implication of a stable succinimide in the structural stability of Methanocaldococcus jannaschii glutaminase. Nat Commun. 2016 Sep 28; 2016 Sep 28. PMID: 27677693

Bandyopadhyay D, Prakash S, Gupta K, Balaram P: Mass spectrometric analysis of dimer-disrupting mutations in Plasmodium triosephosphate isomerase.Anal Biochem. 2016 May 1; 2016 Feb 23. PMID: 26919806

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. Nat Methods. 2016 Apr; 2016 Feb 22. PMID: 26901650

2013

Bhattacharyya M, Gupta K, Gowd KH, Balaram P: Rapid mass spectrometric determination of disulfide connectivity in peptides and proteins. Mol Biosyst. 2013 Jun; 2013 Mar 7. PMID: 23467691

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. J Biol Chem. 2013 May 17; 2013 Apr 3. PMID: 23553634

Kuang Z, Zhang MM, Gupta K, Gajewiak J, Gulyas J, Balaram P, Rivier JE, Olivera BM, Yoshikami D, Bulaj G, Norton RS: Mammalian neuronal sodium channel blocker μ-conotoxin BuIIIB has a structured N-terminus that influences potency. ACS Chem Biol. 2013; 2013 Apr 16. PMID: 23557677

2012

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 Dec 11; 2012 Nov 28. PMID: 23167564

Gupta K, Singh S, Gupta K, Khan N, Sehgal D, Haridas V, Roy RP: A bioorthogonal chemoenzymatic strategy for defined protein dendrimer assembly.Chembiochem. 2012 Nov 26; 2012 Oct 5. PMID: 23042694

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. J Am Soc Mass Spectrom. 2012 Oct; 2012 Jul 31. PMID: 22847390

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. J Proteome Res. 2012 Feb 3; 2011 Dec 28. PMID: 22111579

2011

Banerjee M, Gupta K, Balaram H, Balaram P: Mass spectrometric identification of an intramolecular disulfide bond in thermally inactivated triosephosphate isomerase from a thermophilic organism Methanocaldococcus jannaschii. Rapid Commun Mass Spectrom. 2011 Jul 30. PMID: 21698673

Bhat JY, Venkatachala R, Singh K, Gupta K, Sarma SP, Balaram H: Ammonia channeling in Plasmodium falciparum GMP synthetase: investigation by NMR spectroscopy and biochemical assays. Biochemistry. 2011 Apr 26; 2011 Apr 1. PMID: 21413787

2010

Gupta K, Kumar M, Balaram P: Disulfide bond assignments by mass spectrometry of native natural peptides: cysteine pairing in disulfide bonded conotoxins. Anal Chem. 2010 Oct 1. PMID: 20843009

2009

Thakur SS, Ranganayaki RS, Gupta K, Balaram P: Identification of alpha- and beta-hydroxy acid containing cyclodepsipeptides in natural peptide mixtures using negative ion mass spectrometry. J Am Soc Mass Spectrom. 2009 Dec; 2009 Aug 27. PMID: 19811932