PI: Dr. Soumya De, School of Bio Science, IIT Kharagpur.
Brief CV: Integrated BSc-MSc from IIT Kharagpur; PhD from Cornell University, USA; Postdoc from University of British Columbia, Canada
Office: 2nd Floor, Sir JC Bose Laboratory Complex
Research interests: Biophysics, Biochemistry; Enzymology; Signal Transduction and Gene Expression; Protein engineering; Nuclear Magnetic Resonance (NMR) Spectroscopy
The overarching research goal of Dr. Soumya De's laboratory is to decipher the structural and dynamic principles that govern protein functions and their regulation. This is achieved using solution NMR spectroscopy and other biophysical methods.
Regulation of HOX transcription Factors: Transcription factors play central role in many biological processes that range from cell cycle progression to cell differentiation and organism development. Hence, it is not surprising that the functions of these proteins are under tight regulation and their disruption lead to several diseases raging from developmental disorders to cancer. Regulatory mechanisms of these proteins include post-translational modifications, protein partnerships and DNA-binding autoinhibition.
We are investigating the molecular basis of function, regulation and specificity of HOX transcription factors. We are focussing on Drosophila and Human HOX factors. The Drosophila HOX factors have well-defined biological roles and are ideal systems to explore the molecular basis of their function and regulation. The Human HOX factors, on the other hand, are important therapeutic targets for cancer treatment.
Protein Engineering: Protein splicing involves the excision of an intervening sequence (intein) from a precursor protein, resulting in the ligation of the flanking sequences (exteins) into a single polypeptide chain. The overall goal of this project is to utilize thestructural and dynamic studies to engineer intein proteins for novel applications:
1) design of split inteins
2) design of highly specific proteases
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. J Mol Biol 432 5938-5950 (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)
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)
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)
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 and Functional Studies of Mycobacterium Tuberculosis Peptidyl-tRNA Hydrolase: A Novel Drug Target of Multidrug-resistant Tuberculosis DBT, NEW DELHI
Area of Research: Regulation of HOX transcription factors
Aditya Jyoti Basak
Area of Research: Structure-function Relation of Membrane Proteins/Cell Adhesion Molecules
Area of Research: Regulation of gene transcription
Area of Research: Protein Chemistry
Nikita Veronica Saibo
Area of Research:
Area of Research: Structural Biology
Area of Research: Structural Biochemistry
Area of Research: Structural Biology