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Homology Modelling of Lycopene Cleavage Oxygenase: The Key Enzyme of Bixin Production

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Author(s): Raghunath Satpathy | Rajesh Ku.Guru | Rashmiranjan Behera | Aparajita Priyadarshini

Journal: Journal of Computer Science & Systems Biology
ISSN 0974-7230

Volume: 03;
Issue: 03;
Start page: 059;
Date: 2010;
Original page

Keywords: Homology modelling | Molecular dynamics | Bixin | Model validation

ABSTRACT
Bixin is a natural dye and a high commercial important compound, produced from Bixin synthetic pathway in case ofBixa orellana plant. The particular enzyme Lycopene cleavage Oxygenase catalyzes the fi rst step of reaction pathwaysfrom Trans-lycopene to Bixin synthesis. The 3D structure of the enzyme was predicted by MODELLER program andthe missing side chains were verifi ed by SCRWL4 tool. Model validation was done by using the output of PROCHECKand DOPE score. The Ramachandran plot for the model was observed as 87.3 percentages of residues is in favourableregions that indicate the model is reliable. Molecular dynamics simulation of the model protein was performed in water5 lakh times for 1000 Pico second and at 300K by GROMACS software in a high performance computing environment.The energy value and RMSD (Root men square deviation) fl uctuation of Carbon alpha back bone of the model wascomputed that confi rms the stability of the model protein.
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