Using the Theozyme Model to Study the Dynamical Mechanism of the Post-Transition State Bifurcation Reaction by NgnD Enzyme
Abstract
:1. Introduction
2. Results and Discussion
2.1. Analysis of Energy Barriers
2.2. Bond Length Distributions
2.3. Analysis of Kinetic Trajectory and Dynamics
2.4. Interaction of Key Residues with Tss
3. Computational Methods
3.1. Theozyme Model Construction
3.2. Molecular Dynamics Simulation
3.3. Quantum Mechanical Calculations
3.4. Quasi-Classical Trajectory Simulations
4. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Theozyme Model | [6 + 4] Adduct | [4 + 2] Adduct |
---|---|---|
W67 | 66 | 87 |
Y55 | 79 | 78 |
M69 | 77 | 69 |
Y13 | 57 | 79 |
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Hou, Y.; Chen, J.; Liu, W.; Zhu, G.; Yang, Q.; Wang, X. Using the Theozyme Model to Study the Dynamical Mechanism of the Post-Transition State Bifurcation Reaction by NgnD Enzyme. Molecules 2024, 29, 5518. https://doi.org/10.3390/molecules29235518
Hou Y, Chen J, Liu W, Zhu G, Yang Q, Wang X. Using the Theozyme Model to Study the Dynamical Mechanism of the Post-Transition State Bifurcation Reaction by NgnD Enzyme. Molecules. 2024; 29(23):5518. https://doi.org/10.3390/molecules29235518
Chicago/Turabian StyleHou, Yaning, Jingyun Chen, Weizhe Liu, Gaohua Zhu, Qianying Yang, and Xin Wang. 2024. "Using the Theozyme Model to Study the Dynamical Mechanism of the Post-Transition State Bifurcation Reaction by NgnD Enzyme" Molecules 29, no. 23: 5518. https://doi.org/10.3390/molecules29235518
APA StyleHou, Y., Chen, J., Liu, W., Zhu, G., Yang, Q., & Wang, X. (2024). Using the Theozyme Model to Study the Dynamical Mechanism of the Post-Transition State Bifurcation Reaction by NgnD Enzyme. Molecules, 29(23), 5518. https://doi.org/10.3390/molecules29235518