Developed a theoretical model that relates protein electron transfer rate and protein dynamics with application on cytochrome c.
Completed rigorous solution structural analysis and equilibrium unfolding, by CD and fluorescence spectroscopy, of a 2S seed albumin from Brassica juncea (mustard seeds). The results will help in identifying amino acids that can be mutated for improving the nutritional content of mustard seeds.
Investigated the solution conformation (NMR) of a 20-residue peptide fragment from Protein A that showed important immunological properties.
From known protein structures in the protein data bank, a detailed analysis of protein 310-helices has been completed. This includes, identification of supersecondary structural motifs containing long 310-helices, classification and analysis of shortest protein helices, and, estimation of conformational entropy of protein helices as a function of helix length. In addition, neural network methodology was used to predict 310-helices in proteins. The work has fundamental importance in understanding factors responsible for unique three dimensional structures of proteins.
A series of short peptides were synthesized that exhibit the 310-helical conformation in proteins. The solution conformations of these peptides were studied by NMR and CD spectroscopy. The work is in its preliminary stage, however, our results indicate that some of the peptides can show turn like secondary structure in isolation. This work has important implications in understanding protein folding initiation sites in proteins.
Using a-amino isobutyric acid (Aib) as a strong helix forming amino acid, we have designed and synthesized water soluble peptides that show substantial helicity at ambient temperatures. These designed peptide helices have been used for:
1) Quantitative comparison of helix forming free energies of Ala and Aib, using the Zimm-Bragg model.
2) Identifying artifacts (arising from interfering aromatic side chain contributions) in far-UVCD-monitored peptide unfolding profiles.
3) Designing helical scaffolds (in collaboration with Prof. S. Roy) for designing peptidomimetic drugs.
CURRENT RESEARCH INTERESTS
STRUCTURAL AND SEQUENCE PATTERNS OF INTEGRAL MEMBRANE PROTEINS
ELECTROSTATIC SIGNATURES IN ADENINE AND GUANINE BINDING SITES IN PROTEINS
THEORETICAL AND EXPERIMENTAL STUDY OF 310-HELIX
PUBLICATIONS:
1) Basu, G., Kubasik, M., Anglos, D., Secor, B. & *Kuki, A. "Long-Range Electronic Interactions in Peptides: The Remote Heavy Atom Effect", J. Am. Chem. Soc. 112, 9410-9411 (1990).
2) Basu, G., Bagchi, K. & *Kuki, A. "Conformational Preferences of Oligopeptides Rich in alpha-aminoisobutyric Acid. I. Observation of a 310- / alpha- Helical Transition upon Sequence Permutation", Biopolymers 31, 1763-1774 (1991).
3) Basu, G. & *Kuki, A. "Conformational Preferences of Oligopeptides Rich in alpha-Aminoisobutyric Acid. II. A Model For The 310- / alpha- Helical Transition with Composition and Sequence Sensitivity", Biopolymers 32, 61-71 (1992).
4) Basu, G. & *Kuki, A. "Evidence for a 310- helical Conformation of an Eight-Residue Peptide from 1H-1H Rotating Frame Overhauser Studies", Biopolymers 33, 995-1000 (1993).
5) Basu, G., Anglos, D. and *Kuki, A. "Fluorescence Quenching in a Strongly Helical Peptide Series: The Role of Non-Covalent Pathways in Modulating Electronic Interaction", Biochemistry 32, 3067-3076 (1993).
6) Basu, G., Kubasik, M., Anglos, D. & *Kuki, A. "Spin-Forbidden Excitation Transfer and Heavy Atom Induced Intersystem Crossing in Linear and Cyclic Peptides", J. Phys. Chem. 97, 3956-3967 (1993).
7) Basu, G., Kitao, A., Hirata, F. & *Go, N. "A Collective Motion Description of the 310-/alpha- Helix Transition: Implications For a Natural Reaction Coordinate", J. Am. Chem. Soc. 116, 6307-6315 (1994). pdf file
8) Chong, S., Miura, S., Basu, G., & *Hirata, F. "A Molecular Theory for the Non-Equilibrium Free Energy Surface in Electron Transfer Reaction", J. Phys. Chem. , 99, 10526-10529 (1995).
9) *Kuki, A., Anglos, A., Augspurger, J. D., Basu, G., Bindra, V. A., Kubasik, M. & Pettijohn, A. "Molecular Optical Rails Based on Aib" in Modular Chemistry , J. Michl (ed.). pp 503 - 516 (1997) Kluwer Academic Publishers.
10) *Basu, G., Kitao, A., Kuki, A., & *Go, N. "Protein Electron Transfer Reorganization Energy Spectrum from Normal Mode Analysis. I. Theory", J. Phys. Chem B 102, 2076-2084 (1998). pdf file
11) *Basu, G., Kitao, A., Kuki, A., & *Go, N. "Protein Electron Transfer Reorganization Energy Spectrum from Normal Mode Analysis. II. Application to Ru-modified Cytochrome c", J. Phys. Chem B 102, 2085-2094 (1998). pdf file
12) Pal, L. & *Basu, G. "Novel protein structural motifs containing two-turn and longer 310-helices", Protein Eng. 12, 811-4 (1999). pdf file
13) Kettani, A., Basu, G., Gorin, A., Majumdar, A., Skripkin, E. & *Patel, D. J. "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 (2000). pdf file
14) Pal, L. & *Basu, G. "Neural Network Prediction of 310-helices in proteins", Ind. J. Biochem. Biophys. 38, 107-114 (2001).
15) Sengupta, J., Ray, P. K. & *Basu, G. "Solution structure of an immunoactive peptide from Staphylococcal Protein A", J. Biomol. Struct. Dyn. 18, 773-81. (2001).
16) Pal, D., Mahapatra, P., Manna, T., Chakrabarti, P., Bhattacharyya, B., Banerjee, A., Basu, G. & *Roy, S. "Conformational properties of alpha-tubulin tail peptide: Implications for tail-body interaction", Biochemistry 40, 1512-15519 (2001)
17) Ghose, M., Mandal, S., Roy, D., R. K. Mandal & *Basu, G. "Dielectric Relaxation in a Single Tryptophan Protein", FEBS Lett. 509, 337-340. (2001). pdf file
18) Kar, S., Sakaguchi, K., Shimohigashi, Y., Samaddar, S., Banerjee, R., Basu, G., Swaminathan, V., Kundu, T. K. & *Roy, S. "Effect of Phosphorylation on the Structure and Fold of Transactivation domain of p53", J. Biol. Chem. 277, 15579-15585 (2002).
19) Pal, L., *Basu, G. & *Chakrabarti, P. "Variants of 310-helices in Proteins", Proteins 48, 571-579 (2002). pdf file
20) Banerjee, R., *Basu, G., Chene, P. & *Roy, S. "Aib-based Peptide Backbone as Scaffolds for Helical Peptide Mimics", J. Pep. Res.60, 88-94 (2002). pdf file
21) Banerjee, R. & *Basu, G. "Direct evidence for alteration of unfolding profile of a helical peptide by far-ultraviolet circular dichroism aromatic side-chain contribution", FEBS Lett. 523, 152-156 (2002). pdf file
22) Banerjee, R. & *Basu, G. "A Short Aib/Ala-based Peptide-helix is as Stable as an Ala-based Peptide-Helix Double its Length"
, ChemBioChem 3, 1263-1266 (2002). pdf file
23) Pal, L., *Chakrabarti, P. & *Basu, G. "Sequence and Structural Patterns in Proteins from an Analysis of the Shortest Helices: Implications for helix nucleation", J. Mol. Biol. 326, 273-291 (2003). pdf file
24) Basu, G., Allen, M., Willits, D., Young, M. & *Douglas, T. "Metal Binding to Cowpea Mottle Virus Using Tb(III)
Fluorescence", J. Biol. Inorg. Chem. 8, 721-725 (2003). pdf file
25) Dasgupta, B., Pal, L., Basu, G. & *Chakrabarti, P. "Expanded turn conformations: Characterization and sequence-structure correspondence in alpha-turns with implications in helix folding", Proteins 55, 305-315 (2004).
pdf file
26) *Basu, G., Sivanesan, D., Kawabata, T. & Go, N. "Electrostatic Potential of Nucleotide-free Protein is Sufficient for Discrimination Between Adenine and Guanine-specific Binding Sites", J. Mol. Biol. 342, 1053-1066 (2004). pdf file
When not doing science ... I am involved with
mustard seeds
a project that provides small supports for big results, co-ordinated by Maura Hurley and me
Last updated: September 06, 2004