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bose

Bioinformatics Centre
A.J.C. Bose Centenary Building,
P-1/12, CIT Scheme - VII M,
Kolkata - 700 054, India



Dr. SHUBHRA GHOSH DASTIDAR




RESEARCH I LAB MEMBERS PUBLICATIONS

Associate Professor

sgd(AT)jcbose.ac.in

Tel:+91-33-2569 3332

Fax:+91-33-2355 3886

[BIC Profile]

 

 

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Area of Research: Computational biophysics and physical chemistry, biomolecular modelling and dynamics simulation, ligand design
 

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.

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Research positions:Students/postdocs trained in various disciplines e.g. Chemistry, Physics, Biochemistry, Biophysics, Biological Sciences and Computer Science etc. can participate in our projects.Candidates willing to work as JRF/SRF/RA, may send their query over email; NET/GATE qualification is essential for the JRF/SRF positions.

Infrastructure:
We have computer clusters of High Performance, with different architectures, including CPU and GPU based facilities.



Selected Publications: 2012 -onwards

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

Maity A, Sinha S, Ganguly D, Ghosh Dastidar S.C-terminal tail insertion of Bcl-xL in membrane occurs via partial unfolding and refolding cycle associating microsolvation. Phys Chem Chem Phys. 2016; 18(34):24095-105.

Majumdar S, Maiti S, Ghosh Dastidar S. Dynamic and Static Water Molecules Complement the TN16 Conformational Heterogeneity inside the Tubulin Cavity. Biochemistry. 2016; 55, 335-47.

Priya P, Maity A, Majumdar S, Ghosh Dastidar S, J Mol Graph Model (2015) Mar 6;59:1-13. Interactions between Bcl-xl and its inhibitors: Insights into ligand design from molecular dynamics simulation. 

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 . 

Maity A, Yadav S, Verma CS, Dastidar SG, Dynamics of Bcl-xl in Water and Membrane: Molecular Simulations PLoS One (2013) 8, e76837. 

Chakraborti S, Chakravarty D, Gupta S, Chatterji BP, Dhar G, Poddar A, Panda D, Chakrabarti P, Dastidar SG(*) and Bhattacharyya B (*),Discrimination of Ligands with Different Flexibilities Resulting from the Plasticity of the Binding Site in Tubulin, Biochemistry (2012) 51, 7138-48. 

Dastidar SG, Lane DP, Verma CS. Why is F19Ap53 unable to bind MDM2? Simulations suggest crack propagation modulates binding, Cell Cycle (2012); 11: 2239-47. 


 




© Bioinformatics Centre (BIC), Bose Institute, Kolkata 2011, Last updated on: January 20, 2017