Prediction of Brucella omp25 and BLS antigens epitopes and their interaction with MHC molecules in sheep by in silico methods
Brucellosis is a common disease between humans and livestock that has caused a great deal of damage to the livestock industry in recent years. One way to prevent this disease is to get a vaccine to immunize disease-prone herds. To produce a successful recombinant vaccine, factors such as: selecting...
| Main Authors: | , , |
|---|---|
| Format: | Article |
| Language: | fas |
| Published: |
Shahid Bahonar University of Kerman
2021-12-01
|
| Series: | مجله بیوتکنولوژی کشاورزی |
| Subjects: | |
| Online Access: | https://jab.uk.ac.ir/article_3135_8405a2178ea5520b38df1e77f53500c6.pdf |
| _version_ | 1797389027425386496 |
|---|---|
| author | hashem Honar Hadadan Mojtaba Tahmoorespur Mohammad Hadi Sekhavati |
| author_facet | hashem Honar Hadadan Mojtaba Tahmoorespur Mohammad Hadi Sekhavati |
| author_sort | hashem Honar Hadadan |
| collection | DOAJ |
| description | Brucellosis is a common disease between humans and livestock that has caused a great deal of damage to the livestock industry in recent years. One way to prevent this disease is to get a vaccine to immunize disease-prone herds. To produce a successful recombinant vaccine, factors such as: selecting the right adjuvant, selecting the right antigen and the right delivery system are very important. To this end, epitopes have recently been widely used in clinical research, biomedicine, and the production of recombinant vaccines. Surface proteins of this bacterium, including BLS and Omp25 proteins, have antigenic properties and play an important role in causing this disease. Due to the lack of effective vaccines, today the need to produce new and effective vaccines is felt more than ever. The aim of this study was to bioinformatically predict the epitopes of BLS and Omp25 genes of Brucella bacterium in order to introduce a suitable candidate for vaccine production.
Materials and methods
For this purpose, SYFFPEITHI, PROPRED and IEDB servers were used to predict epitopes. Since the three-dimensional structure of the protein is required to investigate the interaction of antigens with cell surface receptors, in the next step, the predicted epitopes were modeled using the Pepfold 3 server. In addition, in order to evaluate the stability of the predicted structures and to ensure the accuracy of the third structure of the peptides, molecular dynamics simulations were performed using GROMACS software version 2019 and in a duration of 10 nanoseconds. Then, the three-dimensional structure was obtained by modeling homology method and the docking study of the interaction between epitopes with sheep MHCII and MHCI cells was performed using Autodock vina software.
Results
Then, in order to evaluate the stability of the complexes based on the results obtained from molecular docking, complexes with negative values of free binding energy were selected to perform molecular dynamics simulations. Finally, 8 peptides with better numbers were considered as suggested epitopes. The results obtained from molecular dynamics showed that the rmsd values for interleukin and interleukin bound to the polypeptide did not differ much in the two cases, so these results indicate that the activity of interleukin bound to the polypeptope did not change. The rmsf values also indicate the same stability in both proteins.Finally, the obtained results were evaluated in dynamic conditions in GROMACS software. The results of this study showed that in dynamic conditions, 4 predicted epitopes have high binding power to MHC class 1 and 2 receptors.
Conclusions
In addition, docking and molecular dynamics results showed that the polypeptide predicted in this study could be used as a candidate polypeptide in the design of a recombinant vaccine against brucellosis. However, to confirm these results, additional and laboratory studies are needed. |
| first_indexed | 2024-03-08T22:49:51Z |
| format | Article |
| id | doaj.art-a31c512df80b4522a3260038027acfea |
| institution | Directory Open Access Journal |
| issn | 2228-6705 2228-6500 |
| language | fas |
| last_indexed | 2024-03-08T22:49:51Z |
| publishDate | 2021-12-01 |
| publisher | Shahid Bahonar University of Kerman |
| record_format | Article |
| series | مجله بیوتکنولوژی کشاورزی |
| spelling | doaj.art-a31c512df80b4522a3260038027acfea2023-12-16T17:41:19ZfasShahid Bahonar University of Kermanمجله بیوتکنولوژی کشاورزی2228-67052228-65002021-12-01134193410.22103/jab.2021.17658.13233135Prediction of Brucella omp25 and BLS antigens epitopes and their interaction with MHC molecules in sheep by in silico methodshashem Honar Hadadan0Mojtaba Tahmoorespur1Mohammad Hadi Sekhavati2Dept. of Animal Science, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, IranProfessor, Department of Animal Science, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, IranDept. of Animal Science, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, IranBrucellosis is a common disease between humans and livestock that has caused a great deal of damage to the livestock industry in recent years. One way to prevent this disease is to get a vaccine to immunize disease-prone herds. To produce a successful recombinant vaccine, factors such as: selecting the right adjuvant, selecting the right antigen and the right delivery system are very important. To this end, epitopes have recently been widely used in clinical research, biomedicine, and the production of recombinant vaccines. Surface proteins of this bacterium, including BLS and Omp25 proteins, have antigenic properties and play an important role in causing this disease. Due to the lack of effective vaccines, today the need to produce new and effective vaccines is felt more than ever. The aim of this study was to bioinformatically predict the epitopes of BLS and Omp25 genes of Brucella bacterium in order to introduce a suitable candidate for vaccine production. Materials and methods For this purpose, SYFFPEITHI, PROPRED and IEDB servers were used to predict epitopes. Since the three-dimensional structure of the protein is required to investigate the interaction of antigens with cell surface receptors, in the next step, the predicted epitopes were modeled using the Pepfold 3 server. In addition, in order to evaluate the stability of the predicted structures and to ensure the accuracy of the third structure of the peptides, molecular dynamics simulations were performed using GROMACS software version 2019 and in a duration of 10 nanoseconds. Then, the three-dimensional structure was obtained by modeling homology method and the docking study of the interaction between epitopes with sheep MHCII and MHCI cells was performed using Autodock vina software. Results Then, in order to evaluate the stability of the complexes based on the results obtained from molecular docking, complexes with negative values of free binding energy were selected to perform molecular dynamics simulations. Finally, 8 peptides with better numbers were considered as suggested epitopes. The results obtained from molecular dynamics showed that the rmsd values for interleukin and interleukin bound to the polypeptide did not differ much in the two cases, so these results indicate that the activity of interleukin bound to the polypeptope did not change. The rmsf values also indicate the same stability in both proteins.Finally, the obtained results were evaluated in dynamic conditions in GROMACS software. The results of this study showed that in dynamic conditions, 4 predicted epitopes have high binding power to MHC class 1 and 2 receptors. Conclusions In addition, docking and molecular dynamics results showed that the polypeptide predicted in this study could be used as a candidate polypeptide in the design of a recombinant vaccine against brucellosis. However, to confirm these results, additional and laboratory studies are needed.https://jab.uk.ac.ir/article_3135_8405a2178ea5520b38df1e77f53500c6.pdfbrucellosisrecombinant vaccinemolecular dynamicepitope |
| spellingShingle | hashem Honar Hadadan Mojtaba Tahmoorespur Mohammad Hadi Sekhavati Prediction of Brucella omp25 and BLS antigens epitopes and their interaction with MHC molecules in sheep by in silico methods مجله بیوتکنولوژی کشاورزی brucellosis recombinant vaccine molecular dynamic epitope |
| title | Prediction of Brucella omp25 and BLS antigens epitopes and their interaction with MHC molecules in sheep by in silico methods |
| title_full | Prediction of Brucella omp25 and BLS antigens epitopes and their interaction with MHC molecules in sheep by in silico methods |
| title_fullStr | Prediction of Brucella omp25 and BLS antigens epitopes and their interaction with MHC molecules in sheep by in silico methods |
| title_full_unstemmed | Prediction of Brucella omp25 and BLS antigens epitopes and their interaction with MHC molecules in sheep by in silico methods |
| title_short | Prediction of Brucella omp25 and BLS antigens epitopes and their interaction with MHC molecules in sheep by in silico methods |
| title_sort | prediction of brucella omp25 and bls antigens epitopes and their interaction with mhc molecules in sheep by in silico methods |
| topic | brucellosis recombinant vaccine molecular dynamic epitope |
| url | https://jab.uk.ac.ir/article_3135_8405a2178ea5520b38df1e77f53500c6.pdf |
| work_keys_str_mv | AT hashemhonarhadadan predictionofbrucellaomp25andblsantigensepitopesandtheirinteractionwithmhcmoleculesinsheepbyinsilicomethods AT mojtabatahmoorespur predictionofbrucellaomp25andblsantigensepitopesandtheirinteractionwithmhcmoleculesinsheepbyinsilicomethods AT mohammadhadisekhavati predictionofbrucellaomp25andblsantigensepitopesandtheirinteractionwithmhcmoleculesinsheepbyinsilicomethods |