Identification of a Reaction Intermediate and Mechanism of Action of Intermediary Enzymes in Plumbagin Biosynthetic Pathway Using Molecular Dynamics Simulation
The biosynthesis of plumbagin is known to occur via the acetate polymalonate pathway; however there are several intermediary steps that remain unidentified that leads to its synthesis. The study identifies enzyme naphthoate synthase to catalyze the cyclization of O-malonyl benzoyl CoA to form an int...
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MDPI AG
2020-03-01
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| Series: | Catalysts |
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| Online Access: | https://www.mdpi.com/2073-4344/10/3/280 |
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doaj-0998a74d8d174c20b90d452e3388dadc2020-11-25T03:02:17ZengMDPI AGCatalysts2073-43442020-03-0110328010.3390/catal10030280catal10030280Identification of a Reaction Intermediate and Mechanism of Action of Intermediary Enzymes in Plumbagin Biosynthetic Pathway Using Molecular Dynamics SimulationMuralidharan K S0Roopa Lalitha1Shanmugam Girija2Pravin Kumar R3Akshai P S4Meghana N Swamy5Nayana M6Malaiyandi Jayanthi7Research and Development Centre, Bharathiar University, Coimbatore 641046, IndiaKcat Enzymatic Pvt Ltd, #16, Ramakrishnappa Road, Cox Town, Bengaluru 560005, IndiaDepartment of Biotechnology, Bharathiar University, Coimbatore 641046 IndiaKcat Enzymatic Pvt Ltd, #16, Ramakrishnappa Road, Cox Town, Bengaluru 560005, IndiaKcat Enzymatic Pvt Ltd, #16, Ramakrishnappa Road, Cox Town, Bengaluru 560005, IndiaKcat Enzymatic Pvt Ltd, #16, Ramakrishnappa Road, Cox Town, Bengaluru 560005, IndiaKcat Enzymatic Pvt Ltd, #16, Ramakrishnappa Road, Cox Town, Bengaluru 560005, IndiaDepartment of Biotechnology, Bharathiar University, Coimbatore 641046 IndiaThe biosynthesis of plumbagin is known to occur via the acetate polymalonate pathway; however there are several intermediary steps that remain unidentified that leads to its synthesis. The study identifies enzyme naphthoate synthase to catalyze the cyclization of O-malonyl benzoyl CoA to form an intermediate that is acted upon by thioesterase before the reaction proceeds to form plumbagin. Two possible structures were predicted for this intermediate using quantum mechanics studies. A total of 60 ns molecular dynamics simulations revealed the most probable intermediate structure of the predicted two.https://www.mdpi.com/2073-4344/10/3/280plumbaginnaphthoate synthasethioesterasemolecular dynamics simulationquantum mechanics |
| collection |
DOAJ |
| language |
English |
| format |
Article |
| sources |
DOAJ |
| author |
Muralidharan K S Roopa Lalitha Shanmugam Girija Pravin Kumar R Akshai P S Meghana N Swamy Nayana M Malaiyandi Jayanthi |
| spellingShingle |
Muralidharan K S Roopa Lalitha Shanmugam Girija Pravin Kumar R Akshai P S Meghana N Swamy Nayana M Malaiyandi Jayanthi Identification of a Reaction Intermediate and Mechanism of Action of Intermediary Enzymes in Plumbagin Biosynthetic Pathway Using Molecular Dynamics Simulation Catalysts plumbagin naphthoate synthase thioesterase molecular dynamics simulation quantum mechanics |
| author_facet |
Muralidharan K S Roopa Lalitha Shanmugam Girija Pravin Kumar R Akshai P S Meghana N Swamy Nayana M Malaiyandi Jayanthi |
| author_sort |
Muralidharan K S |
| title |
Identification of a Reaction Intermediate and Mechanism of Action of Intermediary Enzymes in Plumbagin Biosynthetic Pathway Using Molecular Dynamics Simulation |
| title_short |
Identification of a Reaction Intermediate and Mechanism of Action of Intermediary Enzymes in Plumbagin Biosynthetic Pathway Using Molecular Dynamics Simulation |
| title_full |
Identification of a Reaction Intermediate and Mechanism of Action of Intermediary Enzymes in Plumbagin Biosynthetic Pathway Using Molecular Dynamics Simulation |
| title_fullStr |
Identification of a Reaction Intermediate and Mechanism of Action of Intermediary Enzymes in Plumbagin Biosynthetic Pathway Using Molecular Dynamics Simulation |
| title_full_unstemmed |
Identification of a Reaction Intermediate and Mechanism of Action of Intermediary Enzymes in Plumbagin Biosynthetic Pathway Using Molecular Dynamics Simulation |
| title_sort |
identification of a reaction intermediate and mechanism of action of intermediary enzymes in plumbagin biosynthetic pathway using molecular dynamics simulation |
| publisher |
MDPI AG |
| series |
Catalysts |
| issn |
2073-4344 |
| publishDate |
2020-03-01 |
| description |
The biosynthesis of plumbagin is known to occur via the acetate polymalonate pathway; however there are several intermediary steps that remain unidentified that leads to its synthesis. The study identifies enzyme naphthoate synthase to catalyze the cyclization of O-malonyl benzoyl CoA to form an intermediate that is acted upon by thioesterase before the reaction proceeds to form plumbagin. Two possible structures were predicted for this intermediate using quantum mechanics studies. A total of 60 ns molecular dynamics simulations revealed the most probable intermediate structure of the predicted two. |
| topic |
plumbagin naphthoate synthase thioesterase molecular dynamics simulation quantum mechanics |
| url |
https://www.mdpi.com/2073-4344/10/3/280 |
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