Prof. Sanjoy Bandyopadhyay

Department of Chemistry and Centre for Computational and Data Sciences

Indian Institute of Technology, Kharagpur-721302, India

E-mail id:sanjoy[at]chem.iitkgp.ac.in

 

Brief Bio-sketch:

PhD from Indian Institute of Science, Bangalore (1997); Post-doctoral research at University of Pennsylvania, USA (1997 to 2001); joined IIT Kharagpur as Asst. Prof. in 2001; currently Professor at the Dept. of Chemistry and Head, Centre for Computational and Data Sciences, IIT Kharagpur. Research interest is in the broad area of biophysical chemistry using state-of-the-art computer simulation methods. Recipient of CRSI Bronze Medal (2017).

 

SOLVENT-MEDIATED PROTEIN-DNA INTERACTIONS

Biomolecular recognition is a necessary step for many biological processes. As proteins are present in great variety in living systems, one of the components in such recognition is almost always a protein¹. For example, single-stranded DNA binding (SSB) proteins bind with single-stranded DNA (ss-DNA) oligomers that are generated as intermediates during DNA metabolic processes. The important issues in protein-DNA binding are how a protein recognizes the target DNA and the role played by water in mediating the interactions between them, and thereby controlling the structure, stability, and dynamics of the hydrated complex formed. We have carried out molecular dynamics (MD) simulations of two DNA binding K homology (KH) domains (KH3 and KH4) of the far upstream element (FUSE) binding protein (FBP) complexed with two ss-DNA oligomers². Calculations were carried out to understand the effects of complexation on the internal motions of the protein domains and the relative free energy changes associated with the formation of such complexes^3,4. Role played by water in freezing the conformational oscillations of the DNA oligomers during complexation has been explored in detail^5,6. Similar findings on other protein-DNA complex systems will also be highlighted⁷.

 

References :

1.    D. L. Nelson and M. M. Cox. Lehninger Principles of Biochemistry (3rd Ed., Worth: New York, 2000).

2.    D. T. Braddock, J. M. Louis, J. L. Baber, D. Levens and G. M. Clore. Nature 2002, 415, 1051.

3.    K. Chakraborty and S. Bandyopadhyay. J. Phys. Chem. B 2015, 119, 10998.

4.    K. Chakraborty, S. K. Sinha and S. Bandyopadhyay. J. Chem. Phys. 2016, 144, 205105.

5.    K. Chakraborty and S. Bandyopadhyay. J. Chem. Phys. 2015, 143, 045106.

6.    K. Chakraborty and S. Bandyopadhyay. Phys. Chem. Chem. Phys. 2016, 18, 7780.

7.    S. Mondal, K. Chakraborty and S. Bandyopadhyay. Phys. Chem. Chem. Phys. 2017, 19, 32459.