PhD: University of California, Los Angeles (1987)
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
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
Important publications in chronological order
Name of group members (in 2010)
Chattopadhyaya, R., Ikuta, S., Grzeskowiak, K. & Dickerson, R. E. (1988)
X-Ray Structure of a DNA hairpin molecule, Nature, 334, 175-179.
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.
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.
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.
Henle, E., Chattopadhyaya, R., Jin, R. & Linn, S. (1994) Detecting DNA
damage caused by iron and hydrogen peroxide, Methods in Enzymology, 234,
Home, D. &
Chattopadhyaya, R. (1996) DNA Molecular Cousin of Schrodinger's Cat : A
curious example of Quantum Measurement, Physical Review Letters, 76,
Home, D. &
Chattopadhyaya, R. (1998) Reply to Comment, Physical Review Letters, 80,
Chattopadhyaya, R. & Goswami, B. (1997) A sturdy box design for sitting drop
crystallization, Journal of Applied Crystallography, 30, 182-183.
V. M. H. & Chattopadhyaya, R. (2000) Purification and Biochemical
Characterization of a Novel Thermostable Lipase from Aspergillus niger,
Lipids, 35, 495-502.
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.
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.
Chattopadhyaya, R. & Ghose, A. C. (2002) Model of Vibrio cholerae toxin
coregulated pilin capable of filament formation, Protein Engineering, 15,
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.
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.
Chattopadhyaya, R. & Pal, A. (2004) Improved Model of a LexA Repressor Dimer
Bound to recA Operator, Journal of Biomolecular Structure and Dynamics, 21,
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.
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.
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.