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Book Chapter
D. Sengupta, G. Kumar, A., Prasanna, X., and Chattopadhyay, A., “Chapter 5: Experimental and computational approaches to study membranes and lipid-protein interactions”, in Computational biophysics of membrane proteins, Royal Society of Chemistry, 2017, pp. 137-160.
D. Sengupta, Sonar, K., and Joshi, M., “Characterizing clinically relevant natural variants of GPCRs using computational approaches”, in Methods in cell biology, 2017.
M. Mohole, G. Kumar, A., Sengupta, D., and Chattopadhyay, A., “Molecular determinants of GPCR oligomerization”, in Molecular determinants of GPCR oligomerization, 2020, pp. 97-108.
M. Joshi, Nikte, S., and Sengupta, D., “Molecular determinants of GPCR pharmacogenetics: deconstructing the population variants in β2-adrenergic receptor”, in Advances in Protein Chemistry and Structural Biology, vol. 128, 2022, pp. 361-396.
X. Prasanna, Chattopadhyay, A., and Sengupta, D., “Role of lipid-mediated effects in beta(2)-adrenergic receptor dimerization”, in biochemical roles of eukaryotic cell surface macromolecules, vol. 842, A. Chakrabarti and Surolia, A., Eds. Heidelberger Platz 3, D-14197 Berlin, Germany : Springer-Verlag Berlin, 2015, pp. 247-261.
D. Sengupta, Joshi, M., Athale, C. A., and Chattopadhyay, A., “What can simulations tell us about GPCRs: integrating the scales”, in G Protein-Coupled Receptors: Signaling, Trafficking and Regulation, vol. 132, A. K. Shukla, Ed. 525 B Street, Suite 1900, San Diego, CA 92101-4495 USA : Elsevier Academic Press Inc., 2016, pp. 429-452.
Journal Article
S. Prakash, Krishna, A., and Sengupta, D., “Actin cytoskeleton and membrane interactions: role in GPCR function and organization”, Proceedings of the Indian National Science Academy, vol. 85, no. 3, 2019.
A. Sonawani, Kharche, S., Dasgupta, D., and Sengupta, D., “Allosteric modulation of the chemokine receptor-chemokine CXCR4-CXCL12 complex by tyrosine sulfation”, International Journal of Biological Macromolecules, vol. 206, pp. 812-822, 2022.
S. Prakash, Krishna, A., and Sengupta, D., “Caveolin induced membrane curvature and lipid clustering: two sides of the same coin?”, Faraday Discussions, vol. 232, pp. 218-235, 2021.
S. Prakash, Krishna, A., and Sengupta, D., “Caveolin mediated curvature and clustering: from simple to complex membrane”, Biophysical Journal, vol. 120, no. 3, p. 232A-233A, 2021.
X. Prasanna, Chattopadhyay, A., and Sengupta, D., “Cholesterol modulates the dimer interface of the beta(2)-adrenergic receptor via cholesterol occupancy sites”, Biophysical Journal, vol. 106, no. 6, pp. 1290-1300, 2014.
D. Sengupta, “Cholesterol modulates the structure, binding modes, and energetics of caveolin-membrane interactions”, Journal of Physical Chemistry B, vol. 116, no. 50, pp. 14556-14564, 2012.
X. Prasanna, Sengupta, D., and Chattopadhyay, A., “Cholesterol-dependent conformational plasticity in GPCR dimers”, Scientific Reports, vol. 6, p. 31858, 2016.
S. Prakash, Krishna, A., and Sengupta, D., “Cofilin-membrane interactions: electrostatic effects in phosphoinositide lipid binding”, ChemPhysChem, vol. 24, no. 3, 2023.
D. Sengupta, Prasanna, X., and Chattopadhyay, A., “Conformational dynamics of GPCR dimers is dependent on membrane cholesterol”, Biophysical Journal, vol. 110, no. 3, p. 356A-356A, 2016.
S. Kharche, Joshi, M., Chattopadhyay, A., and Sengupta, D., “Conformational plasticity and dynamic interactions of the N-terminal domain of the chemokine receptor CXCR1”, Plos Computational Biology, vol. 17, no. 5, 2021.
S. Kar, Sen, S., Maji, S., Saraf, D., Ruturaj,, Paul, R., Dutt, S., Mondal, B., Rodriguez-Boulan, E., Schreiner, R., Sengupta, D., and Gupta, A., “Copper(II) import and reduction are dependent on His-Met clusters in the extracellular amino terminus of human copper transporter-1”, Journal of Biological Chemistry, vol. 298, no. 3, p. 101631, 2022.
S. M. Patra, Chakraborty, S., Shahane, G., Prasanna, X., Sengupta, D., Maiti, P. K., and Chattopadhyay, A., “Differential dynamics of the serotonin(1A) receptor in membrane bilayers of varying cholesterol content revealed by all atom molecular dynamics simulation”, Molecular Membrane Biology, vol. 32, no. 4, pp. 127-137, 2015.
S. Bhosale, V. Nikte, S., Sengupta, D., and Joshi, M., “Differential dynamics underlying the Gln27Glu population variant of the beta(2)-adrenergic receptor”, Journal of Membrane Biology, vol. 252, no. 4-5, pp. 499-507, 2019.
H. Malshikare, Prakash, S., and Sengupta, D., “Differential membrane curvature induced by distinct protein conformers”, Soft Matter, vol. 19, no. 22, pp. 4021-4028, 2023.
G. Moiset, Cirac, A. D., Stuart, M. C. A., Marrink, S. - J., Sengupta, D., and Poolman, B., “Dual action of BPC194: a membrane active peptide killing bacterial cells”, Plos One, vol. 8, no. 4, p. e61541, 2013.
S. Singh, ,, Sengupta, D., and Kulkarni, K., “Dynamic coupling analysis on plant sesquiterpene synthases provides leads for the identification of product specificity determinants”, Biochemical and Biophysical Research Communications, vol. 536, pp. 107-114, 2021.
S. A. Kharche and Sengupta, D., “Dynamic protein interfaces and conformational landscapes of membrane protein complexes”, Current Opinion in Structural Biology, vol. 61, pp. 191-197, 2020.
A. S. Sandholu, Mohole, M., Duax, W. L., Thulasiram, H. V., Sengupta, D., and Kulkarni, K., “Dynamics of loops at the substrate entry channel determine the specificity of iridoid synthases”, Febs Letters, vol. 592, no. 15, pp. 2624-2635, 2018.
A. B. Pawar, Prasanna, X., and Sengupta, D., “Effect of lipid bilayer composition on membrane protein association”, Advances in Planar Lipid Bilayers and Liposomes, vol. 22, pp. 43–63, 2015.
A. Pawar and Sengupta, D., “Effect of membrane composition on receptor association: implications of cancer lipidomics on ErbB receptors”, Journal of Membrane Biology, vol. 251, no. 3, pp. 359-368, 2018.
V. Dubey, Prasanna, X., and Sengupta, D., “Estimating the lipophobic contributions in model membranes”, Journal of Physical Chemistry B, vol. 121, no. 9, pp. 2111-2120, 2017.
D. Sengupta, Prasanna, X., Mohole, M., and Chattopadhyay, A., “Exploring GPCR lipid interactions by molecular dynamics simulations: excitements, challenges, and the way forward”, Journal of Physical Chemistry B, vol. 122, no. 22, pp. 5727-5737, 2018.
X. Prasanna, Jafurulla, M., Sengupta, D., and Chattopadhyay, A., “Ganglioside GM1 interacts with the serotonin1A receptor via the sphingolipid binding domain”, Biochimica et Biophysica Acta, vol. 1858, no. 11, pp. 2818-2826, 2016.
A. Sonawani, Kharche, S., Dasgupta, D., and Sengupta, D., “Graphical Biology Insights into the dynamic interactions at chemokine-receptor interfaces and mechanistic models of chemokine binding”, Journal of Structural Biology, vol. 214, no. 3, p. 107877, 2022.
T. A. Wassenaar, Pluhackova, K., Moussatova, A., Sengupta, D., Marrink, S. - J., D. Tieleman, P., and Boeckmann, R. A., “High-throughput simulations of dimer and trimer assembly of membrane proteins. the DAFT approach”, Journal of Chemical Theory and Computation, vol. 11, no. 5, pp. 2278-2291, 2015.
D. Sengupta and Chattopadhyay, A., “Identification of cholesterol binding sites in the serotonin(1A) receptor”, Journal of Physical Chemistry B, vol. 116, no. 43, pp. 12991-12996, 2012.
S. Nikte, Gahankari, A., Mulla, J., Sengupta, D., Joshi, M., and Tamhane, V., “In vitro and in silico studies on membrane interactions of diverse Capsicum annuum flower gamma-thionin peptides”, Proteins-Structure Function and Bioinformatics, 2019.
A. Krishna and Sengupta, D., “Interplay between membrane curvature and cholesterol: role of palmitoylated caveolin-1”, Biophysical Journal, vol. 116, no. 1, pp. 69-78, 2019.
A. Ghosh, Pawar, A. B., Chirmade, T., Jathar, S. M., Bhambure, R., Sengupta, D., Giri, A. P., and Kulkarni, M. J., “Investigation of the captopril-insulin interaction by mass spectrometry and computational approaches reveals that captopril induces structural changes in insulin”, ACS Omega, vol. 7, no. 27, pp. 23115-23126, 2022.
T. A. Wassenaar, Pluhackova, K., Moussatova, A., Sengupta, D., Marrink, S. - J., D. Tieleman, P., and Boeckmann, R. A., “Landscapes of membrane protein interactions from high-throughput MD simulations using the daft approach”, Biophysical Journal, vol. 108, no. 2, p. 526A-526A, 2015.
S. M. Gopal, Pawar, A. B., Wassenaar, T. A., and Sengupta, D., “Lipid-dependent conformational landscape of the ErbB2 growth factor receptor dimers”, Chemistry and Physics of Lipids, vol. 230, p. 104911, 2020.
S. V. Nikte, Sonar, K., Tandale, A., Joshi, M., and Sengupta, D., “Loss of a water-mediated network results in reduced agonist affinity in a beta(2)-adrenergic receptor clinical variant”, Biochimica ET Biophysica Acta-Proteins and Proteomics, vol. 1869, no. 4, p. 140605, 2021.
S. Kharche, Joshi, M., Sengupta, D., and Chattopadhyay, A., “Membrane-induced organization and dynamics of the N-terminal domain of chemokine receptor CXCR1: insights from atomistic simulations”, Chemistry and Physics of Lipids, vol. 210, pp. 142-148, 2018.
D. Sengupta and Chattopadhyay, A., “Molecular dynamics simulations of GPCR-cholesterol interaction: an emerging paradigm”, Biochimica Et Biophysica Acta-Biomembranes, vol. 1848, no. 9, pp. 1775-1782, 2015.
G. Shahane, Parsania, C., Sengupta, D., and Joshi, M., “Molecular Insights into the dynamics of pharmacogenetically important N-terminal variants of the human beta(2)-adrenergic receptor”, Plos Computational Biology, vol. 10, no. 12, p. e1004006, 2014.
T. Pucadyil, Kulkarni, K., and Sengupta, D., “Molecular interplay at the membrane and impact on cellular physiology”, Journal of Membrane Biology, vol. 254, no. 3, pp. 239-242, 2021.
L. Thukral, Sengupta, D., Ramkumar, A., Murthy, D., Agrawal, N., and Gokhale, R. S., “Molecular mechanism underlying recruitment and insertion of lipid-anchored LC3 protein into membranes”, Biophysical Journal, vol. 109, no. 10, pp. 2067-2078, 2015.
S. Prakash, Malshikare, H., and Sengupta, D., “Molecular mechanisms underlying caveolin-1 mediated membrane curvature”, Journal of Membrane Biology, vol. 255, no. 2-3, pp. 225-236, 2022.
A. Pinjari, Saraf, D., and Sengupta, D., “Molecular mechanisms underlying nanowire formation in pristine phthalocyanine”, Physical Chemistry Chemical Physics, vol. 25, no. 44, pp. 30259-30268, 2023.
G. Moiset, Cirac, A. D., Mika, J. T., Kocer, A., Stuart, M. C. A., Sengupta, D., Marrink, S. - J., and Poolman, B., “Multi-Hit action of membrane active peptides: towards understanding bacterial cell killing”, Biophysical Journal, vol. 102, no. 3, p. 616A, 2012.
L. Thukral, Sengupta, D., and Gokhale, R. S., “Permeation of lipidated protein in bilayer using unbiased simulations reveals signature motif for protein-membrane binding”, Biophysical Journal, vol. 106, no. 2, p. 99A, 2014.
H. Chakraborty and Sengupta, D., “Preface to special issue on protein-mediated membrane remodeling”, Journal of Membrane Biology, vol. 255, no. 6, pp. 633-635, 2022.
A. Chaudhuri, Prasanna, X., Agiru, P., Chakraborty, H., Rydstrom, A., Ho, J. C. S., Svanborg, C., Sengupta, D., and Chattopadhyay, A., “Protein-dependent membrane interaction of a partially disordered protein complex with oleic acid : Implications for cancer lipidomics”, Scientific Reports, vol. 6, 2016.
A. B. Pawar and Sengupta, D., “Resolving the conformational dynamics of ErbB growth factor receptor dimers”, Journal of Structural Biology, vol. 207, no. 2, pp. 225-233, 2019.
D. Sengupta and Raghunathan, A., “Rise of the superbugs: what we need to know overview of antimicrobial resistance”, Resonance, vol. 26, no. 9, pp. 1251 - 1266, 2021.
A. B. Pawar and Sengupta, D., “Role of cholesterol in transmembrane dimerization of the ErbB2 growth factor receptor”, Journal of Membrane Biology, 2021.
X. Prasanna, Mohole, M., Chattopadhyay, A., and Sengupta, D., “Role of cholesterol-mediated effects in GPCR heterodimers”, Chemistry and Physics of Lipids, vol. 227, p. 104852, 2020.
S. A. Deshpande, Pawar, A. B., Dighe, A., Athale, C. A., and Sengupta, D., “Role of spatial inhomogenity in GPCR dimerisation predicted by receptor association-diffusion models”, Physical Biology, vol. 14 , no. 3, p. 036002, 2017.
X. Prasanna, Praveen, P. J., and Sengupta, D., “Sequence dependent lipid-mediated effects modulate the dimerization of ErbB2 and its associative mutants”, Physical Chemistry Chemical Physics, vol. 15, no. 43, pp. 19031-19041, 2013.
S. Prakash and Sengupta, D., “Special issue: membrane and receptor dynamics”, Journal of Membrane Biology, vol. 252, no. 4-5, pp. 207-211, 2019.
A. Krishna, Prakash, S., and Sengupta, D., “Sphingomyelin effects in caveolin-1 mediated membrane curvature published as part of the journal of physical chemistry virtual special issue ``computational and experimental advances in biomembranes''”, Journal of Physical Chemistry B, vol. 124, no. 25, pp. 5177-5185, 2020.
A. Tandale, Joshi, M., and Sengupta, D., “Structural insights and functional implications of inter-individual variability in beta(2)-adrenergic receptor”, Scientific Reports, vol. 6, p. 24379, 2016.
P. Yadav, Shahane, G., Ramasamy, S., Sengupta, D., and Gaikwad, S., “Structural-functional insights and studies on saccharide binding of Sophora japonica seed lectin”, International Journal of Biological Macromolecules, vol. 91, pp. 75-84, 2016.
D. Roy, Sengupta, D., and Kulkarni, K., “Substrate induced dynamical remodeling of the binding pocket generates GTPase specificity in DOCK family of guanine nucleotide exchange factors”, Biochemical and Biophysical Research Communications, vol. 631, pp. 32-40, 2022.
G. S. Bhosle, Kharche, S., Kumar, S., Sengupta, D., Maiti, S., and Fernandes, M., “Superior HIV-1 TAR binders with conformationally constrained R52 arginine mimics in the Tat(48-57) peptide”, Chemmedchem, vol. 13, no. 3, pp. 220-226, 2018.
D. Saraf, Prakash, S., Pinjari, A., Pujari, B., and Sengupta, D., “Surface-induced demixing of self-assembled isomeric mixtures of citral”, Journal of Molecular Liquids, vol. 381, p. 121803, 2023.
M. Mohole, Sengupta, D., and Chattopadhyay, A., “Synergistic and competitive lipid interactions in the serotonin1A receptor microenvironment”, ACS Chemical Neuroscience, vol. 13, no. 23, pp. 3403-3415, 2022.
A. B. Pawar, Deshpande, S. A., Gopal, S. M., Wassenaar, T. A., Athale, C. A., and Sengupta, D., “Thermodynamic and kinetic characterization of transmembrane helix association”, Physical Chemistry Chemical Physics, vol. 17, no. 2, pp. 1390-1398, 2015.
R. Friedman, Khalid, S., Aponte-Santamaria, C., Arutyunova, E., Becker, M., Boyd, K. J., Christensen, M., Coimbra, J. T. S., Concilio, S., Daday, C., van Eerden, F. J., Fernandes, P. A., Graeter, F., Hakobyan, D., Heuer, A., Karathanou, K., Keller, F., M. Lemieux, J., Marrink, S. J., May, E. R., Mazumdar, A., Naftalin, R., Pickholz, M., Piotto, S., Pohl, P., Quinn, P., Ramos, M. J., Schiott, B., Sengupta, D., Sessa, L., Vanni, S., Zeppelin, T., Zoni, V., Bondar, A. - N., and Domene, C., “Understanding conformational dynamics of complex lipid mixtures relevant to biology”, Journal of membrane biology, vol. 251, no. 5-6, pp. 609-631, 2018.
S. V. Nikte, Sonar, K., Tandale, A., Sengupta, D., and Joshi, M., “Water mediated allosteric network in beta 2AR T164I variant modulates agonist binding affinity”, European Biophysics Journal with Biophysics Letters, vol. 50, p. 162, 2021.
Z. Motiwala, Sandholu, A. S., Sengupta, D., and Kulkarni, K., “Wavelet coherence phase analysis decodes the universal switching mechanism of Ras GTPase superfamily”, iScience, vol. 26, no. 7, p. 107031, 2023.