Thermostability mechanisms of β-agarase by analyzing its structure through molecular dynamics simulation
Abstract Agarase is a natural catalyst with a good prospect in the industry. However, most of the currently discovered β-agarases are unsuitable for relatively high-temperature and high-pressure conditions required by industrial production. In this study, molecular dynamics simulations were first us...
| Auteurs principaux: | , , , |
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| Format: | Article |
| Langue: | English |
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SpringerOpen
2022-05-01
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| Collection: | AMB Express |
| Sujets: | |
| Accès en ligne: | https://doi.org/10.1186/s13568-022-01394-x |
| _version_ | 1828791100126527488 |
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| author | Lixing Liu Lixi Cai Yunmeng Chu Min Zhang |
| author_facet | Lixing Liu Lixi Cai Yunmeng Chu Min Zhang |
| author_sort | Lixing Liu |
| collection | DOAJ |
| description | Abstract Agarase is a natural catalyst with a good prospect in the industry. However, most of the currently discovered β-agarases are unsuitable for relatively high-temperature and high-pressure conditions required by industrial production. In this study, molecular dynamics simulations were first used to investigate the dynamic changes of folding and unfolding of mesophile and thermophile β-agarases (i.e., 1URX and 3WZ1) to explore the thermostability mechanism at three high temperatures (300 K, 400 K, and 500 K). Results showed that the sequence identity of 3WZ1 and 1URX reaches 48.8%. 1URX has a higher thermal sensitivity and less thermostability than 3WZ1 as more thermostable regions and hydrogen bonds exist in 3WZ1 compared with 1URX. The structures of 1URX and 3WZ1 become unstable with increasing temperatures up to 500 K. The strategies to increase the thermostability of 1URX and 3WZ1 are discussed. This study could provide insights into the design and modification of β-agarases at a high temperature. |
| first_indexed | 2024-12-12T02:44:50Z |
| format | Article |
| id | doaj.art-d257788b67a744b2874bc17cdea9c6a5 |
| institution | Directory Open Access Journal |
| issn | 2191-0855 |
| language | English |
| last_indexed | 2024-12-12T02:44:50Z |
| publishDate | 2022-05-01 |
| publisher | SpringerOpen |
| record_format | Article |
| series | AMB Express |
| spelling | doaj.art-d257788b67a744b2874bc17cdea9c6a52022-12-22T00:41:04ZengSpringerOpenAMB Express2191-08552022-05-0112111110.1186/s13568-022-01394-xThermostability mechanisms of β-agarase by analyzing its structure through molecular dynamics simulationLixing Liu0Lixi Cai1Yunmeng Chu2Min Zhang3College of Basic Medicine, Putian UniversityCollege of Basic Medicine, Putian UniversityDepartment of Bioengineering and Biotechnology, Huaqiao UniversityCollege of Basic Medicine, Putian UniversityAbstract Agarase is a natural catalyst with a good prospect in the industry. However, most of the currently discovered β-agarases are unsuitable for relatively high-temperature and high-pressure conditions required by industrial production. In this study, molecular dynamics simulations were first used to investigate the dynamic changes of folding and unfolding of mesophile and thermophile β-agarases (i.e., 1URX and 3WZ1) to explore the thermostability mechanism at three high temperatures (300 K, 400 K, and 500 K). Results showed that the sequence identity of 3WZ1 and 1URX reaches 48.8%. 1URX has a higher thermal sensitivity and less thermostability than 3WZ1 as more thermostable regions and hydrogen bonds exist in 3WZ1 compared with 1URX. The structures of 1URX and 3WZ1 become unstable with increasing temperatures up to 500 K. The strategies to increase the thermostability of 1URX and 3WZ1 are discussed. This study could provide insights into the design and modification of β-agarases at a high temperature.https://doi.org/10.1186/s13568-022-01394-xThermostabilityβ-agaraseMolecular simulationRMSDRMSFSalt bridge |
| spellingShingle | Lixing Liu Lixi Cai Yunmeng Chu Min Zhang Thermostability mechanisms of β-agarase by analyzing its structure through molecular dynamics simulation AMB Express Thermostability β-agarase Molecular simulation RMSD RMSF Salt bridge |
| title | Thermostability mechanisms of β-agarase by analyzing its structure through molecular dynamics simulation |
| title_full | Thermostability mechanisms of β-agarase by analyzing its structure through molecular dynamics simulation |
| title_fullStr | Thermostability mechanisms of β-agarase by analyzing its structure through molecular dynamics simulation |
| title_full_unstemmed | Thermostability mechanisms of β-agarase by analyzing its structure through molecular dynamics simulation |
| title_short | Thermostability mechanisms of β-agarase by analyzing its structure through molecular dynamics simulation |
| title_sort | thermostability mechanisms of β agarase by analyzing its structure through molecular dynamics simulation |
| topic | Thermostability β-agarase Molecular simulation RMSD RMSF Salt bridge |
| url | https://doi.org/10.1186/s13568-022-01394-x |
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