Shubhra Ghosh Dastidar
Shubhra Ghosh Dastidar
Associate Professor, Bioinformatics Centre
PhD: University of Calcutta, 2006
2005-2006: Postdoc at UCDavis, CA, USA
2007: Postdoc at UTMB, TX, USA
2007-2010: Postdoc at Bioinformatics Intitute, A*STAR, Singapore
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.
P-1/12 C.I.T. Scheme VII-M
Kolkata - 700054, India
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:
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.
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.
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.
1. 1. Maity A., Majumder S., Ghosh Dastidar S., Computational Biology and Chemistry, Accepted 2018, Flexibility enables to discriminate between ligands: lessons from structural ensembles of Bcl-xl and Mcl-1
2. 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.
3. 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.
4. 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.
5. 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.
6. Majumdar S, Ghosh Dastidar S., Ligand Binding Swaps between Soft Internal Modes of α,β-Tubulin and Alters Its Accessible Conformational Space.J Phys Chem B. 2017 Jan 12;121(1):118-128
7. 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.
8. 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.
9. Bhar K, Maity A, Ghosh A, Das T, Dastidar SG, 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.
10. 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.
11. Maity A, Majumdar S, Priya P, De P, Saha S, Dastidar SG, Adaptability in protein structures: Structural dynamics and implications in ligand design (Review), J Bio Mol Struc Dyn 2015;33(2):298-321
12. Maity A, Yadav S, Verma CS, Dastidar SG, Dynamics of Bcl-xl in Water and Membrane: Molecular Simulations PLoS One 2013, 8, e76837.
13. Sengupta A, Sarkar A, Priya P, Dastidar SG, 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.
14. Chakraborti S, Chakravarty D, Gupta S, Chatterji BP, Dhar G, Poddar A, Panda D, Chakrabarti P, Dastidar SG(*)and Bhattacharyya B(*), Biochemistry 2012, 51,7 138 Discrimination of Ligands with Different Flexibilities Resulting from the Plasticity of the Binding Site in Tubulin
15. Dastidar SG, Lane DP, Verma CS, Cell Cycle 2012, 11: 2239-47 Why is F19Ap53 unable to bind MDM2? Simulations suggest crack propagation modulates binding
16. Brown C. J. £, S. G. Ghosh Dastidar£, Quah S, Lim A, Chia B, Verma. C. S. PLoS One 2011, 6, e24122 C-Terminal Substitution of MDM2 Interacting Peptides Modulates Binding Affinity by Distinctive Mechanisms
17. Fuentes G., Ghosh Dastidar S, Madhumalar A, Verma C. S., Drug Dev. Res 2011 72, 26 Role of protein flexibility in the Discovery of New Drugs (Review Article)
18. Ghosh Dastidar S, Raghunathan D, Nicholson J, Hupp T. R., Lane D. P., Verma C. S., Cell Cycle 2011, 10, 82; Chemical States of the N-terminal “lid” of MDM2 regulate p53 binding
|Debarati Paul||Junior Research Fellow||Bioinformatics Centre||Centenary||25693275||pdebarati|
|Souvik Sinha||Senior Research Fellow||Bioinformatics Centre||Centenary||25693275||souvik|
Postdoctoral Fellows / RA :
|Uttam Kumar Basak||Research Associate||Bioinformatics Centre||Centenary||25693267|
PhD: Multiple positions are available for students willing to pursue PhD in computational chemistry and/or in computational biology. Candidates who have secured fellowships through NET or any other equivalent examination can send their CV along with a cover letter to sgd[at]jcbose.ac.in
RA/Postdoc: Candidates willing to carry out postdoctoral research can also contact by email. We generally encourage them to apply for NPDF of any other equivalent fellowships; we shall help the candidate to design a project.