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Subject: Bioinformatics × Author: Mamatha Y S × End date: 2022 × Thesis Type: M.Sc ×
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    ThesisItemOpen Access
    Structural and Molecular Dynamics Studies of UDP Glucose Pyrophosphorylase Dimerization in Rice (Oryza sativa L.)
    (CCSHAU, 2019) Mamatha Y S; Sudhir Kumar
    UDP-Glucose pyrophosphorylase (UGPase) (EC 2.7.7.9) belongs to family Glycosyltransferace clan (PF01702) which is present in plants as well as animals. UGPase is involved in sucrose synthesis as a catalyzing agent in the reaction, Mg+2-UTP + Glu-1-P PPi + UDP-Glu. It catalyzes both forward and reverse reaction depending on the metabolic status of the tissue. Crystal structure of UGPase shows that it have three domains with N-terminal domain at one end, catalytic domain which have nucleotide binding loop present at the center and the C-terminal domain include insertion loop at another end. C-terminal group is involved in dimer formation and stabilization of protein. Monomer is the active form in most of the parasitic and a plant UGPase. Modelling and dynamic study can uncover the interaction forces involved in UGPase activity. A 469 amino acids long rice UGPase was retrieved from NCBI and further aligned using BLAST program to identify templates for comparative structure prediction. Modelling of UGPase peptide by Modeller9.20, Swiss-model server and I-TASSER server predicted Model1, Model2 and Model3 respectively. All models were subjected to energy minimization using GROMOS96 force field and structure assessment by QMEAN. All models were further verified, validated and evaluated using WHATIF and SAVES server. The RMSD of models on superimposition with template was found to be less than 1.0 Å. Models were further refined using GROMACS-2019, a molecular dynamic (MD) code designed for highperformance simulation of large biomolecular systems. Dimers were generated by using protein-protein docking tools with predicted models. These generated dimers were further evaluated and analyzed. Dimer analysis provides the information about the hydrogen bonding in between the peptides of protein. Solvent accessible area calculated for the residues, which are present in ligand binding site. Solvent accessible area in dimer found to be less compared to monomer. The study showed that protein losses its activity due to dimerization.