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
Autoinhibition of ETV6 DNA-binding is established by the stability of its inhibitory helix by Soumya De, Mark Okon, Barbara Graves & Lawrence McIntosh Journal of molecular biology 428 1515 (2016)
Cyclic cis-Locked Phospho-Dipeptides Reduce Entry of AbetaPP into Amyloidogenic Processing Pathway by 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 55 391 (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 23 161 (2015)
Steric mechanism of auto-inhibitory regulation of specific and non-specific DNA binding by the ETS transcriptional repressor ETV6 by 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 426 1390 (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 5332 (2014)
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 2885 (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 67 (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 Soumya De, Alexander I Greenwood, Monique J Rogals, Evgenii L Kovrigin, Kun Ping Lu, Linda K Nicholson Biochemistry 51 8583 (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 21 (2011)
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 8543 (2009)
Dissecting the Roles of DNA-Binding Autoinhibition , Post-Translational Modification and Protein Partnerships in the Regulation of the HOX Transcription Factors HOXA9 and HOXB4 Science and Engineering Research Board (SERB)
Investigating the Molecular Mechanisms of Functional Regulation and DNA-Binding Specificity in the HOX Transcription Factors ISIRD, SRIC
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