New Insight into the Substrate Selectivity of Bovine Milk γ-glutamyl Transferase via Structural and Molecular Dynamics Predictions
Abstract
:1. Introduction
2. Results and Discussion
2.1. Mechanism behind the Donor Selectivity of BoGGT
2.1.1. Prediction of the 3D Structure of BoGGT
2.1.2. Interactions between BoGGT and Donor
2.1.3. MD Simulations of BoGGT–Donor Complex
2.2. Mechanism behind the Acceptor Selectivity of BoGGT
2.2.1. Construction and Optimization of the BoGGT Intermediate
2.2.2. Interactions between the BoGGT Intermediate and Acceptors
2.2.3. MD Simulations of BoGGT Intermediate–Acceptor Complex
3. Materials and Methods
3.1. Structure Construction of BoGGT and Molecular Docking between γ-glutamyl Donor and BoGGT
3.2. MD Simulation of BoGGT–Donor Complex
3.3. Construction of the BoGGT Intermediate and Optimization of the Intermediate
3.4. Molecular Docking between the BoGGT Intermediate and γ-glutamyl Acceptors
3.5. MD Simulation of BoGGT Intermediate–Acceptor Complexes
3.6. Statistical Analysis
4. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
Sample Availability
References
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Complex | Total Binding Energy (kJ/mol) | Van der Waals Energy (kJ/mol) | Electrostatic Energy (kJ/mol) | Polar Solvation Energy (kJ/mol) | SASA Energy (kJ/mol) |
---|---|---|---|---|---|
BoGGT intermediate–Val-Gly | −141.062 ± 14.829 | −176.361 ± 25.742 | −102.037 ± 36.825 | 165.193 ± 41.980 | −27.857 ± 5.184 |
BoGGT intermediate–Met | −110.784 ± 11.275 | −157.906 ± 32.609 | −76.074 ± 23.259 | 134.209 ± 33.527 | −11.013 ± 4.513 |
BoGGT intermediate–Leu | −75.481 ± 19.973 | −123.524 ± 27.128 | −62.598 ± 19.937 | 124.372 ± 32.252 | −13.731 ± 4.235 |
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Cao, L.; Hunt, C.J.; Meyer, A.S.; Lametsch, R. New Insight into the Substrate Selectivity of Bovine Milk γ-glutamyl Transferase via Structural and Molecular Dynamics Predictions. Molecules 2023, 28, 4657. https://doi.org/10.3390/molecules28124657
Cao L, Hunt CJ, Meyer AS, Lametsch R. New Insight into the Substrate Selectivity of Bovine Milk γ-glutamyl Transferase via Structural and Molecular Dynamics Predictions. Molecules. 2023; 28(12):4657. https://doi.org/10.3390/molecules28124657
Chicago/Turabian StyleCao, Lichuang, Cameron J. Hunt, Anne S. Meyer, and René Lametsch. 2023. "New Insight into the Substrate Selectivity of Bovine Milk γ-glutamyl Transferase via Structural and Molecular Dynamics Predictions" Molecules 28, no. 12: 4657. https://doi.org/10.3390/molecules28124657