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20181
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Subject: Bioinformatics × Author: Jakhar, Ritu × Start date: 1999 × Type: Thesis × Thesis Type: M.Sc ×
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    ThesisItemOpen Access
    Computational modelling and molecular dynamic simulation of glutamate decarboxylase of wheat (Triticum aestivum L.),
    (CCSHAU, 2018) Jakhar, Ritu; Sudhir kumar
    Glutamate decarboxylase (GAD) catalyses the decarboxylation of glutamate amino acid to γ – amino butyrate (GABA) in presence of Pyridoxal phosphate cofactor. GABA build up happens after GAD activation in plants in response to various biotic and abiotic stress such as hypoxia, temperature shock, water stress, salinity stress, acidosis, virus infection and mechanical manipulation. GAD assembled into dimer and subsequently in hexamer for activation. In plants, GAD dimerisation and activation is associated with binding of CaM and C-terminal of GAD. The N-terminal residues are required for the assembly and stabilization of hexameric state of GAD. Modelling and dynamics study can uncover the interaction forces involved in GAD activity. A 500 AA long wheat GAD sequence was retrieved from UniProtKB and further aligned using BLAST program to identify templates for comparative structure prediction. Modelling of GAD peptide (monomer subunit) by Modeller9.19 and Phyre2 server provided Model1 and Model2, respectively. Model1 was generated in two fragments for N- and C- terminal with Modeller9.19 and joined using Chimera visualization tool. Both models were subjected to energy minimisation using GROMOS force field and structure assessment by GROMOS, QMEAN and ANOLEA. Both models were further verified, validated and evaluated using WHATIF and SAVES server. The RMSD of models on superimposition with the template was found to be less than 2.0 Å. Models were further refined using NAMD, a molecular dynamics (MD) code designed for high-performance simulation of large biomolecular systems. Out of two models, Model1 was predicted better model than Model2 on the basis of RMSD between initial and simulated model.