Solubility-Aware Protein Binding Peptide Design Using AlphaFold
Abstract
:1. Introduction
- A library of highly water-soluble peptide sequences is created, and then docking scores and binding affinities are predicted by protein–peptide docking.
- Design peptide sequences that are likely to bind to target proteins using peptide sequence prediction methods such as AfDesign, and then evaluate water solubility and filter out those that exceed water solubility thresholds.
2. Materials and Methods
2.1. AfDesign Settings
2.2. Solubility Loss Calculation
2.3. Calculation of Solubility
2.4. Calculation of Protein–Peptide Binding Affinity
2.5. Creation of Sequence Logos
2.6. Competitive Peptide Binding Predictions Using AlphaFold
2.7. Interatomic Interactions of MDM2 and Peptide
3. Results
3.1. Binder Design Targeting PPI Using AfDesign
3.2. Solubility-Aware Binder Design Using AfDesign
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
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Kosugi, T.; Ohue, M. Solubility-Aware Protein Binding Peptide Design Using AlphaFold. Biomedicines 2022, 10, 1626. https://doi.org/10.3390/biomedicines10071626
Kosugi T, Ohue M. Solubility-Aware Protein Binding Peptide Design Using AlphaFold. Biomedicines. 2022; 10(7):1626. https://doi.org/10.3390/biomedicines10071626
Chicago/Turabian StyleKosugi, Takatsugu, and Masahito Ohue. 2022. "Solubility-Aware Protein Binding Peptide Design Using AlphaFold" Biomedicines 10, no. 7: 1626. https://doi.org/10.3390/biomedicines10071626