Nitin Jain, Ph.D.

Research Statement

My laboratory is primarily interested in application of biochemical and biophysical approaches for elucidation of Structure-Function relationships in biomolecules. Owing to the diverse nature of biological problems investigated, we utilize techniques from wide-ranging areas in biology such as molecular biology, cell biology, protein biochemistry, structural and computational biology. We currently have two active areas of research:

Molecular basis of endotoxin recognition by receptors involved in the innate immune system.

Recognition of endotoxins released by microbial pathogens during infection of higher organisms leads to an appropriate innate immune response from the host cell. This response if uncontrolled, often leads to sepsis and septic shock, a major cause of mortality in hospitals. Onset of sepsis occurs in a series of signaling steps, initiated by binding of endotoxins to a key host cell receptor CD14 expressed on the surface of monocytes and tissue macrophages of the host. A precise understanding of the molecular mechanism underlying CD14-dependent endotoxin recognition and signaling is thus essential for the control of immune response and endotoxin septic shock. Efforts in our laboratory are currently focused on understanding the molecular basis of endotoxin recognition by CD14, mainly using site-directed mutagenesis, cell-based functional assays and structural techniques such as Fluorescence and NMR spectroscopy. This will provide insights into the mechanism of CD14-mediated response and will be quite useful in the design of effective antagonists and development of new strategies for prevention and therapeutic treatment of sepsis as well as infectious diseases.

Molecular design of proteins involved in catalysis and biological electron transfer.

Electron transfer in biological systems, although essential to numerous biological processes, is often not well characterized in terms of its molecular mechanism. An example of a prototype biological electron transfer system is the complex between two metalloproteins, putidaredoxin (a Cys4Fe2S2 ferredoxin) and CYP101 (a heme-containing cytochrome P450 catalytic enzyme), that belong to the camphor hydroxylase pathway of the bacteria Pseudomonas putida. This redox pair represents a model system for the investigation of catalytic properties of the very important cytochrome P450 systems and for electron transfer in general. We are interested in structural and dynamic characterization of this protein-protein complex to identify structural and molecular elements inherent to these two proteins in terms of their ligand binding and electron transfer properties. This will be important in explaining the catalytic efficiency of this protein system towards certain organic substrates. Our long-term goals are to use this information in design of more efficient catalytic systems for commercially useful organic substrates. We are currently developing novel structural and computational approaches for protein molecular design to achieve these goals.

Selected Publications

Jain NU, Wyckoff TJ, Raetz CR and Prestegard JH (2004) Rapid analysis of large protein-protein complexes using NMR-derived orientational constraints: the 95 kDa complex of LpxA with acyl carrier protein. J. Mol. Biol. 343: 1379-1389.
 
Jain NU, Noble S and Prestegard JH (2003) Structural Characterization of Mannose-Binding Protein-Trimannoside complex using residual dipolar couplings. J. Mol. Biol. 328: 451-462. 
 
Prestegard JH, Jain NU, Al-Hashimi HM, Morris LC and Venot AP (2001) NMR Assisted Design of High Affinity Ligands for Structurally Uncharacterized Proteins. U.S. Patent Application Pending.
 
Prestegard JH, Jain NU and Levery SB (2001) Saccharide-Protein Interactions. Encyclopedia of NMR.
 
Jain NU, Venot A, Umemoto K, Leffler H and Prestegard JH (2001) Distance Mapping of protein-binding sites using spin-labeled oligosaccharide ligands. Protein Science 10: 2393.
 
Pochapsky TC, Kostic M, Jain NU and Pejchal R (2001) Redox-Dependent Conformational Selection in a Cys4Fe2S2 ferredoxin. Biochemistry 40: 5602.
 
Jain NU and Pochapsky TC (1999) A new assignment strategy for the hyperfine-shifted 13C and 15N resonances in Fe2S2 ferredoxins. Biochem. Biophys. Res. Comm. 258: 54.
 
Pochapsky TC, Jain NU, Kuti M, Lyons TA and Heymont J (1999) A refined model for the solution structure of oxidized Putidaredoxin. Biochemistry 38: 4681.
 
Pochapsky TC, Arakaki T, Jain N, Kazanis S, Lyons TA, Mo H, Patera A, Ratnaswamy G and Ye X (1997) How does the oxidation state of a metalloprotein affect its structure, dynamics and function? Journal of Biomolecular Structure and Dynamics 16: 79-84.
 
Jain NU and Pochapsky TC (1998) Redox dependence of the hyperfine-shifted 13C and 15N resonances in Putidaredoxin. J. Am. Chem. Soc. 120: 12984-12985.

Contact Information

Office:
Room F-325
Walters Life Sciences
Phone: (865) 974-4045

Lab:
Room D-301
Walters Life Sciences
Phone: (865) 974-8091

Email: njain@utk.edu