OPEN RESEARCH POSITIONS: Masters degree holders in any branch of science who possess a fellowship from CSIR, UGC, DBT, ICMR etc. may apply through email. Queries regarding postdoctoral positions are also most welcome. Interested individuals can apply in any of the two major projects that are ongoing:
1. DBT (Govt. of India) project entitled, “Characterization of few blue light sensing photoreceptors with transcription factor activity: A molecular approach”
2. Dept of Higher Education, Science & Technology and Biotechnology, Govt. of West Bengal entitled “Assessing the role of Cryptochrome/Photolyase protein in circadian rhythm and DNA repair activity”
1. SERB DST-EMR (Govt. of India) project entitled, “Identification and validation of structural hotspots in signalling network of few blue light responsive photoreceptors using complex networks and biophysical techniques”
Outline of research:
Could light cure diseases?
In the last decade and a half, the world has witnessed the emergence of two fields with revolutionary potential -- namely, Optogenetics and Synthetic Biology. The goal of synthetic biology is to enable the design and engineering of biological systems in a systematic and rational manner. Optogenetics aims to impart light-sensitivity to genetically encoded molecules -- otherwise insensitive to light.
Our interdisciplinary lab is interested in optogenetics inspired synthetic biology.
Besides investigating the structure-function-dynamics of blue-light sensitive photoreceptors particularly those with transcription factor activity, we also pursue design and engineering of artificial photoreceptors suitable for optogenetic/imaging applications. We are also fascinated with the versatility of nature's extraordinary co-factor, Fe-S cluster, in metalloproteins.
We use techniques from molecular biology, biochemistry and biophysics. Our recently published work draws on collaborations from physics, systems biology, and plant science.
Our research is generously funded by SERB (DST-EMR), Govt. of India; DBT (under Basic Research in Modern Biology), Govt. of India, DHESTBT, Govt. of West Bengal as well as FRPDF, Presidency University. We also gratefully acknowledge DBT BUILDER and DST FIST funding for central instrumentation facilities.
PhD - Biotechnology [Indian Institute of Technology, Kharagpur; 2002-2006]
M.Sc. - Biochemistry [University of Calcutta, 2001]
B.Sc. - Chemistry (Honours) [University of Calcutta, 1999]
Jan 2013 - present - Assistant Professor, DBS, Presidency University, Kolkata
Dec 2009 – Nov 2012 Center for Advanced Radiation Sources & Dept of Biochemistry and Molecular Biology, The University of Chicago (Mentor: Prof. Keith Moffat)
Mar 2007 – Dec 2009 Depts. of Applied Science / Chemistry, University of California, Davis (Mentors: Profs. Stephen Cramer, Sheila David)
Research / Administrative Experience+
Current research focus:
Optogenetics – the conferring of light sensitivity on the genetically encoded molecules, forms an emerging area with effective applications in neurobiology, synthetic biology and synthetic physiology. The approach that started with the usage of naturally occurring signaling photoreceptors to monitor living neural circuitry, has since been extended to accommodate "biologically-inspired design" of synthetic photoreceptors. It is of utmost importance to understand the signaling mechanism in already-existing natural photoreceptors to develop synthetic photoreceptors. Perhaps the best way to progress is to study their crystal structures, a branch recently described as “Structural Optogenetics”. Blue-light responsive LOV (Light-Oxygen-Voltage) domains, being one of the most-targeted design modules, my current research is involves kinetic and biophysical characterization of different photosensors, predominantly LOV-based photoreceptors. My other major research interest is to explore the versatility of nature's extraordinary, modular co-factor, Fe-S cluster, in metalloproteins. The ubiquitous Fe-S clusters have a major role in electron transfer pathway and regulate conformational changes in signaling proteins. Given the limitations of static crystallography and other widely-used spectroscopic techniques, I am interested in observing Fe-S cluster-dynamics by Synchrotron based spectroscopic techniques especially, Extended X-ray Absorption Fine Structure (EXAFS) and recently introduced Nuclear Resonance Vibrational Spectroscopy (NRVS). I study the importance of polypeptide environment in modulating the Fe-S cluster dynamics through normal mode analyses of the Fe-S clusters from proteins as well as inorganic synthetic compounds.
I am currently serving as the member of academic committee, admissions committee, biosafety committee as well as cultural committee. Previously, I had also served as a member of PhD committee.
Teaching / Other Experience+
I am actively involved in postgraduate and undergraduate (including GenEd) teaching. My primary teaching interests are Biochemistry (e.g. protein engineering, downstream processing of enzymes, protein structure-function relations, protein-ligand interactions), Bioinorganic Chemistry (e.g. metals in biology), Basics of Synthetic Biology and Bioinformatics and Biophysical Methods.
Presidency University PG students from DLS (max. limit - 2) who want to do their Master's dissertation projects at the final semester are welcome to apply.
Post Graduate Supervision+
Current Lab Members:
(1) Ms. Aparna Boral, ICMR SRF [Joined October 2018]
(MSc. in Botany, Burdwan university)
(2) Ms. Madhurima Khamaru, UGC SRF [Joined January 2020]
(MSc. in Botany, Visva-Bharati)
(3) Ms. Piu Sarkar, CSIR JRF [Joined December 2021]
(MSc in Zoology, University of Calcutta
MSc Dissertation Students (2023 batch):
(1) Pracheta Pal [Since January 2023]
(pursuing MSc in Life Sciences, Presidency University)
(2) Saptarshi Pal [Since January 2023]
(pursuing MSc in Life Sciences, Presidency University)
Undergrad Research Students (2023 batch):
(1) Dibyajyoti Ghosh (research intern for Value Added Course, 2022)
1. Dr. Anwesha Deb [2021; currently Assistant Professor, JIS University]
12. Tiasa Biswas [2022 batch; research intern]
11. Bidisha Chakraborty [2021 batch; research intern]
10. Shreyasi Neogi [2021 batch, pursuing PhD at University of Illinois at Urbana Champaign, USA
9. Rajat Shubhra Nath [2021 batch]
8. Titir De [2020 batch, pursuing PhD at New York University, USA]
7. Namrata Ganguli [2020 batch, pursuing PhD at IIT-Kharagpur, India]
6. Kumari Vaishnavi [2019 batch]
5. Sudakshina Banerjee [2018 batch, pursuing PhD at International Max Planck Research School in Chemical and Molecular Biology, Dortmund, Germany]
4. Kankana Banerjee [2017 batch]
3. Payel Mandal [2017 batch; pursuing PhD at NICED, Kolkata, India]
2. Sk. Asik Ali [2015 batch; Technical Specialist at International Cancer Genome Consortium, NIBMG, Kalyani, India]
1. Natasha Khan [2015 batch; pursuing PhD at NISER, Bhubaneswar, India]
Project/summer/winter interns (Undergrad/postgrad):
25. Anwesha Banerjee (Life Sciences, Presidency University)
24. Sarbartha Mukherjee (IIT-IACS MSc program)
23. Pratichi Sarkar (Biophysics, Molecular Biology and Bioinformatics, University of Calcutta)
22. Ankita Saha (Biophysics, Molecular Biology and Bioinformatics, University of Calcutta)
21. Sanjana Mullick (St Xavier's College, Kolkata)
20. Akshssmita Somani (Biophysics, Molecular Biology and Bioinformatics, University of Calcutta)
19. Koyel Nandy (Biophysics, Molecular Biology and Bioinformatics, University of Calcutta)
18. Debapriya Kundu (SERB project assistant)
17. Tiasa Biswas (Life Sciences, Presidency University)
16. Simantan Dutta (KIIT, Bhubaneswar)
15. Aritra Biswas (St Xavier's College, Kolkata)
14. Titir De (Life Sciences, Presidency University)
13. Souvik Das Naskar (Life Sciences, Presidency University)
12. Sohini Barua (Life Sciences, Presidency University)
11. Sudipta Das
10. Roopsali Banerjee (Life Sciences, Presidency University)
9. Megha Ghosh (Life Sciences, Presidency University)
8. Mahasweta Das (Life Sciences, Presidency University)
7. Samriddhi Gupta (Life Sciences, Presidency University)
6. Atreyee Mukherjee (Life Sciences, Presidency University)
5. Anusha Singh (Life Sciences, Presidency University)
4. Sudakshina Banerjee (Life Sciences, Presidency University)
3. Sk Asik Ali (SERB Project Assistant, Life Sciences, Presidency University)
2. Sudipta Mukherjee (Life Sciences, Presidency University)
1. Arpan Som (Life Sciences, Presidency University)
(23) Journal of Cellular Biochemistry (Accepted, 2023)
Heterogeneity in winged Helix-Turn-Helix and Substrate DNA Interactions: Insights from Theory and Experiments
- Boral A and Mitra D*.
(22) Preprint (2022)
bioRxiv 2022.05.19.492614; doi: https://doi.org/10.1101/2022.05.19.492614
Basic Leucine Zippers: Aureochromes Versus the Rest
- Khamaru M, Deb A, Mitra D*.
(21) Cells Tissues Organs (Accepted, 2022)
[bioRxiv 2022.06.05.494858; doi: https://doi.org/10.1101/2022.06.05.494858]
Assessing combinatorial diversity of aureochrome bZIPs through genome-wide screening
- Khamaru M, Nath D, Mitra D*, Roy S*.
(20) Advances in Protein Chemistry and Structural Biology 2022; 130:245-287, Designing synthetic transcription factors: A structural perspective.
- Boral A^, Khamaru M^ and Mitra D*. [^ equal contribution]
(19) Scientific Reports 2021; 11:7849, Identification and functional characterization of two bamboo FD gene homologs having contrasting effects on shoot growth and flowering.
- Dutta S, Deb A, Biswas P, Chakraborty S, Guha S, Mitra D, Geist B, Schaffner AR, Das M.
(18) Proteins: Structure, Function, and Bioinformatics 2020; 88(12): 1660-1674, Residue Interaction Dynamics in Vaucheria Aureochrome1 LOV: Bridging Theory and Experiments
- Deb A, Kaur Grewal R, Roy S* and Mitra D*
(17) Trends in Plant Science 2020; 25:35-65, Structural basis of design and engineering for advanced plant optogenetics
- Banerjee S and Mitra D*
(16) BMC Genomics, 2018; 19:190, Identification, characterization and gene expression analyses of important flowering genes related to photoperiodic pathway in bamboo
- Dutta S, Biswas P, Chakraborty S, Mitra D, Pal A, Das M
(15) Bioinformatics (Oxford), 2015; 31: 3608-16, Mapping networks of light-dark transition in LOV photoreceptors
- Kaur Grewal R, Mitra D* and Roy S*
(14) International X-ray Absorption Society (IXAS) research review, 10 (2013) EXAFS and NRVS: A perfect marriage made at the Synchrotron.
- Mitra D and Cramer SP.
(13) J. Am. Chem. Soc., 2013; 135: 2530-43 Characterization of [4Fe-4S] Cluster Vibrations and Structure in Nitrogenase Fe Protein at Three Oxidation Levels via Combined NRVS, EXAFS, and DFT Analyses.
- Mitra D, George SJ, Guo Y, Peters JW, Keable S, Pelminschikov V, Case DA, Cramer SP.
(12) Angew Chem Int Ed Engl., 2013; 52(2):724-8 Active Site Fe-CN and Fe-CO vibrations in [NiFe] Hydrogenase – Observation by Nuclear Resonance Vibrational Spectroscopy.
- Kamali S, Wang H, Mitra D, Ogata H, Lubitz W, Manor BC, Rauchfuss TB, Byrne D, Bonnefoy V, Jenney FE Jr, Adams MW, Yoda Y, Alp E, Zhao J, Cramer SP. (On cover)
(11) Structure 2012; 20: 698-706. Crystal structures of Aureochrome1 LOV suggest new design strategies for Optogenetics.
- Mitra D, Yang X, Moffat K.
(10) J. Inorg. Biochem. 2012; 112: 85-92. EXAFS and NRVS reveal a conformational distortion of the FeMo-cofactor in the MoFe Nitrogenase propargyl alcohol complex.
- George SJ, Barney BM, Mitra D, Igarashi RY, Guo Y, Dean DR, Cramer SP, Seefeldt L.
(09) Biochemistry 2011; 50(23): 5220-5235. Dynamics of the [4Fe-4S] Cluster in Pyrococcus furiosus Ferredoxin via Nuclear Resonance Vibrational Spectroscopy (NRVS) and Resonance Raman Spectroscopy – Quantitative Simulation by Density Functional Theory.
- Mitra D, Pelmentschikov V, Guo Y, Case DA, Wang H, Dong W, Tang ML, Ichiye T, Jenney FE Jr., Adams MW, Yoda Y, Zhao J, Cramer SP.
(08) Eur. J. Inorg. Chem. 2011; 2011(13): 2064-2074. Photolysis of Hi-CO Nitrogenase – Observation of a plethora of distinct CO Species using Infrared spectroscopy.
- Yan L, Dapper CH, Gorge SJ, Wang H, Mitra D, Dong W, Newton WE, Cramer SP.
(07) J Am. Chem. Soc. 2010; 132: 6914–6916. Identification of Protein-Bound Dinitrosyl Iron Complexes by Nuclear Resonance Vibrational Spectroscopy.
- Tonzetich ZJ, Wang H, Mitra D, Tinberg CE, Do LH, Jenney FE Jr., Adams MWW, Cramer SP, and Lippard SJ.
(06) PLoS One 2010; 5(8): e12225. An Oligopeptide Transporter of Mycobacterium tuberculosis Regulates Cytokine Release and Apoptosis of Infected Macrophages.
- Dasgupta A, Sureka K, Mitra D, Saha B, Sanyal S, Das AK, Chakrabarti P, Jackson M, Gicquel B, Kundu M and Basu J.
(05) FEBS Lett. 2006; 580: 6846-6860. Cyclosporin A binding to Mycobacterium tuberculosis Peptidyl-prolyl cis-trans isomerase A: Investigation by CD, FTIR and Fluorescence spectroscopy.
- Mitra D, Mukherjee S and Das AK.
(04) Tuberculosis. 2005; 85(5-6): 337-45. Correlating sequential homology of Mce1A, Mce2A, Mce3A and Mce4A with their possible functions in mammalian cell entry of Mycobacterium tuberculosis performing homology modeling.
- Mitra D, Saha B, Das D, Wiker HG and Das AK.
(03) J. Bacteriol. 2005; 187(6): 2175-81. Crystal structure of low-molecular-weight protein tyrosine phosphatase from Mycobacterium tuberculosis at 1.9-A resolution.
- Madhurantakam C, Rajakumara E, Mazumdar PA, Saha B, Mitra D, Wiker HG, Sankaranarayanan R and Das AK.
(02) Scand. J. Immunol. 2004; 59(2): 190-7. Immunodominant B-cell epitope in the Mce1A mammalian cell entry protein of Mycobacterium tuberculosis cross-reacting with glutathione S-transferase.
- Harboe M, Das AK, Mitra D, Ulvund G, Ahmad S, Harkness RE, Das D, Mustafa AS and Wiker HG. (On cover)
(01) Biochem Biophys Res Commun. 2003; 302(3): 442-7. Predicted molecular structure of the mammalian cell entry protein Mce1A of Mycobacterium tuberculosis.
- Das AK, Mitra D, Harboe M, Nandi B, Harkness RE, Das D and Wiker HG.
* denotes Corresponding author / Co-Corresponding author
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