Conserved Domains in Variable Surface Lipoproteins A-G of Mycoplasma hyorhinis May Serve as Probable Multi-Epitope Candidate Vaccine: Computational Reverse Vaccinology Approach
Abstract
:Simple Summary
Abstract
1. Introduction
2. Materials and Methods
2.1. Sequences and Alignment and Prediction of Epitopes
2.2. Construction of Multi-Epitope Vaccine
2.3. Prediction of Antigenicity
2.4. Physicochemical Properties
2.5. Prediction of Secondary Structure
2.6. Prediction and Validation of Tertiary Structure
2.7. Prediction of Discontinuous Epitopes
2.8. Molecular Docking
2.9. Molecular Dynamic Simulation
2.10. Immune Simulation
2.11. Codon Optimization and In Silico Cloning
3. Results
3.1. Multiple Sequence Alignment
3.2. B Cell Epitopes
3.3. Prediction of CTL Epitopes
3.4. Prediction of HTL Epitopes
3.5. MEV Construct
3.6. Physicochemical Properties
3.7. Secondary Structure and Solubility
3.8. Prediction and Refinement of Tertiary Structure
3.9. Discontinuous B Cell Epitopes
3.10. Molecular Docking
3.11. Molecular Dynamics Simulation
3.12. Molecular Cloning
3.13. Immune Simulation
4. Discussion
5. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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No. | Start | End | Peptide | Length |
---|---|---|---|---|
1 | 5 | 14 | IFSKKLLVSF | 10 |
2 | 30 | 38 | CGQTSQQPG | 9 |
Peptide Sequence | Binding Affinity | Affinity Rescaled | Cleavage | TAP | Combined Score |
---|---|---|---|---|---|
LLVSFGSLV | 0.0872 | 0.3701 | 0.9251 | 0.5170 | 0.5347 |
Peptide Sequence | Start | End | Score |
---|---|---|---|
SIFSKKLLV | 4 | 12 | 0.194 |
VALAAIPLI | 18 | 26 | 0.24 |
Physicochemical Properties | Score |
---|---|
Number of amino acids | 138 |
Molecular weight | 14,153.88 |
Theoretical pI | 9.42 |
Total number of negatively charged residues (Asp + Glu) | 3 |
Total number of positively charged residues (Arg + Lys) | 13 |
Ext. coefficient | 4970 |
Estimated half-life | >20 h (yeast, in vivo) >10 h (Escherichia coli, in vivo) |
Instability index (II) | 26.53 (Stable) |
Aliphatic index | 103.26 |
Grand average of hydropathicity (GRAVY) | 0.484 (Polar protein) |
Scaled solubility | 0.707 |
Number of amino acids | 138 |
No. | Residues | Number of Residues | Score |
---|---|---|---|
1 | A:M1, A:R2, A:A3, A:L4, A:C5, A:L6, A:L7, A:L8, A:L9, A:T10, A:V11, A:L14, A:S15, A:S16, A:Q17, A:L18, A:A20, A:G21, A:L24, A:L25, A:T26, A:G27, A:L28, A:G29, A:Q30, A:R31, A:S32, A:D33, A:C44, A:N45, A:F46, A:S47, A:P48, A:C49, A:P50, A:L51, A:F52, A:N53, A:R54, A:I55, A:E56, A:G57, A:T58, A:C59, A:Y60, A:S61, A:G62, A:K63, A:A64, A:K65, A:C66, A:C67, A:I68, A:R69, A:E70, A:K73, A:K77, A:L80, A:V81, A:S82, A:F83, A:G84, A:P85, A:G86, A:P87, A:G88, A:P89, A:C90, A:G91, A:Q92, A:T93, A:S94, A:Q95, A:Q96, A:P97, A:G98, A:G99, A:P100, A:G101, A:P102, A:G103, A:S104, A:I105, A:F106, A:S107, A:K108, A:K109, A:V112, A:G113, A:P114, A:G115, A:P116, A:A121, A:A122, A:I123, A:P124, A:L125, A:I126, A:S133, A:F134, A:G135, A:S136, A:L137, A:V138 | 104 | 0.58 |
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Zubair, M.; Wang, J.; Yu, Y.; Rasheed, M.A.; Faisal, M.; Dawood, A.S.; Ashraf, M.; Shao, G.; Feng, Z.; Xiong, Q. Conserved Domains in Variable Surface Lipoproteins A-G of Mycoplasma hyorhinis May Serve as Probable Multi-Epitope Candidate Vaccine: Computational Reverse Vaccinology Approach. Vet. Sci. 2023, 10, 557. https://doi.org/10.3390/vetsci10090557
Zubair M, Wang J, Yu Y, Rasheed MA, Faisal M, Dawood AS, Ashraf M, Shao G, Feng Z, Xiong Q. Conserved Domains in Variable Surface Lipoproteins A-G of Mycoplasma hyorhinis May Serve as Probable Multi-Epitope Candidate Vaccine: Computational Reverse Vaccinology Approach. Veterinary Sciences. 2023; 10(9):557. https://doi.org/10.3390/vetsci10090557
Chicago/Turabian StyleZubair, Muhammad, Jia Wang, Yanfei Yu, Muhammad Asif Rasheed, Muhammad Faisal, Ali Sobhy Dawood, Muhammad Ashraf, Guoqing Shao, Zhixin Feng, and Qiyan Xiong. 2023. "Conserved Domains in Variable Surface Lipoproteins A-G of Mycoplasma hyorhinis May Serve as Probable Multi-Epitope Candidate Vaccine: Computational Reverse Vaccinology Approach" Veterinary Sciences 10, no. 9: 557. https://doi.org/10.3390/vetsci10090557