Banaras Hindu University, India
Banaras Hindu University, India
The University of Iowa, Iowa State University,
RCSB, Rutgers-The State University of New Jersey
Structure-function relationship studies, protein structure, interactions, surface energetics, binding studies using NMR
Ambrish Kumar, Rohit Singh Dangi, Pinakin K. Makhwana
Summary of Research
- Structure-function relationship studies on the fatty acid biosynthesis pathways
Fatty acid biosynthesis pathway has been regarded as an important drug target against several tropical diseases owing to the remarkable structural and functional differences in their proteins. Most microorganisms synthesize fatty acids via a type II pathway, while their human counterpart synthesizes by type I pathway. In the type II pathway, fatty acids are synthesized by multiple enzymes catalyzing different reactions, whereas in type I pathway, fatty acids are synthesized by one single multidomain, multifunctional fatty acid synthase, each domain catalyzing a particular reaction. Interestingly, ACP’s of type I and II pathway share a similar fold though they differ remarkably in their mechanism of function.
The primary function of ACP is to shuttle the lengthening acyl chains to the catalytic site of FAS enzymes. It is expressed as an apo protein (inactive), and modified to holo-ACP (active) by the transfer of a 4’-phosphopantetheine moiety (4’-PP) from coenzyme A (CoA) to a conserved serine residue, Ser 36/37, ACP synthase acting as a catalyst. The acyl chain gets covalently tethered to the terminal cysteamine thiol of the 4’-PP prosthetic group, which in turn transfers the acyl chain to the respective enzymes during elongation. Several structural studies have shown that the hydrophobic cavity accommodates the growing acyl chain in the type II pathway, which expands with increasing length of the acyl chain. However, a few questions still remain unanswered viz. how does thioesterase recognize and release the acyl chain, how are the acyl intermediates recognized by their enzymes. Moreover, in type I fatty acid biosynthesis pathway, the mechanism of protection of the acyl chain by ACP still remains elusive. To address these questions, we are studying the structure and interactions of some key proteins of this pathway from three different organisms, P. falciparum, Leishmania and human using NMR. Understanding the structural features that dictate ACP function and its interaction with other enzymes could offer new avenues for inhibitor design.
- Structure, dynamics and interactions of ubiquitin
Ubiquitin is a remarkable protein, with innumerable non-covalent interactions playing an indispensable role in the regulation of a multitude of cellular processes. Ubiquitin still remains a mystery with regard to its expanding number of interactions. What are the structural features that impart it with this unique ability to bind a wide range of structures? Identification of the structural properties important for its recognition is necessary to understand the regulation of ubiquitin mediated pathways. We are using NMR spectroscopy to understand the structure, dynamics and interactions of ubiquitin.
- Sundd M. (2012) Conformational and dynamic changes at the interface contribute to ligand binding by ubiquitin. Biochemistry (epub).
- Kumar, A., Surolia, A., Sundd, M. (2012) Backbone and side chain (1)H, (15)N & (13)C chemical shift assignments of the holo-acyl carrier protein (ACP) of Leishmania major. Biomol NMR Assign. 6: 221-223.
- Sidhu, A., Surolia, A., Robertson, A.D., Sundd, M. (2011) A hydrogen bond regulates slow motions in ubiquitin by modulating a b-turn flip. J Mol Biol 411: 1037-1048.
- Upadhyay, S.K., Misra, A., Surolia, N., Surolia, A., Sundd, M. (2010) Backbone chemical shift assignments of the acyl-acyl carrier protein intermediates of the fatty acid biosynthesis pathway of Plasmodium falciparum. Biomol NMR Assign. 4: 83-85.
- Upadhyay SK, Misra A, Srivastava R, Surolia N, Surolia A and Sundd M. (2009) Structural Insights into the acyl-intermediates of Plasmodium falciparum fatty acid synthesis pathway; the mechanism of expansion of acyl carrier protein core. J Biol Chem 284: 22390-22400.