Rajagopal Chattopadhyaya

Rajagopal Chattopadhyaya
Professor

Previous appointments:

During October 1987 through April 1988, was postdoctoral in the same laboratory under Prof. Richard E Dickerson at UCLA to finish up writing papers.

During April 1988 through July 1990, postdoctoral at U.C. Berkeley under Prof. Stuart M. Linn, Biochemistry Department, on DNA damage.

During July 1990 through October 1993, HHMI postdoctoral at Baylor College of Medicine under Prof. Florante A. Quiocho, protein crystallography.

Research interests:

This section describes only my current and future research interests being carried out, while the rest is given below in detail.

The 1.74Å crystal structure of the dietary storage protein, a lectin from Colocasia esculenta was been solved and deposited to the PDB in August 2015 (code 5D5G).  Recently, our paper describing that structure is in the press (publication #43).  Two more papers are being prepared about the same lectin : one about the biophysical properties and another about the crystal structure of the same lectin when complexed with mannose (PDB ID 5D9Z).

Efforts are continuing to solve the crystal structure of the transcription-activator protein C1 of bacteriophage P22 in complex with PRE promoter element, which was crystallized and X-ray data collected by Avisek Mondal in 2014 (publication #37 is a preliminary report), by molecular replacement and some progress was made in 2016 by noting the Patterson function.  Have to get the R-factor down !

Contact:

Address: Department of Biochemistry
Centenary Campus
Bose Institute
P-1/12 C.I.T. Scheme VII-M
Kolkata - 700054, India
E-Mail: raja[at]jcbose.ac.in
Phone: +91-33-25693239

Research:

Prof. Chattopadhyaya’s primary interest is determining three dimensional structures of macromolecules by crystallography and other methods.  His group is also interested in biochemical characterization of purified proteins. 

Prof. Chattopadhyaya 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 #20 below). Later, crystal structures of several operator-free mutants of LexA were reported by another group, largely verifying Chattopadhyaya’s original model.  Prof. Chattopadhyaya’s group 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 #27).  These have been described in the 3rd edn (2008) of the classic text by Burton E. Tropp, Molecular Biology : Genes to Proteins, a continuation of David Freifelder's classic molecular biology textbook (1st edn, 1983; 2nd edn, 1987).  It has further been shown that this is the only original work done in India to be mentioned in that undergraduate textbook.

Three different alternative models of the lambda cI repressor tetramer bound to adjacent operator sites was published by Prof. Chattopadhyaya in 2003 (publication #25), 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 (processed June 22, 2000) was found to be nearly identical (1.24Å  R.M.S. 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.  This study has also been used and studied in graduate level courses in several universities in the USA between 2004 and 2010 roughly.

Prof. Chattopadhyaya has 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 #24 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.  Prof. Chattopadhyaya’s group suggested an improved model for the enteropathogenic E. coli pilin BfpA (publication#39) based on the crystal structure.

Prof. Chattopadhyaya deposited a three dimensional model for the mycobacteriophage L1 repressor bound to its cognate operator (PDB entry 1z0l).  Work in constructing models for several nucleotide binding domains associated with disease resistance / apoptosis in a wide range of organisms completed (Publication # 28, PDB entries 2b84, 2b85, 2ft4, 2ft5, 2g2m).  Work is also completed towards the digestion of cI repressor by six different proteases (publication #29) and the understanding of RecA mediated self-cleavage of the lambda cI repressor (publications #30, #41).

Prof. Chattopadhyaya has also constructed a 3D model (PDB entry 2G7D) of dyhydrolipoamide dehydrogenase from Plasmodium falciparum in collaboration with Dr. Debjani Roy of Bose Institute.  Our studies are continuing for computationally predicting some drug molecules that will selectively bind to this protein generated by the malaria parasite, but not to its human counterpart.

Prof. Chattopadhyaya is currently also reviving his old interest in nucleic acids, particularly Fenton reaction-mediated damage of DNA constituents.  He has published two studies based on his old experimental work (deoxyadenosine family, publication#31) and the other (thymidine family, publication#33).  Graduate student Indrani Kar, who submitted her doctoral thesis on January 25, 2017, studied how the presence of several plant extracts influence the amount of Fenton reaction-mediated DNA damage; these plants have been studied by Prof. Chattopadhyaya’a Bose Institute colleague, Dr. Nripendranath Mandal.  The study has already been published around August 2016 (publication #40).  In collaboration with Dr. Hemanta K. Majumder of IICB, an expert on topoisomerases, we have also reported in early 2017 the inhibitory activities in these plant extracts regarding human topoisomerases I and II (publication #42), thus explaining their use as cancer drugs, as found by Dr. N. Mandal and colleagues.

Another of Prof. Chattopadhyaya’s former graduate student at Bose Institute, Dr. Himadri Biswas has completed his studies on several plant lectins for characterizing them by biochemical, biophysical and crystallographic methods (publications #34, #38).

The 1.74Å crystal structure of the dietary storage protein, a lectin from Colocasia esculenta was been solved and deposited to the PDB in August 2015 (code 5D5G).  Recently, our paper describing that structure is in the press (publication #43).  Two more papers are being prepared about the same lectin : one about the biophysical properties and another about the crystal structure of the same lectin when complexed with mannose (PDB ID 5D9Z).

Efforts are continuing to solve the crystal structure of the transcription-activator protein C1 of bacteriophage P22 in complex with PRE promoter element, which was crystallized and X-ray data collected by Avisek Mondal in 2014 (publication #37 is a preliminary report), by molecular replacement and some progress was made in 2016 by noting the Patterson function.

Publications:

Publication from research conducted at High School under my name in use at that time :

0. Chatterjee, Rajagopal (1975)  Friction -- Absolute and Relative, Physics Teacher,17(2), 68-72.

PUBLICATIONS (40 journal articles + 4 abstracts);  from no. 17 onwards, research performed at Bose Institute.

  1. Chattopadhyaya, R. & Ghosh, P. K. (1980)  QUISTOR : Conical injection of Ions around the Z-axis, Int. J. Mass Spectrom. Ion Phys., 36, 365-370.
  2. Chattopadhyaya, R. & Ghosh, P. K. (1981)  QUISTOR : injection of two concentric rings of ions in the X-Y plane, Int. J. Mass Spectrom. Ion Phys., 41, 1-6.
  3. Ikuta, S., Chattopadhyaya, R. & Dickerson, R. E. (1984) The kinetics of phosphodiester condensation reactions on solid support, Nucleic Acids Research, 12, 6511-6522.
  4. Chattopadhyaya, R., Ikuta, S. & Dickerson, R. E. (1985) Preliminary Crystallographic Studies of d(CGCGCGTTTTCGCGCG), Book of Abstracts, Fourth Conversation in Biomolecular Stereodynamics, State University of New York, p.118.
  5. Ikuta, S., Chattopadhyaya, R. & Dickerson, R. E. (1985) Reverse Phase Polystyrene column for Purification and Analysis of DNA Oligomers, Analytical Chemistry, 56, 2253-2256.
  6. Ikuta, S., Chattopadhyaya, R., Ito, H., Dickerson, R. E. & Kearns, D. E. (1986) NMR study of a Synthetic DNA Hairpin, Biochemistry, 25, 4840-4849.
  7. Chattopadhyaya, R. Ikuta, S., Grzeskowiak, K. & Dickerson, R. E. (1987) Progress towards the structure of d(CGCGCGTTTTCGCGCG), a DNA hairpin molecule, Book of Abstracts, Fifth Conversation in Biomolecular Stereodynamics, State University of New York, Albany, pp.47-48.
  8. Chattopadhyaya, R., Ikuta, S., Grzeskowiak, K. & Dickerson, R. E. (1988) X-Ray Structure of a DNA hairpin molecule, Nature, 334, 175-179.
  9. Chattopadhyaya, R. & Chakrabarti, P. (1988) Solving DNA Structures by MERLOT, Acta Crystallographica, B44, 651-657.
  10. Benight, A. S., Wang, Y., Chattopadhyaya, R., Amaratunga, M., Henderson, J., Hanlon, S. & Ikuta, S. (1989)  Conformation and Dynamics of a Left-Handed Z-DNA Hairpin : Studies of d(CGCGCGTTTTCGCGCG) in solution, Biochemistry, 28, 3323-3332.
  11. 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.
  12. Linn, S., Chin, S. M., Henle, E. & Chattopadhyaya, R. (1990) Hydrogen Peroxide toxicity, J. Cellular Biochem., Supplement 14A, p.31
  13. Henle, E., Chattopadhyaya, R. & Linn, S. (1990) Damage of DNA constituents by hydrogen peroxide/iron compared to radiation, J. Cellular Biochem., Supplement 14A, p.74.
  14. 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, State University of New York, Albany, p.25.
  15. 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.
  16. 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.
  17. Home, D. & Chattopadhyaya, R. (1996) DNA Molecular Cousin of Schrodinger's Cat : A curious example of Quantum Measurement, Physical Review Letters, 76, 2836-2839.
  18. Chattopadhyaya, R. & Goswami, B. (1997) A sturdy box design for sitting drop crystallization, Journal of Applied Crystallography, 30, 182-183.
  19. Home, D. & Chattopadhyaya, R. (1998) Reply to Comment, Physical Review Letters, 80, 1349.
  20. Namboodiri, V. M. H. & Chattopadhyaya, R. (2000) Purification and Biochemical Characterization of a Novel Thermostable Lipase from Aspergillus niger, Lipids, 35, 495-502.
  21. 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.
  22. Chattopadhyaya, R. & Ghose, A. C. (2000) Three different abstracts on Vibrio Cholerae toxin coregulated pilin, Bundle forming pilin of enteropathogenic Escherichia coli, and major pilin of human enterotoxigenic Escherichia coli, on CD-ROM for the 5th International meeting of Molecular Epidemiology and Evolutionary Genetics of Infectious Diseases, November 12-16, Hyderabad.  One abstract in Journal of Biomolecular Structure and Dynamics, 18, 1017.  Two abstracts in July 2001, Protein Science, 10, suppl. 2, 117-118.
  23. 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.
  24. Chattopadhyaya, R. & Ghose, A. C. (2002) Model of Vibrio cholerae toxin coregulated pilin capable of filament formation, Protein Engineering, 15, 297-304.
  25. 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.
  26. 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.
  27. 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.
  28. 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.
  29.  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.
  30. 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.
  31. Chattopadhyaya, R. & Goswami, B. (2012) Oxidative damage to DNA constituents by iron-mediated Fenton reactions -- the deoxyadenosine family, Journal of Biomolecular Structure and Dynamics, 30, 394-406.
  32. Biswas, H., Kar, I & Chattopadhyaya, R. Deoxyadenosine family : improved synthesis, DNA damage and repair, analogs as drugs. Biomolecular Concepts, 4, 401-410 (2013).
  33. Chattopadhyaya, R. (2014) Oxidative damage to DNA constituents by iron-mediated Fenton reactions -- the thymidine family, Journal of Biomolecular Structure and Dynamics, 32, 155-169.
  34. Biswas, H. & Chattopadhyaya, R. (2014) Thermal, Chemical and pH induced unfolding of turmeric root lectin: modes of denaturation Modes of Denaturation. PLoS ONE 9(8): e103579. doi:10.1371/journal.pone.0103579
  35. Chattopadhyaya, R. (2014) Book Review in Current Science, July 10 issue, 125-126.
  36. Polley, S., Chakravarty, D., Chakrabarti, G., Chattopadhyaya, R. & Sau, S. (2015) Proline substitutions in a Mip-like peptidyl-prolyl cis-trans isomerase severely affects its structure, stability, shape and activity. Biochimie Open, 1, 28-39.
  37. Mondal, A., Chattopadhyaya, R., Datta, A. B. & Parrack, P. (2015) Crystallization and X-ray analysis of the transcription-activator protein C1 of bacteriophage P22 in complex with PRE promoter element. Acta Crystallographica, F71, 1286-1291.
  38. Biswas, H. & Chattopadhyaya, R. (2016) Stability of Curcuma longa rhizome lectin : Role of N-linked glycosylation. Glycobiology, 26, 410-426.
  39. Chattopadhyaya, R. & Biswas, H. (2016) Sequence, structure and functional comparisons suggest an alternative structure for the bundle-forming pilin BfpA. Clinical Proteomics & Bioinformatics, 1, 9-14. doi: 10.15761.
  40. Kar, I. & Chattopadhyaya, R. (2016) Effect of seven Indian plant extracts on Fenton reaction-mediated damage to DNA constituents. Journal of Biomolecular Structure and Dynamics, http://dx.doi.org/10.1080/07391102.2016.1244493
  41. Kar, I. & Chattopadhyaya, R. (2016) Role of Histidine163 in the co-protease Activity of RecA Verified by Chemical Modification, followed by MALDI mass Spectrometry.  Science and Culture, 82 (11-12), 382-385.
  42. Kar, I., Majumder, H. K. & Chattopadhyaya, R. (2017) Extracts of Seven Indian Plants Inhibit Human Topoisomerase I and Partially Inhibit Human Topoisomerase II. Molecular Enzymology and Drug Targets, 3 (1):1. http://www.imedpub.com
  43. Chattopadhyaya, R., Biswas, H. & Sarkar, A. (2017) Crystal structure Colocasia esculenta tuber agglutinin at 1.74Å resolution and its quaternary interactions. Journal of Glycobiology, accepted 5 April, 2017.
  44. Biswas, H. & Chattopadhyaya, R. (2017) Thermal and chemical denaturation of Colocasia esculenta tuber agglutinin from a2b2 to unfolded state. Journal of Biomolecular Structure and Dynamics, http://dx.doi.org/10.1080/07391102.2017.1345327


 


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Recognition:

  • First position among 1,80,000 candidates in the High School Board examination in West Bengal, India., 1975
  • Doctoral work published in Nature and called notable by The Scientist, 1988
  • About 2,000 citations received for my published papers, 1980-
  • Work at Bose Institute in the boundary of biology and physics (publication #17) described at length in the (Encylcopedia) Britannica Book of the Year, 1996 as being among the four best works in physics during 1995, 1996
  • Recent work on an improved model of LexA repressor bound to operator DNA (Figure 3a of publication # 27) used in an undergaduate textbook by Burton E. Tropp titled Molecular Biology: Genes to Proteins, 3rd edition (Jones and Bartlett Publishers, Massachusetts, USA, 2008) on pages 430, 431 and 439. Tropp’s 3rd edn. is a continuation of David Freifelder’s classic textbook, Molecular Biology (2nd edn. 1987), 2008

Teaching:

Prof. Chattopadhyaya generally used to teach a course on Macromolecular Crystallography for doctoral students at Bose Institute once every three years.  Among other courses taught at Bose Institute, there used to be one titled ‘DNA and its Enzymes’, a third titled ‘Protein Structure’, a fourth titled ‘Ribosome’.  Each one of these four courses was designed by him independently.  Other than this, he taught upper division and lower division tutorial sections at UCLA as a TA in Physical Chemistry, lower division courses in Biochemistry during 1981-1985.


Present:

Image Name Designation Department Campus Contact number Email

Former:

Kaushik Ghosh was Dr. Chattopadhyaya's first doctoral student, awarded Ph.D. in 2001 from Jadavpur University.  Dr. Kaushik Ghosh (Jan 1994-Dec 1999), awarded PhD in 2001, was postdoctoral fellow and later research associate at the University of Pennsylvania, USA until Jan 2008.  Has joined BioCon at Bangalore under joint program with Bristol-Myers Squibb.

Veriketta M. Haridasan Namboodiri submitted his thesis next, awarded Ph.D. in 2001 also from Jadavpur University. Dr. V. M. H. Namboodiri (March 1994-May 2000), awarded PhD in 2001, was postdoctoral fellow at Boston University Medical School, later joined Locus Pharmaceuticals, Blue Bell, Pennsylvania, USA, was head of crystallography there, now associated with Drexel University and a company in the USA associated with final drug applications / approval.

Atasi Pal submitted her thesis and was awarded her Ph.D. in Oct 2007 from Jadavpur University.  Dr. Atasi Pal (July 2002-November 2006), awarded PhD in Oct 2007, now housewife (married Prof. Chattopadhyaya !!!).

Himadri Biswas submitted his thesis to University of Calcutta and awarded in 2016. Currently, postdoctoral fellow at the Rutgers State University Medical School, New Jersey, USA.

Indrani De (nee Kar), submitted her doctoral thesis on January 25, 2017 to the University of Calcutta.


Group News:

Former postdoctoral fellows :

Dr. Bhaswati Goswami (PhD, Rutgers University) (postdoctoral, March 1994-Dec 1997), currently housewife.

Dr. Kajari Dhar (nee Ghosh) (postdoctoral, Nov 1995-Nov 1997), previously research scientist in Univ of Nebraska Medical Center, currently faculty member, Creighton University School of Medicine, Omaha, Nebraska, USA.

Dr. Swati Ray (postdoctoral, Mar 1999-Mar 2000), teaches at Barrackpore Surendranath College

Dr. Pushpankur Ghosal (postdoctoral, Mar 2000-Mar 2001), postdoctoral at SUNY Buffalo Medical Center, currently research associate at Georgia Health Sciences University, Georgia, USA

Joined as doctoral student, but did not complete under Dr. Chattopadhyaya :

Dr. Alakesh Bera (March 2002-Mar 2003), left to continue his PhD in France, was postdoctoral at John’s Hopkins Medical School, Maryland, USA, currently in San Antonio, Texas as Research Scientist.

Dr. Sanjukta Mallik (June 2003-Dec 2003), left after her marriage due to commuting problem, later completed her PhD at Indian Statistical Institute, Calcutta.

Mrs. Manjari Tharad (Nov 2004-Nov 2005), left after her marriage, lives in Bombay