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Krishnan P. Nambiar
Associate Professor

Email: nambiar@chem.ucdavis.edu
Phone:(530) 752-4757

BS, University of Calicut, India, 1971.
MS, University of Calicut, India, 1973.
Ph.D, University of New Brunswick, Canada, 1978.
Research Fellow / Research Associate, Harvard University, 1978-87.
Chemistry Faculty at UC Davis, 1987-present.

Group Page
Principal Research Interests
Our research focuses on understanding the chemical interactions involved in macromolecular recognition relevant to biological systems and the utilization of the resulting information in the design of novel molecules with chemical and biological applications.

Peptides and Peptidomimetics
We have been investigating the parameters that influence the folding of peptides into specific secondary structures. We have shown that short a-helices can be stabilized by end capping. We have been active in the area of stabilizing beta ribbon structures as well. We have shown that incorporation of a strain-free disulfide bridge between two peptide strands results in a large increase in the stability of b-ribbon structures formed by the peptides. In addition, we have designed and synthesized a turn structure which upon incorporation into a peptide forces it to adopt a stable beta ribbon structure.
Nucleic Acids
This project involves the chemical synthesis of an unnatural analog of DNA having the bases connected to the sugar via a-anomeric linkages rather than the natural b- linkages, and the phosphodiester linkage replaced with a sulfone linkage, in order to study their chemical and biological properties.

Designing Catalysts
Another project involves the design and synthesis of organic catalysts. By synthesizing a designed binding pocket and incorporating specific catalytic functional groups at the mouth of the cavity, we hope to attain substrate binding followed by catalysis. We designed an organic molecule (compound I, Figure 2) with a hydrophobic binding pocket, whose synthesis is now half way through.
Representative Publications

“A Practical Synthesis of C-14 labeled 5-Methyl Tetrahydrofolic Acid” Matel, H., Snyder, D., Owens, J., Clifford, A.J. and Nambiar, K.P., ( 2006, in preparation).

“Exploring a-Helix N-Capping Preferences of Asparagine and Glutamine”. Couch, V.A.; Nambiar, K. P., Fink, W. H ( 2006, in preparation).

“Investigation of protein turn over in human ocular lenses by AMS” Stewart, D., Buchholz, B., Knezovich, J. and Nambiar, K.P., (2006, in preparation).

“A novel fluorometric method for the rapid and sensitive quantitation of snake venom metalloproteases and their inhibitors”, Biardi, J.E., Nguyen, K.T., Leachman, S.L. and Nambiar, K.P. (2006, in preparation).

“Site Selective Cleavage of Oligodeoxynucleotides containing 2-thiopyrimidine Residues”, Nambiar, K.P and Saiki, T. (2006, in preparation).

“Structural Characterization of a-Helices of Implicitly Solvated Poly-Alanine.”, Couch, V. A.; Cheng, N.; Nambiar, K. P.; Fink, W. H. Journal of Physical Chemistry B (2006), ASAP Article; DOI: 10.1021/jp055209j

“Design, Synthesis and Incorporation in Peptides of a b-turn Mimetic”, Janardhanam, S.; Balachari, D. and Nambiar, K.P., Peptides: Proceedings of the 2nd International/17th American Peptide Symposium. Richard Houghton (Eds), Kluwer Academic Publishers 2001 , 440-441.

"Strain-Free Disulfide Bridge and Stabilization of b-Ribbon Structures in Short Peptides" Nambiar, K.P, Janardhanam, S. and Balachari, D., Peptides for the New Millenium, Proceedings of the 16th American Peptide Symposium, G.B Fields, J.P. Tam and G. Barany (Eds), Kluwer Academic Publishers 2000, 311-312.

"End Capping and Helix Stabilization in Short Peptides", Reddy, H. K. and Nambiar, K. P., Peptides: Frontiers of Peptide Science, Proceedings of the 15th American Peptide Symposium, J.P. Tam and P.T.P. Kaumaya (Eds), Kluwer Academic Publishers, 1999, 114-115.

"Redesigning Nucleic Acids", Benner S.A. et al, Pure and Appl. Chem., 70, 263-266 (1998).

"The Role of a strain free disulfide bridge in stabilizing b-sheet structures in short peptides", anardhanam, S., Balachari, D., Corson, D.T. and Nambiar, K.P., Proceedings of the 14th American Peptide Symposuim, Peptides: Chemistry, Structure and Biology. Pravin T.P. Kaumaya and Robert S. Hodges (Eds), Mayflower Scientific Ltd, 575-576 (1996).

"Extraordinary Helicity in Short Peptides via End Capping Design", Forood, B., Reddy, H. R. and Nambiar, K. P. J. Am. Chem. Soc., 116, 6935-6936 (1994).

"Stabilization of b-Ribbon Structures in Peptides using Disulfide Bonds", Aberle, A. M., Heeb, N. V. and Nambiar, K. P. Biochem. Biophys. Res.Commun., 200, 102-107 (1994).

"Synthesis of Oligodeoxynucleotides Containing 2-Thiopyrimidine Residues -A New Protection Scheme", Kuimelis, R. G. and Nambiar, K. P.Nucleic Acids Research, 22, 1429-1436 (1994).

"Investigation of Stereoselectivities in the Coupling Reactions between 1-O-Methyl-3',5'-di-O-p-toluoyl-2-deoxyribofuranoside with Purines and Pyrimidines" Salvasekaran, J. and Nambiar, K. P. Tetrahedron Letters, 35, 3657-3660 (1994).