In silico study of Bacillus spB201 amylase through protein sequence inspection
Background/aim Bioinformatics is the automatic processing of biological information, and it is a helpful tool to study the structure-function relationship of various proteins. Here, it was used in the in silico study of an AmyB201 from Bacillus strain, named AmyB201 to describe its origin and proper...
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| Format: | Article |
| Language: | English |
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Wolters Kluwer Medknow Publications
2024-12-01
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| Series: | Journal of the Arab Society for Medical Research |
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| Online Access: | https://journals.lww.com/10.4103/jasmr.jasmr_20_24 |
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| author | Sameh Ben Mabrouk Bouthaina Ben Hadj Hmida Ikram Boukthir Slim Cherif |
| author_facet | Sameh Ben Mabrouk Bouthaina Ben Hadj Hmida Ikram Boukthir Slim Cherif |
| author_sort | Sameh Ben Mabrouk |
| collection | DOAJ |
| description | Background/aim
Bioinformatics is the automatic processing of biological information, and it is a helpful tool to study the structure-function relationship of various proteins. Here, it was used in the in silico study of an AmyB201 from Bacillus strain, named AmyB201 to describe its origin and properties, which could help us to improve the performance of this enzyme through mutagenesis.
Materials and methods
The protein sequence of AmyB201 was purchased from NCBI data Base. The Signal P and the Protparam were used to determine the properties of AmyB201. In addition, programs like Swiss-model, Phyre2 and PyMOL were used to generate and manipulate the AmyB201 models.
Results
Comparaison study of Amy B201using Blast program showed an identity of 94% and 91% with amylases from Bacillus spUS586 and Bacillus spUS572, respectively. Subsequently, the analysis of the sequence by the Signal P. program revealed the presence of a signal peptide, which confirms the extracellular nature of the enzyme. Furthermore, the examination of the AmyB201 sequence by Espript showed that it has the same secondary structure with amylases from Bacillus spUS586 and Bacillus spUS572, with the exception of a few differences that could explain the specificity of each enzyme. In addition, the inspection of the 3D models showed the presence of three typical domains of amylases, namely the domains: A, B, C. Using these structures, we have been able to explain some properties of AmyB201.
Conclusion
This study was able to describe the origin of some properties of AmyB201, and could help us to improve the performance of this enzyme through mutagenesis. |
| format | Article |
| id | doaj-art-ad413eefe178483dbdaae6f247a7de76 |
| institution | Kabale University |
| issn | 1687-4293 |
| language | English |
| publishDate | 2024-12-01 |
| publisher | Wolters Kluwer Medknow Publications |
| record_format | Article |
| series | Journal of the Arab Society for Medical Research |
| spelling | doaj-art-ad413eefe178483dbdaae6f247a7de762025-01-04T13:59:20ZengWolters Kluwer Medknow PublicationsJournal of the Arab Society for Medical Research1687-42932024-12-0119215816610.4103/jasmr.jasmr_20_24In silico study of Bacillus spB201 amylase through protein sequence inspectionSameh Ben MabroukBouthaina Ben Hadj HmidaIkram BoukthirSlim CherifBackground/aim Bioinformatics is the automatic processing of biological information, and it is a helpful tool to study the structure-function relationship of various proteins. Here, it was used in the in silico study of an AmyB201 from Bacillus strain, named AmyB201 to describe its origin and properties, which could help us to improve the performance of this enzyme through mutagenesis. Materials and methods The protein sequence of AmyB201 was purchased from NCBI data Base. The Signal P and the Protparam were used to determine the properties of AmyB201. In addition, programs like Swiss-model, Phyre2 and PyMOL were used to generate and manipulate the AmyB201 models. Results Comparaison study of Amy B201using Blast program showed an identity of 94% and 91% with amylases from Bacillus spUS586 and Bacillus spUS572, respectively. Subsequently, the analysis of the sequence by the Signal P. program revealed the presence of a signal peptide, which confirms the extracellular nature of the enzyme. Furthermore, the examination of the AmyB201 sequence by Espript showed that it has the same secondary structure with amylases from Bacillus spUS586 and Bacillus spUS572, with the exception of a few differences that could explain the specificity of each enzyme. In addition, the inspection of the 3D models showed the presence of three typical domains of amylases, namely the domains: A, B, C. Using these structures, we have been able to explain some properties of AmyB201. Conclusion This study was able to describe the origin of some properties of AmyB201, and could help us to improve the performance of this enzyme through mutagenesis.https://journals.lww.com/10.4103/jasmr.jasmr_20_24amyb201in silico analysismodelingprotein sequence |
| spellingShingle | Sameh Ben Mabrouk Bouthaina Ben Hadj Hmida Ikram Boukthir Slim Cherif In silico study of Bacillus spB201 amylase through protein sequence inspection Journal of the Arab Society for Medical Research amyb201 in silico analysis modeling protein sequence |
| title | In silico study of Bacillus spB201 amylase through protein sequence inspection |
| title_full | In silico study of Bacillus spB201 amylase through protein sequence inspection |
| title_fullStr | In silico study of Bacillus spB201 amylase through protein sequence inspection |
| title_full_unstemmed | In silico study of Bacillus spB201 amylase through protein sequence inspection |
| title_short | In silico study of Bacillus spB201 amylase through protein sequence inspection |
| title_sort | in silico study of bacillus spb201 amylase through protein sequence inspection |
| topic | amyb201 in silico analysis modeling protein sequence |
| url | https://journals.lww.com/10.4103/jasmr.jasmr_20_24 |
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