deepak

B.Sc (Chemistry) from Fergusson College, Pune University, Pune (1992-1994).
M.Sc (Biotechnology) from the Department of Biotechnology, University of Pune, Pune (1994-1996).
Ph.D (Life Sciences) from the Structural Biology Unit, National Institute of Immunology, New Delhi (1996-2001).Thesis supervisor: Dr. Dinakar M. Salunke
(2002-7/2004) Post-doctoral fellow with the Aggarwal Group (Structural Biology Program, Dept. of Physiology & Biophysics, Mt.Sinai School of Medicine
Principal Investigator: Prof. Aneel K. Aggarwal
(7/2004-present) Instructor at the Mt. Sinai School of Medicine in Prof. Aggarwal's lab in the Department of Physiology and Biophysics

We work in collaboration with the laboratories of Prof. Satya Prakash and Prof. Louise Prakash (located at UTMB in Galveston, Texas) to understand the structural basis of the function and unusual biochemical properties exhibited by lesion-bypass Y-family polymerases. Towards this end I have been able to determine the structures of the ternary complexes of the catalytic cores of two Y-family Polymerases human DNA polymerase Iota and yeast REV1.
The structure of the catalytic core of the enzyme REV1 from yeast in complex with DNA and incoming nucleotide was determined to a resolution of 2.3 Angstroms (Science, 2005). This enzyme is a Y-family polymerase which plays a pivotal role in the bypass of DNA lesions. This DNA polymerase shows extreme specificty for template G as well as incoming C. The structure of the catalytic core shows that instead of the template base G the incoming nucleotide C pairs do not base pair with each other. The template G is flipped out of the active site and is held in place by specific interactions with a long loop of the protein. The incoming nucleotide instead of base pairing with the template, instead forms specific hydrogen bonds with the guanidinium group of an Arginine residue. Thus the specificity of the incoming nucleotide is determined by the protein itself which is a novel mode of DNA synthesis.We believe that this extreme nature of the enzyme allows it to accurately bypass N2-adducted Guanine lesions which would otherwise lead to mutations and cause cancer.

The crystal structure of the catalytic core of the enzyme human DNA Polymerase Iota (hPoli) in complex with DNA and incoming nucleotide was determined to 2.3 Angstroms (Nature, 2004). This enzyme is also an error prone DNA lesion bypass polymerase and belongs to theY-family of DNA polymerases. It has been implicated in the bypass of a number of DNA lesions that can cause cancer. The structure of the catalytic core in complex with DNA and dTTP shows that the enzyme stabilizes the incoming nucleotide through Hoogsteen base pairing (as against the normally observed Watson-Crick base pairing). This has been seen for both template A and template G (Structure, 2005) and explains why this enzyme is more efficient at DNA synthesis opposite template purines than pyrimidines. In addition, I have shown -through a comparison of the binary and ternary complexes of hPoli - that the template purine nucleotide flips from anti to syn conformation on nucleotide binding (Structure, 2006). Overall, the enzymes ability to favor Hoogsteen base pairing must enable it to bypass a variety of carcinogenic DNA lesions. I have recently determined the structure of hPoli with the carcinogenic lesion 1,N6 ethenodeoxyadenosine (whose Watson-Crick edge is disrupted by an exocyclic ring) in its active site (with both incoming dTTP and dCTP). The structure shows that the enzyme forces this adduct to adopt a syn conformation in the active site (thus rotating the exocyclic ring away from the active site) and hydrogen bonds with the incoming nucleotide through its unaffected Hoogsteen edge (NSMB, 2006). I am presently trying to determine the structure of this enzyme in complex with other lesions.These structures will provide valuable insight into how DNA lesions formed by environmental, food and chemical carcinogens lead to cancer and how Y-family polymerases can prevent this.

Previous Research Contributions
My doctoral thesis describes the crystallographic analysis of a panel of three monoclonal antibodies raised against the same peptide antigen PS1 (HQLDPAFGANSTNPD). (J Immunol, 2000; J. Immunol 2002). I also carried out a computational analysis of the conformational propensities of native and retro-inverso versions of B-cell and T-cell epitopes (J. Immunol, 2003). I was also involved in the crystal structure determination of the antibacterial protein from tasar silkworm Antheraea mylitta (J. Biol. Chem., 2001). In addition, I modelled the complex of the ribonuclease restrictocin and its rRNA substrate (Biochemistry, 2001).

From Mt. Sinai School of Medicine, New York.
1. Nair DT*, Johnson RE*, Prakash L, Prakash S, Aggarwal AK. Hoogsteen base pair formation promotes synthesis opposite the 1,N(6)-ethenodeoxyadenosine lesion by human DNA polymerase iota. Nat Struct Mol Biol. 2006 Jul 2; [Epub ahead of print]
2. Nair DT, Johnson RE, Prakash L, Prakash S, Aggarwal AK. An Incoming Nucleotide Imposes an anti to syn Conformational Change on the Templating Purine in the Human DNA Polymerase-iota Active Site. Structure. 2006 Apr;14(4):749-55.
3: Nair DT, Johnson RE, Prakash L, Prakash S, Aggarwal AK. Human DNA Polymerase iota Incorporates dCTP Opposite Template G via a G.C+ Hoogsteen Base Pair.
Structure (Camb). 2005 Oct;13(10):1569-77.
4: Nair DT, Johnson RE, Prakash L, Prakash S, Aggarwal AK. Rev1 employs a novel mechanism of DNA synthesis using a protein template.
Science. 2005 Sep 30;309(5744):2219-22.
5: Nair DT, Johnson RE, Prakash S, Prakash L, Aggarwal AK. Replication by human DNA polymerase-iota occurs by Hoogsteen base-pairing.
Nature. 2004 Jul 15;430(6997):377-80.

From National Insitute of Immunology, New Delhi.
6: Nair DT, Kaur KJ, Singh K, Mukherjee P, Rajagopal D, George A, Bal V, Rath S, Rao KV, Salunke DM. Mimicry of native peptide antigens by the corresponding retro-inverso analogs is dependent on their intrinsic structure and interaction propensities. J Immunol. 2003 Feb 1;170(3):1362-73.
7: Nair DT, Singh K, Siddiqui Z, Nayak BP, Rao KV, Salunke DM. Epitope recognition by diverse antibodies suggests conformational convergence in an antibody response. J Immunol. 2002 Mar 1;168(5):2371-82.
8: Jain D*, Nair DT*, Swaminathan GJ, Abraham EG, Nagaraju J, Salunke DM. Structure of the induced antibacterial protein from tasar silkworm, Antheraea mylitta. Implications to molecular evolution. J Biol Chem. 2001 Nov 2;276(44):41377-82. Epub 2001 Aug 24.
9: Nayak SK, Bagga S, Gaur D, Nair DT, Salunke DM, Batra JK. Mechanism of specific target recognition and RNA hydrolysis by ribonucleolytic toxin restrictocin. Biochemistry. 2001 Aug 7;40(31):9115-24.
10: Nair DT, Singh K, Sahu N, Rao KV, Salunke DM. Crystal structure of an antibody bound to an immunodominant peptide epitope: novel features in peptide-antibody recognition. J Immunol. 2000 Dec 15;165(12):6949-55.