Welcome to Protein Crystallography Lab, IIT Bombay

About our Lab

Proteins are important biological macromolecules as they play key roles in almost every biological process of a living organism. Protein molecules function as enzymes, transporters, mechanical strength enhancers, protective immune systems, signal transducers, etc. Three dimensional structure of a protein dictates its functional properties. Hence, determination and understanding of three dimensional structure a protein is essential for deciphering the mechanistic details about how a protein performs its activities. Our research group at IIT Bombay is focused in elucidating the structure-function relationship of proteins, rational design of enzymes and structure based drug development. We determine crystal structures of proteins. We perform extensive biochemical and biophysical studies on proteins, which enables us to obtain information complementary to that obtained from structure analysis. We have determined high resolution crystal structures of multiple proteins. The crystal structures on P. falciparum plasmepsins (PMs) complexed with KNI compounds solved in our group provide detailed molecular insights for antimalarial drug development. We also perform molecular dynamics simulations in order to capture different dynamic motions and interactions in proteins and their complexes.

We have performed extensive structural studies on glutamate dehydrogenase (GDH) to decipher the catalytic mechanism and for understanding the molecular basis of cofactor recognition of this enzyme. Recently we have determined multiple Cryo-EM structures of GDHs. Following movie presents some of the exciting structural features of Aspergillus niger GDH (AnGDH) complexed with substrate alpha-ketoglutarate (AKG) and cofactor NADP.

Our structural and biophysical studies indicate a novel mechanism of activation of vacuolar plasmepsins. Following videos show the structural changes during the activation of histo-aspartic protease (HAP), a vacuolar PM.

Our recent studies on artificial metalloenzyme published in Nature Synthesis

		Tetrameric streptavidin along with a biotinylated metal complex is a promising artificial metalloenzyme for its industrial application in diverse non-natural reactions. In this collaborative work with Prof. Debabrata Maiti group (Department of Chemistry, IIT Bombay), a streptavidin-biotin-Rh(III) platform has been utilized to synthesize chiral isoindolones. We have determined a high-resolution crystal structure of streptavidin with unique conformations of the biotinylated Rh(III) cofactor, and the information from the structural analysis has aided to develop better biocatalyst.

Our efforts towards drug repurposing: anti-HIV drugs as antimalrials

		We have shown that FDA approved HIV-1 drugs ritonavir (RTV) and lopinavir (LPV) exhibit the highest inhibition activity against plasmepsin II (PMII) and plasmepsin X (PMX) of P. falciparum, the parasite that causes the deadliest form of malaria. Crystal structures of the complexes of PMII with both RTV and LTV have been determined. Our structural investigations and biochemical data emphasize PMs as crucial targets for repurposing anti-HIV drugs as antimalarials.

Our exciting structural studies on PMX publsihed in Protein Science

		Plasmodium falciparum plasmepsin X (PfPMX), involved in the invasion and egress of this deadliest malarial parasite, is essential for its survival and hence considered as an important drug target. We report the first crystal structure of PfPMX zymogen containing a novel fold of its prosegment. A unique twisted loop from the prosegment and arginine 244 from the mature enzyme are involved in zymogen inactivation; such mechanism, not previously reported, might be common for apicomplexan proteases similar to PfPMX. Our data provide thorough insights into the mode of binding of a substrate and a potent inhibitor 49c to PfPMX.

Recent paper on GDH published in PROTEINS

		The function of glutamate dehydrogenase (GDH) is extensively regulated by both metabolites(citrate, succinate, etc.) and non-metabolites (ATP, NADH, etc.) but sufficient molecular evidences are lacking to rationalize the inhibitory effects by the metabolites. We have expressed and purified NADP+-dependent Aspergillus terreus GDH (AtGDH) in recombinant form. Succinate, malonate, maleate, fumarate, and tartrate independently inhibit the activity of AtGDH to different extents. The crystal structures of AtGDH complexed with the dicarboxylic acid metabolites and the coenzyme NADPH have been determined.

Our review article on Protein Crystallography

		Our paper in Emerging Topics in Life Sciences presents advancements in the field of protein crystallography or macromolecular crystallography (MX). The paper provides a brief history about the developments in methods as well as technologies in MX. With many exciting current techniques like X-ray Free Electron Lasers (XFELs) and more developments awaiting in the upcoming years, MX has the potential to contribute significantly to the growth of modern biology