Identification of a Reaction Intermediate and Mechanism of Action of Intermediary Enzymes in Plumbagin Biosynthetic Pathway Using Molecular Dynamics Simulation
Abstract
:1. Introduction
2. Results
2.1. Hypothetical Enzyme Reaction for Biosynthesis of Plumbagin
2.2. Enzyme Substrate Interaction of NS–OMB CoA
2.3. Transition and Intermediate Sates of the Intermediary Compound
2.4. Enzyme Substrate Interaction Studies of Intermediate Structure 1 and 2 with Thioesterase
2.5. Results of Molecular Dynamics Simulation
2.5.1. Free Energy of Binding of OMB with Naphthoate Synthase after Simulations Reveals Stable Interactions
2.5.2. Simulations Reveal That Intermediate Structure 2 is More Stable in Its Interaction with Thioesterase
3. Materials and Methods
3.1. Molecular Modeling and Docking
3.2. Molecular Dynamics Simulations and Quantum Mechanics Optimization
3.3. Calculation of Free Energy of Binding Using the MM/PBSA Method
3.4. Prediction of Intermediates by Quantum Mechanics Studies
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Conflicts of Interest
References
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K S, M.; Lalitha, R.; Girija, S.; Kumar R, P.; P S, A.; N Swamy, M.; M, N.; Jayanthi, M. Identification of a Reaction Intermediate and Mechanism of Action of Intermediary Enzymes in Plumbagin Biosynthetic Pathway Using Molecular Dynamics Simulation. Catalysts 2020, 10, 280. https://doi.org/10.3390/catal10030280
K S M, Lalitha R, Girija S, Kumar R P, P S A, N Swamy M, M N, Jayanthi M. Identification of a Reaction Intermediate and Mechanism of Action of Intermediary Enzymes in Plumbagin Biosynthetic Pathway Using Molecular Dynamics Simulation. Catalysts. 2020; 10(3):280. https://doi.org/10.3390/catal10030280
Chicago/Turabian StyleK S, Muralidharan, Roopa Lalitha, Shanmugam Girija, Pravin Kumar R, Akshai P S, Meghana N Swamy, Nayana M, and Malaiyandi Jayanthi. 2020. "Identification of a Reaction Intermediate and Mechanism of Action of Intermediary Enzymes in Plumbagin Biosynthetic Pathway Using Molecular Dynamics Simulation" Catalysts 10, no. 3: 280. https://doi.org/10.3390/catal10030280
APA StyleK S, M., Lalitha, R., Girija, S., Kumar R, P., P S, A., N Swamy, M., M, N., & Jayanthi, M. (2020). Identification of a Reaction Intermediate and Mechanism of Action of Intermediary Enzymes in Plumbagin Biosynthetic Pathway Using Molecular Dynamics Simulation. Catalysts, 10(3), 280. https://doi.org/10.3390/catal10030280