Machine Learning-Driven Discovery and Evaluation of Antimicrobial Peptides from Crassostrea gigas Mucus Proteome
Abstract
:1. Introduction
2. Results
2.1. Mucus Proteome Functional Enrichment Analysis
2.2. The Hydrophobicity Scales of Peptides and the Correlation of Length and Relative Scores
2.3. Performance of Peptide Sets Functional Activities According to iAMPCN
2.4. Characterization of Candidate Peptide Sequences
2.5. Antimicrobial Effects of Six Polypeptides against Escherichia coli, Staphylococcus aureus, and Vibrio parahaemolyticus
2.6. Evaluation of In Vitro Cytotoxicity and Hemolytic Activity
3. Discussion
4. Materials and Methods
4.1. Animals Culture and Mucus Collection
4.2. Protein Extraction
4.3. Proteolysis and Peptide Fractionation
4.4. LC-MS/MS
4.5. Protein Identification and Bioinformatics Analysis
4.6. Generation and Analysis of Oyster Mucus Peptide Libraries
4.7. iAMPCN Model Prediction on Polypeptides Functional Activity
4.8. Polypeptides Physicochemical Properties Prediction
4.9. Antimicrobial Activity Assay
4.10. Cytotoxicity Assay
4.11. Hemolysis Assay
4.12. Statistical Analysis
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Sample Name | Total Spectra | Spectra | Unique Spectra | Peptide | Unique Peptide | Protein |
---|---|---|---|---|---|---|
Crassostrea_gigas | 388,065 | 39,974 | 29,987 | 18,642 | 15,113 | 4490 |
Sequence | Score | AMP | Antibacterial | Anti-Gram-Positive | Anti-Gram-Negative | Antifungal | Antiviral | Anti-Mammalian-Cells | Hemolytic | Cytotoxic | Endotoxin | |
---|---|---|---|---|---|---|---|---|---|---|---|---|
P1 | FAKLLLRLPALR | 0.602235 | Yes | Yes | Yes | Yes | Yes | No | No | No | No | No |
P2 | WKQIKFYVYNRILKKRK | 0.565195 | Yes | Yes | Yes | Yes | Yes | No | No | No | No | No |
P3 | KVWQRVKVKML | 0.564499 | Yes | Yes | Yes | Yes | Yes | No | No | No | No | No |
P4 | RRRAKKMRAIYLIMNRFKKYKI | 0.562785 | Yes | Yes | Yes | Yes | Yes | No | No | No | No | No |
S1 | LLFRRRLL | 0.947085 | Yes | Yes | Yes | Yes | No | No | Yes | No | No | Yes |
S2 | LLRRKFFF | 0.927233 | Yes | Yes | Yes | Yes | No | No | Yes | No | No | Yes |
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Song, J.; Liu, K.; Jin, X.; Huang, K.; Fu, S.; Yi, W.; Cai, Y.; Yu, Z.; Mao, F.; Zhang, Y. Machine Learning-Driven Discovery and Evaluation of Antimicrobial Peptides from Crassostrea gigas Mucus Proteome. Mar. Drugs 2024, 22, 385. https://doi.org/10.3390/md22090385
Song J, Liu K, Jin X, Huang K, Fu S, Yi W, Cai Y, Yu Z, Mao F, Zhang Y. Machine Learning-Driven Discovery and Evaluation of Antimicrobial Peptides from Crassostrea gigas Mucus Proteome. Marine Drugs. 2024; 22(9):385. https://doi.org/10.3390/md22090385
Chicago/Turabian StyleSong, Jingchen, Kelin Liu, Xiaoyang Jin, Ke Huang, Shiwei Fu, Wenjie Yi, Yijie Cai, Ziniu Yu, Fan Mao, and Yang Zhang. 2024. "Machine Learning-Driven Discovery and Evaluation of Antimicrobial Peptides from Crassostrea gigas Mucus Proteome" Marine Drugs 22, no. 9: 385. https://doi.org/10.3390/md22090385