Publications

2020-Current

Negi H, Ravichandran A, Dasgupta P, Reddy S, Das R, (2024), “Plasticity of the proteasome-targeting signal Fat10 enhances substrate degradation,” Elife, 13:e91122.

Ravichandran A and Das R, (2024), “The Thermodynamic Properties of Fat10ylated Proteins Are Regulated by the Fat10ylation Site,” ACS Omega, 9(20):22265-22276.

Singh G, Kumar S, Das R, (2023), "Decoding the Assembly of Mixed and Branched Heterotypic Ubiquitin Chains", ACS Analytical Chemsitry, 95(26):10061-10067.

Bhate S, Udgaonkar JB, Das R, (2021), “Destabilization of polar interactions in the prion protein triggers misfolding and oligomerization,” Protein Science, 30(11):2258-2271.

Mohanty P, Chatterjee KS, Das R, (2021), “NEDD8 Deamidation Inhibits Cullin RING Ligase Dynamics,” Frontiers in Immunology, 12, 3289.

Chatterjee KS, Das R, (2021), “An "up" oriented methionine-aromatic structural motif in SUMO is critical for its stability and activity,” Journal of Biological Chemistry, 297(2):100970.

Tripathi V, Chatterjee KS, Das R, (2021), “Non-covalent Interaction with SUMO Enhances the Activity of Human Cytomegalovirus Protein IE1,” Frontiers in Cell and Developmental Biology, 9:662522.

Sullivan T, Thirthagiri E, Chong CE, Stauffer S, Reid S, Southon E, Hassan T, Ravichandran A, Wijaya E, Lim J, Taib NAM, Fadzli F, Yip CH, Hartman M, Li J, van Dam RM, North SL, Das R, Easton DF, Biswas K, Teo SH, Sharan SK, (2021), “Epidemiological and ES cell-based functional evaluation of BRCA2 variants identified in families with breast cancer,” Human Mutations 42(2), 200-212.

Negi H, Reddy PP, Vengayil V, Patole C, Laxman S, Das R, (2020), A novel polyubiquitin chain linkage formed by viral Ubiquitin is resistant to host deubiquitinating enzymes, Biochemical Journal, 477(12), 2193-2219.

Habibullah, BI, Tripathi, V, Surana P, Das R, (2020), Monitoring Protein Ubiquitination and SUMOylation in real-time by NMR, Chemical Communications, 2020, 56, 6735 – 6738.

Hembram DSS, Negi H, Biswas P, Tripathi V, Bhushan L, Shet D, Kumar V, Das R, (2020), The viral SUMO-targeted Ubiquitin Ligase ICP0 is phosphorylated and activated by host kinase Chk2, Journal of Molecular Biology, 432(7):1952-1977.

Chatterjee KS, Hembram DSS, Das R., (2020), Amide temperature coefficients in characterizing the allosteric effects of ligand binding on local stability in proteins, Biochem Biophys Res Commun. 524(3):677-682.

Mukherjee A, Singh R, Udayan S, Biswas S, Reddy PP, Manmadhan S, George G, Kumar S, Das R, Rao BM, Gulyani A., (2020), A Fyn biosensor reveals pulsatile, spatially localized kinase activity and signaling crosstalk in live mammalian cells, eLife 9: e50571.

Nair A, Chatterjee KS, Jha V, Das R, Shivaprasad PV, (2020), “Stability of Begomoviral pathogenicity determinant βC1 is modulated by mutually antagonistic SUMOylation and SIM interactions,” BMC Biology, 18(1):110.

Kesarwani S, Lama P, Chandra A, Reddy PP, Jijumon AS, Bodakuntla S, Rao BM, Janke C, Das R, Sirajuddin M, (2020), “Genetically encoded live cell sensor for tyrosinated microtubules”, Journal of Cell Biology, 219(10): e201912107.

2014-2019

Mohanty P, Agrata R, Habibullah BI, Geetha Surendran A, Das R, (2019), Deamidation disrupts native and transient contacts to weaken the interaction between UBC13 and RING-finger E3 ligases, eLife 8:e492238.

Tripathi V, Chatterjee KS, Das R. (2019), Casein kinase-2 mediated phosphorylation increases the SUMO-dependent activity of the cytomegalovirus transactivator IE2, J Biol Chem. 294(40):14546-14561.

Chatterjee KS, Tripathi V, Das R, (2019) A conserved and buried edge-to-face aromatic interaction in Small Ubiquitin-like Modifier (SUMO) has a role in SUMO stability and function, J Biol Chem. 294(17):6772-6784.

Nandwani N, Surana P, Negi H, Mascarenhas NM, Udgaonkar JB, Gosavi S, Das R, (2019) A five-residue motif for the design of domain swapping in proteins, Nature Comm. 10(1):452.

Surana P^#, Gowda CM^#, Tripathi V, Broday L, Das R., (2017), Structural and functional analysis of SMO-1, the SUMO homolog in Caenorhabditis elegans, PLoS One. 12(10):e0186622. ^#Equal Contribution

Nandwani N^#, Surana P^#, Udgaonkar JB, Gosavi S, Das R, (2017), Amino-acid composition after loop deletion drives domain swapping, Protein Sci. 26(10):1994-2002. ^#Equal Contribution.

Amanullah A, Mishra R, Upadhyay A, Reddy PP, Das R, Mishra A., (2017), Indomethacin Elicits Proteasomal Dysfunctions Develops Apoptosis Through Mitochondrial Abnormalities, J Cell Physiol., doi: 10.1002/jcp.26081.

Sengupta I, Bhate S, Das R*, Udgaonkar J*, (2017), Salt-binding induced oligomerization of the mouse proin protein monitored by real time NMR, J. Mol. Biol., 429(12): 1852-1872. *Corresponding authors.

Chakrabarti KS, Li J, Das R*, Byrd RA*, (2017), Conformational dynamics and allostery in E2:E3 interactions driving ubiquitination: Ube2g2 and gp78, Structure, 25(5):794-805. *Corresponding authors.

Surana P, Das R, (2016), Observing a late folding intermediate of Ubiquitin at atomic resolution by NMR, Protein Science, 25(8): 1438–1450.

Moulick R, Das R, Udgaonkar JB, (2015), Partially Unfolded Forms of the Prion Protein Populated Under Misfolding promoting conditions: Characterization by Hydrogen Exchange and NMR, J Biol Chem, 290(42):25227-40.

2007-2013

Das R, Liang YH, Mariano J, Li J, Huang T, King A, Tarasov SG, Weissman AM, Ji X, Byrd RA, (2013), Allosteric regulation of E2:E3 interactions promote a processive ubiquitination machine, EMBO J., 32(18):2504-16.

Metzger MB, Liang YH, Das R, Mariano J, Li S, Li J, Kostova Z, Byrd RA, Ji X, Weissman AM, (2013), “A structurally unique E2-binding domain activates ubiquitination by the ERAD E2, Ubc7p, through multiple mechanisms”, Molecular Cell, 50(4): 516-27.

Liu S, Chen Y, Li J, Huang T, Tarasov S, King A, Weissman AM, Byrd RA, Das R, (2012), “Promiscuous interactions of gp78 E3 ligase CUE domain with polyubiquitin chains”, Structure, 20(12):2138-50.

Biswas K, Das R, Eggington JM, Qiao H, North SL, Stauffer S, Burkett SS, Martin BK, Southon E, Sizemore SC, Pruss D, Bowles KR, Roa BB, Hunter N, Tessarollo L, Wenstrup RJ, Byrd RA, Sharan SK, (2012), “Functional evaluation of BRCA2 variants mapping to the PALB2-binding and C-terminal DNA-binding domains using a mouse ES cell-based assay”, Human Molecular Genetics, 21(18):3993-4006.

Biswas K, Das R, Alter BP, Kuznetsov SG, Stauffer S, North SL, Burkett S, Brody LC, Meyer S, Byrd RA, Sharan SK, (2011), “A comprehensive functional characterization of BRCA2 variants associated with Fanconi anemia using mouse ES cell-based assay”, Blood, 118(9):2430-42.

Das R, Mariano J, Tsai YC, Kalathur RC, Kostova Z, Li J, Tarasov SG, McFeeters RL, Altieri AS, Ji X, Byrd RA, Weissman AM, (2009), “Allosteric activation of E2-RING finger-mediated ubiquitylation by a structurally defined specific E2-binding region of gp78”, Molecular Cell, 34(6):674-85.

Das R., Loss S., Li J., Waugh D.S., Tarasov S., Wingfield P.T., Byrd R. A., and Altieri A. S., (2008), “Structural Biophysics of the NusB:NusE antitermination complex,” J. Mol. Biol., 376(3), 705-20.

2002-2006

Ghosh A, Das R., Gopinath T., and Kumar A., (2006), “Use of Geometric Phase in Quantum Information Processing by Nuclear Magnetic Resonance,” Proceedings of Quantum Information, Computation and Communication IIT-Kharagpur, 57-98.

Das, R., Bhattacharya, R., and Kumar, A., (2006), “Investigation of a dipolar coupled 8-qubit system for Quantum Information Processing by NMR,” AIP Conference Proceedings, 864, 313.

Das R., Kumar S. K., and Kumar A., (2005), “Use of non-adiabatic geometric phase for quantum computing by NMR,” J. Magn. Reson., 177(2), 318-28.

Mitra A., Ghosh A., Das R., Patel A., and Kumar A., (2005), “Experimental implementation of local adiabatic evolution algorithms by an NMR quantum information processor,” J. Magn.  Reson., 177(2), 285-98.

Bhattacharya, R., Das, R., Ramanathan, K.V., and Kumar, A., (2005), “Implementation of parallel search algorithms using spatial encoding by nuclear magnetic resonance,” Phys. Rev. A., 71, 052313.

Gopinath, T., Das, R., and Kumar, A., (2005), “Programmable quantum state discriminatory by nuclear magnetic resonance,” Phys. Rev. A., 71, 042307.

Das, R., Chakraborty, S., Rukmani, K. and Kumar, A., (2004), “Search for optimum labeling schemes in qubit systems for quantum information processing by NMR,” Phys. Rev. A., 70, 012314.

Das, R., Bhattacharya, R., and Kumar, A., (2004), “Quantum information processing by NMR using a 5-qubit system formed by dipolar coupled spins in an oriented molecule,” J. Magn. Reson., 170(2), 310.

Das, R., and Kumar, A., (2004), “Spectral implementation of quantum algorithms by one-and two- dimensional NMR, J. Chem. Phys., 121(16), 7601-13.

Gopinath, T., Das, R., and Kumar, A., (2004), “Quantum information processing by NMR:   Implementation of inversion-on-equality gate, Parity gate, and Fanout gate,” Proc. Indian Natn. Sci. Acad., 70(5), 649-658.

Mahesh, T.S., Sinha, N., Ghosh, A., Das, R., Suryaprakash, N., Levitt, M.H., Ramanathan, K.V. and Kumar, A., (2003), “Quantum information processing by NMR using strongly coupled spins,” Current Science, 85(7), 932-944.

Das, R., Mitra, A., Vijay Kumar, V., and Kumar, A., (2003) “Quantum Information processing by NMR:  Preparation of pseudopure states and implementation of Unitary operations in a single-qutrit system,” Int’l. J. of Quant. Infor., 1(3), 387-394.

Das, R., and Kumar, A., (2003), “Use of quadrupolar nuclei for quantum-information processing by nuclear magnetic resonance: Implementation of a quantum algorithm,” Phys. Rev. A., 68, 032304.

Das, R., Mahesh, T.S. and Kumar, A., (2003), “Experimental implementation of Grover’s search algorithm using efficient quantum state tomography,” Chem. Phys. Lett., 369, 8-15.

Das, R., Mahesh, T.S. and Kumar, A., (2003), “Efficient Quantum State Tomography for Quantum Information Processing using two-dimensional Fourier Transform Technique,” Phys. Rev. A., 67, 062304.

Das, R., Mahesh, T.S. and Kumar, A., (2002), “Implementation of the conditional phase-shift gate for quantum information processing by NMR, using transition-selective pulses,” J. Magn. Reson., 159, 46-54.