Molecular analysis of a fibrin-degrading enzyme from Bacillus subtilis K2 isolated from the Indonesian soybean-based fermented food moromi
| Autor: | Fathma Syahbanu, Raymond R. Tjandrawinata, Puspo Edi Giriwono, Maggy Thenawidjaja Suhartono |
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| Rok vydání: | 2020 |
| Předmět: |
0301 basic medicine
Bacillus subtilis Serine 03 medical and health sciences chemistry.chemical_compound 0302 clinical medicine Bacterial Proteins Protein Domains RNA Ribosomal 16S Catalytic triad Genetics Amino Acid Sequence Subtilisins Molecular Biology Histidine chemistry.chemical_classification Serine protease Fibrin Binding Sites biology Sequence Homology Amino Acid Subtilisin General Medicine Sequence Analysis DNA biology.organism_classification Molecular Docking Simulation 030104 developmental biology Enzyme Biochemistry chemistry Indonesia 030220 oncology & carcinogenesis Proteolysis biology.protein Soybeans Fermented Foods Nattokinase |
| Zdroj: | Molecular biology reports. 47(11) |
| ISSN: | 1573-4978 |
| Popis: | The screening of proteolytic and fibrinolytic bacteria from moromi (an Indonesian soybean-based fermented food) yielded a number of isolates. Based on morphological and biochemical analyses and sequencing of the 16S rRNA gene, the isolate that exhibited the highest proteolytic and fibrinolytic activity was identified as Bacillus subtilis K2. The study was performed to analyze molecular characteristic of a fibrin-degrading enzyme from B. subtilis K2. BLASTn analysis of the nucleotide sequence encoding this fibrinolytic protein demonstrated 73.6% homology with the gene encoding the fibrin-degrading enzyme nattokinase of the B. subtilis subsp. natto, which was isolated from fermented soybean in Japan. An analysis of the putative amino-acid sequence of this protein indicated that it is a serine protease enzyme with aspartate, histidine, and serine in the catalytic triad. This enzyme was determined to be a 26-kDa molecule, as confirmed with a zymogram assay. Further bioinformatic analysis using Protparam demonstrated that the enzyme has a pI of 6.02, low instability index, high aliphatic index, and low GRAVY value. Molecular docking analysis using HADDOCK indicated that there are favorable interactions between subtilisin K2 and the fibrin substrate, as demonstrated by a high binding affinity (ΔG: − 19.4 kcal/mol) and low Kd value (6.3E-15 M). Overall, the study concluded that subtilisin K2 belong to serine protease enzyme has strong interactions with its fibrin substrate and fibrin can be rapidly degraded by this enzyme, suggesting its application as a treatment for thrombus diseases. |
| Databáze: | OpenAIRE |
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