Pinakpani Chakrabarti
J. C. Bose Fellow
Pinakpani Chakrabarti
J. C. Bose Fellow, Biochemistry
PhD: Indian Institute of Science, Bangalore, 1981
Previous appointments:
1990-97 Senior Scientist, In-charge of the X-ray Diffractometer Facility, National Chemical Laboratory, Pune.
1989-90 Research Fellow, California Institute
of Technology,
1984-89 Research Associate, Professor D.C.
Rees,
1982-84 Post doctoral Fellow, Professor M.G.
Rossmann,
1981-82 Post doctoral Fellow, Professor J.D.
Dunitz, Swiss Federal Institute ofTechnology, Switzerland
Research interests:
Understanding the structure and folding of proteins and their interactions with other molecules, large and small, and nanoparticles using biophysical techniques (especially, X-ray crystallography), modelling and database analysis. Some specific topics are:
- Identification of stabilizing interactions (like CH-p, CH-O,
electrophile-nucleophile,
aromatic-aromatic
etc.) and their implications
in protein structures and function
- Analysis of protein conformation and identification of structural
motifs
- Protein folding, threading and prediction of structures
- Molecular modelling and dynamics to understand protein function
- Molecular recognition, protein-protein/DNA complexation and
ion-binding by proteins
- Biophysical studies on proteins from phage lambda and Vibrio cholerae
- Design of peptides with specific structure
- Structural bioinformatics and development of algorithms
- Vibrio
cholerae proteomics
- Interaction of nanoparticles with proteins
and their antibacterial effect.
Contact:
Address: |
Department of Biochemistry Centenary Campus Bose Institute P-1/12 C.I.T. Scheme VII-M Kolkata - 700054, India |
E-Mail: | pinak[at]jcbose.ac.in |
Phone: | +91-33-25693253 |
Research:
1)
Following the tradition of GN
Ramachandran we have done extensive work on protein structure, conformation. From
an analysis of protein structures a
new secondary structure has been identified, which because of its shape is termed topi (hat in many Indian languages), thus
introducing an Indian term in scientific lexicon (Dhar et al. Scientific Reports, 6:31483 (2016)).
2) Our work has identified many weak
interactions that stabilize the native fold. A review article with authors from
three other countries on C-H···p interactions (Nishio et al. Phys. Chem. Chem. Phys. 16, 12648
(2014)) has been highly acclaimed. Motifs containing C-H···O (Dhar et
al. Proteins, 83, 203 (2015), Chakrabarti and Chakrabarti, J Mol Biol 284 (1998))
, N-H···N(pz) (Dhar et al. Scientific Reports, 6:31483 (2016)) interactions have been characterized
3) We have been involved in understanding the process of molecular recognition by
analyzing the physicochemical and evolutionary properties of interfaces formed
in protein-protein/DNA complexes. The dissection
of the interface into core and rim (Chakrabarti and Janin, Proteins, 47, 334 (2002)) is now referred to as CJ model (Levy E. J Mol Biol 403, 660 (2010)). This is one
of the most highly cited papers from the institute (~700 citations). The
residues in the core are more conserved than those in rim, which has led to the
development of an algorithm of for predicting the hotspot residues in
interfaces (Guharoy and Chakrabarti. Proc.
Natl. Acad. Sci. USA, 102, 15447 (2005)).
4) Many of the webservers (on protein-protein
interaction) developed in the lab (http://www.jcbose.ac.in/resources/bioinfo/stag.html)
are being widely used (Saha et al. BMC Struct. Biol. 6, 11 (2006)).
5) The group is involved in crystallographic analysis of a
number of interesting proteins, such as CII from bacteriophage lambda, which is
the deciding factor in which of the two alternative modes (lysis or lysogeny)
bacteriophage lambda develops. The structure explains why this transcription
activator binds a direct repeat DNA sequence (Datta et al. Proc. Natl. Acad. Sci. USA, 102, 11242 (2005)).
6) Another topic of interest is the structural
proteomics of Vibrio chholerae.
Structures have been elucidated for HlyU (transcriptional activator of the
hemolysin gene hlyA) (Mukherjee et al. Biochim. Biophys. Acta 1844, 2346-2354
(2014)) and PIMT (a repair enzyme) (Chatterjee et al. Arch. Biochem. Biophys.
583, 140 (2015)). EMSA has been used to delineate the DNA binding sequence (173
bp upstream of hlyA promoter), and mutational studies carried out to identify
the residues in the recognition helix and the wing region of HlyU involved in
the interaction (Mukherjee et al. Nucleic
Acids Res. 43, 1407-1417 (2015)). The effect of virstatin on the DNA
binding property of ToxR, a transcriptional activator of two major virulence
factors for cholera pathogenesis, cholera toxin (CT) and toxin coregulated
pilus (TCP), has been elucidated.
7) The work involving the antimicrobial and
anti-tumor activity of ZnO nanoparticles and their surface-coated derivatives
is likely to find niche applications in pharmaceutical industry (Sarwar et al.
J Biol Chem 292, 18303, Sarwar et al. Nanomedicine,
12, 1499-1509 (2016)). The effect of morphology and size of gold nanoparticles
on the growth of V. cholerae biotypes
and accessory cholera enterotoxin (Ace) have been studied using biophysical
methods and animal studies (Chatterjee et al. Biochem Biophys Acta, 1861, 977 (2017)). The bacterial growth
kinetics has been modeled to incorporate the antibacterial effect of silver
nanoparticles (Chatterjee et al. Biochim.
Biophys. Acta, 1850, 299 (2015)).
8) Biophysical techniques and MD simulations have
been used to understand the binding of small molecules to proteins and the
dynamics of binding (Chakraborti et al. Biochemistry 52, 7449 (2013)). In silico mutations and
molecular dynamics have been used to understand the importance of flexibility
in the N-terminal actin-binding domain (Chakravarty et al. Proteins, 83, 696 (2015)). |
9) An exciting
observation has recently been made (Chatterjee et al (under submission)) which
shows that protein L-isoaspartyl methyltransferase (PIMT) can prevent fibril
formation in iso-aspartyl containing peptides and the efficacy is enhanced in
presence of anti-epileptic drugs (AEDs). It was the first time that it has been
shown that PIMT is the target of AEDs.
Publications:
1.
Bera S, Dhar J, Dasgupta R, Basu G,
Chakraborti S and Chakrabarti P (2018). Molecular features
of interaction involving hen egg white lysozyme immobilized on graphene oxide
and the effect on activity. Int
J Biol Macromol, 120, 2390-2398 (doi: 10.1016/j.ijbiomac.2018.09.007).
2.
Dhar J and Chakrabarti P (2018). Structural motif, topi and its role in protein function and fibrillation. Mol. Omics, 14, 247-256. (DOI: 10.1039/c8mo00048d)
3. Podder S, Chakravarty D and Chakrabarti P
(2018). Structural changes in DNA-binding proteins on complexation. Nucleic Acids Res. 46, 3298-3308 (doi:
10.1093/nar/gky170).
4. Sarwar
S, Ali A, Pal M and Chakrabarti P
(2017). Zinc oxide nanoparticles provide anti-cholera activity by disrupting
the interaction of cholera toxin with the human GM1 receptor. J Biol Chem, 292 18303-18311.
5. Chatterjee T, Chatterjee BK and Chakrabarti
P (2017). Modelling of growth kinetics of Vibrio
cholerae in presence of gold nanoparticles: effect of size and morphology. Scientific Reports, 7: 9671.
6. Maji A, Beg M, Mandal AM, Das S, Jha PK,
Kumar A, Sarwar S, Hossain M and Chakrabarti P (2017). Spectroscopic
interaction study of human serum albumin and human haemoglobin with Mersilea quadrifolia leaves extract
mediated silver nanoparticles having antibacterial and anticancer activity. J Mol Struct, 1141, 584-592.
7.
Jana TK, Pal A, Mandal AK, Sarwar S,
Chakrabarti P and Chatterjee K (2017). Photocatalytic and antibacterial
performance of -Fe2O3 nanostructures. Chemistry Select 2, 1-11 (DOI:
10.1002/slct.201700294).
8. Chatterjee T, Chatterjee B, Saha T, Hoque KM
and Chakrabarti P (2017). Structure and function of Vibrio cholerae accessory cholera enterotoxin in presence of gold
nanoparticles: Dependence on morphology. Biochim.
Biophys. Acta, 1861, 977-986.
9. Chakraborti S, Chakraborty S, Saha S, Manna A, Banerjee S, Adhikary A, Sarwar S, Hazra TK, Das T and Chakrabarti
P (2017). PEG-functionalized zinc oxide nanoparticles induce apoptosis in
breast cancer cells through reactive oxygen species-dependent impairment of DNA
damage repair enzyme NEIL2. Free Radical
Biology & Medicine, 103, 35-47.
10.
Aoun J, Hayashi M, Sheikh IA, Sarkar P, Saha
T, Ghosh P, Bhowmick R, Ghosh D, Chatterjee T, Chakrabarti P, Chakrabarti MK,
Hoque KM (2016). Anoctamin 6 contributes to Cl- secretion in
accessory cholera enterotoxin (Ace) stimulated diarrhea: an essential role for
PIP2 signaling in cholera. J Biol Chem,
291, 26816-26836.
11.
Dhar J, Kishore R and Chakrabarti P (2016). A novel secondary structure based on fused
five-membered rings motif. Scientific
Reports, 6:31483.
12.
Ghosh T, Barik S, Bhuniya A, Dhar J,
Dasgupta S, Ghosh S, Sarkar M, Guha I, Sarkar K, Chakrabarti P, Saha B, Storkus
WJ, Baral R and Bose A (2016). Tumor-associated mesenchymal stem cells inhibit
naïve T cell expansion by blocking cysteine export from dendritic cells. Int J Cancer, 139, 2068-2081.
13.
Karaman DS, Sarwar S, Desai D, Björk EM, Odén M, Chakrabarti P, Rosenholm JM and Chakraborti S
(2016). Shape engineering boosts
antibacterial activity of chitosan coated mesoporous silica nanoparticle doped
with silver: a mechanistic investigation. J. Mater. Chem. B, 4,
3292-3304.
14.
Sarwar
S, Chakraborti S, Bera S, Sheikh IA, Hoque KM and Chakrabarti
P (2016). The antimicrobial activity of ZnO nanoparticles against Vibrio cholerae: Variation in response
depends on biotype. Nanomedicine, 12,
1499-1509.
15.
Biswas S and Chakrabarti P (2016). Analysis
of interactions and dissection of interfaces involved in RNA-protein
recognition. Protein & Peptide
Letters, 23, 777-784.
16.
Chatterjee T, Sheikh IA, Chakravarty D, Chakrabarti
P, Sarkar P, Saha T, Chakrabarti MK and Hoque KM (2015). Effects of small
molecule calcuium-activated chloride channel inhibitors on structure and
function of Accessory cholera enterotoxin (Ace) of Vibrio cholerae. PLoS ONE,
10(11): e0141283.
17.
Chakravarty D, Janin J, Robert CH and
Chakrabarti P (2015). Changes in protein structure at the interface accompanying
complex formation. IUCr J, 2, 643-652.
(Scientific Commentary on the article: Laskowski RA and Thornton JM. ibid, 609-610).
18.
Chatterjee T, Mukherjee D, Banerjee M, Chatterjee BK
and Chakrabarti P (2015). Crystal structure and activity of protein
L-isoaspartyl-O-methyltransferase from Vibrio
cholerae, and the effect of AdoHcy binding. Arch. Biochem. Biophys. 583, 140-149.
19.
Dhar J and Chakrabarti P (2015). Defining
the loop structures in proteins based on composite -turn mimics. Protein Engng, Design & Selection,
28, 153-161.
20.
Chakravarty D, Chakraborti S and Chakrabarti P (2015).
Flexibility in the N-terminal actin-binding domain: Clues from in sillico mutations and molecular
dynamics. Proteins, 83, 696-710.
21.
Dhar G, Chakravarty D, Hazra J, Dhar J,
Poddar A, Pal M, Chakrabarti P, Surolia A and Bhattacharyya B (2015). Actin-curcumin
interaction: Insights into the mechanism of actin polymerization inhibition. Biochemistry, 54, 1132-1143.
22.
Mukherjee D, Pal A, Chakravarty D and Chakrabarti P
(2015). Identification
of the target DNA sequence and characterization of DNA binding features of
HlyU, and suggestion of a redox switch for hlyA
expression in the human pathogen Vibrio
cholerae from in silico studies. Nucleic Acids Res. 43, 1407-1417.
23.
Chatterjee T,
Chatterjee BK, Majumdar D and Chakrabarti P. Antibacterial effect of silver
nanoparticles and the modeling of bacterial growth kinetics using a modified
Gompertz model (2015). Biochim. Biophys.
Acta, 1850, 299-306.
24.
Dhar J, Chakrabarti P, Saini
H, Raghava GPS, Kishore R (2015). w-Turn: a novel b-turn mimic in globular
proteins stabilized by main-chain to side-chain C-H×××O interaction. Proteins, 83, 203-214.
25.
Mukherjee D, Datta AB and Chakrabarti P (2014). Crystal structure of HlyU, the hemolysin gene
transcription activator, from Vibrio
cholerae N16961 and functional implications. Biochim. Biophys. Acta 1844, 2346-2354.
26.
Chakraborti S, Mandal AK, Sarwar S, Singh P,
Chakraborty R and Chakrabarti P (2014). Bactericidal effect of polyethyleneimine
capped ZnO nanoparticles on multiple antibiotic resistant bacteria harboring
genes of high-pathogenicity island. Colloids
and Surfaces B: Biointerfaces, 121, 44-53.
27.
Nishio M, Umezawa Y, Fantini J, Weiss MS,
and Chakrabarti P (2014). CH/p hydrogen
bonds in biological macromolecules. Phys.
Chem. Chem. Phys. 16, 12648-12683.
28.
Dasgupta B, Dey S
and Chakrabarti P (2014). Water and side-chain embedded -turns. Biopolymers, 101, 441-453.
29.
Chakraborti S, Dhar
G, Dwivedi V, Das A, Poddar A, Chakraborti G, Basu G, Chakrabarti P, Surolia A
and Bhattacharyya B (2013). Stable and potent analogues derived from the
modification of the dicarbonyl moiety of curcumin. Biochemistry 52, 7449-7460.
30.
Chakraborti S,
Sarwar S and Chakrabarti P (2013). The effect of the binding of ZnO
nanoparticle on the structure and stability of -lactalbumin: a comparative
study. J. Phys. Chem. B 117, 13397-13408.
31.
Chakravarty D,
Guharoy M, Robert CH, Chakrabarti P and Janin J (2013). Reassessing buried
surface areas in protein-protein complexes. Protein
Sci. 22, 1453-1457.
32.
Chakraborti S, Bhattacharya S, Chowdhury R
and Chakrabarti P (2013). The molecular basis of inactivation of metronidazole-resistant
Helicobacter pylori using
polyethyleneimine functionalized zinc oxide nanoparticles. PLoS ONE, 8(8): e70776.
33.
Chatterjee T, Pal A,
Chakravarty D, Dey S, Saha RP and Chakrabarti P (2013). Protein
L-isoaspartyl-O-methyltransferase of Vibrio
cholerae: Interaction with cofactors and effect of osmolytes on unfolding. Biochimie, 95, 912-921.
34.
Chakraborti S,
Chakravarty D, Gupta S, Chatterje, BP, Dhar G, Poddar A, Panda D, Chakrabarti
P, Dastidar SG, Bhattacharyya B (2012). Discrimination of ligands with
different flexibilities resulting from the plasticity of the binding site in
tubulin. Biochemistry, 51, 7138-7148.
35.
Chakraborti S, Joshi P, Chakravarty D, Shanker V, Ansari ZA, Singh SP and Chakrabarti P (2012). Interaction
of polyethyleneimine functionalized ZnO nanoparticles with bovine serum albumin.
Langmuir, 28, 11142-11152.
36.
Dey S, Pal A, Guharoy
M, Sonavane S and Chakrabarti P (2012). Characterization and prediction of the binding site in DNA-binding
proteins: improvement of accuracy by combining residue composition,
evolutionary conservation and structural parameters. Nucleic Acids Res. 40, 7150-7161.
37.
Chatterjee T, Pal A, Dey S,
Chatterjee BK and Chakrabarti P (2012). Interaction of virstatin with human
serum albumin: spectroscopic analysis and molecular modeling. PLoS ONE, 7(5): e37468.
38.
Joshi P, Chakraborti S, Chakrabarti P, Sing
SP, Ansari ZA, Husain M and Shanker V (2012). ZnO nanoparticles as an antibacterial
agent against E.coli. Sci. Adv. Mater. 4(1), 173-178.
39.
Joshi P, Chakraborti S, Ramirez-Vick JE, Ansari ZA,
Shanker V, Chakrabarti P and Singh SP (2012). The anticancer activity of
chloroquine-gold nanoparticles against MCF-7 breast cancer cells. Colloids Surfaces B: Biointerfaces, 95,
195-200.
40.
Mazumder A, Bandyopadhyay S,
Dhar A, Lewis DEA, Deb S, Dey S, Chakrabarti P and Roy S (2012). A genetic
network that balances two outcomes utilizes asymmetric recognition of operator
sites. Biophys. J. 102, 1580-1589.
41.
Ganguly HK, Majumder B, Chattopadhyay S,
Chakrabarti P and Basu G (2012). Direct evidence for CH···p interaction
mediated stabilization of Pro-cisPro
bond in peptides with Pro-Pro-Aromatic motifs. J. Amer. Chem. Soc. 134, 4661-4669.
42.
Dey S, Chakrabarti P and Janin J (2011). A
survey of hemoglobin quaternary structures. Proteins,
79, 2861-2870.
43.
Chakraborti S, Das L, Kapoor N, Das A, Dwivedi
V, Poddar A, Chakraborti G, Janik M, Basu G, Panda D, Chakrabarti P, Surolia A
and Bhattacharyya B (2011). Curcumin recognizes a unique binding site of
tubulin. J. Med. Chem. 54, 6183-6196.
44.
Kumar A, Chakraborti S, Joshi P, Chakrabarti
P and Chakraborty R (2011). A multiple antibiotic and serum
resistant oligotrophic strain, Klebsiella
pneumoniae MB45 having novel dfrA30, is sensitive to ZnO
QDs. Ann Clin Microbiol Antimicrob 10:19.
45.
Chakraborty S, Joshi P, Shanker V, Ansari ZA, Singh SP
and Chakrabarti P (2011). Contrasting effect of gold nanoparticles and
nanorods on the structure and activity of bovine serum albumin. Langmuir, 27, 7722-7731.
46.
Chatterjee T, Mukherjee D,
Dey S, Pal A, Hoque KM and Chakrabarti P (2011). Accessory cholera enterotoxin,
Ace, from Vibrio cholerae: Structure, unfolding, and virstatin binding. Biochemistry 50, 2962-2972.
47.
Guharoy M, Pal A, Dasgupta M and Chakrabarti P (2011).
PRICE (PRotein Interface Conservation and Energetics): a server for the
analysis of protein-protein interfaces. J.
Struct. Func. Genom. 12, 33-41.
48.
Joshi P, Chakraborty S, Dey
S, Shanker V, Ansari ZA, Singh SP and Chakrabarti P (2011). Binding of
choloroquine-conjugated gold nanoparticles with bovine serum albumin. J. Colloid Interface Sci. 355, 402-409.
49.
Sonavane S and Chakrabarti P
(2010). Prediction of active site cleft using support vector machines. J. Chem. Inform. Modeling, 50, 2266-2273.
50.
Chatterjee T, Chakraborti S, Joshi P, Singh SP, Gupta
V and Chakrabarti P (2010). The effect of zinc oxide nanoparticles on the structure of the
periplasmic domain of the Vibrio cholerae
ToxR protein. FEBS J. 277, 4184-4194.
51.
Debnath A, Saha A, Gomes A, Biswas S,
Chakrabarti P, Giri B, Biswas AK, Das Gupta S and Gomes A (2010). A lethal cardiotoxic-cytotoxic protein from
the Indian monocellate cobra (Naja
kaouthia) venom. Toxicon 56,
569-579.
52.
Guharoy M and Chakrabarti P (2010). Conserved residue
clusters at protein-protein interfaces and their use in binding site
identification. BMC Bioinformatics
11: 286.
53.
Dey S, Pal A, Chakrabarti P and Janin J (2010). The subunit interfaces of weakly associated homdimeric proteins. J. Mol. Biol. 398, 146-160.
54.
Chakraborti S, Chatterjee T, Joshi P, Poddar A,
Bhattacharyya B, Singh SP, Gupta V and Chakrabarti P (2010). Structure and
activity of lysozyme on binding to ZnO nanoparticles. Langmuir, 26(5), 3506-3513.
55.
Bahadur RP and Chakrabarti P (2009). Discriminating the native structure
from decoys using scoring functions based on the residue packing in globular
proteins. BMC Struct.
Biol. 9: 76.
56.
Guharoy M and Chakrabarti P (2009). Empirical
estimation of the energetic contribution of individual interface residues in
structures of protein-protein complexes. J.
Comput. Aided Mol. Des. 23, 645-654.
57.
Mukherjee D,
Saha RP and Chakrabarti P (2009). Structural and unfolding features of HlyT, a
tetrameric LysR type transcription regulator of Vibrio cholerae. Biochim. Biophys. Acta, 1794, 1134-1141.
58.
Sonavane S and Chakrabarti P (2009). Cavities
in protein-DNA and protein-RNA interfaces. Nucleic
Acids Res. 37, 4613-4620.
59. Joshi P, Chakraborti S, Chakrbarti P, Haranath D Shanker V,
Ansari ZA, Singh SP and Gupta V (2009). Role of surface
adsorbed anionic species in antibacterial activity of ZnO quantum dots against Escherichia coli. J. Nanosci. Nanotechnol. 9,
6427-6433.
60.
Pal A, Bahadur RP, Ray PS and Chakrabarti P
(2009). Accessibility and partner number of protein residues, their
relationship and a webserver, ContPlot for their display. BMC Bioinformatics 10: 103.
61.
Pal A,
Bhattacharyya R, Dasgupta M, Mandal S and Chakrabarti P (2009). IntGeom: a
server for the calculation of the interaction geometry between planar groups in
proteins. J. Proteomics &
Bioinformatics 2(1), 60-63.
62.
Biswas
S, Guharoy M and Chakrabarti P (2009). Dissection, residue conservation,
and structural classification of protein-DNA interfaces. Proteins 74(3), 643-654.
63.
Sonavane S and Chakrabarti P (2008). Cavities and atomic packing in protein structures and interfaces. PLoS Comput. Biol. 4(9): e1000188.
64.
Dasgupta B and
Chakrabarti P (2008). pi-Turns: types, systematics and the context of their
occurrence in protein structures. BMC
Struct. Biol. 8: 39.
65.
Biswas S, Guharoy M and Chakrabarti P
(2008). Structural segments and residue propensities in protein-RNA interfaces:
comparison with protein-protein and protein-DNA complexes. Bioinformation 2(10), 422-427.
66.
Janin J, Bahadur RP and Chakrabarti P (2008). Protein-protein
interaction and quaternary structure. Q.
Rev. Biophys. 41 (2) 133-180.
67.
Chatterjee T, Saha RP and Chakrabarti P
(2007). Structural studies on Vibrio
cholerae ToxR periplasmic and cytoplasmic domains. Biochim. Biophys. Acta 1774, 1331-1338.
68.
Dasgupta B, Chakrabarti P and Basu G (2007).
Enhanced stability of cis Pro-Pro peptide
bond in Pro-Pro-Phe sequence motif. FEBS
Letters, 581, 4529-4532.
69. Guharoy M
and Chakrabarti P (2007). Secondary structure based analysis and classification
of biological interfaces: identification of binding motifs in protein-protein
interactions. Bioinformatics, 23,
1909-1918.
70. Chakrabarti
P and Bhattacharyya R (2007). Geometry of nonbonded interactions involving
planar groups in proteins. Prog. Biophys.
Mol. Biol. 95, 83-137.
71. The
NMITLI-BioSuite Team (Vidyasagar et al.) (2007). BioSuite: a comprehensive
bioinformatics software package (A unique industry-academia collaboration). Curr. Sci. 92, 29-38.
72. Janin
J, Rodier F, Chakrabarti P and Bahadur R (2007). Macromolecular recognition in
the Protein Data Bank. Acta Crystallogr. D63, 1-8.
73. Pal
A, Chakrabarti P, Bahadur R, Rodier F and Janin J (2007). Peptide segments in
protein-protein interfaces. J. Biosci.
32, 101-111.
74. Saha
RP, Bhattacharyya R and Chakrabarti P (2007). Interaction geometry involving
planar groups in protein-protein interfaces. Proteins, 67, 84-97.
75.
Saha, RP and Chakrabarti
P (2006). Molecular modeling and characterization of Vibrio cholerae transcription regulator HlyU. BMC Struct. Biol. 6, 24.
76.
Saha RP, Bahadur
R, Pal A, Mandal S and Chakrabarti P (2006).
ProFace: a server for the analysis of the physicochemical features of
protein-protein interfaces. BMC Struct. Biol.
6, 11.
77. Raichaudhuri
A, Bhattacharyya R, Chaudhuri S, Chakrabarti P and DasGupta M (2006). Domain
analysis of a groundnut calcium-dependent protein kinase: nuclear localization
sequence in the junction domain is coupled with nonconsensus calcium binding
domains. J. Biol. Chem.
281, 10399-10409.
78. Saha
RP, Basu G and Chakrabarti P (2006).Cloning, expression, purification, and characterization
of Vibrio cholerae transcriptional activator, HlyU. Protein
Expression and Purification, 48, 118-125.
79. Saha
RP and Chakrabarti P (2006). Parity in the number of atoms in residue
composition in proteins and contact preferences. Curr. Sci. 90, 558-561.
80. Singha
S, Lahiri T, Dasgupta AK and Chakrabarti P (2006). Structural classification of
protein using surface roughness index. Online Journal of Bioinformatics, 7(2), 74-84.
81. Guharoy
M and Chakrabarti P (2005). Conservation and relative importance of residues
across protein-protein interfaces. Proc.
Natl. Acad. Sci. USA, 102, 15447-15452.
82. Datta
AB, Panjikar S, Weiss MS, Chakrabarti P and Parrack P (2005). Structure of l
CII: implications for recognition of direct-repeat DNA by an unusual tetrameric
organization. Proc. Natl. Acad. Sci. USA,
102, 11242-11247.
83. Saha
RP, Bahadur RP and Chakrabarti P (2005). Inter-residue contacts in proteins and
protein-protein interfaces and their use in characterizing the homodimeric
interface. J. Proteome Res.
4, 1600-1609.
84. Rodier
F, Bahadur RP, Chakrabarti P and Janin J (2005). Hydration of protein-protein
interfaces. Proteins, 60, 36-45.
85. Pal
L, Dasgupta B and Chakrabarti P (2005). 310-helix adjoining -helix
and -strand: sequence, structural features and their conservation. Biopolymers, 78, 147-162.
86. Bhattacharyya
R, Pal D and Chakrabarti, P (2004). Disulfide bonds, their stereospecific
environment and conservation in protein structures. Protein Eng. Design Selection, 17, 795-808.
87. Bahadur
RP, Chakrabarti P, Rodier F and Janin J (2004). A dissection of specific and
non-specific protein-protein interfaces. J.
Mol. Biol. 336, 943-955.
88. Dasgupta
B, Pal L, Basu G and Chakrabarti P (2004). Expanded turn conformations:
characterization and sequence-structure correspondence in -turns with
implications in helix folding. Proteins,
55, 305-315.
89. Bhattacharyya
R and Chakrabarti P (2003). Stereospecific interactions of proline residues in
protein structures and complexes. J. Mol.
Biol. 331, 925-940.
90. Bahadur
RP, Chakrabarti P, Rodier F and Janin J (2003). Dissecting subunit interfaces
in homodimeric proteins. Proteins,
53, 708-719.
91. Bhattacharyya
R, Saha, R, Samanta, U and Chakrabarti P (2003). Geometry of interaction of
histidine ring with other planar and basic residues. J. Proteome Res. 2, 255-263.
92. Pal
L, Chakrabarti P and Basu G (2003). Sequence and structure patterns in proteins
from an analysis of the shortest helices: implications for helix nucleation. J. Mol. Biol. 326, 273-291.
93. Chakrabarti
P and Janin J (2002). Dissecting
protein-protein recognition sites. Proteins,
47, 334-343.
94. Bhattacharyya
B, Pal D and Chakrabarti P (2002). Secondary structures at polypeptide
chain-termini and their features. Acta
Crystallogr. D56,
1793-1802.
95. Samanta
U, Bahadur RP and Chakrabarti P (2002). Quantifying the accessible surface area
of protein residues in their local environment. Protein Engng. 15, 659-667.
96. Pal
L, Basu G and Chakrabarti P (2002). Variants of 310-helices in
proteins. Proteins, 48, 571-579.
97. Praveen
T, Das T, Sureshan KM, Shashidhar MS, Samanta U, Pal D and Chakrabarti P (2002). Silver(I) oxide – silver halide mediated
alcoholysis of O-benzoyl-myo-inositol 1,3,5-orthoformates:
intramolecular assistance by the sulfonyl group. J.C.S., Perkin Trans. 2, 358-365.
98. Pal
D and Chakrabarti P (2002). On residues in the disallowed region of the
Ramachandran map. Biopolymers, 63,
195-206.
99. Bhattacharyya
R, Samanta U and Chakrabarti P (2002). Aromatic-aromatic
interactions in and around α-helices. Protein
Engng. 15, 91-100.
100. Datta
AB, Chakrabarti P, Subramanya HS and Parrack P (2001). Purification and
crystallization of CII: an unstable transcription activator from phage l.
Biochem. Biophys. Res. Commun. 288,
997-1000.
101. Pal
D, Mahapatra P, Manna T, Chakrabarti P, Bhattacharyya B, Banerjee A, Basu G,
Roy S (2001). Conformational properties of α-tubulin tail peptide: implications
for tail-body interaction. Biochemistry,
40, 15512-15519.
102. Pal
D and Chakrabarti P (2001). Non-hydrogen bond interactions involving the
methionine sulfur atom. J. Biomol. Struct. Dyn. 19, 115-128.
103. Chakrabarti
P and Pal D (2001). The interrelationships of side-chain and main-chain
conformations in proteins. Prog. Biophys. Mol. Biol. 76, 1-102.
104. Samanta
U and Chakrabarti P (2001). Assessing the role of tryptophan residues in the
binding site. Protein Engng.
14, 7-15.
105. Pal
D and Chakrabarti P (2000). Conformational similarity indices between different
residues in proteins and-helix propensities. J. Biomol. Struct. Dyn. 18, 273-280.
106. Chakrabarti
P, Puranik VG, Naskar JP, Hati S and Datta D (2000). New copper complexes of
diacetyl hydrazone oxime and its acetone azine. Ind. J. Chem. 39A, 571-578.
107. Hazra
BG, Basu S, Pore VS, Joshi PL, Pal D and Chakrabarti P (2000). Synthesis of 11-(4-dimethylaminophenyl)-17-hydroxy-17-(3-methyl-1-butynyl)-4,9-estradien-3-one
and 11-(4-acetophenyl)-17-hydroxy-17-(3-methyl-1-butynyl)-4,9-estradien-3-one:
two new analogs of mifepristone (RU-486). Steroids, 65, 157-162.
108. Pal
D and Chakrabarti P (2000). -sheet propensity and its correlation with
parameters based on conformation. Acta Crystallogr. D56, 589-594.
109. Pal
D and Chakrabarti P (2000). Terminal residues in protein chains: residue
preference, conformation and interaction. Biopolymers, 53, 467-475.
110. Samanta
U, Pal D and Chakrabarti P (2000). Environment of tryptophan side-chains in
proteins. Proteins, 38,
288-300.
111. Pal
D and Chakrabarti P (1999). Cis
peptide bonds in proteins: residues involved, their conformations, interactions
and locations. J. Mol. Biol.
294, 271-288.
112. Maji
M, Hossain M, Chatterjee M, Chattopadhyay SK, Puranik VG, Chakrabarti P and
Ghosh S (1999). Synthesis, characterisation and reactivity of trans-[Ru(L)(PPh3)Br2];
L = 2-pyridyl-N-(2’-methylthiophenyl)methyleneimine.
Crystal structure of trans-[Ru(L)(PPh3)Br2].
Polyhedron, 18,
3735-3739.
113. Samanta
U, Chakrabarti P, Naskar JP, Haiti S and Datta D (1999). Structure and metal
binding of an 1H-1,5-benzodiazepine. Ind.
J. Chem. 38A, 553-557.
114. Samanta
U, Pal D and Chakrabarti P (1999). Packing of aromatic rings against tryptophan
residues in proteins. Acta Crystallogr. D55, 1421-1427.
115. Pal
D and Chakrabarti P (1999). Graphical representation of salient conformational
features of residues in protein. Protein Engng. 12, 523-526.
116. Pal
D and Chakrabarti P (1999). Estimates of the loss of main-chain conformational
entropy of different residues on protein folding. Proteins, 36, 332-339.
117. Chakrabarti
P and Chakrabarti S (1998). C-H×××O
hydrogen bond involving proline residues in a-helices.
J. Mol. Biol. 284,
867-873.
118. Samanta
U, Chakrabarti P and Chandrasekhar J (1998). Ab initio study of energetics of
X-H×××p (X = N,O and C) interactions involving a
heteroaromatic ring. J. Phys. Chem.
A 102, 8964-8969.
119. Chakrabarti
P and Pal D (1998). Main-chain
conformational features at different conformations of the side-chains in
proteins. Protein Engng. 11,
631-647.
120. Pal
D and Chakrabarti P (1998). Different types of interactions involving cysteine
sulfhydryl group in proteins. J. Biomol. Struct. Dyn. 15, 1059-1072.
121. Praveen
T, Samanta U, Das T, Shashidhar MS and
Chakrabarti P (1998). Reactivity controlled by lattice interactions in crystal:
intermolecular acyl transfer in (±)-2,4-di-O-benzoyl-myo-inositol-1,3,5-orthoformate. J.
Amer. Chem. Soc. 120,
3842-3845.
122. Samanta
U, Puranik VG, Chakrabarti P, Thoniyot P and Shashidhar MS (1998). 2-O-Benzoyl-myo-inositol-1,3,5-orthoformate. Acta Crystallogr. C54, 1289-1291.
123. Naskar
JP, Hati S, Datta D, Samanta U and Chakrabarti P (1998). The crystal structure
of 2,3-dihydro-2,2,4-trimethyl-1H-1,5-benzodiazepinium
perchlorate. Z. Krist. 213,
112-114.
124. Rajeev
KG, Samanta U, Chakrabarti P, Shashidhar MS and Samuel AG (1998). Molecular
association of 2,3-dihydro-2-alkyl-3-hydroxybenzisothiazole-1,1-dioxides:
formation of novel bicyclic dimers containing 12/14 membered rings. J. Org.
Chem. 63, 230-234.
125. Maurya
MR, Jayaswal MN, Puranik VG, Chakrabarti P, Gopinathan S and Gopinathan C
(1997). Dioxomolybdenum (VI) and dioxotungsten (VI) complexes of isomeric ONO
donor ligands and the X-ray crystal structure of [MoO2(o-OC6H4CH=NCH2C6H4O)(MeOH)]2.MeOH.
Polyhedron, 16,
3977-3983.
126. Surange
SS, Kumaran G, Rajappa S, Pal D and Chakrabarti P (1997). Push-pull butadienes:
evidence for a possible C-H×××S
hydrogen bond in 4-(methylthio)-4-nitro-1-(pyrrolidin-1-yl)buta-1,3-diene. Helv.
Chim. Acta, 80, 2329-2336.
127. Chakrabarti
P and Pal D (1997). An eletrophile-nucleophile interaction in metalloprotein
structures. Protein Sci. 6,
851-859.
128. Sur
S, Ganesh S, Pal D, Puranik VG, Chakrabarti P and Sarkar A (1996).
Stereodivergent C-C bond formation on arene-chromium template: endo-selectivity allylation by
Hosomi-Sakurai reaction. J. Org. Chem. 61, 8362-8363.
129. Chakrabarti
P and Samanta U (1995). CH/p interaction in the packing of the
adenine ring in protein structures. J. Mol. Biol. 251, 9-14.
130. Joshi
VS, Sathe KM, Nandi M, Chakrabarti P and Sarkar A (1995). Severe distortion of p-allyl
orientation in a molybdenum complex containing a sterically demanding ligand:
crystal structure of hydrotris(3,5-dimethylpyrazolyl)boraoto-(p-cinnamyl)-dicarbonyl
molybdenum(II). J. Organomet. Chem.
485, C1-C5.
131. Chakrabarti P (1994). Conformational analysis of
carboxylate and carboxamide side-chains bound to cations. J. Mol. Biol. 239, 306-314.
132. Chakrabarti
P (1994). An assessment of the effect of helix dipole in protein strucrures. Protein
Engng. 7, 471-474.
133. Chakrabarti
P and Hsu BT (1994). Cation binding by the phenolate group in small molecules
and proteins. Inorg. Chem. 33,
1165-1170.
134. Chakrabarti
P (1994). Conformations of arginine and lysine side chains in association with
anions. Int. J. Pept. Protein Res.
43, 284-291.
135. Chakrabarti
P (1993). Anion binding sites in protein structures. J. Mol. Biol. 234, 463-482.
136. Chakrabarti
P and Pal S (1993). Differences in the energies of interactions at the binding
sites in protein structures. Chem. Phys. Lett. 201, 24-26.
137. Rees
DC, Kim J, Georgiadis MM, Komiya H, Chirino AJ, Woo D, Schlessman J, Chan MK,
Joshua-Tor L, Santillan G, Chakrabarti P and Hsu BT (1993). Crystal structures
of the iron protein and molybdenum-iron protein of nitrogenase. In Molybdenum Enzymes, Cofactors, and Model
Systems (edited by Stiefel EI, Coucouvanis D and Newton WE), ACS Symposium
Series 535, Chapter 11, 170-185.
138. Ganesh
S, Sathe KM, Nandi M, Chakrabarti P and Sarkar A (1993). Complete reversal of
stereoselectivity in cyclopropanation of 2-arylidene-1-tetralone
tricarbonylchromium complexes. J. Chem. Soc., Chem. Commun. 224-226.
139. Georgiadis
MM, Komiya H, Chakrabarti P, Woo D, Kornuc JJ and Rees DC (1992).
Crystallographic structure of the nitrogenase iron protein from Azotobacter vinelandii. Science, 257, 1653-1659.
140. Chakrabarti
P (1991). Does helix dipole have any role in binding metal ions in protein
structures? Arch. Biochem. Biophys.
290, 387-390.
141. Chakrabarti
P (1990). Systematics in the interaction of metal ions with the main-chain
carbonyl group in protein structures. Biochemistry, 29, 651-658.
142. Chakrabarti
P (1990). Interaction of metal ions with carboxylic and carboxamide groups in
protein structures. Protein Engng.
4, 49-56.
143. Chakrabarti
P (1990). Geometry of interaction of metal ions with histidine residues in
protein structures. Protein Engng.
4, 57-63.
144. Piontek
K, Chakrabarti P, Schär HP, Rossmann MG and Zuber H (1990). Structure
determination and refinement of Bacillus
stearothermophilus lactate dehydrogenase. Proteins, 7, 74-92.
145. Georgiadis
MM, Chakrabarti P and Rees DC (1990). Crystal structure of the nitrogenase iron
protein from Azotobacter vinelandii.
In Nitrogen Fixation: Achievements and
Objectives (Gresshoff PM, Roth E, Stacy G and Newton WE, eds.), Chapman
& Hill: New York, 111-116.
146. Chakrabarti
P (1989). Geometry of interaction of metal ions with sulfur-containing ligands
in protein strcutures. Biochemistry, 28, 6081-6085.
147. Chattopadhyaya
R and Chakrabarti P (1988). Solving DNA structures by MERLOT. Acta Crystallogr. B44, 651-657.
148. Chakrabarti
P, Bernard M and Rees DC (1986). Peptide bond distortions and the curvature of a-helices.
Biopolymers, 25, 1087-1093.
149. Rees
DC, Howard JB, Chakrabarti P, Yeates T, Hsu BT, Hardman KD and Lipscomb WN
(1986). Crystal structures of metallosubstituted carboxypeptidase A. Zinc Enzymes (Progress in Inorganic
Biochemistry and Biophysics, Vol. 1, edited by
Gray H and Bertini I), 155-166.
150. Chakrabarti
P, Venkatesan K, Cameron TS, Demir T and Shaw RA (1985). Aromatic amines and
their derivatives. Part 2. Synthesis, spectroscopic properties, and molecular
and crystal structure of N-acetyl-4,N-dimethyl-6-(N-acetyl-p-
toluidinomethyl)-aniline. J. Cryst. Spectros. Res. 15, 229-245.
151. Chakrabarti
P and Dunitz JD (1982). Directional preferences of ether O-atoms towards alkali
and alkaline earth cations. Helv. Chim. Acta, 65, 1482-1487.
152. Chakrabarti
P and Dunitz JD (1982). Structural characteristics of the carboxylic amide
group. Helv. Chim. Acta, 65,
1555-1562.
153. Chakrabarti
P, Venkatesan K and Rao CNR (1981). Structure and bonding in N-methylacetamide complexes of alkali
and alkaline earth metals. Proc. R. Soc.
(Lond.), A375, 127-153.
154. Chakrabarti
P, Venkatesan K, Singh UC and Rao CNR (1981). Systematic variation in bond
lengths in peptides. Biochim. Biophys. Acta, 670, 134-137.
155. Chakrabarti
P, Venkatesan K, Cameron TS, Demir T, Shaw RA (1981). Aromatic amines and their
derivatives. Part 3. The synthesis and crystal structure of 4,4’,NN’-tetramethyl-NN’-dinitroso-2,2’-methylenedianiline. J. Chem. Soc. (Perkin I), 206-211.
156. Chakrabarti
P, Banerjee DK and Venkatesan K (1981). The crystal and molecular structure of dl-17b-hydroxy-8a-androst-4-en-3-one
(8- isotesto-sterone). Steroids,
37, 269-279.
157. Bhadbhade
MM, Chakrabarti P, Banerjee DK and Venkatesan K (1981). X-ray crystallographic
investigations of testosterones and 19-nor-testosterones. Proc. Indian Natn.
Sci. Acad. 47A, 100-109.
158. Chakrabarti
P and Venkatesan K (1981). The structure of 9b-methyl-3ab,3ba,5aa,9aa,9bb,11ab-perhydrophenanthro[2,1-b]furan-7-one.
Acta Crystallogr. B37,
1142-1144.
159. Chakrabarti P,
Seiler P, Dunitz JD, Schlüter AD and Szeimies G (1981). Experimental evidence
for the absence of bonding electron density between inverted carbon atoms. J.
Amer. Chem. Soc. 103,
7378-7380.
Recognition:
- The Jagadis Chandra Bose Medal, INSA, 2016
- Distinguished Alumnus Award, IIT Kharagpur, 2012
- Fellow, TWAS (The World Academy of Sciences), 2011
- JC Bose National Fellow , 2007-
- Fellow, Indian National Science Academy, 2006
- Fellow, Indian Academy of Sciences, 1998
- Fellow, The National Academy of Sciences, 2006
- Prof. YT Thathachari Prestigious Award for Science, 2005
- P.S. Sarma Memorial Award for contributions in the field of Biochemistry and Allied Sciences, by the Society of Biological Chemists , 2004
- Fellow, West Bengal Academy of Science and Technology,
Teaching:
Students:
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