Rational Design of Pepsin for Enhanced Thermostability via Exploiting the Guide of Structural Weakness on Stability
Enzyme thermostability is an important parameter for estimating its industrial value. However, most naturally produced enzymes are incapable of meeting the industrial thermostability requirements. Software programs can be utilized to predict protein thermostability. Despite the fast-growing number o...
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Frontiers Media S.A.
2021-09-01
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fphy.2021.755253/full |
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doaj-09c9fb8521af4de2832ab5fb9f695f6c2021-09-30T08:07:11ZengFrontiers Media S.A.Frontiers in Physics2296-424X2021-09-01910.3389/fphy.2021.755253755253Rational Design of Pepsin for Enhanced Thermostability via Exploiting the Guide of Structural Weakness on StabilityYue Zhao0Yulu Miao1Fengdong Zhi2Yue Pan3Jianguo Zhang4Xuepeng Yang5John Z. H. Zhang6John Z. H. Zhang7John Z. H. Zhang8Lujia Zhang9Lujia Zhang10Shanghai Engineering Research Center of Molecular Therapeutics & New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, ChinaShanghai Engineering Research Center of Molecular Therapeutics & New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, ChinaShanghai Engineering Research Center of Molecular Therapeutics & New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, ChinaShanghai Engineering Research Center of Molecular Therapeutics & New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, ChinaInstitute of Food Science and Engineering, School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai, ChinaSchool of Food and Biological Engineering, Zhengzhou University of Light Industry, Zhengzhou, ChinaShanghai Engineering Research Center of Molecular Therapeutics & New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, ChinaNYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai, ChinaDepartment of Chemistry, New York University, New York, NY, United StatesShanghai Engineering Research Center of Molecular Therapeutics & New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, ChinaNYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai, ChinaEnzyme thermostability is an important parameter for estimating its industrial value. However, most naturally produced enzymes are incapable of meeting the industrial thermostability requirements. Software programs can be utilized to predict protein thermostability. Despite the fast-growing number of programs designed for this purpose; few provide reliable applicability because they do not account for thermodynamic weaknesses. Aspartic proteases are widely used in industrial processing; however, their thermostability is not able to meet the large-scale production requirements. In this study, through analyzing structural characteristics and modifying thermostability using prediction software programs, we improved the thermostability of pepsin, a representative aspartic protease. Based on the structural characteristics of pepsin and the experimental results of mutations predicted by several energy-based prediction software programs, it was found that the majority of pepsin’s thermodynamic weaknesses lie on its flexible regions on the surface. Using computational design, mutations were made based on the predicted sites of thermodynamic weakness. As a result, the half-lives of mutants D52N and S129A at 70°C were increased by 200.0 and 66.3%, respectively. Our work demonstrated that in the effort of improving protein thermostability, identification of structural weaknesses with the help of computational design, could efficiently improve the accuracy of protein rational design.https://www.frontiersin.org/articles/10.3389/fphy.2021.755253/fullthermostabilityaspartic proteaseprediction software programsstructural weaknesssite-specific mutagenesis |
| collection |
DOAJ |
| language |
English |
| format |
Article |
| sources |
DOAJ |
| author |
Yue Zhao Yulu Miao Fengdong Zhi Yue Pan Jianguo Zhang Xuepeng Yang John Z. H. Zhang John Z. H. Zhang John Z. H. Zhang Lujia Zhang Lujia Zhang |
| spellingShingle |
Yue Zhao Yulu Miao Fengdong Zhi Yue Pan Jianguo Zhang Xuepeng Yang John Z. H. Zhang John Z. H. Zhang John Z. H. Zhang Lujia Zhang Lujia Zhang Rational Design of Pepsin for Enhanced Thermostability via Exploiting the Guide of Structural Weakness on Stability Frontiers in Physics thermostability aspartic protease prediction software programs structural weakness site-specific mutagenesis |
| author_facet |
Yue Zhao Yulu Miao Fengdong Zhi Yue Pan Jianguo Zhang Xuepeng Yang John Z. H. Zhang John Z. H. Zhang John Z. H. Zhang Lujia Zhang Lujia Zhang |
| author_sort |
Yue Zhao |
| title |
Rational Design of Pepsin for Enhanced Thermostability via Exploiting the Guide of Structural Weakness on Stability |
| title_short |
Rational Design of Pepsin for Enhanced Thermostability via Exploiting the Guide of Structural Weakness on Stability |
| title_full |
Rational Design of Pepsin for Enhanced Thermostability via Exploiting the Guide of Structural Weakness on Stability |
| title_fullStr |
Rational Design of Pepsin for Enhanced Thermostability via Exploiting the Guide of Structural Weakness on Stability |
| title_full_unstemmed |
Rational Design of Pepsin for Enhanced Thermostability via Exploiting the Guide of Structural Weakness on Stability |
| title_sort |
rational design of pepsin for enhanced thermostability via exploiting the guide of structural weakness on stability |
| publisher |
Frontiers Media S.A. |
| series |
Frontiers in Physics |
| issn |
2296-424X |
| publishDate |
2021-09-01 |
| description |
Enzyme thermostability is an important parameter for estimating its industrial value. However, most naturally produced enzymes are incapable of meeting the industrial thermostability requirements. Software programs can be utilized to predict protein thermostability. Despite the fast-growing number of programs designed for this purpose; few provide reliable applicability because they do not account for thermodynamic weaknesses. Aspartic proteases are widely used in industrial processing; however, their thermostability is not able to meet the large-scale production requirements. In this study, through analyzing structural characteristics and modifying thermostability using prediction software programs, we improved the thermostability of pepsin, a representative aspartic protease. Based on the structural characteristics of pepsin and the experimental results of mutations predicted by several energy-based prediction software programs, it was found that the majority of pepsin’s thermodynamic weaknesses lie on its flexible regions on the surface. Using computational design, mutations were made based on the predicted sites of thermodynamic weakness. As a result, the half-lives of mutants D52N and S129A at 70°C were increased by 200.0 and 66.3%, respectively. Our work demonstrated that in the effort of improving protein thermostability, identification of structural weaknesses with the help of computational design, could efficiently improve the accuracy of protein rational design. |
| topic |
thermostability aspartic protease prediction software programs structural weakness site-specific mutagenesis |
| url |
https://www.frontiersin.org/articles/10.3389/fphy.2021.755253/full |
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