Exploring the impact of taurine on the biochemical properties of urate oxidase: response surface methodology and molecular dynamics simulation
Abstract This paper investigates the impact of taurine as an additive on the structural and functional stability of urate oxidase. First, the effect of the processing parameters for the stabilization of Urate Oxidase (UOX) using taurine was examined using the response surface methodology (RSM) and t...
| Main Authors: | , , |
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| Format: | Article |
| Language: | English |
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BMC
2024-01-01
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| Series: | Journal of Biological Engineering |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s13036-023-00397-x |
| _version_ | 1827329183688163328 |
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| author | Parisa Shahmoradipour Maryam Zaboli Masoud Torkzadeh-Mahani |
| author_facet | Parisa Shahmoradipour Maryam Zaboli Masoud Torkzadeh-Mahani |
| author_sort | Parisa Shahmoradipour |
| collection | DOAJ |
| description | Abstract This paper investigates the impact of taurine as an additive on the structural and functional stability of urate oxidase. First, the effect of the processing parameters for the stabilization of Urate Oxidase (UOX) using taurine was examined using the response surface methodology (RSM) and the central composite design (CCD) model. Also, the study examines thermodynamic and kinetic parameters as well as structural changes of urate oxidase with and without taurine. Fluorescence intensity changes indicated static quenching during taurine binding. The obtained result indicates that taurine has the ability to preserve the native structural conformation of UOX. Furthermore, molecular dynamics simulation is conducted in order to get insights into the alterations in the structure of urate oxidase in the absence and presence of taurine under optimal conditions. The molecular dynamics simulation section investigated the formation of hydrogen bonds (H-bonds) between different components as well as analysis of root mean square deviation (RMSD), root mean square fluctuations (RMSF) and secondary structure. Lower Cα-RMSD and RMSF values indicate greater stabilization of the taurine-treated UOX structure compared to the free enzyme. The results of molecular docking indicate that the binding of taurine to the UOX enzyme through hydrophobic interactions is associated with a negative value for the Gibbs free energy. |
| first_indexed | 2024-03-07T15:29:15Z |
| format | Article |
| id | doaj.art-f560776a73024148b0da468ecb0ddef8 |
| institution | Directory Open Access Journal |
| issn | 1754-1611 |
| language | English |
| last_indexed | 2024-03-07T15:29:15Z |
| publishDate | 2024-01-01 |
| publisher | BMC |
| record_format | Article |
| series | Journal of Biological Engineering |
| spelling | doaj.art-f560776a73024148b0da468ecb0ddef82024-03-05T16:32:32ZengBMCJournal of Biological Engineering1754-16112024-01-0118112010.1186/s13036-023-00397-xExploring the impact of taurine on the biochemical properties of urate oxidase: response surface methodology and molecular dynamics simulationParisa Shahmoradipour0Maryam Zaboli1Masoud Torkzadeh-Mahani2Department of Biotechnology, , Institute of Science, High Technology and Environmental Sciences, Graduate University of Advanced TechnologyDepartment of chemistry, faculty of science, University of BirjandDepartment of Biotechnology, , Institute of Science, High Technology and Environmental Sciences, Graduate University of Advanced TechnologyAbstract This paper investigates the impact of taurine as an additive on the structural and functional stability of urate oxidase. First, the effect of the processing parameters for the stabilization of Urate Oxidase (UOX) using taurine was examined using the response surface methodology (RSM) and the central composite design (CCD) model. Also, the study examines thermodynamic and kinetic parameters as well as structural changes of urate oxidase with and without taurine. Fluorescence intensity changes indicated static quenching during taurine binding. The obtained result indicates that taurine has the ability to preserve the native structural conformation of UOX. Furthermore, molecular dynamics simulation is conducted in order to get insights into the alterations in the structure of urate oxidase in the absence and presence of taurine under optimal conditions. The molecular dynamics simulation section investigated the formation of hydrogen bonds (H-bonds) between different components as well as analysis of root mean square deviation (RMSD), root mean square fluctuations (RMSF) and secondary structure. Lower Cα-RMSD and RMSF values indicate greater stabilization of the taurine-treated UOX structure compared to the free enzyme. The results of molecular docking indicate that the binding of taurine to the UOX enzyme through hydrophobic interactions is associated with a negative value for the Gibbs free energy.https://doi.org/10.1186/s13036-023-00397-xTaurineMolecular dynamics simulationUrate oxidaseResponse surface methodologyMolecular docking |
| spellingShingle | Parisa Shahmoradipour Maryam Zaboli Masoud Torkzadeh-Mahani Exploring the impact of taurine on the biochemical properties of urate oxidase: response surface methodology and molecular dynamics simulation Journal of Biological Engineering Taurine Molecular dynamics simulation Urate oxidase Response surface methodology Molecular docking |
| title | Exploring the impact of taurine on the biochemical properties of urate oxidase: response surface methodology and molecular dynamics simulation |
| title_full | Exploring the impact of taurine on the biochemical properties of urate oxidase: response surface methodology and molecular dynamics simulation |
| title_fullStr | Exploring the impact of taurine on the biochemical properties of urate oxidase: response surface methodology and molecular dynamics simulation |
| title_full_unstemmed | Exploring the impact of taurine on the biochemical properties of urate oxidase: response surface methodology and molecular dynamics simulation |
| title_short | Exploring the impact of taurine on the biochemical properties of urate oxidase: response surface methodology and molecular dynamics simulation |
| title_sort | exploring the impact of taurine on the biochemical properties of urate oxidase response surface methodology and molecular dynamics simulation |
| topic | Taurine Molecular dynamics simulation Urate oxidase Response surface methodology Molecular docking |
| url | https://doi.org/10.1186/s13036-023-00397-x |
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