Publications from IIT Kharagpur (click fulltext to download the PDF)
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The intrinsically disordered transactivation region of HOXA9 regulates its function by auto-inhibition of its DNA-binding activity. (2024) Nikita V Saibo, Snigdha Maiti, Soumendu Boral, Puja Banerjee, Tushar Kushwaha, Krishna K Inampudi, Ritobrata Goswami, Soumya De* [fulltext] [supporting info]
Stability and dynamics of extradenticle modulates its function. (2024) Aakanksha Singh, Bidisha Acharya, Beas Mukherjee, Veda Sheersh Boorla, Soumendu Boral, Snigdha Maiti, Soumya De* [fulltext] [supporting info]
Experimental methods to study the structure and dynamics of intrinsically disordered regions in proteins. (2024) Snigdha Maiti, Aakanksha Singh, Tanisha Maji, Nikita V Saibo, Soumya De* [fulltext]
Expressional vagaries of OsCAMTA genes under differential abiotic stresses supported with protein–protein interaction study and prediction of miRNA target sites. (2024) Hena Gain, Soumya De, Joydeep Banerjee* [fulltext]
Deciphering the conformational stability of MazE7 antitoxin in Mycobacterium tuberculosis from molecular dynamics simulation study (2023) Rituparna Saha, Gourab Bhattacharje, Soumya De*, Amit Kumar Das* [fulltext]
Crystal structure of a mycobacterial secretory protein Rv0398c and in silico prediction of its export pathway (2023) Rituparna Saha, Somnath Mukherjee, Bina Singh, Soumya De, Manfred S. Weiss, Amit Kumar Das* [fulltext]
Extein residues regulate the catalytic function of Spl DnaX intein enzyme by restricting the near‐attack conformations of the active‐site residues (2023) Soumendu Boral, Srijon Sen, Tushar Kushwaha, Krishna K Inampudi, Soumya De* [fulltext]
Crystal structure of a mycobacterial secretory protein Rv0398c and in silico prediction of its export pathway (2023) Rituparna Saha, Somnath Mukherjee, Bina Singh, Soumya De, Manfred S Weiss, Amit Kumar Das* [fulltext]
Nuclear Magnetic Resonance Spectroscopy to Analyse Protein Folding and Dynamics (2023) Nikita V. Saibo, Soumendu Boral, Rituparna Saha, Amit K. Das, Soumya De* [fulltext]
Non-enzymatic glycation of human angiogenin: Effects on enzymatic activity and binding to hRI and DNA (2023) Atashi Panda, Kabira Sabnam, Soumya De, Swagata Dasgupta* Biochimie [fulltext]
Thermodynamics of the association of aminoglycoside antibiotics with human angiogenin (2022) Atashi Panda, Krishna Halder, Debkumar Debnath, Soumya De, Swagata Dasgupta* Protein & Peptide Letters [fulltext]
Lineshape Analysis as a Tool for Probing Functional Motions at Biological Interfaces (2022) Soumya De, Alexander I Greenwood, L Andrea Acevedo, Nathan E Korson, Linda K Nicholson* Book: NMR Spectroscopy for Probing Functional Dynamics at Biological Interfaces.
β-cyclodextrin encapsulation of curcumin elicits an altered mode of angiogenin inhibition: In vitro and in vivo studies (2022) Atashi Panda, Pritam Roy, Debopriya Goon, Harinarayanan Kottala, SoumyaDe, Swagata Dasgupta* International Journal of Biological Macromolecules [fulltext]
Analysis of structure and dynamics of intrinsically disordered regions in proteins using solution NMR methods (2021) Nikita V Saibo, Snigdha Maiti, Bidisha Acharya, Soumya De* Book: Advances in Protein Molecular and Structural Biology Methods. [fulltext]
Identification of potential short linear motifs (SLiMs) in intrinsically disordered sequences of proteins by fast time-scale backbone dynamics (2021) Snigdha Maiti, Soumya De* Journal of Magnetic Resonance Open. [fulltext]
Structural and dynamic studies of the human RNA binding protein RBM3 reveals the molecular basis of its oligomerization and RNA recognition (2021) Sayantani Roy*, Soumendu Boral, Snigdha Maiti, Tushar Kushwaha, Aditya J Basak, Woonghee Lee, Amit Basak, Shivajirao L Gholap, Krishna K Inampudi, Soumya De* The FEBS Journal. [fulltext]
Enhancement of angiogenin inhibition by polyphenol‐capped gold nanoparticles (2021) Atashi Panda, Siddhant Karhadkar, Bidisha Acharya, Anwesha Banerjee, Soumya De, Swagata Dasgupta* Biopolymers. [fulltext]
Structural, Dynamic, and Functional Characterization of a DnaX Mini-intein Derived from Spirulina platensis Provides Important Insights into Intein-Mediated Catalysis of Protein Splicing (2020) Soumendu Boral, Snigdha Maiti, Aditya J. Basak, Woonghee Lee, Soumya De* Biochemistry. [fulltext]
Characterization of active/binding site residues of peptidyl-tRNA hydrolase using biophysical and computational studies (2020) Rajkumar Kulandaisamy, Tushar Kushwaha, Vikas Kumar, Soumya De, Saroj Kumar, Santosh Kumar Upadhyay, Manoj Kumar, Krishna K Inampudi* International journal of biological macromolecules. [fulltext]
Structural Insights into N-terminal IgV Domain of BTNL2, a T Cell Inhibitory Molecule, Suggests a Non-canonical Binding Interface for Its Putative Receptors (2020) Aditya Basak, Snigdha Maiti, Anita Hansda, Dhrunajyoti Mahata, Kheerthana Duraivelan, Shankar Kundapura, Wonghee Lee, Gayatri Mukherjee*, Soumya De*, Dibyendu Samanta* Journal of Molecular Biology. [fulltext]
Molecular Details of A Salt-Bridge and Its Role in Insulin Fibrillation by NMR and Raman Spectroscopic Analysis (2020) Bhisma N Ratha, Rajiv Kumar Kar, Zuzana Bednarikova, Zuzana Gazova, Samuel A Kotler, Sreyan Raha, Soumya De, Nakul Chandra Maiti, Anirban Bhunia* The Journal of Physical Chemistry B. [fulltext]
Dynamic Studies on Intrinsically Disordered Regions of Two Paralogous Transcription Factors Reveal Rigid Segments with Important Biological Functions (2019) Snigdha Maiti, Bidisha Acharya, Veda Sheersh Boorla, Bharat Manna, Amit Ghosh, Soumya De* Journal of Molecular Biology. [fulltext]
Structural characterization of VapB46 antitoxin from Mycobacterium tuberculosis : insights into VapB46 – DNA binding (2018) Madhurima Roy, Anirban Kundu, Anirban Bhunia, Sujoy Das Gupta, Soumya De*, Amit Kumar Das* The FEBS Journal. [fulltext]
Cyclic cis-Locked Phospho-Dipeptides Reduce Entry of AβPP into Amyloidogenic Processing Pathway (2016) Carolyn L Fisher, Ross J Resnick, Soumya De, Lucila A Acevedo, Kun Ping Lu, Frank C Schroeder, Linda K Nicholson* Journal of Alzheimer's Disease. [fulltext]
Publications from Postdoctoral, PhD and MSc research
Autoinhibition of ETV6 DNA binding is established by the stability of its inhibitory helix (2016) Soumya De, Mark Okon, BarbaraJ Graves and Lawrence P McIntosh. Journal of Molecular Biology. [fulltext]
The Modular Structure of the Inner-Membrane Ring Component PrgK Facilitates Assembly of the Type III Secretion System Basal Body (2014) 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 and Natalie CJ Strynadka Structure.
Structural characterization of the C3 domain of cardiac myosin binding protein C and its hypertrophic cardiomyopathy-related R502W mutant (2014) XL Zhang, Soumya De, Lawrence P McIntosh and Mark Paetzel Biochemistry. [fulltext]
Steric mechanism of auto-inhibitory regulation of specific and non-specific DNA binding by the ETS transcriptional repressor ETV6 (2014) Soumya De, Anson CK Chan, H Jerome Coyne, Niraja Bhachech, Ulrike Hermsdorf, Mark Okon, Michael EP Murphy, Barbara J Graves, Lawrence P McIntosh Journal of Molecular Biology. [fulltext]
TCR scanning of peptide/MHC through complementary matching of receptor and ligand molecular flexibility (2014) 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.
Complete thermodynamic and kinetic characterization of the isomer-specific interaction between Pin1-WW domain and the amyloid precursor protein cytoplasmic tail phosphorylated at Thy668 (2012) Soumya De, Alexander I Greenwood, Monique J Rogals, Evgenii L Kovrigin, Kun P Lu and Linda K Nicholson Biochemistry. [fulltext]
Autoinhibition of ETV6 (TEL) DNA binding: appended helices sterically block the ETS domain (2012) Harold J Coyne, Soumya De, Mark Okon, Shaun M Green, Niraja Bhachech, Barbara J Graves and Lawrence P McIntosh Journal of Molecular Biology. [fulltext]
Putting a Stop to l,d-Transpeptidases (2012) Soumya De and Lawrence P McIntosh Structure.
Complete determination of the Pin1 catalytic domain thermodynamic cycle by NMR lineshape analysis (2012) Alexander I Greenwood, Monique J Rogals, Soumya De, Kun P Lu, Evgenii L Kovrigin and Linda K Nicholson Journal of Biomolecular NMR. [fulltext]
Structural biology: The twist in Crk signaling revealed (2010) Linda K Nicholson and Soumya De Nature Chemical Biology.
Elucidation of a pH-folding switch in the Pseudomonas syringae effector protein AvrPto (2009) Jennifer E Dawson, Jolita Šečkutė, Soumya De, Samuel A Schueler, Aaron B Oswald and Linda K Nicholson Proceedings of the National Academy of Sciences.
Alzheimer's disease therapeutics based on pin-1 catalyzed conformational changes in phosphorylated amyloid precursor protein (2008) Kun Ping Lu, Linda Nicholson, Lucia Pastorino, Xiao Zhou, Soumya De US Patent App. 11/623,672
3'-N-Alkylamino-3'-deoxy-ara-uridines: A new class of potential inhibitors of ribonuclease A and angiogenin (2006) Tushar K Maiti, Soumya De, Swagata Dasgupta and Tanmaya Pathak Bioorganic & Medicinal Chemistry.
A docking interaction study of the effect of critical mutations in ribonuclease a on protein‐ligand binding (2005) Sayan Mukherjee, Soumya De, Zhumur Ghosh and Swagata Dasgupta Biochemistry and Molecular Biology Education.