
Shubhra Ghosh Dastidar
Professor
Shubhra Ghosh Dastidar
Professor, Biological Sciences
PhD: University of Calcutta, 2006
Previous appointments:
2005-2006: Postdoc at UCDavis, CA, USA
2007: Postdoc at UTMB, TX, USA
2007-2010: Postdoc at Bioinformatics Intitute, A*STAR, Singapore
Research interests:
Broader areas of interest: Computational Chemistry and Biology, Bioinformatics, Structural Dynamics of Biomolecules, Molecular Modelling and Drug Design
Biomolecules and their assemblies
are complex chemical systems. Understanding their mechanisms of functions require
various methods of investigations, in truly interdisciplinary mode, covering theoretical,
experimental, computational methods and even data analytics. In our group we address
those questions on the mechanism of functions Biomolecular systems, which would
require insights not only from the molecular structures but also would need the
information on the dynamics of the constituent atoms; in fact in real systems the
atoms and molecules in a cell are always jiggling, dancing and bumping into
each other at any given temperature. For example, one may figure out a model structure
of a protein from the experimental measurement or may obtain from from a structure
database, but that may not be sufficient to guess the mechanical flexibility of
the system which could have relation with the function. The dynamics could be
simulated in computer using fundamental principles of Chemistry, Biochemistry, Physics
and the obtained datasets are analyzed using statistical methods to interpret
the observations in Life sciences. The computations are done on large scale
parallel computing platforms, often using GP-GPU based machines.
Our systems of specific interests are proteins, lipids, nucleic acids, small molecule (drugs). These exercises only tells us how do the biomolecules function but also lead to understand the kind of errors at the molecular level that can result functional defect and diseases. Once this is understood, it provides a direction for designing a lead compound (drug molecule) in a rational manner. Some of our recent interests include (i) mechanism of conformational modulations on αβ-Tubulin dimer and their control over cell divisions, (ii) structural dynamics of the Bcl2 family of proteins and their role in apoptosis and cancer therapy, (iii) Kinase allosteric and their inhibition using drug molecules, (iv) ligand design and various others.
Primarily we use standard molecular dynamics methods to simulate the all-atom dynamics of the systems and also use more advanced methods of accelerated molecular dynamics to compute the free energy landscapes of the biomolecular functions. We are also using machine learning based approaches to analyze conformational ensembles.
Here is a list of selected publications:
J Chem Inf Model. 2023, 63, 224-239.
Comput Biol Chem 2022; 96, 107617.
Biochemistry 2020, 59, 45, 4353
J. Chem. Inf. Model. 2019, 59, 5, 2274
J. Chem. Inf. Model. 2018, 58, 2, 370
J. Phys. Chem. B 2017, 121, 1, 118
Biochemistry 2016, 55, 2, 335
Phys Chem Chem Phys 2016, 18, 24095
Biochemistry 2012, 51, 36, 7138
Click here for the complete list
(Movies, with specific scientific insights, are available as the supporting information of these articles, which are usually available free of charges from the journal websites)
Group Members (current): Debadrita Basu (SRF), Debarati Paul (SRF), Nibedita Ray Chaudhuri (SRF), Premananda Basak (SRF), Megha Ghosh (JRF), Jit Ghosh (JRF)
Ph.D. positions: Our group is looking for at least 2-3 motivated students. Candidates with Masters in Chemistry/ Biophysics/ Biochemistry/ Physics/ Biotechnology/ Statistics/ Computer Applications, etc. and with NET-JRF or equivalent qualification for fellowship may send their CV by email to sgd[at]jcbose.ac.in.
Postdoc/RA positions: Currently we are looking for candidates with knowledge on Machine Learning based data analytics or at least the candidate who have interest to learn these methods to make applications. Anyone willing to apply for N-PDF (SERB)/ DBT-RA or equivalent, may contact by email.
Contact:
Address: |
Biological Sciences Unified Academic Campus Bose Institute EN-80, Sector V Bidhan Nagar Kolkata - 700 091, India |
E-Mail: | sgd[at]jcbose.ac.in |
Phone: | +91-33-25693218 |
Research:
Publications:
Publications: 2011 - 2021
1. De A, Maity
A, Mazumder M, Mondal B, Mukherjee A, Ghosh S, Ray P, Polley S, Ghosh Dastidar S, Basu D., Plant Sci. 2021, 309:110953, Overexpression of LYK4, a lysin motif
receptor with non-functional kinase domain, enhances tolerance to Alternaria
brassicicola and increases trichome density in Brassica juncea.
2.
Paul D, Basu D, Ghosh Dastidar S., J Mol
Model. 2021;27(5):128. Multi-conformation
representation of Mpro identifies promising candidates for drug repurposing
against COVID-19.
3. Sinha S, Ghosh Dastidar S., Biochemistry 2020; 59(45):4353-4366. Shifting Polar Residues Across Primary Sequence Frames of Transmembrane
Domains Calibrates Membrane Permeation Thermodynamics.
4. Bhattacharyya
R, Dhar J, Ghosh Dastidar S,
Chakrabarti P, Weiss MS., IUCrJ. 2020;7(Pt
5):825-834.’ The susceptibility of
disulfide bonds towards radiation damage may be explained by S⋯O interactions.
5. Shohan MUS, Sinha S, Nabila FH, Ghosh Dastidar S, Seraj ZI. Front
Plant Sci. 2019 Nov 4;10:1420. HKT1;5
Transporter Gene Expression and Association of Amino Acid Substitutions With
Salt Tolerance Across Rice Genotypes.
6. Meher G, Sinha S, Pattnaik
GP, Ghosh Dastidar S, Chakraborty H., J Phys Chem B. 2019 [Accepted]
Cholesterol Modulates Membrane Properties and the Interaction of gp41 Fusion
Peptide to Promote Membrane Fusion.
7. Maity A, Sinha S, Ghosh
Dastidar S., Chem Phys Lipids. 2019 Jan;218:112-124.
,Dissecting the thermodynamic contributions of the charged residues in the
membrane anchoring of Bcl-xl C-terminal domain.
8. Majumdar S, Basu D, Ghosh
Dastidar S., J Chem Inf Model. 2019 May
28;59(5):2274-2286. ,Conformational States of E7010 Is Complemented by
Microclusters of Water Inside the α,β-Tubulin Core.
9. Chakraborty J, Priya P, Ghosh
Dastidar S, Das S., Plant Sci. 2018 Nov;276:111-133. ,
Physical interaction between nuclear accumulated CC-NB-ARC-LRR protein and
WRKY64 promotes EDS1 dependent Fusarium wilt resistance in chickpea.
10. Maity A, Majumdar S, Ghosh
Dastidar S., Comput Biol Chem. 2018 Dec;77:17-27. ,
Flexibility enables to discriminate between ligands: Lessons from structural
ensembles of Bcl-xl and Mcl-1.
11. Sinha S, Maity A, Ghosh
Dastidar S., J Chem Inf Model. 2018 Feb 26;58(2):370-382.
, BIM Binding Remotely Regulates BAX Activation: Insights from the Free Energy
Landscapes.,
12. Basak P, Maitra-Majee S, Das JK,
Mukherjee A, Ghosh Dastidar S, Pal Choudhury P, Lahiri Majumder A.,
PLoS One. 2017 Sep 26;12(9):e0185351. ,An evolutionary
analysis identifies a conserved pentapeptide stretch containing the two
essential lysine residues for rice L-myo-inositol 1-phosphate synthase catalytic
activity.
13. Priya P, Maity A, Ghosh
Dastidar S., Proteins. 2017 Aug;85(8):1567-1579. ,The long
unstructured region of Bcl-xl modulates its structural dynamics.
14. Majumdar S, Ghosh
Dastidar S., J Phys Chem B. 2017 Jan 12;121(1):118-128. ,
Ligand Binding Swaps between Soft Internal Modes of α,β-Tubulin and Alters Its
Accessible Conformational Space.
15. Maity A, Sinha S, Ganguly
D, Ghosh Dastidar S., Phys Chem Chem Phys. 2016 Aug
24;18(34):24095-105. C-terminal tail insertion of Bcl-xL in membrane occurs via
partial unfolding and refolding cycle associating microsolvation.
16. Majumdar S, Maiti S, Ghosh
Dastidar S, Biochemistry. 2016; 55, 335-47.Dynamic and
Static Water Molecules Complement the TN16 Conformational Heterogeneity inside
the Tubulin Cavity.
17. Sinha A, Ray A, Ganguly S, Ghosh
Dastidar S, Sarkar S., Biol Direct. 2015 Sep 30;10(1):56.
Variation in the ribosome interacting loop of the Sec61α from Giardia lamblia.
18. Bhar K, Maity A, Ghosh A, Das
T, Ghosh Dastidar S, Siddhanta A., Protein J. 2015 Apr;34(2):158-67.,
Phosphorylation of Leghemoglobin at S45 is Most Effective to Disrupt the
Molecular Environment of Its Oxygen Binding Pocket.
19. Priya P, Maity A, Majumdar
S, Ghosh Dastidar S., J Mol Graph Model. 2015 Jun;59:1-13.
Interactions between Bcl-xl and its inhibitors: Insights into ligand design
from molecular dynamics simulation.
20. Maity A, Majumdar S, Priya P, De
P, Saha S, Ghosh Dastidar S, Adaptability in protein structures:
Structural dynamics and implications in ligand design (Review), J Bio Mol
Struc Dyn J Biomol Struct Dyn. 2015;33(2):298-321
21. Maity A, Yadav S, Verma
CS, Ghosh Dastidar S, Dynamics of Bcl-xl in Water and Membrane:
Molecular Simulations PLoS One (2013) 8, e76837.
22. Sengupta A, Sarkar A, Priya
P, Ghosh Dastidar S, Das
S, New Insight to Structure-Function Relationship of GalNAc Mediated Primary
Interaction between Insecticidal Cry1Ac Toxin and HaALP Receptor of Helicoverpa
armigeraí. PLoS One (2013) 8,
e78249.
23. Chakraborti S, Chakravarty D,
Gupta S, Chatterji BP, Dhar G, Poddar A, Panda D, Chakrabarti P, Ghosh Dastidar S(*)and
Bhattacharyya B(*), Biochemistry 51,7 138 (2012), Discrimination
of Ligands with Different Flexibilities Resulting from the Plasticity of the
Binding Site in Tubulin
24. Ghosh Dastidar S, Lane DP, Verma CS, Cell
Cycle 11: 2239-47 (2012) Why is F19Ap53 unable to
bind MDM2? Simulations suggest crack propagation modulates binding
25. C. J. Brown, S. Ghosh
Dastidar, S. T. Quah, A. Lim, B. Chia, C. S. Verma. PLoS One 6, e24122 (2011) C-Terminal
Substitution of MDM2 Interacting Peptides Modulates Binding Affinity by
Distinctive Mechanism
26. G. Fuentes, S. Ghosh Dastidar, A. Madhumalar, C. S.
Verma, Drug Dev. Res. 72, 26 (2011) Role
of protein flexibility in the Discovery of New Drugs (Review Article)
27. S. Ghosh Dastidar, D. Raghunathan, J. Nicholson, T. R.
Hupp, D. P. Lane, C. S. Verma, Cell Cycle 10, 82 (2011); Chemical
States of the N-terminal “lid” of MDM2 regulate p53 binding
Recognition:
Teaching:
Students:
Image | Name | Designation | Department | Campus | Contact number | |
---|---|---|---|---|---|---|
![]() |
Jit Ghosh | Junior Research Fellow | Bioinformatics Centre | Unified | gjit226@gmail.com | |
![]() |
Megha Ghosh | Junior Research Fellow | Bioinformatics Centre | Unified | ghoshmegha39@gmail.com | |
![]() |
Premananda Basak | Senior Research Fellow | Bioinformatics Centre | Centenary | premabasaknanda@gmail.com |
Former:
Ex students who have already been awarded with the doctoral degree:
1. Souvik
Sinha, Ph.D. (2021), Postdoctoral Fellow, University of California at Irvine
2. Sarmistha Majumdar, Ph.D. (2019), Scientist-I at Schrödinger, Inc.; Former Postdoctoral Fellow, Istituto Italiano di Tecnologia, Italy
3. Prerna Priya, Ph.D. (2019), Guest Lecturer at Department of Botany, Purnea University,
India
Trainee/Interns, etc.
To be updated .......
Group News:
Group Members (current): Debadrita Basu (SRF), Debarati Paul (SRF), Nibedita Ray Chaudhuri (SRF), Premananda Basak (SRF), Premananda Basak (SRF), Megha Ghosh (JRF), Jit Ghosh (JRF)
Ph.D. positions: Our group is looking for at least 2-3 motivated candidates. Candidates with Masters in Chemistry/ Biophysics/ Biochemistry/ Physics/ Biotechnology/ Statistics/ Computer Applications, etc. and with NET-JRF or equivalent qualification for fellowship may send their CV by email to sgd[at]jcbose.ac.in.
Postdoc/RA positions: Currently we are looking for candidates with knowledge on Machine Learning based data analytics or at least a candidate who has interest to learn these methods to make applications. Anyone willing to apply for N-PDF (SERB)/ DBT-RA or equivalent, may contact by email.