Structural Insights into the Ligand-Binding and -Releasing Mechanism of Helicoverpa armigera Pheromone-Binding Protein PBP1
Abstract
:1. Introduction
2. Results
2.1. Crystal Structures of Apo-HarmPBP1 and HarmPBP1/Z9-16:Ald Complex
2.2. Structural Comparison Revealed a Specific Conformation of Apo-HarmPBP1
2.3. The Binding of Ligand in the HarmPBP1 Binding Cavity
2.4. A New Releasing Mechanism at Low pH Conditions
3. Discussion
4. Materials and Methods
4.1. Expression and Purification of Recombinant HarmPBP1
4.2. Protein Crystallization and Data Collection
4.3. Structure Determination and Refinement
4.4. Fluorescence Binding Assays
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Apo-HarmPBP1 at pH 7.5 (PDB ID:7VW8) | Apo-HarmPBP1 at pH 5.5 (PDB ID:7VW9) | HarmPBP1/Z9-16:Ald Complex at pH 8.5 (PDB ID: 7VWA) | |
---|---|---|---|
Wavelength, Å | 0.9792 | 0.9792 | 1.0000 |
Space group | P21 | P21 | P21 |
Cell dimensions | |||
a, b, c, Å | 32.03, 32.60, 54.79 | 32.43, 33.38, 55.38 | 32.91, 33.36, 56.04 |
α, β, γ, ° | 90, 97.88, 90 | 90, 99.66, 90 | 90, 98.79, 90 |
Resolution, Å | 50-1.30 (1.32–1.30) a | 50-2.05 (2.09–2.05) a | 50-2.09 (2.13–2.09) a |
Rmerge, % | 6.6 (59.9) | 5.0 (21.4) | 5.7 (30.2) |
I/σI | 17.7 (1.8) | 41.2 (7.6) | 31.1 (3.0) |
Completeness, % | 93.1 (97.5) | 95.6 (93.5) | 98.2 (81.0) |
Redundancy | 4.3 (3.9) | 3.5 (3.1) | 4.9 (3.7) |
Refinement | |||
Resolution, Å | 50-1.3 (1.33–1.30) | 50-2.05 (2.10–2.05) | 50-2.10 (2.15–2.10) |
No. of unique reflections | 21224 (736) | 6834 (465) | 6682 (432) |
Rwork/Rfree, % | 17.9/19.8 (22.3/24.9) | 22.2/26.5 (28.4/36.7) | 19.9/23.6 (24.2/37.1) |
No. of atoms (protein/ligand/water) | 1048/0/62 | 1015/0/56 | 1059/17/40 |
Average B factor (Å2) (protein/ligand/water) | 21.44/0/30.79 | 43.69/0/47.31 | 31.07/37.11/36.18 |
rms deviations | |||
Bond lengths, Å | 0.008 | 0.007 | 0.009 |
Bond angles, ° | 1.378 | 0.994 | 1.515 |
Ramachandran Plot, % b | 95.9/4.1/0/0 | 91.1/8.9/0/0 | 92.9/7.1/0/0 |
Ligand | pH 7.5 | pH 5.5 |
---|---|---|
(Z)-11-Hexadecenal | 0.67 ± 0.05 | 13.09 ± 1.78 |
(Z)-9-Hexadecenal | 0.56 ± 0.05 | 13.61 ± 1.33 |
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Zheng, J.; Yang, M.; Dong, K.; Zhang, J.; Wang, H.; Xie, M.; Wu, W.; Zhang, Y.-J.; Chen, Z. Structural Insights into the Ligand-Binding and -Releasing Mechanism of Helicoverpa armigera Pheromone-Binding Protein PBP1. Int. J. Mol. Sci. 2022, 23, 1190. https://doi.org/10.3390/ijms23031190
Zheng J, Yang M, Dong K, Zhang J, Wang H, Xie M, Wu W, Zhang Y-J, Chen Z. Structural Insights into the Ligand-Binding and -Releasing Mechanism of Helicoverpa armigera Pheromone-Binding Protein PBP1. International Journal of Molecular Sciences. 2022; 23(3):1190. https://doi.org/10.3390/ijms23031190
Chicago/Turabian StyleZheng, Jiangge, Meiting Yang, Kun Dong, Jianbo Zhang, Huali Wang, Mengjia Xie, Wei Wu, Yong-Jun Zhang, and Zhongzhou Chen. 2022. "Structural Insights into the Ligand-Binding and -Releasing Mechanism of Helicoverpa armigera Pheromone-Binding Protein PBP1" International Journal of Molecular Sciences 23, no. 3: 1190. https://doi.org/10.3390/ijms23031190