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:

The broader areas of interests of our group cover different areas of Chemistry, Biophysics, Biochemistry, Molecular Biology, etc. with aims to understand the molecular mechanisms of biological events. We primarily explore the computational methods to answer the scientific questions which we aim to address and we often collaborate with the experimentalists to validate the understanding and predictions. We investigate the chemical structures of the Proteins, Lipids, Nucleic acids, small molecule (drugs) and their assemblies to understand their mechanism of functions. These exercises 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.

The atoms and molecules in a cell are always jiggling, dancing and bumping into each other and therefore the molar structures are not frozen objects; they are continuously changing their shape/conformation, mode of interactions etc. Therefore the investigations of the structural properties requires the mimicry of such dynamic charters of the molecules. Our work begins by mimicking such realistic molecular situations using computer simulations and then their events of changes in structures and encounters are witnessed, analyzed and utilized for making predictions.  A few and more specific examples of our direction of work would be available in the Research page  and in the list of publications.

Ph.D. positions: We accept students with masters in Chemistry, Physics, BioPhysics, Biochemistry, etc. to pursue research for Ph.D. Interested candidates can contact by email by sending their CV to sgd[at]jcbose.ac.in.  Having NET or equivalent qualification would be an advantage.   

Postdoc/RA positions: Candidateds willing to join our group as a postdoc/RA with NPDF/DBT-RA (and any other equivalent fellowships) may contact us through email. Currently we are looking for candidates with some experience in machine learning/AI etc. with programming skills.

Contact:

Address: Bioinformatics Centre
Centenary Campus
Bose Institute
P-1/12 C.I.T. Scheme VII-M
Kolkata - 700054, India
E-Mail: sgd[at]jcbose.ac.in
Phone: +91-33-25693332

Research:

The atoms and molecules in a cell are always jiggling, dancing and bumping into each other and occasionally carrying out a specific reaction or a process. Hence it is important to understand how exactly this is choreographed, i.e. how such motions influence the molecular structures. Such dynamics of the molecular structures forms the basis of the conformational changes of the molecules, their interaction with other molecules and thus determines the function of the molecules. Therefore dissecting the characteristics of the dynamics of a bimolecular systempaves the way to the understanding of the molecular mechanism of their function. The general interest of our group is to gain novel insight into biology analyzing the structure, dynamics and the statistical thermodynamics of the molecular systems using computer simulations. These methods not only help to understand the biomolecular mechanism of functions but can also reveal how the molecular defects can lead to a disease, which becomes useful for designing drugs in a rational manner. Overall, we are dealing with protein-protein, protein-lipid bilayers, and protein-ligand interactions in all atom description.  A few examples of the research directions are the following:

Kinase allostery: Understanding the molecules mechanims of allosteric regulation in kinases is one of our major intesrests. This is not only for fundametal understandg but also for designing suitiable inhibtors to interfere with the intrinsic allostery with therapeutic interests. 

α,β-dimer of tubulin: Arresting the cell cycle discouraging the mitotic spindle formation by disintegrating the microtubules is a promising strategy to combat cancer. This could be achieved by influencing the conformational states of the constitutional unit of microtubule, i.e. the α,β-dimer of tubulin. Though several ligands were already known to be able to do this, we have made a fundamental contribution by revealing how the ligands achieve this by causing disturbance on the vibrational states of the dimer. We are in process to take this concept forward by demonstrating the mechanism on analogous systems.

Bcl2 family: The apoptotic machinery of the cell sets the defective cells to suicide and thus prevents the growth of a disease and Bcl2 is a family of proteins that has a direct role to activate this pathway. In recent years we have contributed to the understanding of the conformational dynamics of these proteins which are correlated with the activation of the apoptotic machinery. We have been investigating the thermodynamics of the insertion of these proteins in the membrane and their conformational alterations. These proteins are highly flexible and yet are lucrative drug target for cancer therapy. We are deeply engaged in the design of novel compounds to target these proteins.

Bridging water: The water is everywhere but the significance of their presence is not same in every place. In general, the water as the natural solvent creates the surrounding environment of a biomolecule and determines its shape as well as their interactions with others. But often the individual water moleculesare found to mediate the molecular recognition, whose role in the biomolecular functionis significantly different from the bulk water (i.e. solvent). Identifying such water bridging the interactions between two molecular entities and quantifying their role are extremely important for the accuracy of the computational analysis of molecular recognition and drug design. We are carrying out such investigations and have recently reported the role of few such water in Tubulin-ligand binding as well as the microsolvation of peptides during its membrane insertion.

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 SO 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 Tubuli

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 Chandradeep Basu Senior Research Fellow Biophysics Centenary 25693215
    profile image Debarati Paul Senior Research Fellow Bioinformatics Centre Centenary 25693275 pdebarati
    profile image Premananda Basak Junior Research Fellow Bioinformatics Centre Centenary
    profile image Premananda Basak Junior Research Fellow Bioinformatics Centre Centenary

    Former:

    1.    Souvik Sinha, submitted thesis for PhD in 2020, currently is a Postdoctoral Fellow at University of California at Irvine

    2.    Sarmistha Majumdar, Ph.D. (2019), currently is a Postdoctoral Fellow at Istituto Italiano di Tecnologia, Italy

    3.    Prerna Priya, Ph.D. (2019), currently is a Guest Lecturer at Department of Botany, Purnea University, India

    4.    Atanu Maity, Ph.D. (2018), currently is a postdoctoral fellow at Department of Chemistry, IIT Bombay, India


    Group News:

    Openings: 

     

    Ph.D. positions: We accept students with masters in Chemistry, Physics, BioPhysics, Biochemistry, etc. to pursue research for Ph.D. Interested candidates can contact by email by sending their CV to sgd[at]jcbose.ac.in.  Having NET or equivalent qualification would be an advantage.   

    Postdoc/RA positions: Candidateds willing to join our group as a postdoc/RA with NPDF/DBT-RA (and any other equivalent fellowships) may contact us through email. Currently we are looking for candidates with some experience in machine learning/AI etc. with programming skills.