Pinakpani Chakrabarti

Pinakpani Chakrabarti
J. C. Bose Fellow

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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,                             Pasadena., USA.

1984-89           Research Associate, Professor D.C. Rees, University of                             California, Los Angeles, USA.

1982-84          Post doctoral Fellow, Professor M.G. Rossmann, Purdue                            University, USA.

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.

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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,

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