Research Activities
Protein Three-dimensional Models
1.1. Three-dimensional model of plasmepsin V from Plasmodium falciparum :
The virulent form of malaria is caused by Plasmodium falciparum that infects red blood cells. In order to survive inside the host, the parasite remodels the infected erythrocytes by exporting more than 300 effector proteins outside the parasitophorous vacuole membrane into the cytosol.The main feature of all the export proteins is the presence of a pentapeptide sequence motif; RxLxE/Q/D. This sequence motif is hydrolysed between L – x and the proteins with the acetylated new N-terminus xE/Q/D are exported. The enzyme responsible for this hydrolysis is plasmepsin V which is one of the ten aspartic proteases in P. falciparum . In order to understand the structural rationale for the specificity of this protease towards cleavage of the above motif, we generated three-dimensional models of seven plasmepsins (I, V to X) for which experimental structures were not available and compared these along with the crystal structures of three P. falciparum plasmepsins (II to IV). The structure comparisons revealed the importance of Tyr13, Glu77 and Ala117 specific to plasmepsin V that facilitates the accommodation of arginine at P3 in the RxLXE/Q/D motif. Our analysis correlates the structure-function relationship of plasmepsin V.
Researcher(s) / References :
- Guruprasad, L., Tanneeru, K., Guruprasad, K. (2011) Protein Pept. Lett. Feb 21.
1.2. Three-dimensional models corresponding to corynemycolyltransferases from C. glutamicum and C. efficiens :
The three-dimensional structures of Mycobacterium tuberculosis mycolyltransferases, antigen 85 B and C are known. In all Actinobacteria, these mycolyltransferases are responsible for the synthesis of trehalose dimycolate that is a constituent of the glycolipid cell wall. In order to understand whether this is the case in corynemycolyltransferases that share less than 20% sequence identity with mycolyltransferases, we constructed three-dimensional models of the corynemycolyltransferases. Significant difference was observed between Trp82-Trp97 and Ala222-Asn223. Further, it was observed that trehalose may not bind some corynemycolyltransferases owing to critical mutations that lead to loss of equivalent side-chain interactions with trehalose and unfavorable steric interactions in the binding subsites. Further, the fibronectin binding region (Phe58-Val69), in mycolyltransferases associated with mediating host-pathogen interactions in M. tuberculosis comprises amino acid residue mutations in the corresponding region in the soil bacterium - Corynebacterium corynemycolyltransferases that suggest a different epitope and therefore possible lack of binding to fibronectin.
Researcher(s) / References :
- Adindla, S., Guruprasad, K., Guruprasad, L. (2004) Int. J. Biol. Macromol. 34, 181-189.
1.3. IspC protein models from genomes of bacterial sub-groups :
Isopentenyl diphosphate is the precursor of various isoprenoids that are essential to all living organisms. It is produced by the mevalonate pathway in humans but by an alternate route in plants, protozoa, and many bacteria. The pathway relies on eight enzymes exploiting different cofactors and metal ions. The IspC is the first enzyme committed to isoprenoid biosynthesis in the non-mevalonate pathway. As it is present in many pathogens and plants, but not in man, this pathway has attracted considerable interest as a target for novel antibiotics and herbicides. Fosmidomycin represents a specific high-affinity inhibitor of IspC. Recently, its anti-malaria activity in man has been demonstrated in clinical trials.
We have constructed three-dimensional models of 27 IspC sequences representing a particular sub-group of bacterial genomes and assessed the nature of the active site and interactions with fosmidomycin. The different bacterial-sub-groups are associated with diseases, such as, tuberculosis, malaria, typhoid, cholera, salmonellosis, bubonic plague, childhood meningitis, leprosy, syphilis. Despite the low sequence similarities between some of these proteins, 21 amino acid residues are conserved that include the active site residues. The amino acid residues responsible for the IspC activity are conserved in all the genomes, except in Actinobacteria. The IspCs corresponding to eighteen sub-groups are associated with one or two sites of loop insertions varying between 4 and 34 amino acid residues. These insertions are distant from the active site. All the IspCs display the ability to accommodate fosmidomycin in the binding site, although the binding poses are likely to vary in IspCs from certain bacterial sub-groups.
Researcher(s):
- Dr. K. Guruprasad
1.4. Three-dimensional models corresponding to the C-terminal domain of human alphaA and alphaB crystallins :
We have proposed three-dimensional models corresponding to the C-terminal domain of human alphaA- and alphaB-crystallins. Our models reflect the relative shifts in the beta-strands corresponding to the beta-sandwich associated with the core C-terminal domain that is common to small heat-shock proteins and the alpha-crystallins. The loop between the equivalent beta5-beta7 strands corresponding to a region of seven amino acid residues deletion in alpha-crystallins defined the new set of amino acid residues likely to be associated with a dimer interface. The models provide the structural basis to examine sites of mutations known to affect chaperone-like activity and dimerization in alpha-crystallins.
Researcher(s) / References :
- Guruprasad, K., Kumari, K. (2003) Int. J. Biol. Macromol. 33, 107-112.