Rajagopal Chattopadhyaya
Professor , Biochemistry
PhD: University of California, Los Angeles (1987)

Research interest
 

My primary interest is determining three dimensional structures of macromolecules by crystallography and other methods.  We are also interested in biochemical characterization of purified proteins.  We proposed the first 3D model of the LexA repressor bound to the recA operator (PDB code 1qaa), the first structure processed (02.02.1999) from Bose Institute (see also publication #10 below). Later, crystal structures of several operator-free mutants of LexA were reported by another group, largely verifying our original model.  We then used these crystal structures to generate an improved model (PDB code 1mvd) of the LexA dimer bound to the recA operator, and also to show how good our original model was (publication #15).

 Three different alternative models of the lambda cI repressor tetramer bound to adjacent operator sites was published in 2003 (publication #13), easily one of the important structures reported from India in recent years.  These are available in the PDB as entries 1gfx, 1j5g and 1lwq.  The structure of region 136-230 predicted in 1gfx (processes June 22, 2000) was found to be nearly identical (1.24 Angstrom RMS deviation) to the independently determined crystal structure of the 132-236 fragment, 1f39, released later by the PDB.  The study correlates these models with functional, biochemical, biophysical and immunological data on the repressor in the literature.

 I have also deposited full 3D models of type IV pilins in some enteropathogenic organisms like Vibrio cholerae, enteropathogenic E. coli, enterotoxigenic E. coli (vide PDB entries 1qqz, 1qt2 and 1c4h) built from biochemical data available in the literature about the V. cholerae pilin.  Publication #12 below describes the model and its rationality.  Subsequently, a crystal structure of a truncated V. cholerae pilin was published and partly verified our predicted model.  We would like to improve the models for the two other E. coli pilins based on this crystal structure using our approach.

A 3D model for the mycobacteriophage L1 repressor bound to its cognate operator (PDB entry 1z0l) was deposited.  Work has been completed in constructing three dimensional models of NB-ARC domains in five different proteins of which two are for tomato species, one each for flax, Arabidopsis and nematode, based on the recently published (2005) crystal structure of the apoptotic protease activating factor 1. The plant proteins are the so-called R proteins that lead to host cell defense through some signal transduction pathway.  This works was done in collaboration with Prof Amita Pal of PMCG (publication #16 below). Atasi’s work is also completed in studying protease mediated cleavage in lambda cI repressor (publication #17 below) and correlating results with various of our own models and those found in crystal structures. Understanding of RecA mediated self-cleavage of the lambda cI repressor has been advanced to a great extent through Atasi’s recent paper (publication # 18). At present we are attempting crystallographic studies of some plant proteins


Name of group members (in 2010)

  • Mr. Himadri Biswas (JRF)
     
Important publications in chronological order

1.      Chattopadhyaya, R., Ikuta, S., Grzeskowiak, K. & Dickerson, R. E. (1988) X-Ray Structure of a DNA hairpin molecule, Nature, 334, 175-179.

2.      Chattopadhyaya, R., Grzeskowiak, K. & Dickerson, R. E. (1990) Structure of a T4 Hairpin Loop on a Z-DNA Stem and Comparison with A-RNA and B-DNA Loops, Journal of Molecular Biology, 211, 189-210.

3.      Chattopadhyaya, R., Luecke, H. & Quiocho, F. A. (1991) Phosphate Binding Protein -- extension of studies to 1.18A, Book of Abstracts, Seventh Conversation in Biomolecular Stereodynamics, p.25.

4.      Chattopadhyaya, R., Meador, W. E., Means, A. & Quiocho, F. A. (1992) Structure of calmodulin refined at 1.7A resolution, Journal of Molecular Biology, 228, 1177-1192.

5.      Luo, Y., Henle, E., Chattopadhyaya, R., Jin, R. & Linn, S. (1994) Detecting DNA damage caused by iron and hydrogen peroxide, Methods in Enzymology, 234, 51-59.

6.      Home, D. & Chattopadhyaya, R. (1996) DNA Molecular Cousin of Schrodinger's Cat : A curious example of Quantum Measurement, Physical Review Letters, 76, 2836-2839.

7.      Home, D. & Chattopadhyaya, R. (1998) Reply to Comment, Physical Review Letters, 80, 1349.

8.      Chattopadhyaya, R. & Goswami, B. (1997) A sturdy box design for sitting drop crystallization, Journal of Applied Crystallography, 30, 182-183.

9.      Namboodiri, V. M. H. & Chattopadhyaya, R. (2000) Purification and Biochemical Characterization of a Novel Thermostable Lipase from Aspergillus niger, Lipids, 35, 495-502.

10.  Chattopadhyaya, R., Ghosh, K. & Namboodiri, V. M. H. (2000) Model of LexA Repressor Dimer Bound to recA Operator, Journal of Biomolecular Structure and Dynamics, 18, 181-197. Our figures on the front cover of this number.

11.  Ghosh, K. & Chattopadhyaya, R. (2001) Papain does not cleave operator-bound lambda repressor : structural characterization of the carboxy terminal domain and the hinge, Journal of Biomolecular Structure and Dynamics, 18, 557-567.

12.  Chattopadhyaya, R. & Ghose, A. C. (2002) Model of Vibrio cholerae toxin coregulated pilin capable of filament formation, Protein Engineering, 15, 297-304.

13.  Chattopadhyaya, R. & Ghosh, K. (2003) A comparative three-dimensional model of the carboxy-terminal domain of the lambda repressor and its use to build intact repressor tetramer models bound to adjacent operator sites, Journal of Structural Biology, 141, 103-114.

14.  Ghosh, K., Pal, A. & Chattopadhyaya, R. (2004) pH-dependent autocleavage of λ repressor occurs in the operator-bound form : characterization of λ repressor autocleavage, Biochemical Journal, 379, 325-330.

15.  Chattopadhyaya, R. & Pal, A. (2004) Improved Model of a LexA Repressor Dimer Bound to recA Operator, Journal of Biomolecular Structure and Dynamics, 21, 681-689.

16.  Chattopadhyaya, R. & Pal, A. (2008) Three-dimensional Models of NB-ARC Domains of Disease Resistance Proteins in Tomato, Arabidopsis, and Flax, Journal of Biomolecular Structure and Dynamics, 25, 357-372.

17.   Pal, A. & Chattopadhyaya, R. (2008) Digestion of the λ cI repressor with various serine proteases and correlation with its three dimensional structure, Journal of Biomolecular Structure and Dynamics, 26, 339-354.

18.  Pal, A. & Chattopadhyaya, R (2009) RecA-mediated cleavage of λ cI repressor accepts repressor dimers : probable role of prolyl cis-trans isomerization and catalytic involvement of H163, K177 and K232 of RecA, Journal of Biomolecular Structure and Dynamics, 27, 221-234.

Contact

raja@boseinst.ernet.in