Shubhra Ghosh Dastidar

Shubhra Ghosh Dastidar
Professor

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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, Drug Design, Data Science, Machine Learning and AI, Structure and Dynamics of Biomolecules,  Molecular Modelling and Simulations


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 developing machine learning based protocols to analyze conformational ensembles. 


Ongoing project: DBT funded 'Bioinformatics Centre' at Bose Institute (Role:  PI and Coordinator)


Here is a list of selected publications:

 

Comput Biol Chem. 2024;108:108004

Proteins. 2023, doi: 10.1002/prot.26634

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)

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

 

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Recognition:

    Teaching:

    Students:

    Image Name Designation Department Campus Contact number Email
    profile image Jit Ghosh Junior Research Fellow Bioinformatics Centre Unified gjit226@gmail.com
    profile image Megha Ghosh Junior Research Fellow Bioinformatics Centre Unified ghoshmegha39@gmail.com
    profile image 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

    4.    Atanu Maity, Ph.D. (2018), Postdoctoral Fellow, Department of Chemistry, IIT Bombay, 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.