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Educational Package
• Introduction to complex biological systems by De S., Samanta D. - (2025)
• Experimental Biochemistry by Dasgupta S., De S. - (2024)
• Experimental Biochemistry by Dasgupta S., De S. - (2023)
• Experimental Biochemistry by Dasgupta S., De S. - (2022)
• Experimental Biochemistry by Dasgupta S., De S. - (2019)
Journal
• Deciphering the conformational stability of MazE7 antitoxin in Mycobacterium tuberculosis from molecular dynamics simulation study by Saha R., Bhattacharje G., De S., Das A.K. Journal of Biomolecular Structure and Dynamics 43 127-143 (2025)
• Redefining NSP12 activity in SARS-CoV-2 and its regulation by NSP8 and NSP7 by Singh D., Kushwaha T., Kulandaisamy R., Kumar V., Baswal K., Tiwari S.H., Ghorai A., Kumar M., Kumar S., De S., Polamarasetty A., Sehgal D., Katika M.R., Gadde S., Côté M., Kayampeta S.R., Appaiahgari M.B., Inampudi K.K. Molecular Therapy Nucleic Acids 36 - (2025)
• Experimental methods to study the structure and dynamics of intrinsically disordered regions in proteins by Maiti S., Singh A., Maji T., Saibo N.V., De S. Current Research in Structural Biology 7 100138- (2024)
• Expressional vagaries of OsCAMTA genes under differential abiotic stresses supported with protein protein interaction study and prediction of miRNA target sites by Gain H., De S. , Banerjee J. Plant Biotechnology Reports - (2024)
• The intrinsically disordered transactivation region of HOXA9 regulates its function by auto-inhibition of its DNA-binding activity by Saibo N. V., Maiti S. , Boral S. , Banerjee P. , Kushwaha T. , Inampudi K. K., Goswami R. , De S. International Journal of Biological Macromolecules - (2024)
• Stability and dynamics of extradenticle modulates its function by Singh A., Acharya B. , Mukherjee B. , Boorla V. S., Boral S. , Maiti S. , De S. Current Research in Structural Biology 7 100150- (2024)
• Deciphering the conformational stability of MazE7 antitoxin in Mycobacterium tuberculosis from molecular dynamics simulation study by Saha R., Bhattacharje G. , De S. , Das A. K. Journal of Biomolecular Structure and Dynamics - (2023)
• Thermodynamics of the association of aminoglycoside antibiotics with human angiogenin. by Panda A., Halder K. , Debkumar D. , De S. , Dasgupta S. Protein & Peptide Letters 30 92-101 (2023)
• Thermodynamics of the Association of Aminoglycoside Antibiotics with Human Angiogenin by Panda A., Halder K., Debnath D., De S., Dasgupta S. Protein and Peptide Letters 30 92-101 (2023)
• Non-enzymatic glycation of human angiogenin: Effects on enzymatic activity and binding to hRI and DNA by Panda A., Sabnam K., De S., Dasgupta S. Biochimie - (2023)
• Extein residues regulate the catalytic function of Spl DnaX intein enzyme by restricting the near attack conformations of the active site residues by Boral S., Sen S. , Kushwaha T. , Inampudi K. K., De S. Protein Science - (2023)
• Crystal structure of a mycobacterial secretory protein Rv0398c and in silico prediction of its export pathway by Saha R., Mukherjee S. , Singh B. , De S. , Weiss M. S., Das A. K. Biochemical and Biophysical Research Communications 672 45-53 (2023)
• beta-cyclodextrin encapsulation of curcumin elicits an altered mode of angiogenin inhibition: In vitro and in vivo studies by Panda A., Roy P., Goon D., Kottala H., De S., Dasgupta S. International Journal of Biological Macromolecules 208 654-666 (2022)
• Enhancement of angiogenin inhibition by polyphenol capped gold nanoparticles by Panda A., Karhadkar S. , Acharya B. , Banerjee A. , De S. , Dasgupta S. Biopolymers - (2021)
• Structural and dynamic studies of the human RNA binding protein RBM3 reveals the molecular basis of its oligomerization and RNA recognition by Roy S., Boral S. , Maiti S. , Kushwaha T. , Basak A. J., Lee W. , Basak A. , Gholap S. L., Inampudi K. K., De S. The FEBS journal - (2021)
• Identification of potential short linear motifs (SLiMs) in intrinsically disordered sequences of proteins by fast time-scale backbone dynamics by Maiti S., De S. Journal of Magnetic Resonance Open - (2021)
• Characterization of active/binding site residues of peptidyl-tRNA hydrolase using biophysical and computational studies by Kulandaisamy R., Kushwaha T. , Kumar V. , De S. , Kumar S. , Upadhyay S. K., Kumar M. , Inampudi K. K. International Journal of Biological Macromolecules 159 877-885 (2020)
• Molecular Details of a Salt Bridge and Its Role in Insulin Fibrillation by NMR and Raman Spectroscopic Analysis by Ratha B. N., Kar R. K., Bednarikova Z. , Gazova Z. , Kotler S. S., Raha S. , De S. , Maiti N. C., Bhunia A. The Journal of Physical Chemistry B 124 1125-1136 (2020)
• Structural, Dynamic, and Functional Characterization of a DnaX Mini-intein Derived from Spirulina platensis Provides Important Insights into Intein-Mediated Catalysis of Protein Splicing by Boral S., Maiti S. , Basak A. J., Lee W. , De S. Biochemistry 59 4711-4724 (2020)
• Structural Insights into N-terminal IgV Domain of BTNL2, a T Cell Inhibitory Molecule, Suggests a Non-canonical Binding Interface for Its Putative Receptors by Basak A. J., Maiti S. , Hansda A. , Mahata D. , Duraivelan K. , Kundapura . V., Lee . , Mukherjee G. , De S. , Samanta D. Journal of Molecular Biology 432 5938-5950 (2020)
• Dynamic Studies on Intrinsically Disordered Regions of Two Paralogous Transcription Factors Reveal Rigid Segments with Important Biological Functions by Maiti S., Acharya B. , Sheersh Boorla V. , Manna B. , Ghosh A. , De S. Journal of Molecular Biology 431 1353-1369 (2019)
• Structural characterization of VapB46 antitoxin from Mycobacterium tuberculosis: insights into VapB46 DNA binding by Roy M., Kundu A. , Bhunia A. , Das Gupta S. , De S. , Das A. K. The FEBS journal 286 1174-1190 (2019)
• Cyclic cis-Locked Phospho-Dipeptides Reduce Entry of AbetaPP into Amyloidogenic Processing Pathway by Fisher C. L., Resnick R. J., De S. , Acevedo L. A., Lu K. P., Schroeder F. C., Nicholson L. K. Journal of Alzheimer's Disease 55 391-410 (2017)
• Autoinhibition of ETV6 DNA-binding is established by the stability of its inhibitory helix by De S., Okon M. , Graves B. , Mcintosh L. Journal of molecular biology 428 1515-1530 (2016)
• The Modular Structure of the Inner-Membrane Ring Component PrgK Facilitates Assembly of the Type III Secretion System Basal Body by Julien RC Bergeron, Liam J Worrall, Soumya De, Nikolaos G Sgourakis, Adrienne H Cheung, Emilie Lameignere, Mark Okon, Gregory A Wasney, David Baker, Lawrence P McIntosh, Strynadka Natalie CJ Structure 23 - (2015)
• TCR scanning of peptide/MHC through complementary matching of receptor and ligand molecular flexibility by William F Hawse, Soumya De, Alex I Greenwood, Linda K Nicholson, Jaroslav Zajicek, Evgenii L Kovrigin, David M Kranz, K Christopher Garcia, Brian M Baker The Journal of Immunology 192 - (2014)
• Steric mechanism of auto-inhibitory regulation of specific and non-specific DNA binding by the ETS transcriptional repressor ETV6 by De S., Chan A. C., Coyne H. J., Bhachech N. , Hermsdorf U. , Okon M. , Murphy M. E., Graves B. J., Mcintosh L. P. Journal of molecular biology 426 1390-1406 (2014)
• Structural Characterization of the C3 Domain of Cardiac Myosin Binding Protein C and Its Hypertrophic Cardiomyopathy-Related R502W Mutant by Xiaolu Linda Zhang, Soumya De, Lawrence P McIntosh, Mark Paetzel Biochemistry 53 - (2014)
• Autoinhibition of ETV6 (TEL) DNA binding: appended helices sterically block the ETS domain by H Jerome Coyne, Soumya De, Mark Okon, Sean M Green, Niraja Bhachech, Barbara J Graves, Lawrence P McIntosh Journal of molecular biology 421 - (2012)
• Complete thermodynamic and kinetic characterization of the isomer-specific interaction between Pin1-WW domain and the amyloid precursor protein cytoplasmic tail phosphorylated at Thr668 by De S., Greenwood A. I., Rogals M. J., Kovrigin E. , Lu K. P., Nicholson L. K. Biochemistry 51 - (2012)
• Putting a Stop to l,d-Transpeptidases by De S., Mcintosh L. P. Structure 20 753-754 (2012)
• Complete determination of the Pin1 catalytic domain thermodynamic cycle by NMR lineshape analysis by Alexander I Greenwood, Monique J Rogals, Soumya De, Kun Ping Lu, Evgenii L Kovrigin, Linda K Nicholson Journal of biomolecular NMR 51 - (2011)
• Structural biology: The twist in Crk signaling revealed by Nicholson L. K., De S. Nature Chemical Biology 7 5-6 (2010)
• Elucidation of a pH-folding switch in the Pseudomonas syringae effector protein AvrPto by Jennifer E Dawson, Jolita Seckute, Soumya De, Samuel A Schueler, Aaron B Oswald, Linda K Nicholson Proceedings of the National Academy of Sciences 106 - (2009)
• 3'-N-Alkylamino-3'-deoxy-ara-uridines: A new class of potential inhibitors of ribonuclease A and angiogenin by Maiti T. K., De S. , Dasgupta S. , Pathak T. Bioorganic & medicinal chemistry 14 1221-1228 (2006)
• A docking interaction study of the effect of critical mutations in ribonuclease a on protein ligand binding by Mukherjee S., De S. , Ghosh Z. , Dasgupta S. Biochemistry and Molecular Biology Education 33 335-343 (2005)
Book Chapter/Section
• Intrinsically disordered proteins: functionality of chaos by Singh A., Maji T. , Banerjee P. , De S. The Three Functional States of Proteins 45-61 (2024)
• Nuclear Magnetic Resonance Spectroscopy to Analyse Protein Folding and Dynamics by Saibo N., Boral S. , Saha R. , Das A. K., De S. Protein Folding Dynamics and Stability 61-81 (2023)
• Analysis of structure and dynamics of intrinsically disordered regions in proteins using solution NMR methods by Saibo N.V., Maiti S., Acharya B., De S. Advances in Protein Molecular and Structural Biology Methods 535-550 (2022)
• Lineshape Analysis as a Tool for Probing Functional Motions at Biological Interfaces by De S., Greenwood A. I., Acevedo L. A., Korson N. E., Nicholson L. K. NMR Spectroscopy for Probing Functional Dynamics at Biological Interfaces 82-121 (2022)
Conferences
• Understanding the structural basis of protein splicing mechanism mediated by Spl DnaX intein enzyme using solution NMR spectroscopy and molecular dynamics simulations by Boral S., Kushwaha T. , Inampudi K. K., De S. IBS: 44th annual meeting of the Indian Biophysical Society - (2022)
• Structural and dynamic investigations of murine BTNL2, an orphan T cell co-inhibitor by Basak A. J., Maiti S. , Hansda A. , Mukherjee G. , De S. , Samanta D. 27th conference of the National Magnetic Resonance Society (NMRS 2022) - (2022)
• Understanding the Catalytic Mechanism of Spl DnaX Intein mediated Protein Splicing guided by Solution NMR Spectroscopy and Molecular Dynamics Simulations by Boral S., Kushwaha T. , Inampudi K. K., De S. 35th Annual Symposium of the Protein Society - (2021)
• Elucidating the Role of Protein Partnerships in Modulating DNA Binding Specifi city of Transcription Factors by Acharya B., Maiti S. , Basak A. J., De S. 33rd Annual Symposium of The Protein Society - (2019)
• The Role of dynamics in transcription factor DNA-binding specificity by Sheu K., De S. , Mcintosh L. 33rd Annual Symposium of The Protein Society - (2019)
Symposium
• Understanding the Structural Basis of Protein Splicing Mechanism mediated by Spl DnaX Intein Enzyme using Solution NMR Spectroscopy and Molecular Dynamics Simulations by Boral S., Kushwaha T. , Inampudi K. K., De S. NMRS: 27th annual meeting of the National Magnetic Resonance Society - (2022)
• Structural Characterization by Solution NMR Spectroscopy of a DnaX Mini-intein Derived from Spirulina platensis by Boral S., Lee W. , De S. PDB50: A special symposium celebrating the 50th anniversary of the Protein Data Bank - (2021)
• Solution state structural and dynamic studies of mouse BTNL2, an orphan T cell coinhibitory molecule by Basak A. J., Maiti S. , Hansda A. , Mahata D. , Lee W. , Mukherjee G. , De S. , Samanta D. 33rd Annual Symposium of The Protein Society 152-152 (2019)
Patent
• Alzheimer's disease therapeutics based on pin-1 catalyzed conformational changes in phosphorylated amyloid precursor protein by Lu K. P., Nicholson L. K., Pastorino L. , Zhou X. , De S. - (2008)

Principal Investigator

• Investigating the Molecular Mechanisms of Functional Regulation and DNA-Binding Specificity in the HOX Transcription Factors
• Dissecting the Roles of DNA-Binding Autoinhibition , Post-Translational Modification and Protein Partnerships in the Regulation of the HOX Transcription Factors HOXA9 and HOXB4
• Structural and Functional Studies of Mycobacterium Tuberculosis Peptidyl-tRNA Hydrolase: A Novel Drug Target of Multidrug-resistant Tuberculosis
• In vitro and in Vivo Investigation of the Role of Intrinsically Disordered Regions in the Regulation of HOX Transcription Factor Function
• Bioconjugation of proteins by Mandovi Green 444
• Reimbursement of travel grant to Aakanksha Singh for attending workshop in Germany

Co-Principal Investigator

• Structural and Functional Characterization of Mycobacterium Tuberculosis Beta-hydroxyacyl-ACP Dehydrataes and Monooxygenases for Understanding its Thiourea Mediated Mode of Inhibition