MD Simulation Reveals Regulation of Mechanical Force and Extracellular Domain 2 on Binding of DNAM-1 to CD155
Abstract
:1. Introduction
2. Results and Discussion
2.1. The Second Extracellular Domain D2 Improved DNAM-1 Affinity to CD155
2.2. Dissociation of the Stretched DNAM-1/CD155 Complex Was Biphasic Force-Dependent
2.3. Force-Induced Allostery of the DNAM-1/CD155 Complex
2.4. The Key Residues in the Binding of DNAM-1 to CD155 under Tensile Force
3. Conclusions
4. Materials and Methods
4.1. System Setup
4.2. MD Simulation
4.3. Data Analysis
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
Sample Availability
References
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No. | DNAM-1 | CD155 | WT | ΔD2 |
---|---|---|---|---|
Residue | Residue | Occupancy | Occupancy | |
1 | E49 | S132 | 0.90 ± 0.02 | 0.86 ± 0.07 |
2 | T46 | Q63 | 0.86 ± 0.07 | 0.80 ± 0.14 |
3 | Q47 | T127 | 0.78 ± 0.02 | 0.76 ± 0.05 |
4 | Q115 | S74 | 0.67 ± 0.02 | 0.45 ± 0.24 |
5 | Q47 | S62 | 0.62 ± 0.33 | 0.70 ± 0.14 |
6 | T112 | Q63 | 0.49 ± 0.42 | 0.40 ± 0.19 |
7 | Y113 | G83 | 0.49 ± 0.07 | 0.44 ± 0.23 |
8 | R72 | E57 | 0.33 ± 0.57 | 0.26 ± 0.44 |
9 | R72 | D28 | 0.28 ± 0.49 | 0.04 ± 0.07 |
10 | S59 | R133 | 0.25 ± 0.38 | 0.08 ± 0.08 |
11 | E49 | R133 | 0.24 ± 0.42 | 0.14 ± 0.25 |
12 | K190 | E71 | 0.23 ± 0.22 | 0.00 ± 0.00 |
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Fang, L.; Zhao, Y.; Guo, P.; Fang, Y.; Wu, J. MD Simulation Reveals Regulation of Mechanical Force and Extracellular Domain 2 on Binding of DNAM-1 to CD155. Molecules 2023, 28, 2847. https://doi.org/10.3390/molecules28062847
Fang L, Zhao Y, Guo P, Fang Y, Wu J. MD Simulation Reveals Regulation of Mechanical Force and Extracellular Domain 2 on Binding of DNAM-1 to CD155. Molecules. 2023; 28(6):2847. https://doi.org/10.3390/molecules28062847
Chicago/Turabian StyleFang, Liping, Yang Zhao, Pei Guo, Ying Fang, and Jianhua Wu. 2023. "MD Simulation Reveals Regulation of Mechanical Force and Extracellular Domain 2 on Binding of DNAM-1 to CD155" Molecules 28, no. 6: 2847. https://doi.org/10.3390/molecules28062847
APA StyleFang, L., Zhao, Y., Guo, P., Fang, Y., & Wu, J. (2023). MD Simulation Reveals Regulation of Mechanical Force and Extracellular Domain 2 on Binding of DNAM-1 to CD155. Molecules, 28(6), 2847. https://doi.org/10.3390/molecules28062847