Dr. Sibani Chakraborty Ph.D
Designation: Assistant Professor
Email: [email protected]
Dr. Chakraborty earned her Masters in Biochemistry from the University of Kalyani. She
received her Ph.D degree from Jadavpur University while working at the Biophysics
Department of Bose Institute, Kolkata under the direction of Prof. Asok Banerjee. Further she
went for her post-doctoral training at the Department of Biochemistry & Molecular Biology,
Brain Institute, University of Florida, Gainesville, USA and at the Crystallography &
Molecular Biology Division, Saha Institute of Nuclear Physics, Kolkata, India. Her research
interests focused on the structural, biochemical and molecular elucidation of “interactions”
that govern life processes. Models exploited includes both proteases and their inhibitors of
the serine, cysteine, aspartic and metallo protease family with the ultimate goal of designing
novel inhibitors that can be used as therapeutic agents for combating diseases. With an aim to
understand the role of various micro-organisms in industry and biotechnology, she is
currently working with different beneficial microbes isolated from environment.
Professional Membership
Society of Biological Chemists, India.
Indian Science Congress Association
Teaching
Biochemistry, Carbohydrate Metabolism, Bioinformatics, Proteomics.
Laboratory courses on Biochemistry and Environmental Microbiology.
Teaching Experience
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Assistant Professor, Microbiology Department, West Bengal State University from
January 2009 till date.
Lecturer (contractual), Life Sciences and Biotechnology Dept. of Jadavpur University
Lecturer (contractual), Post–Graduate Dept. of Microbiology at Acharya Prafulla
Chandra College, Calcutta University
Completed/Ongoing Research Project(s)
DBT, Govt. of India “Comparative structural analysis of substrate specificity in astacin
metalloendopeptidases by homology modeling” 2012-15, Rs 30, 15000/-
Oral presentations
1. Ankur Chaudhuri, Asim K. Bera, Indrani Sarkar and Sibani Chakraborty* (2013).
Screening inhibitors of human meprins: Insights from analysis of binding sites by
molecular dynamics simulation. Symposium on “Frontiers in Modern Biology 2013”,
IISER- Kolkata, 9th and 10th. November
2.
Sibani Chakraborty, Sampa Biswas, Chandana Chakrabarti and J.K.Dattagupta (2005).
Structure and Function of a Highly Active Cysteine Protease from Ervatamia coronaria.
National Seminar on Crystallography, Guwahati University, Guwahati, Assam, 10th.
Jan- 12th. Jan
3. Sibani Chakraborty, S.Bhattacharya, A.K.Bera, S.Ghosh and Asok Banerjee (1999).
Designing of clinically potential inhibitors for thiol and serine proteases: An attempt for
blunting the “Nature‟s Swiss Army Knife”. National Symposium on Trends in
Environmental Biology. North – Eastern Hill University, Shillong, June 23rd-25th
Poster presentations
1. Subrata Ghosh, Ankur Chaudhuri and Sibani Chakraborty (2012). Department of
Microbiology, West Bengal State University, Barasat. “Knowledge based molecular
modeling of astacin metalloproteases”. InCoB 2012, 3rd-5th Oct, Bangkok, Thailand.
2. Sampa Biswas, Sibani Chakraborty, Chandana Chakrabarti, Debi Chowdhury, J.K.
Dattagupta (2005). Crystallography and Molecular Biology Division, Saha Institute of
Nuclear Physics, Kolkata. “Rational design of a model of thermostable papain – a
proteolytic enzyme, based on the structures of naturally occuring thermostable
proteins of the same family”. Discussion Meeting on Crystallography, CCMB,
Hyderabad, 15th-16th. Nov.
3. Amrita Madabushi, Sibani Chakraborty, S. Zoe Fisher, Jose C. Clemente, Charles
Yowell, John Dame, Ben Dunn, Mavis Agbandje-Mckenna and Robert Mckenna (2005)
Department of Biochemistry and Pathobiology, College of Veterinary Medicine,
University of Florida. "Crystal structure of the aspartic protease plasmepsin4 from the
malarial parasite Plasmodium malariae". ACA, 2005, Orlando, USA.
4.
S. Chakraborty, R. Mckenna, B. Dunn, J. Dame and M. Agbandje-Mckenna.
Department of Biochemistry and Pathobiology, College of Veterinary Medicine.
“Structural Basis Of Inactivation Of Food Vacuole Plasmepsins By Pepstatin A”.
College of Medicine- Research Day, April 11, 2003, University of Florida.
5.
N. Bryant, S. Chakraborty, L. Govindaswamy, J. Sequeira, R. Mckenna and M.
Agbandje-Mckenna. Department of Biochemistry and Pathobiology, College of
Veterinary Medicine. “X-Ray Crystallographic Studies Of Variants Of The Murine
Parvovirus Of Mice: Structural Elucidation Of Tissue Tropism and Pathogenicity
Determinants”. College of Medicine-Research Day, April 11, 2003, University of
Florida
6. N. Bryant, S. Chakraborty, L. Govindaswamy, J. Sequeira, R. Mckenna and M.
Agbandje-Mckenna. Department of Biochemistry,
University of Florida. “X-Ray
Crystallographic Studies Of Variants Of The Murine Parvovirus Of Mice: Structural
Elucidation Of Tissue Tropism and Pathogenicity Determinants”. American Society for
Virology, 22nd. Annual Meeting, University of California, Davis; Davis, California,
July12-16, 2003
7. S. Chakraborty, U.Haldar, A.K.Bera, A.K.Pal, S.Bhattacharya, S.Ghosh, B.P.
Mukhopadhyay and Asok Banerjee (2001). Recognition and stabilization of an unique
CPRI- structural motif in Cucurbitaceae family trypsin inhibitor peptides: Molecular
dynamics based homology modelling using the X-ray structure of MCTI-II. Interational
Symposium on Crystallography and Bioinformatics in Structural Biology, Molecular
Biophysics Unit & Bioinformatics Centre, I.I.Sc,Bangalore, Nov.22nd-25th
8. S.Chakraborty, S.Bhattacharya, A.Bera, A.K.Pal, S.Ghosh, B.P.Mukhopadhyay,
U.Halder, and A.Banerjee (1998). Designing of inhibitors for thiol and serine proteasesAn attempt for blunting „Nature‟s Swiss Army Knife‟. Discussion meeting on
macromolecular crystallography, Molecular Biophysics Unit, I.I.Sc, Bangalore, Feb.6-7th
9. S.Ghosh, A.Bera, A.K.Pal, S.Bhattacharya, B.P.Mukhopadhyay, U.Halder, S.
Chakraborty and A.Banerjee(1998). The structural view of Nature‟s another „Swiss
Army Knife‟, Calotropin DII, a thiol protease at 2.1Å resolution. Discussion meeting on
macromolecular crystallography, Molecular Biophysics Unit, I.I.Sc., Bangalore, Feb.6-7th
Important Publications
Molecular Modeling
Screening inhibitors of human meprins: Insights from analysis of binding sites by molecular
dynamics simulation. Ankur Chaudhuri, Indrani Sarkar, A. K. Bera, Sibani Chakraborty*
(communicated)
Ankur Chaudhuri, Indrani Sarkar and Sibani Chakraborty*(2013). Comparative analysis of
binding sites of human meprins with hydroxamic acid derivative by molecular dynamics
simulation study. Journal of Biomolecular Structure and Dynamics, USA. Vol.32 , Issue
Number- 12, pp1969-1978 .
Ankur Chaudhuri, Indrani Sarkar, Sibani Chakraborty* (2012). Topological Analysis of
Protease Domain of Astacin Metalloproteases by Homology Modeling. JOURNAL OF
PROTEINS AND PROTEOMICS, ISSN : 0975-8151; 3(2), pp62.
S.Chakraborty, U. Haldar, A.K.Bera, A.K.Pal, S.Bhattacharya, S.Ghosh, B.P.Mukhopadhyay
and Asok Banerjee (2001). Recognition and stabilisation of a unique CPRI-structural motif in
Cucurbitaceae family Trypsin inhibitor peptides: Molecular dynamics based homology modeling
using the X-ray structure of MCTI-II. Journal of Biomolecular Structure and Dynamics, USA.
Vol. 18, Issue Number-4, 569-578.
Asok K. Pal, S.Sen, S.Ghosh, A.K.Bera, S.Bhattacharya, S.Chakraborty and Asok Banerjee
(2001). Research strategies for design and development of NSAIDs: clue to balance potency and
toxicity of acetanilide compounds. Journal of Biomolecular Structure and Dynamics,USA.
Vol. 19, Issue Number-1, 85-93.
Suparna Bhattacharya, S.Ghosh, S.Chakraborty, A.K.Bera, B.P. Mukhopadhyay I.Dey and
Asok Banerjee (2001). Insight to subsite recognition in thiol protease-inhibitor
complexes:Understanding specificity,the basis of differential inhibition.. BMC Structural
Biology, 1:4, 345-352.
S.Chakraborty, S.Bhattacharya, S.Ghosh, A.K.Bera, A.K.Pal, U.C.Halder, B.P.Mukhopadhyay
and Asok Banerjee (2000). Structural and interactional homology of clinically potential trypsin
inhibitors: molecular modeling of Cucurbitaceae family peptides using X-ray structure of MCTIII. Protein Engineering, Vol.13, no.8, 551-555.
Asok K. Pal, Sreya Ghosh, Asim K. Bera, Suparna Bhattacharya, Sibani Chakraborty, Kanai
L.Ghatak and Asok Banerjee (2000). Structural basis of inactivation of thiol protease by Nacetyl-p-benzoquinone Imine (NAPQI). A knowledge based molecular modeling of the adduct of
NAPQI with thiol protease of papain family. Journal of Molecular Modeling, Vol.6, 648-653.
Biochemical studies
Raka Ghosh, Sibani Chakraborty, Chandana Chakrabarti, Jiban K. Dattagupta and sampa
Biswas (2008). Structural insight into the substrate specificity and activity of Ervatamins: the
papain-like cysteine proteases from a tropical plant Ervatamia coronaria. FEBS Journal, Vol.
275, No.3, pp.421-434.
Rebecca Moose, Jose Clemente, Larry Jackson, Minh Ngo, Kimberly Worten, Richard Chang,
Antonetle Bennetle, Sibani Chakraborty, Charles Yowell, John Dame, Mavis AgbandjeMckenna, Ben Dunn (2007). Analysis of Binding Interactions of Pepsin Inhibitor-3 To
Mammalian and Malarial Aspartic Proteases. Biochemistry, 46 (49), pp 14198-14205.
Macromolecular Crystallography
Sibani Chakraborty, Sampa Biswas, Chandana Chakrabarti and Jiban K. Dattagupta (2005).
Crystallization and Preliminary X-ray diffraction studies of a cysteine protease Ervatamin A from
Ervatamia coronaria. Acta Crystallographica, F61, 562-564.
Amrita Madabushi, Sibani Chakraborty, S. Zoe Fisher, Jose C. Clemente, Charles Yowell,
John Dame, Ben Dunn, Mavis Agbandje-Mckenna & Robert Mckenna (2005). Crystallization
and Preliminary X-ray analysis of the aspartic protease plasmepsin 4 from the malarial parasite
Plasmodium malariae.Acta Crystallographica, F61, 228-231.
S. Ghosh, A. Bera, A. K. Pal, S. Bhattacharya, B. P. Mukhopadhyay, U. Halder, S. Chakraborty
and Asok Banerjee (1999). The structural view of Nature‟s another „Swiss Army Knife‟,
Calotropin DII, a thiol protease at 2.1Å resolution. Journal of Biosciences, vol.24, Supplement
1.
Small-molecule Crystallography
S.Chakraborty, A.K.Bera, S.Bhattacharya, S.Ghosh, A.K.Pal, Soumen.Ghosh and Asok
Banerjee (2002). Synthesis ,microbiological study and X-ray structural characterization of a Tri-
n-butylstannyl2-[4-(diethylamino)arylazo] benzene carboxylate. Journal of
Chemistry,USA. Vol. 645, 33-38.
Organometallic
S.Chakraborty, U.Haldar, A.K.Bera, A.K.Pal, S.Bhattacharya, S.Ghosh, B. P. Mukhopadhyay
and Asok Banerjee (2001). Hydrogen bonding potentiality of serine in more aquated
environment: Crystal and molecular structure of dihydrated D-L Serine,C3H7NO3.2H2O. Indian
Journal of Physics.Vol.75, PartA, no 5, 599-601.
S.Bhattacharya, A.K.Bera, S.Ghosh, S.Chakraborty, B.P.Mukhopadhyay, A.Pal and Asok
Banerjee (2001). Regiospecificity of nucleotide-Amino acid mating Vs water dynamics: A key to
Protein-Nucleic acid assemblies: Structure of unidecahydrated Inosine-5'-monophosphate and Lglutamic acid (2C10H13N4O3P.C5H11NO4.11H2O) cocrystal at atomic resolution.. Journal of
Chemical Crystallography,USA Vol 30,no.10,655-663.
A. Bera, B.P. Mukhopadhyay, S.Ghosh, S.Bhattacharya, S.Chakraborty and Asok Banerjee
(1999). Influences of cooperative hydrogen bonding economy of protein-nucleic acid
complexation: structure of unidecahydrated inosine C5‟-monophosphate and L-glutamine
(2C10H13N4O8P.C5H10N2O3.11H2O) cocrystal at atomic resolution. Journal of Chemical
Crystallography,USA Vol.29, no.5, 531-540.