Project titles for:
Project titles for: 2010-12
- Multiple Sequence Alignment:Comparison and Evaluation
- Prediction of Codon Bias in Rice (Oryza sativa) genes
- Subunit-Subunit interactions in Heterotetrameric structure of rice (Oryza sativa) ADP Glucose pyrophosphorylase
- Identification of microRNA in rice (Oryza sativa)
- Virtual High-Throughput Screening of Peroxisome proliferator-activated receptor Inhibitors
- In silico idetentification and analysis of Simple Sequence Repeats (SSRs) in rice (Oryza sativa) ESTs
- Effect on virulence in Streptococcus pneumonia due to the presence of rlrA gene
ADP-glucose pyrophosphorylase, a key allosteric enzyme involved in higher plant starch biosynthesis, is composed of pairs of large (LS) and small subunits (SS). Current evidence indicates that the two subunits play distinct roles in enzyme function. The LS is involved in mainly allosteric regulation through its interaction with the catalytic SS. Recently the crystal structure of the SS homotetramer from potato tuber has been solved, but no crystal structure of the native heterotetrameric enzyme is currently available for any species. In this study, homology modelling of the three-dimensional structure of the LS and SS from rice (Oryza sativa) was done using Swiss Model Server to construct the heterotetrameric assembly of the enzyme. The SS from the crystal structure of potato tuber was taken as the template. The models were evaluated using PROCHECK, VERIFY3D and ERRAT from SAVES. Further the two subunits were docked using GRAMM-X rigid docking server first to obtain the stable heterodimer orientation (LS as receptor and SS as ligand) and then the heterotetrameric orientation. The initial heterotetrameric orientation was further refined using RosettaDock Server and idealization of bond geometry and removal of unfavorable non-bonded contacts was performed by energy minimization with force field GROMOS96 from Swiss- Pdb Viewer. A minimized energy state of -69853 KJ/mol for the heterotetramer was obtained. MD simulation of the representative heterodimer/tetramer was performed using NAMD on an 8-node Linux cluster operating at 0.1 TFLOPS. The studies indicated that the tail-to-tail interaction of the LS and SS was more stable with -437086 kcal/mol energy as compared to the head-to-head orientation (-396097 kcal/mol) also the heterotetramer energy was minimized to -767011 kcal/mol. Following this the subunit-subunit interaction studies were carried out on the heterotetramer using NACCESS and Dimplot programs. NACCESS indicated interface residues; 57 residues for SS out of which 30 were hydrophobic and 27 were hydrophilic and 63 residues (31 hydrophobic and 32 hydrophilic residues) for LS. Dimplot plotted the hydrophobic interactions and hydrogen bonds between different chains of the heterotetramer. Lastly superimposition of the deduced heterotetramer on the template homotetramer (1YP2) was done and found to be quite similar as evident by 0.822Å RMSD.