The Molecular Docking of MAX Fungal Effectors with Plant HMA Domain-Binding Proteins
Abstract
:1. Introduction
2. Results
2.1. Benchmarking of Bound Complexes
2.1.1. Evaluation of Docking Output Using DockQ
2.1.2. Re-Scoring and Re-Ranking with ZRANK
2.1.3. Comparison of Docking Predictions with ZDOCK and ZRANK Scores
2.1.4. Assessment of Docking Output with and without Residue Restraints
2.2. Optimisation of Parameters for the Prediction of Near-Native Docking Poses
2.2.1. Docking Parameters
2.2.2. Unbound Docking Results
3. Discussion
3.1. Interactions with MAX Regions 1 and 2
3.2. Polymorphic Residues and Engineered Plant HMA Domain Proteins
3.3. Best Scoring Function for MAX Regions 1 and 2
3.4. Limitations of Molecular Docking and Future Improvements
4. Materials and Methods
4.1. Experimental 3D Structures
4.2. Protein Structure Modelling
4.3. Protein Structure Processing
4.4. Protein–Protein Docking
4.5. Re-Scoring and Re-Ranking
5. 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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Effector–Host Receptor Binding Partner Complex | PDB ID | Pose with Best DockQ Score | Pose with Best ZDOCK Score | ||||
---|---|---|---|---|---|---|---|
DockQ Score | ZDOCK | ZDOCK Score | DockQ | ||||
Score | Rank | Score | Rank | ||||
Avr1CO39-RGA5 | 5zngAC | 0.967 | 34.19 | 756 | 46.35 | 0.022 | 1480 |
AvrPia-PikpHMA | 6q76AB | 0.962 | 42.47 | 3 | 43.46 | 0.024 | 1605 |
AvrPikC-PikhHMA | 7a8xBC | 0.971 | 60.16 | 2 | 61.74 | 0.910 | 2 |
7a8xEF | 0.919 | 73.13 | 1 | 73.13 | 0.919 | 1 | |
AvrPikD-PikmHMA | 6fu9AB | 0.942 | 59.69 | 9 | 69.34 | 0.833 | 13 |
6fu9CD | 0.941 | 62.21 | 3 | 63.39 | 0.915 | 2 | |
AvrPikE-PikmHMA | 6fubAB | 0.935 | 58.90 | 4 | 64.49 | 0.925 | 2 |
AvrPikE-PikpHMA | 6g11BC | 0.908 | 51.14 | 29 | 65.69 | 0.885 | 5 |
6g11EF | 0.947 | 58.82 | 4 | 62.28 | 0.753 | 34 | |
6r8mFG | 0.924 | 63.82 | 2 | 67.90 | 0.901 | 2 | |
AvrPikF-OsHIPP19 | 7b1iBC | 0.928 | 63.75 | 9 | 75.98 | 0.887 | 8 |
ApikL2F-sHMA94 | 7nmmAI | 0.952 | 62.99 | 3 | 68.51 | 0.922 | 2 |
7nmmBJ | 0.940 | 53.48 | 12 | 59.6 | 0.876 | 8 | |
7nmmCK | 0.933 | 61.34 | 3 | 65.57 | 0.858 | 9 | |
7nmmDL | 0.943 | 70.17 | 1 | 70.17 | 0.943 | 1 | |
7nmmEM | 0.922 | 59.95 | 5 | 62.04 | 0.831 | 18 | |
7nmmFN | 0.933 | 61.17 | 4 | 66.76 | 0.866 | 9 | |
7nmmGO | 0.941 | 64.19 | 2 | 64.39 | 0.913 | 2 | |
7nmmHP | 0.914 | 57.23 | 8 | 63.64 | 0.890 | 5 |
Effector–Host Receptor Binding Partner Complex. | PDB ID | Pose with Best DockQ Score | Pose with Best ZRANK Score | ||||
---|---|---|---|---|---|---|---|
DockQ Score | ZRANK | ZRANK Score | DockQ | ||||
Score | Rank | Score | Rank | ||||
Avr1CO39-RGA5 | 5zngAC | 0.967 | −74.5563 | 35 | −89.5292 | 0.912 | 8 |
AvrPia-PikpHMA | 6q76AB | 0.962 | −64.0926 | 212 | −95.9139 | 0.24 | 204 |
AvrPikC-PikhHMA | 7a8xBC | 0.971 | −88.0183 | 1 | −88.0183 | 0.971 | 1 |
7a8xEF | 0.919 | −85.0809 | 25 | −109.556 | 0.904 | 4 | |
AvrPikD-PikmHMA | 6fu9AB | 0.942 | −92.2094 | 19 | −120.033 | 0.833 | 13 |
6fu9CD | 0.941 | −100.436 | 14 | −129.325 | 0.12 | 296 | |
AvrPikE-PikmHMA | 6fubAB | 0.935 | −90.305 | 15 | −106.179 | 0.162 | 239 |
AvrPikE-PikpHMA | 6g11BC | 0.908 | −76.3809 | 31 | −110.703 | 0.892 | 4 |
6g11EF | 0.947 | −79.1564 | 22 | −96.3179 | 0.875 | 6 | |
6r8mFG | 0.924 | −61.0644 | 254 | −112.655 | 0.807 | 13 | |
AvrPikF-OsHIPP19 | 7b1iBC | 0.928 | −66.7719 | 94 | −125.125 | 0.88 | 10 |
ApikL2F-sHMA94 | 7nmmAI | 0.952 | −103.174 | 1 | −103.174 | 0.952 | 1 |
7nmmBJ | 0.94 | −102.48 | 1 | −102.48 | 0.94 | 1 | |
7nmmCK | 0.933 | −88.5095 | 14 | −102.381 | 0.834 | 15 | |
7nmmDL | 0.943 | −100.989 | 3 | −104.301 | 0.931 | 2 | |
7nmmEM | 0.922 | −89.2384 | 14 | −98.7345 | 0.065 | 413 | |
7nmmFN | 0.933 | −107.157 | 1 | −107.157 | 0.933 | 1 | |
7nmmGO | 0.941 | −96.1059 | 4 | −107.128 | 0.901 | 5 | |
7nmmHP | 0.914 | −91.2643 | 10 | −103.77 | 0.061 | 522 |
Effector–Host Receptor Binding Partner Complex | PDB ID | DockQ Score | |
---|---|---|---|
Best Docking Pose ZDOCK Score 54k and 2k | Best Docking Pose ZRANK Score 2k | ||
Avr1CO39-RGA5 | 5zngAC | 0.022 | 0.912 |
AvrPia-PikpHMA | 6q76AB | 0.024 | 0.240 |
AvrPikC-PikhHMA | 7a8xBC | 0.910 | 0.971 |
7a8xEF | 0.919 | 0.904 | |
AvrPikD-PikmHMA | 6fu9AB | 0.833 | 0.833 |
6fu9CD | 0.915 | 0.120 | |
AvrPikE-PikmHMA | 6fubAB | 0.925 | 0.162 |
AvrPikE-PikpHMA | 6g11BC | 0.885 | 0.892 |
6g11EF | 0.753 | 0.875 | |
6r8mFG | 0.901 | 0.807 | |
AvrPikF-OsHIPP19 | 7b1iBC | 0.887 | 0.880 |
ApikL2F-sHMA94 | 7nmmAI | 0.922 | 0.952 |
7nmmBJ | 0.876 | 0.940 | |
7nmmCK | 0.858 | 0.834 | |
7nmmDL | 0.943 | 0.931 | |
7nmmEM | 0.831 | 0.065 | |
7nmmFN | 0.866 | 0.933 | |
7nmmGO | 0.913 | 0.901 | |
7nmmHP | 0.890 | 0.061 |
CCharPPI Scoring Functions | Avr1CO39-RGA5 (5zngAC) | AvrPia-PikpHMA (6q76AB) | |||||
---|---|---|---|---|---|---|---|
Total Poses | DockQ < 0.5 | DockQ > 0.5 | Total Poses | DockQ < 0.5 | DockQ > 0.5 | ||
Positive filter | (1) CP_PIE > 0.8 | 76 | 48 | 28 | 81 | 48 | 33 |
(2) AP_GOAP_ALL < 0 | 39 | 15 | 23 | 29 | 5 | 23 | |
(3) AP_OPUS_PSP < −100 | 7 | 1 | 6 | 5 | 0 | 5 | |
Negative filter | (4) CP_SKOa > 0 | 6 | 0 | 6 | 5 | 0 | 5 |
(5) CP_ZLOCAL_CB < 3 | 6 | 0 | 6 | 5 | 0 | 5 |
Host Receptor Binding Partner/Effector | AvrPikA (6fubD) | AvrPikC (7a8xC) | ||||||
---|---|---|---|---|---|---|---|---|
Rank | ZDOCK Score | Rank | ZRANK Score | Rank | ZDOCK Score | Rank | ZRANK Score | |
PikmHMA/6fu9 | 3 | 60.52 | 2 | −106.805 | 22 | 51.30 | 14 | −88.187 |
PikhHMA/7a8x | 10 | 51.64 | 21 | −79.4618 | 15 | 54.24 | 1 | −114.65 |
PikpHMA/5a6w | 16 | 51.31 | 1 | −91.1659 | 10 | 51.82 | 3 | −87.068 |
PikpHMA-mut/6r8m | 3 | 61.01 | 3 | −92.2020 | 1 | 63.85 | 1 | −111.540 |
ancHMA/7bnt | 8 | 51.34 | 5 | −92.3646 | 4 | 53.23 | 89 | −67.468 |
osHIPP19/7b1i | 1 | 71.15 | 2 | −107.887 | 11 | 57.32 | 5 | −94.782 |
sHMA94/7nmm | 19 | 50.38 | 39 | −81.2881 | 5 | 54.58 | 4 | −93.776 |
ApikL2F (7nmmI) | AvrPikD (5a6wC) | |||||||
PikmHMA/6fu9 | 3 | 57.53 | 17 | −82.0646 | 5 | 62.53 | 2 | −101.76 |
PikhHMA/7a8x | 2 | 54.29 | 1 | −92.6857 | 9 | 55.61 | 2 | −113.11 |
PikpHMA/5a6w | 1 | 56.14 | 13 | −78.5247 | 13 | 56.28 | 1 | −116.840 |
PikpHMA-mut/6r8m | 11 | 51.88 | 6 | −81.2988 | 1 | 71.46 | 1 | −115.93 |
ancHMA/7bnt | 1 | 55.86 | 3 | −96.2088 | 1 | 65.07 | 3 | −104.54 |
osHIPP19/7b1i | 2 | 69.92 | 1 | −100.196 | 12 | 60.54 | 1 | −116.76 |
sHMA94/7nmm | 1 | 66.00 | 1 | −100.020 | 2 | 68.34 | 1 | −112.6 |
AvrPikE (6g11C) | AvrPikF (7b1iC) | |||||||
PikmHMA/6fu9 | 53 | 50.43 | 1 | −113.286 | 8 | 57.30 | 1 | −103.87 |
PikhHMA/7a8x | 2 | 57.46 | 1 | −104.541 | 4 | 55.99 | 19 | −76.509 |
PikpHMA/5a6w | 12 | 52.19 | 1 | −98.2134 | 15 | 51.03 | 1 | −92.64 |
PikpHMA-mut 6r8m | 8 | 62.33 | 1 | −112.241 | 6 | 61.70 | 1 | −102.24 |
ancHMA/7bnt | 6 | 54.53 | 1 | −94.1270 | 7 | 52.77 | 4 | −83.268 |
osHIPP19/7b1i | 3 | 72.65 | 1 | −128.358 | 4 | 70.92 | 1 | −125.13 |
sHMA94/7nmm | 4 | 61.76 | 1 | −104.071 | 4 | 62.12 | 1 | −96.3480 |
Unbound Complexes | Number of Interacting Residues on the Effector | Number of Interacting Residues on the Host Receptor Binding Partner | ||
---|---|---|---|---|
Known | Predicted | Known | Predicted | |
AvrPikA-osHIPP19 | 28 | 27 (87.5%) | 21 | 21 (100%) |
AvrPikC-PikpHMAmutant | 21 | 21 (100%) | 23 | 23 (100%) |
AvrPikD-PikpHMAmutant | 30 | 26 (86.6%) | 21 | 21 (100%) |
AvrPikE-osHIPP19 | 27 | 25 (92.5%) | 24 | 24 (100%) |
AvrPikF-osHIPP19 | 29 | 29 (100%) | 21 | 20 (95%) |
ApikL2F-osHIPP19 | 24 | 24 (100%) | 21 | 21 (100%) |
Unbound Complexes (PDB ID) | Number of Interacting Residues on the Effector | Number of Interacting Residues on the Host Receptor Binding Partner | ||
---|---|---|---|---|
Known | Predicted | Known | Predicted | |
AvrPia (6q76B)-RGA5 (5zngA) | 10 | 10 (100%) | 13 | 10 (76.9%) |
Avr1CO39 (5zngC)-PikpHMA (6q76A) | 8 | 8 (100%) | 11 | 11 (100%) |
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Rozano, L.; Hane, J.K.; Mancera, R.L. The Molecular Docking of MAX Fungal Effectors with Plant HMA Domain-Binding Proteins. Int. J. Mol. Sci. 2023, 24, 15239. https://doi.org/10.3390/ijms242015239
Rozano L, Hane JK, Mancera RL. The Molecular Docking of MAX Fungal Effectors with Plant HMA Domain-Binding Proteins. International Journal of Molecular Sciences. 2023; 24(20):15239. https://doi.org/10.3390/ijms242015239
Chicago/Turabian StyleRozano, Lina, James K. Hane, and Ricardo L. Mancera. 2023. "The Molecular Docking of MAX Fungal Effectors with Plant HMA Domain-Binding Proteins" International Journal of Molecular Sciences 24, no. 20: 15239. https://doi.org/10.3390/ijms242015239
APA StyleRozano, L., Hane, J. K., & Mancera, R. L. (2023). The Molecular Docking of MAX Fungal Effectors with Plant HMA Domain-Binding Proteins. International Journal of Molecular Sciences, 24(20), 15239. https://doi.org/10.3390/ijms242015239