Gautam Basu
Professor, Biophysics

Research interest

The focus of my research group is to understand biological problems at the molecular level where molecular structure plays a vital role. We use both experimental and theoretical / computational tools to achieve our goals. The problems we tackle range from fundamental science to more applied aspects.

Here is a partial list of some of our ongoing projects:

a) Analysis of electrostatic interactions in protein-protein complexes.
b) Understanding the mechanism of substrate recognition by bacterial glutamyl-tRNA synthetase.
c) Deciphering interactions responsible for Pro-Pro cis peptide bonds in proteins.
d) Molecular and evolutionary origin of differential binding of colchicine to tubulin from different eukaryotic families.

Current Group Members

Dr. Saumya Dasgupta (Research Associate)
Madhurima Das (Extended Senior Research Fellow)
Himal Ganguly (Senior Research Fellow)
Nipa Chongdar (Senior Research Fellow)
Sarbani Chatterjee (Senior Research Fellow)
Kalyan Reddy (MSc. project student from NIPER, Kolkata)

Group: 1997


Group: 2012

Publications

1. O'Neil, A., Prevelige, P. E., Basu, G., Douglas, T. (2012) Co-Confinement of Fluorescent Proteins: Spatially Enforced Communication of GFP and mCherry Encapsulated Within the P22 Capsid.   Biomacromolecules 13:3902-3907. 

2. Das, M., Basu, G. (2012) Glycine Rescue of β-Sheets from cis-Proline.   J. Am. Chem. Soc. 5134:13536-13539. 

3. Das, L., Bhattacharya, B., Basu, G. (2012) Rationalization of paclitaxel insensitivity of yeast β-tubulin and human βIII-tubulin isotype using principal component analysis.   BMC Research Notes 5:395. 

4. Saha, R., Dasgupta, S., Banerjee, R., Mitra-Bhattacharyya, A., Soll, D., Basu, G., Roy, S. (2012) A functional loop spanning distant domains of glutaminyl-tRNA synthetase also stabilizes a molten globule state.   Biochemistry 51:4429-4437. 

5. Dasgupta, S., Manna, D., Basu, G. (2012) Structural and functional consequences of mutating a proteobacteria-specific surface residue in the catalytic domain of E. coli GluRS.   FEBS Lett. 586:1724-1730. 

6. Ganguly, H. K., Majumder, B., Chattopadhyay, S., Chakrabarti, P., Basu, G. (2012) Direct Evidence for CH-π Interaction Mediated Stabilization of Pro-cisPro Bond in Peptides with Pro-Pro-Aromatic motifs.   J. Am. Chem. Soc. 134:4661-4669. 

7. Banerjee, S., Bhowmik, D., Verma, P. K., Mitra, R. K., Sidhhanta, A., Basu, G., Pal, S. (2011) Ultrafast Spectroscopic Study on Caffeine Mediated Dissociation of Mutagenic Ethidium from Synthetic DNA and Various Cell Nuclei.   J. Phys. Chem. B 115:14776-83. 

8. Banerjee, S., Verma, P. K., Mitra, R. K., Basu, G., Pal, S. K. (2011) Probing the Interior of Self-Assembled Caffeine Dimer at Various Temperatures.   J. Fluoresc. 22:753-69. 

9. Chakraborti, S., Das, L., Kapoor, N., Das, A., Dwivedi, V., Poddar, A., Chakrabarti, G., Janik, M. E., Basu, G., Panda, D., Chakrabarti, P., Surolia, A., Bhattacharyya, B. (2011) Curcumin recognizes a unique binding site of tubulin.   J. Med. Chem. 54:6183-6196. 

10. Cheema, J. and Basu G. (2011) MAPS: An interactive web server for membrane annotation of transmembrane proteins.   Ind. J. Biochem. Biophys. 48:106-110.  MAPS Webserver

11. Pradhan, S. K., Dasgupta, D., Basu G. (2011) Human telomere d[(TTAGGG)₄] undergoes a conformational transition to the Na+-form upon binding with sanguinarine in presence of K+.   Biochem. Biophys. Res. Comm. 404:139-142.  

12. Neogy, R. K., Nath, R., Basu, G., Raychaudhuri, A. K. (2010) Single step precursor free synthesis and characterisation of stable Au nanochains by laser ablation.   arXiv:1010.1999v1 [cond-mat.mtrl-sci] . 

13. Dasgupta, S., Saha, R., Dey, C., Banerjee, R., Roy S, Basu G. (2009) The role of the catalytic domain of E. coli GluRS in tRNAGln discrimination.   FEBS Lett. 583:2114-2120. 

14. Banerjee R, Chattopadhyay S, Basu G. (2009) Conformational preferences of a short Aib/Ala-based water-soluble peptide as a function of temperature,  Proteins 76:184-200. 

15. Das M, Basu G. (2009) Coulomb energies of protein-protein complexes with monopole-free charge distributions. J. Mol. Graph. Model. 27:846-51. 

16. Saha R, Dasgupta S, Basu G, Roy S. (2009) A chimaeric glutamyl:glutaminyl-tRNA synthetase: implications for evolution. Biochem. J. 417:449-55.  

17. Dasgupta, B, Chakrabarti, P, Basu, G. (2007) Enhanced stability of cis Pro-Pro peptide bond in Pro-Pro-Phe sequence motif. FEBS Lett. 581:4529-32.  

18. Banerjee M, Bhattacharyya, B., Basu, G. (2007) Differential colchicine-binding across eukaryotic families: the role of highly conserved Pro268β and Ala248β residues in animal tubulin. FEBS Lett. 581:5019-23.  

19. Saha. R. P., Basu, G., Chakrabarti P. (2006) Cloning, expression, purification, and characterization of Vibrio cholerae transcriptional activator. HlyU. Protein Expr. Purif. 48:118-25. 

20. Allen M, Bulte JW, Liepold L, Basu G, Zywicke HA, Frank JA, Young M, Douglas T. (2005) Paramagnetic viral nanoparticles as potential high-relaxivity magnetic resonance contrast agents. Magn. Reson. Med. 54:807-812.  

21. Gupta S, Banerjee M, Poddar A, Banerjee A, Basu G, Roy D, Bhattacharyya B. (2005) Biphasic kinetics of the colchicine-tubulin interaction: role of amino acids surrounding the a ring of bound colchicine molecule.   Biochemistry 44:10181-10188.  

22. Basu, G., Sivanesan, D., Kawabata, T., Go, N. (2004) Electrostatic Potential of Nucleotide-free Protein is Sufficient for Discrimination Between Adenine and Guanine-specific Binding Sites.   J. Mol. Biol. 342:1053-1066.  

23. Dasgupta, B., Pal, L., Basu, G. & Chakrabarti, P. (2004) Expanded turn conformations: Characterization and sequence-structure correspondence in α-turns with implications in helix folding.   Proteins 55:305-315.  

24. Basu, G., Allen, M., Willits, D., Young, M. & Douglas, T. (2003) Metal Binding to Cowpea Mottle Virus Using Tb(III) Fluorescence.   J. Biol. Inorg. Chem. 8:721-725.  

25. Pal, L., Chakrabarti, Basu, G. (2003) Sequence and Structural Patterns in Proteins from an Analysis of the Shortest Helices: Implications for helix nucleation.  J. Mol. Biol. 326:273-291.  

26. Banerjee, R., Basu, G. (2002) A Short Aib/Ala-based Peptide-helix is as Stable as an Ala-based Peptide-Helix Double its Length.   ChemBioChem 3:1263-1266.  

27. Banerjee, R., Basu, G. (2002) Direct evidence for alteration of unfolding profile of a helical peptide by far-ultraviolet circular dichroism aromaticside-chain contribution.  FEBS Lett. 523:152-156.. 

28. Banerjee, R., Basu, G., Chene, P., Roy, S. (2002) Aib-based Peptide Backbone as Scaffolds for Helical Peptide Mimics. J. Pep. Res. 60:88-94.  

29. Pal, L., Basu, G., Chakrabarti, P. (2002) Variants of 3₁₀-helices in Proteins. Proteins 48, 571:579.

30. Kar, S., Sakaguchi, K., Shimohigashi, Y., Samaddar, S., Banerjee, R., Basu, G., Swaminathan, V., Kundu, T. K., Roy, S. (2002) Effect of Phosphorylation on the Structure and Fold of Transactivation domain of p53. J. Biol. Chem. 277:15579-15585. 

31. Ghose, M., Mandal, S., Roy, D., R. K. Mandal, Basu, G. (2001) Dielectric Relaxation in a Single Tryptophan Protein. FEBS Lett. 509:337-340.  

32. 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 40:1512-15519. 

33. Sengupta, J., Ray, P. K. & Basu, G. (2001) Solution structure of an immunoactive peptide from Staphylococcal Protein A. J. Biomol. Struct. Dyn. 18:773-881. 

34. Pal, L. & Basu, G. (2001) Neural Network Prediction of 3₁₀-helices in proteins. Ind. J. Biochem. Biophys. 38:107-114. 

35. Kettani, A., Basu, G., Gorin, A., Majumdar, A., Skripkin, E. & Patel, D. J. (2000) A two-stranded template-based approach to G.(C-A) triad formation: designing novel structural elements into an existing DNA framework. J. Mol. Biol. 301:129-146.  

36. Pal, L. & Basu, G. (1999) Novel protein structural motifs containing two-turn and longer 3₁₀-helices. Protein Eng. 12:811-814.  

37. Basu, G., Kitao, A., Kuki, A., & Go, N. (1998) Protein Electron Transfer Reorganization Energy Spectrum from Normal Mode Analysis. II. Application to Ru-modified Cytochrome c. J. Phys. Chem. B 102:2085-2094.  

38. Basu, G., Kitao, A., Kuki, A., & Go, N. (1998) Protein Electron Transfer Reorganization Energy Spectrum from Normal Mode Analysis. I. Theory. J. Phys. Chem. B 102:2076-2084.  

39. Kuki, A., Anglos, A., Augspurger, J. D., Basu, G., Bindra, V. A., Kubasik, M., Pettijohn, A. (1997) Molecular Optical Rails Based on Aib, in Modular Chemistry , J. Michl (ed.) pp 503 - 516 Kluwer, Academic Publishers. 

40. Chong, S., Miura, S., Basu, G., & Hirata, F. (1995) A Molecular Theory for the Non-Equilibrium Free Energy Surface in Electron Transfer Reaction. J. Phys. Chem. 99:10526-10529.  

41. Basu, G., Kitao, A., Hirata, F., Go, N. (1994) A Collective Motion Description of the 3₁₀-/α-Helix Transition: Implications For a Natural Reaction Coordinate. J. Am. Chem. Soc. 116:6307-6315.  

42. Basu, G., Kubasik, M., Anglos, D. & Kuki, A. (1993) Spin-Forbidden Excitation Transfer and Heavy Atom Induced Intersystem Crossing in Linear and Cyclic Peptides. J. Phys. Chem. 97:3956-3967. 

43. Basu, G., Anglos, D., Kuki, A. (1993) Fluorescence Quenching in a Strongly Helical Peptide Series: The Role of Non-Covalent Pathways in Modulating Electronic Interaction. Biochemistry 32:3067-3076. 

44. Basu, G., Kuki, A. (1993) Evidence for a 3₁₀- helical Conformation of an Eight-Residue Peptide from 1H-1H Rotating Frame Overhauser Studies. Biopolymers 33:995-1000. 

45. Basu, G., Kuki, A. (1992) Conformational Preferences of Oligopeptides Rich in α-Aminoisobutyric Acid. II. A Model For The 3₁₀- / α-Helical Transition with Composition and Sequence Sensitivity. Biopolymers 32:61-71. 

46. Basu, G., Bagchi, K., Kuki, A. (1991) Conformational Preferences of Oligopeptides Rich in α-aminoisobutyric Acid. I. Observation of a 3₁₀- / α-Helical Transition upon Sequence Permutation.   Biopolymers 31:1763-1774. 

47. Basu, G., Kubasik, M., Anglos, D., Secor, B. & Kuki, A. (1990) Long-Range Electronic Interactions in Peptides: The Remote Heavy Atom Effect. J. Am. Chem. Soc. 112:9410-9411.

Ongoing projects with external financial support

• Theoretical and experimental analyses of bacterial GlxRS/tRNA-Glx/gatCAB co-evolution and the molecular basis of their interaction (CSIR; 2012-14)