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Zhang Z, Li Z, Yang M, Zhao F, Han S. Machine learning-guided multi-site combinatorial mutagenesis enhances the thermostability of pectin lyase. Int J Biol Macromol 2024; 277:134530. [PMID: 39111490 DOI: 10.1016/j.ijbiomac.2024.134530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2024] [Revised: 07/25/2024] [Accepted: 08/04/2024] [Indexed: 08/13/2024]
Abstract
Enhancing the thermostability of enzymes is crucial for industrial applications. Methods such as directed evolution are often limited by the huge sequence space and combinatorial explosion, making it difficult to obtain optimal mutants. In recent years, machine learning (ML)-guided protein engineering has become an attractive tool because of its ability to comprehensively explore the sequence space of enzymes and discover superior mutants. This study employed ML to perform combinatorial mutation design on the pectin lyase PMGL-Ba from Bacillus licheniformis, aiming to improve its thermostability. First, 18 single-point mutants with enhanced thermostability were identified through semi-rational design. Subsequently, the initial library containing a small number of low-order mutants was utilized to construct an ML model to explore the combinatorial sequence space (theoretically 196,608 mutants) of single-point mutants. The results showed that the ML-predicted second library was successfully enriched with highly thermostable combinatorial mutants. After one iteration of learning, the best-performing combinatorial mutant in the third library, P36, showed a 67-fold and 39-fold increase in half-life at 75 °C and 80 °C, respectively, as well as a 2.1-fold increase in activity. Structural analysis and molecular dynamics simulations provided insights into the improved performance of the engineered enzyme.
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Affiliation(s)
- Zhihui Zhang
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Zhixuan Li
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Manli Yang
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Fengguang Zhao
- School of Light Industry and Engineering, South China University of Technology, Guangzhou 510006, China
| | - Shuangyan Han
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China.
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Wang L, Meng J, Yu X, Wang J, Zhang Y, Zhang M, Zhang Y, Wang H, Feng H, Tian Q, Zhang L, Liu H. Construction of highly active and stable recombinant nattokinase by engineered bacteria and computational design. Arch Biochem Biophys 2024; 760:110126. [PMID: 39154817 DOI: 10.1016/j.abb.2024.110126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 08/13/2024] [Accepted: 08/15/2024] [Indexed: 08/20/2024]
Abstract
Nattokinase (NK) is an enzyme that has been recognized as a new potential thrombolytic drug due to its strong thrombolytic activity. However, it is difficult to maintain the enzyme activity of NK during high temperature environment of industrial production. In this study, we constructed six NK mutants with potential for higher thermostability using a rational protein engineering strategy integrating free energy-based methods and molecular dynamics (MD) simulation. Then, wild-type NK and NK mutants were expressed in Escherichia coli (E. coli), and their thermostability and thrombolytic activity were tested. The results showed that, compared with wild-type NK, the mutants Y256P, Q206L and E156F all had improved thermostability. The optimal mutant Y256P showed a higher melting temperature (Tm) of 77.4 °C, an increase of 4 °C in maximum heat-resistant temperature and an increase of 51.8 % in activity at 37 °C compared with wild-type NK. Moreover, we also explored the mechanism of the increased thermostability of these mutants by analysing the MD trajectories under different simulation temperatures.
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Affiliation(s)
- Lianxin Wang
- School of Life Science, Liaoning University, Shenyang, 110036, China
| | - Jinhui Meng
- School of Life Science, Liaoning University, Shenyang, 110036, China
| | - Xiaomiao Yu
- School of Life Science, Liaoning University, Shenyang, 110036, China
| | - Jie Wang
- School of Pharmacy, Liaoning University, Shenyang, 110036, China
| | - Yuying Zhang
- School of Pharmacy, Liaoning University, Shenyang, 110036, China
| | - Man Zhang
- School of Life Science, Liaoning University, Shenyang, 110036, China
| | - Yuxi Zhang
- School of Life Science, Liaoning University, Shenyang, 110036, China
| | - Hengyi Wang
- School of Pharmacy, Liaoning University, Shenyang, 110036, China
| | - Huawei Feng
- Liaoning Provincial Key Laboratory of Computational Simulation and Information Processing of Biomacromolecules, Shenyang, 110036, China; Engineering Laboratory for Molecular Simulation and Designing of Drug Molecules of Liaoning, Shenyang, 110036, China; School of Pharmacy, Liaoning University, Shenyang, 110036, China
| | - Qifeng Tian
- School of Life Science, Liaoning University, Shenyang, 110036, China
| | - Li Zhang
- School of Life Science, Liaoning University, Shenyang, 110036, China; Liaoning Provincial Key Laboratory of Computational Simulation and Information Processing of Biomacromolecules, Shenyang, 110036, China; Engineering Laboratory for Molecular Simulation and Designing of Drug Molecules of Liaoning, Shenyang, 110036, China.
| | - Hongsheng Liu
- Liaoning Provincial Key Laboratory of Computational Simulation and Information Processing of Biomacromolecules, Shenyang, 110036, China; Engineering Laboratory for Molecular Simulation and Designing of Drug Molecules of Liaoning, Shenyang, 110036, China; School of Pharmacy, Liaoning University, Shenyang, 110036, China.
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3
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Albayati SH, Nezhad NG, Taki AG, Rahman RNZRA. Efficient and easible biocatalysts: Strategies for enzyme improvement. A review. Int J Biol Macromol 2024; 276:133978. [PMID: 39038570 DOI: 10.1016/j.ijbiomac.2024.133978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Revised: 06/19/2024] [Accepted: 07/16/2024] [Indexed: 07/24/2024]
Abstract
Owing to the environmental friendliness and vast advantages that enzymes offer in the biotechnology and industry fields, biocatalysts are a prolific investigation field. However, the low catalytic activity, stability, and specific selectivity of the enzyme limit the range of the reaction enzymes involved in. A comprehensive understanding of the protein structure and dynamics in terms of molecular details enables us to tackle these limitations effectively and enhance the catalytic activity by enzyme engineering or modifying the supports and solvents. Along with different strategies including computational, enzyme engineering based on DNA recombination, enzyme immobilization, additives, chemical modification, and physicochemical modification approaches can be promising for the wide spread of industrial enzyme usage. This is attributed to the successful application of biocatalysts in industrial and synthetic processes requires a system that exhibits stability, activity, and reusability in a continuous flow process, thereby reducing the production cost. The main goal of this review is to display relevant approaches for improving enzyme characteristics to overcome their industrial application.
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Affiliation(s)
- Samah Hashim Albayati
- Enzyme and Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia; Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia
| | - Nima Ghahremani Nezhad
- Enzyme and Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia; Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia
| | - Anmar Ghanim Taki
- Department of Radiology Techniques, Health and Medical Techniques College, Alnoor University, Mosul, Iraq
| | - Raja Noor Zaliha Raja Abd Rahman
- Enzyme and Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia; Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia; Institute Bioscience, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia.
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4
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Bergeson AR, Alper HS. Advancing sustainable biotechnology through protein engineering. Trends Biochem Sci 2024:S0968-0004(24)00185-3. [PMID: 39232879 DOI: 10.1016/j.tibs.2024.07.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Revised: 07/20/2024] [Accepted: 07/31/2024] [Indexed: 09/06/2024]
Abstract
The push for industrial sustainability benefits from the use of enzymes as a replacement for traditional chemistry. Biological catalysts, especially those that have been engineered for increased activity, stability, or novel function, and are often greener than alternative chemical approaches. This Review highlights the role of engineered enzymes (and identifies directions for further engineering efforts) in the application areas of greenhouse gas sequestration, fuel production, bioremediation, and degradation of plastic wastes.
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Affiliation(s)
- Amelia R Bergeson
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Hal S Alper
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA; Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, USA.
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5
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Zhou J, Huang M. Navigating the landscape of enzyme design: from molecular simulations to machine learning. Chem Soc Rev 2024; 53:8202-8239. [PMID: 38990263 DOI: 10.1039/d4cs00196f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/12/2024]
Abstract
Global environmental issues and sustainable development call for new technologies for fine chemical synthesis and waste valorization. Biocatalysis has attracted great attention as the alternative to the traditional organic synthesis. However, it is challenging to navigate the vast sequence space to identify those proteins with admirable biocatalytic functions. The recent development of deep-learning based structure prediction methods such as AlphaFold2 reinforced by different computational simulations or multiscale calculations has largely expanded the 3D structure databases and enabled structure-based design. While structure-based approaches shed light on site-specific enzyme engineering, they are not suitable for large-scale screening of potential biocatalysts. Effective utilization of big data using machine learning techniques opens up a new era for accelerated predictions. Here, we review the approaches and applications of structure-based and machine-learning guided enzyme design. We also provide our view on the challenges and perspectives on effectively employing enzyme design approaches integrating traditional molecular simulations and machine learning, and the importance of database construction and algorithm development in attaining predictive ML models to explore the sequence fitness landscape for the design of admirable biocatalysts.
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Affiliation(s)
- Jiahui Zhou
- School of Chemistry and Chemical Engineering, Queen's University, David Keir Building, Stranmillis Road, Belfast BT9 5AG, Northern Ireland, UK.
| | - Meilan Huang
- School of Chemistry and Chemical Engineering, Queen's University, David Keir Building, Stranmillis Road, Belfast BT9 5AG, Northern Ireland, UK.
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6
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Wang B, Zhou X, Wang Y, Gao Y, Nakanishi H, Fujita M, Li Z. Enhancement of thermostability and expression level of Rasamsonia emersonii lipase in Pichia pastoris and its application in biodiesel production in a continuous flow reactor. Int J Biol Macromol 2024; 278:134481. [PMID: 39127275 DOI: 10.1016/j.ijbiomac.2024.134481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Revised: 07/27/2024] [Accepted: 08/02/2024] [Indexed: 08/12/2024]
Abstract
The acidic lipase from Rasamsonia emersonii named LIPR has great potential for biodiesel synthesis due to its strong methanol tolerance. Nonetheless, the limited thermostability of LIPR and low expression level in Escherichia coli remain major obstacles to its use in biodiesel synthesis. To enhance the thermostability, the mutant LIPR harboring mutations A126C-P238C for the formation of a new disulfide bond and amino acid substitution D214L was obtained through rational design. To our delight, the thermostability of LIPR mutant was greatly improved. Moreover, a comprehensive optimization strategy, such as employing the Mss signal peptide, co-expressing the molecular chaperone protein disulfide isomerase (PDI), knocking out the vacuolar sorting receptor gene VPS10-01, and overexpressing the dihydroxyacetone synthase gene DAS2, was adopted to obtain the combination-optimized mutant Pichia pastoris strain GS54. Furthermore, the biodiesel synthetic capability with the mutant GS54-LIPR was verified and the production yield was 52.2 % after 24 h in a shake flask. Subsequently, a continuous flow system was adopted to increase the biodiesel yield to 73.6 % within 3 h, demonstrating its efficacy in enhancing enzyme biocatalysis. The engineered GS54-LIPR mutant lipase is an efficient and reusable biocatalyst for the sustained production of biodiesel in a continuous flow reaction.
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Affiliation(s)
- Buqing Wang
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Xiaoman Zhou
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Yasen Wang
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Yahui Gao
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Hideki Nakanishi
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Morihisa Fujita
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China; Institute for Glyco-Core Research, Gifu University, Gifu, Japan
| | - Zijie Li
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China.
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Huang JP, Yun ST, Zhao JX, Wang XT, Wang XC, Guo XY, San DM, Zhou YX. The two-step strategy for enhancing the specific activity and thermostability of alginate lyase AlyG2 with mechanism for improved thermostability. Int J Biol Macromol 2024; 273:132685. [PMID: 38823749 DOI: 10.1016/j.ijbiomac.2024.132685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 04/01/2024] [Accepted: 05/24/2024] [Indexed: 06/03/2024]
Abstract
To overcome the trade-off challenge encountered in the engineering of alginate lyase AlyG2 from Seonamhaeicola algicola Gy8T and to expand its potential industrial applications, we devised a two-step strategy encompassing activity enhancement followed by thermal stability engineering. To enhance the specific activity of efficient AlyG2, we strategically substituted residues with bulky steric hindrance proximal to the active pocket with glycine or alanine. This led to the generation of three promising positive mutants, with particular emphasis on the T91S mutant, exhibiting a 1.91-fold specific activity compared to the wild type. To mitigate the poor thermal stability of T91S, mutants with negative ΔΔG values in the thermal flexibility region were screened out. Notably, the S72Ya mutant not only displayed 17.96 % further increase in specific activity but also exhibited improved stability compared to T91S, manifesting as a remarkable 30.97 % increase in relative activity following a 1-hour incubation at 42 °C. Furthermore, enhanced kinetic stability was observed. To gain deeper insights into the mechanism underlying the enhanced thermostability of the S72Ya mutant, we conducted molecular dynamics simulations, principal component analysis (PCA), dynamic cross-correlation map (DCCM), and free energy landscape (FEL) analysis. The results unveiled a reduction in the flexibility of the surface loop, a stronger correlation dynamic and a narrower motion subspace in S72Ya system, along with the formation of more stable hydrogen bonds. Collectively, our findings suggest amino acids substitutions resulting in smaller side chains proximate to the active site can positively impact enzyme activity, while reducing the flexibility of surface loops emerges as a pivotal factor in conferring thermal stability. These insights offer valuable guidance and a framework for the engineering of other enzyme types.
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Affiliation(s)
- Jin-Ping Huang
- Marine College, Shandong University, Weihai, Shandong 264209, China
| | - Shuai-Ting Yun
- Marine College, Shandong University, Weihai, Shandong 264209, China
| | - Jin-Xin Zhao
- Monash Biomedicine Discovery Institute, Infection Program and Department of Microbiology, Monash University, Clayton, Victoria 3800, Australia
| | - Xue-Ting Wang
- Marine College, Shandong University, Weihai, Shandong 264209, China
| | - Xiao-Chen Wang
- Marine College, Shandong University, Weihai, Shandong 264209, China
| | - Xiang-Yi Guo
- SDU-ANU joint science college, Shandong University, Weihai, Shandong 264209, China
| | - Dong-Mei San
- Marine College, Shandong University, Weihai, Shandong 264209, China
| | - Yan-Xia Zhou
- Marine College, Shandong University, Weihai, Shandong 264209, China
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8
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Zhang X, Zhang X, Shi H, Zhang H, Zhang J, Yue C, Li D, Yao L, Tang C. Combining Flexible Region Design and Automatic Design to Enhance the Thermal Stability and Catalytic Efficiency of Leucine Dehydrogenase. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024. [PMID: 38838197 DOI: 10.1021/acs.jafc.4c02152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2024]
Abstract
Leucine dehydrogenase (LeuDH, EC 1.4.1.9) can reversibly catalyze the oxidative deamination of l-leucine and some other specific α-amino acids to form the corresponding α-ketoacids. This reaction has great significance in the field of food additives and the pharmaceutical industry. The LeuDH from Exiguobacterium sibiricum (EsLeuDH) has high catalytic efficiency but limited thermal stability, hindering its widespread industrial application. In this study, a mutant N5F/I12L/A352Y of EsLeuDH (referred to as M2) was developed with enhanced thermal stability and catalytic activity through rational modification. The M2 mutant exhibits a half-life at 60 °C (t1/2(60 °C)) of 975.7 min and a specific activity of 69.6 U mg-1, which is 5.4 and 2.1 times higher than those of EsLeuDH, respectively. This research may facilitate the utilization of EsLeuDH at elevated temperatures, enhancing its potential for industrial applications. The findings offer a practical and efficient approach for optimizing LeuDH and other industrial enzymes.
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Affiliation(s)
- Xiang Zhang
- College of Life Science, Nanyang Normal University, 1638 Wolong Road, Nanyang, Henan 473061, People's Republic of China
| | - Xichuan Zhang
- College of Life Science, Nanyang Normal University, 1638 Wolong Road, Nanyang, Henan 473061, People's Republic of China
| | - Hongling Shi
- College of Life Science, Nanyang Normal University, 1638 Wolong Road, Nanyang, Henan 473061, People's Republic of China
| | - Huimin Zhang
- College of Animal Science and Technology, Yangzhou University, 88 South Daxue Road, Yangzhou, Jiangsu 225009, People's Republic of China
| | - Jianhui Zhang
- Postdoctoral Innovation Training Base, She Dian Lao Jiu Co. Ltd., 2 Liquor Avenue, Nanyang, Henan 473300, People's Republic of China
| | - Chao Yue
- College of Life Science, Nanyang Normal University, 1638 Wolong Road, Nanyang, Henan 473061, People's Republic of China
| | - Dandan Li
- College of Life Science, Nanyang Normal University, 1638 Wolong Road, Nanyang, Henan 473061, People's Republic of China
| | - Lunguang Yao
- College of Life Science, Nanyang Normal University, 1638 Wolong Road, Nanyang, Henan 473061, People's Republic of China
| | - Cunduo Tang
- College of Life Science, Nanyang Normal University, 1638 Wolong Road, Nanyang, Henan 473061, People's Republic of China
- Postdoctoral Innovation Training Base, She Dian Lao Jiu Co. Ltd., 2 Liquor Avenue, Nanyang, Henan 473300, People's Republic of China
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9
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Datta Darshan VM, Arumugam N, Almansour AI, Sivaramakrishnan V, Kanchi S. In silico energetic and molecular dynamic simulations studies demonstrate potential effect of the point mutations with implications for protein engineering in BDNF. Int J Biol Macromol 2024; 271:132247. [PMID: 38750847 DOI: 10.1016/j.ijbiomac.2024.132247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 05/01/2024] [Accepted: 05/07/2024] [Indexed: 05/26/2024]
Abstract
Protein engineering by directed evolution is time-consuming. Hence, in silico techniques like FoldX-Yasara for ∆∆G calculation, and SNPeffect for predicting propensity for aggregation, amyloid formation, and chaperone binding are employed to design proteins. Here, we used in silico techniques to engineer BDNF-NTF3 interaction and validated it using mutations with known functional implications for NGF dimer. The structures of three mutants representing a positive, negative, or neutral ∆∆G involving two interface residues in BDNF and two mutations representing a neutral and positive ∆∆G in NGF, which is aligned with BDNF, were selected for molecular dynamics (MD) simulation. Our MD results conclude that the secondary structure of individual protomers of the positive and negative mutants displayed a similar or different conformation from the NTF3 monomer, respectively. The positive mutants showed fewer hydrophobic interactions and higher hydrogen bonds compared to the wild-type, negative, and neutral mutants with similar SASA, suggesting solvent-mediated disruption of hydrogen-bonded interactions. Similar results were obtained for mutations with known functional implications for NGF and BDNF. The results suggest that mutations with known effects in homologous proteins could help in validation, and in silico directed evolution experiments could be a viable alternative to the experimental technique used for protein engineering.
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Affiliation(s)
- V M Datta Darshan
- Disease Biology Lab, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Andhra Pradesh 515134, India
| | - Natarajan Arumugam
- Department of Chemistry, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Abdulrahman I Almansour
- Department of Chemistry, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Venketesh Sivaramakrishnan
- Disease Biology Lab, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Andhra Pradesh 515134, India.
| | - Subbarao Kanchi
- Department of Physics, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Andhra Pradesh 515134, India.
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Zhu X, Zhao YF, Wen HJ, Lu Y, You S, Herman RA, Wang J. Silkworm pupae protein co-degradation by magnetic nanoparticles immobilized proteinase K and Mucor circinelloides aspartic protease for further utilization of sericulture by-products. ENVIRONMENTAL RESEARCH 2024; 249:118385. [PMID: 38331140 DOI: 10.1016/j.envres.2024.118385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Revised: 01/18/2024] [Accepted: 01/30/2024] [Indexed: 02/10/2024]
Abstract
Silkworm pupae, by-product of sericulture industry, is massively discarded. The degradation rate of silkworm pupae protein is critical to further employment, which reduces the impact of waste on the environment. Herein, magnetic Janus mesoporous silica nanoparticles immobilized proteinase K mutant T206M and Mucor circinelloides aspartic protease were employed in the co-degradation. The thermostability of T206M improved by enhancing structural rigidity (t1/2 by 30 min and T50 by 5 °C), prompting the degradation efficiency. At 65 °C and pH 7, degradation rate reached the highest of 61.7%, which improved by 26% compared with single free protease degradation. Besides, the immobilized protease is easy to separate and reuse, which maintains 50% activity after 10 recycles. Therefore, immobilized protease co-degradation was first applied to the development and utilization of silkworm pupae resulting in the release of promising antioxidant properties and reduces the environmental impact by utilizing a natural and renewable resource.
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Affiliation(s)
- Xuan Zhu
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, 212100, China
| | - Yi-Fan Zhao
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, 212100, China
| | - Hong-Jian Wen
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, 212100, China
| | - Yu Lu
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, 212100, China
| | - Shuai You
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, 212100, China; Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture and Rural Affairs, The Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, 212100, China
| | - Richard Ansah Herman
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, 212100, China; Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture and Rural Affairs, The Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, 212100, China
| | - Jun Wang
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, 212100, China; Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture and Rural Affairs, The Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, 212100, China.
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11
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Ali I, Wei DQ, Khan A, Feng Y, Waseem M, Hussain Z, Iqbal A, Ali SS, Mohammad A, Zheng J. Improving the substrate binding of acetyl-CoA carboxylase (AccB) from Streptomyces antibioticus through computational enzyme engineering. Biotechnol Appl Biochem 2024; 71:402-413. [PMID: 38287712 DOI: 10.1002/bab.2548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 12/15/2023] [Indexed: 01/31/2024]
Abstract
Malonyl-CoA serves as the main building block for the biosynthesis of many important polyketides, as well as fatty acid-derived compounds, such as biofuel. Escherichia coli, Corynebacterium gultamicum, and Saccharomyces cerevisiae have recently been engineered for the biosynthesis of such compounds. However, the developed processes and strains often have insufficient productivity. In the current study, we used enzyme-engineering approach to improve the binding of acetyl-CoA with ACC. We generated different mutations, and the impact was calculated, which reported that three mutations, that is, S343A, T347W, and S350W, significantly improve the substrate binding. Molecular docking investigation revealed an altered binding network compared to the wild type. In mutants, additional interactions stabilize the binding of the inner tail of acetyl-CoA. Using molecular simulation, the stability, compactness, hydrogen bonding, and protein motions were estimated, revealing different dynamic properties owned by the mutants only but not by the wild type. The findings were further validated by using the binding-free energy (BFE) method, which revealed these mutations as favorable substitutions. The total BFE was reported to be -52.66 ± 0.11 kcal/mol for the wild type, -55.87 ± 0.16 kcal/mol for the S343A mutant, -60.52 ± 0.25 kcal/mol for T347W mutant, and -59.64 ± 0.25 kcal/mol for the S350W mutant. This shows that the binding of the substrate is increased due to the induced mutations and strongly corroborates with the docking results. In sum, this study provides information regarding the essential hotspot residues for the substrate binding and can be used for application in industrial processes.
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Affiliation(s)
- Imtiaz Ali
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, P. R. China
| | - Dong-Qing Wei
- Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, P. R. China
| | - Abbas Khan
- Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, P. R. China
- Sunway Microbiome Centre, School of Medical and Life Sciences, Sunway University, Sunway City, Malaysia
| | - Yuanyuan Feng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, P. R. China
| | - Muhammad Waseem
- Faculty of Rehabilitation and Allied Health Science, Riphah International University, Islamabad, Pakistan
| | - Zahid Hussain
- Centre for Biotechnology and Microbiology, University of Swat, Charbagh, Khyber Pakhtunkhwa, Pakistan
| | - Arshad Iqbal
- Centre for Biotechnology and Microbiology, University of Swat, Charbagh, Khyber Pakhtunkhwa, Pakistan
| | - Syed Shujait Ali
- Centre for Biotechnology and Microbiology, University of Swat, Charbagh, Khyber Pakhtunkhwa, Pakistan
| | - Anwar Mohammad
- Department of Biochemistry and Molecular Biology, Dasman Diabetes Institute, Dasman, Kuwait
| | - Jianting Zheng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, P. R. China
- Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University, Shanghai, P. R. China
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12
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Eskandari A, Leow TC, Rahman MBA, Oslan SN. Recent insight into the advances and prospects of microbial lipases and their potential applications in industry. Int Microbiol 2024:10.1007/s10123-024-00498-7. [PMID: 38489100 DOI: 10.1007/s10123-024-00498-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 03/04/2024] [Accepted: 03/07/2024] [Indexed: 03/17/2024]
Abstract
Enzymes play a crucial role in various industrial sectors. These biocatalysts not only ensure sustainability and safety but also enhance process efficiency through their unique specificity. Lipases possess versatility as biocatalysts and find utilization in diverse bioconversion reactions. Presently, microbial lipases are gaining significant focus owing to the rapid progress in enzyme technology and their widespread implementation in multiple industrial procedures. This updated review presents new knowledge about various origins of microbial lipases, such as fungi, bacteria, and yeast. It highlights both the traditional and modern purification methods, including precipitation and chromatographic separation, the immunopurification technique, the reversed micellar system, the aqueous two-phase system (ATPS), and aqueous two-phase flotation (ATPF), moreover, delves into the diverse applications of microbial lipases across several industries, such as food, vitamin esters, textile, detergent, biodiesel, and bioremediation. Furthermore, the present research unveils the obstacles encountered in employing lipase, the patterns observed in lipase engineering, and the application of CRISPR/Cas genome editing technology for altering the genes responsible for lipase production. Additionally, the immobilization of microorganisms' lipases onto various carriers also contributes to enhancing the effectiveness and efficiencies of lipases in terms of their catalytic activities. This is achieved by boosting their resilience to heat and ionic conditions (such as inorganic solvents, high-level pH, and temperature). The process also facilitates the ease of recycling them and enables a more concentrated deposition of the enzyme onto the supporting material. Consequently, these characteristics have demonstrated their suitability for application as biocatalysts in diverse industries.
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Affiliation(s)
- Azadeh Eskandari
- Enzyme and Microbial Technology Research Centre, Universiti Putra Malaysia, UPM, 43400, Serdang, Selangor, Malaysia
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, UPM, 43400, Serdang, Selangor, Malaysia
| | - Thean Chor Leow
- Enzyme and Microbial Technology Research Centre, Universiti Putra Malaysia, UPM, 43400, Serdang, Selangor, Malaysia
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, UPM, 43400, Serdang, Selangor, Malaysia
- Enzyme Technology and X-ray Crystallography Laboratory, VacBio 5, Institute of Bioscience, Universiti Putra Malaysia, UPM, 43400, Serdang, Selangor, Malaysia
| | | | - Siti Nurbaya Oslan
- Enzyme and Microbial Technology Research Centre, Universiti Putra Malaysia, UPM, 43400, Serdang, Selangor, Malaysia.
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, UPM, 43400, Serdang, Selangor, Malaysia.
- Enzyme Technology and X-ray Crystallography Laboratory, VacBio 5, Institute of Bioscience, Universiti Putra Malaysia, UPM, 43400, Serdang, Selangor, Malaysia.
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13
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Huang J, Xie X, Zheng W, Xu L, Yan J, Wu Y, Yang M, Yan Y. In silico design of multipoint mutants for enhanced performance of Thermomyces lanuginosus lipase for efficient biodiesel production. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2024; 17:33. [PMID: 38402206 PMCID: PMC10894483 DOI: 10.1186/s13068-024-02478-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 02/15/2024] [Indexed: 02/26/2024]
Abstract
BACKGROUND Biodiesel, an emerging sustainable and renewable clean energy, has garnered considerable attention as an alternative to fossil fuels. Although lipases are promising catalysts for biodiesel production, their efficiency in industrial-scale application still requires improvement. RESULTS In this study, a novel strategy for multi-site mutagenesis in the binding pocket was developed via FuncLib (for mutant enzyme design) and Rosetta Cartesian_ddg (for free energy calculation) to improve the reaction rate and yield of lipase-catalyzed biodiesel production. Thermomyces lanuginosus lipase (TLL) with high activity and thermostability was obtained using the Pichia pastoris expression system. The specific activities of the mutants M11 and M21 (each with 5 and 4 mutations) were 1.50- and 3.10-fold higher, respectively, than those of the wild-type (wt-TLL). Their corresponding melting temperature profiles increased by 10.53 and 6.01 °C, [Formula: see text] (the temperature at which the activity is reduced to 50% after 15 min incubation) increased from 60.88 to 68.46 °C and 66.30 °C, and the optimum temperatures shifted from 45 to 50 °C. After incubation in 60% methanol for 1 h, the mutants M11 and M21 retained more than 60% activity, and 45% higher activity than that of wt-TLL. Molecular dynamics simulations indicated that the increase in thermostability could be explained by reduced atomic fluctuation, and the improved catalytic properties were attributed to a reduced binding free energy and newly formed hydrophobic interaction. Yields of biodiesel production catalyzed by mutants M11 and M21 for 48 h at an elevated temperature (50 °C) were 94.03% and 98.56%, respectively, markedly higher than that of the wt-TLL (88.56%) at its optimal temperature (45 °C) by transesterification of soybean oil. CONCLUSIONS An integrating strategy was first adopted to realize the co-evolution of catalytic efficiency and thermostability of lipase. Two promising mutants M11 and M21 with excellent properties exhibited great potential for practical applications for in biodiesel production.
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Affiliation(s)
- Jinsha Huang
- Key Laboratory of Molecular Biophysics, Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, People's Republic of China
| | - Xiaoman Xie
- Key Laboratory of Molecular Biophysics, Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, People's Republic of China
| | - Wanlin Zheng
- Key Laboratory of Molecular Biophysics, Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, People's Republic of China
| | - Li Xu
- Key Laboratory of Molecular Biophysics, Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, People's Republic of China.
| | - Jinyong Yan
- Key Laboratory of Molecular Biophysics, Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, People's Republic of China
| | - Ying Wu
- Key Laboratory of Molecular Biophysics, Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, People's Republic of China
| | - Min Yang
- Key Laboratory of Molecular Biophysics, Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, People's Republic of China
| | - Yunjun Yan
- Key Laboratory of Molecular Biophysics, Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, People's Republic of China.
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14
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Kamble A, Singh R, Singh H. Structural and Functional Characterization of Obesumbacterium proteus Phytase: A Comprehensive In-Silico Study. Mol Biotechnol 2024:10.1007/s12033-024-01069-x. [PMID: 38393631 DOI: 10.1007/s12033-024-01069-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 01/09/2024] [Indexed: 02/25/2024]
Abstract
Phytate, also known as myoinositol hexakisphosphate, exhibits anti-nutritional properties and possesses a negative environmental impact. Phytase enzymes break down phytate, showing potential in various industries, necessitating thorough biochemical and computational characterizations. The present study focuses on Obesumbacterium proteus phytase (OPP), indicating its similarities with known phytases and its potential through computational analyses. Structure, functional, and docking results shed light on OPP's features, structural stability, strong and stable interaction, and dynamic conformation, with flexible sidechains that could adapt to different temperatures or specific functions. Root Mean Square fluctuation (RMSF) highlighted fluctuating regions in OPP, indicating potential sites for stability enhancement through mutagenesis. The systematic approach developed here could aid in enhancing enzyme properties via a rational engineering approach. Computational analysis expedites enzyme discovery and engineering, complementing the traditional biochemical methods to accelerate the quest for superior enzymes for industrial applications.
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Affiliation(s)
- Asmita Kamble
- Department of Biological Sciences, Sunandan Divatia School of Science, NMIMS Deemed to be University, Vile Parle (W), Mumbai, Maharashtra, India
| | - Rajkumar Singh
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Station 19, Lausanne, Switzerland
- Division of Physiological Chemistry II, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17177, Stockholm, Sweden
| | - Harinder Singh
- Department of Biological Sciences, Sunandan Divatia School of Science, NMIMS Deemed to be University, Vile Parle (W), Mumbai, Maharashtra, India.
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15
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Cui Y, Yang M, Liu N, Wang S, Sun Y, Sun G, Mou H, Zhou D. Computer-Aided Rational Design Strategy to Improve the Thermal Stability of Alginate Lyase AlyMc. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:3055-3065. [PMID: 38298105 DOI: 10.1021/acs.jafc.3c07215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2024]
Abstract
Alginate lyase degrades alginate by the β-elimination mechanism to produce unsaturated alginate oligosaccharides (UAOS), which have better bioactivities than saturated AOS. Enhancing the thermal stability of alginate lyases is crucial for their industrial applications. In this study, a feasible and efficient rational design strategy was proposed by combining the computer-aided ΔΔG value calculation with the B-factor analysis. Two thermal stability-enhanced mutants, Q246V and K249V, were obtained by site-directed mutagenesis. Particularly, the t1/2, 50 °C for mutants Q246V and K249V was increased from 2.36 to 3.85 and 3.65 h, respectively. Remarkably, the specific activities of Q246V and K249V were enhanced to 2.41- and 2.96-fold that of alginate lyase AlyMc, respectively. Structural analysis and molecular dynamics simulations suggested that mutations enhanced the hydrogen bond networks and the overall rigidity of the molecular structure. Notably, mutant Q246V exhibited excellent thermal stability among the PL-7 alginate lyase family, especially considering the heightened enzymatic activity. Moreover, the rational design strategy used in this study can effectively improve the thermal stability of enzymes and has important significance in advancing applications of alginate lyase.
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Affiliation(s)
- Yongyan Cui
- College of Food Science, Ocean University of Shanghai, Shanghai 201306, China
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong 266071, China
| | - Min Yang
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong 266071, China
- College of Food Science and Engineering, Ocean University of China, Qingdao, Shandong 266003, China
| | - Nan Liu
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong 266071, China
| | - Shanshan Wang
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong 266071, China
| | - Yong Sun
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong 266071, China
| | - Guohui Sun
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong 266071, China
| | - Haijin Mou
- College of Food Science and Engineering, Ocean University of China, Qingdao, Shandong 266003, China
| | - Deqing Zhou
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong 266071, China
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16
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Melnik TN, Majorina MA, Vorobeva DE, Nagibina GS, Veselova VR, Glukhova KA, Pak MA, Ivankov DN, Uversky VN, Melnik BS. Design of stable circular permutants of the GroEL chaperone apical domain. Cell Commun Signal 2024; 22:90. [PMID: 38303060 PMCID: PMC10836027 DOI: 10.1186/s12964-023-01426-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 12/08/2023] [Indexed: 02/03/2024] Open
Abstract
Enhancing protein stability holds paramount significance in biotechnology, therapeutics, and the food industry. Circular permutations offer a distinctive avenue for manipulating protein stability while keeping intra-protein interactions intact. Amidst the creation of circular permutants, determining the optimal placement of the new N- and C-termini stands as a pivotal, albeit largely unexplored, endeavor. In this study, we employed PONDR-FIT's predictions of disorder propensity to guide the design of circular permutants for the GroEL apical domain (residues 191-345). Our underlying hypothesis posited that a higher predicted disorder value would correspond to reduced stability in the circular permutants, owing to the increased likelihood of fluctuations in the novel N- and C-termini. To substantiate this hypothesis, we engineered six circular permutants, positioning glycines within the loops as locations for the new N- and C-termini. We demonstrated the validity of our hypothesis along the set of the designed circular permutants, as supported by measurements of melting temperatures by circular dichroism and differential scanning microcalorimetry. Consequently, we propose a novel computational methodology that rationalizes the design of circular permutants with projected stability. Video Abstract.
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Affiliation(s)
- Tatiana N Melnik
- Institute of Protein Research, Russian Academy of Sciences, Institutskaja Str. 4, Pushchino, Moscow Region, 142290, Russia
| | - Maria A Majorina
- Institute of Protein Research, Russian Academy of Sciences, Institutskaja Str. 4, Pushchino, Moscow Region, 142290, Russia
| | - Daria E Vorobeva
- Institute of Protein Research, Russian Academy of Sciences, Institutskaja Str. 4, Pushchino, Moscow Region, 142290, Russia
| | - Galina S Nagibina
- Institute of Protein Research, Russian Academy of Sciences, Institutskaja Str. 4, Pushchino, Moscow Region, 142290, Russia
| | - Victoria R Veselova
- Institute of Protein Research, Russian Academy of Sciences, Institutskaja Str. 4, Pushchino, Moscow Region, 142290, Russia
| | - Ksenia A Glukhova
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Institutskaja Str. 3, Puschino, Moscow Region, 142290, Russia
| | - Marina A Pak
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, Bld. 1, Moscow, 121205, Russia
| | - Dmitry N Ivankov
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, Bld. 1, Moscow, 121205, Russia
| | - Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Center and Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA.
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia.
| | - Bogdan S Melnik
- Institute of Protein Research, Russian Academy of Sciences, Institutskaja Str. 4, Pushchino, Moscow Region, 142290, Russia.
- Pushchino Branch, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Prospekt Nauki 6, Pushchino, Moscow Region, 142290, Russia.
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17
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Kadam V, Dhanorkar M, Patil S, Singh P. Advances in the co-production of biosurfactant and other biomolecules: statistical approaches for process optimization. J Appl Microbiol 2024; 135:lxae025. [PMID: 38308506 DOI: 10.1093/jambio/lxae025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Revised: 01/24/2024] [Accepted: 02/01/2024] [Indexed: 02/04/2024]
Abstract
An efficient microbial conversion for simultaneous synthesis of multiple high-value compounds, such as biosurfactants and enzymes, is one of the most promising aspects for an economical bioprocess leading to a marked reduction in production cost. Although biosurfactant and enzyme production separately have been much explored, there are limited reports on the predictions and optimization studies on simultaneous production of biosurfactants and other industrially important enzymes, including lipase, protease, and amylase. Enzymes are suited for an integrated production process with biosurfactants as multiple common industrial processes and applications are catalysed by these molecules. However, the complexity in microbial metabolism complicates the production process. This study details the work done on biosurfactant and enzyme co-production and explores the application and scope of various statistical tools and methodologies in this area of research. The use of advanced computational tools is yet to be explored for the optimization of downstream strategies in the co-production process. Given the complexity of the co-production process and with various new methodologies based on artificial intelligence (AI) being invented, the scope of AI in shaping the biosurfactant-enzyme co-production process is immense and would lead to not only efficient and rapid optimization, but economical extraction of multiple biomolecules as well.
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Affiliation(s)
- Vaibhav Kadam
- Symbiosis Centre for Waste Resource Management, Symbiosis International (Deemed University), Lavale, Pune-412115, India
| | - Manikprabhu Dhanorkar
- Symbiosis Centre for Waste Resource Management, Symbiosis International (Deemed University), Lavale, Pune-412115, India
| | - Shruti Patil
- Symbiosis Institute of Technology, Symbiosis International (Deemed University), Lavale, Pune-412115, India
| | - Pooja Singh
- Symbiosis Centre for Waste Resource Management, Symbiosis International (Deemed University), Lavale, Pune-412115, India
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18
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Sang Y, Huang X, Li H, Hong T, Zheng M, Li Z, Jiang Z, Ni H, Li Q, Zhu Y. Improving the thermostability of Pseudoalteromonas Porphyrae κ-carrageenase by rational design and MD simulation. AMB Express 2024; 14:8. [PMID: 38245573 PMCID: PMC10799840 DOI: 10.1186/s13568-024-01661-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 12/28/2023] [Indexed: 01/22/2024] Open
Abstract
The industrial applications of the κ-carrageenases have been restricted by their poor thermostability. In this study, based on the folding free energy change (ΔΔG) and the flexibility analysis using molecular dynamics (MD) simulation for the alkaline κ-carrageenase KCgCD from Pseudoalteromonas porphyrae (WT), the mutant S190R was identified with improved thermostability. After incubation at 50 °C for 30 min, the residual activity of S190R was 63.7%, 25.7% higher than that of WT. The Tm values determined by differential scanning calorimetry were 66.2 °C and 64.4 °C for S190R and WT, respectively. The optimal temperature of S190R was 10 °C higher than that of WT. The κ-carrageenan hydrolysates produced by S190R showed higher xanthine oxidase inhibitory activity compared with the untreated κ-carrageenan. MD simulation analysis of S190R showed that the residues (V186-M194 and P196-G197) in F5 and the key residue R150 in F3 displayed the decreased flexibility, and residues of T169-N173 near the catalytic center displayed the increased flexibility. These changed flexibilities might be the reasons for the improved thermostability of mutant S190R. This study provides a useful rational design strategy of combination of ΔΔG calculation and MD simulation to improve the κ-carrageenase's thermostability for its better industrial applications.
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Affiliation(s)
- Yuyan Sang
- College of Ocean Food and Biological Engineering, Jimei University, 361021, Xiamen, China
| | - Xiaoyi Huang
- College of Ocean Food and Biological Engineering, Jimei University, 361021, Xiamen, China
| | - Hebin Li
- Department of Pharmacy, Xiamen Medical College, 361008, Xiamen, China
| | - Tao Hong
- College of Ocean Food and Biological Engineering, Jimei University, 361021, Xiamen, China
- Fujian Provincial Key Laboratory of Food Microbiology and Enzyme Engineering, 361021, Xiamen, China
- Research Center of Food Biotechnology of Xiamen City, 361021, Xiamen, China
| | - Mingjing Zheng
- College of Ocean Food and Biological Engineering, Jimei University, 361021, Xiamen, China
- Fujian Provincial Key Laboratory of Food Microbiology and Enzyme Engineering, 361021, Xiamen, China
- Research Center of Food Biotechnology of Xiamen City, 361021, Xiamen, China
| | - Zhipeng Li
- College of Ocean Food and Biological Engineering, Jimei University, 361021, Xiamen, China
- Fujian Provincial Key Laboratory of Food Microbiology and Enzyme Engineering, 361021, Xiamen, China
- Research Center of Food Biotechnology of Xiamen City, 361021, Xiamen, China
| | - Zedong Jiang
- College of Ocean Food and Biological Engineering, Jimei University, 361021, Xiamen, China
- Fujian Provincial Key Laboratory of Food Microbiology and Enzyme Engineering, 361021, Xiamen, China
- Research Center of Food Biotechnology of Xiamen City, 361021, Xiamen, China
| | - Hui Ni
- College of Ocean Food and Biological Engineering, Jimei University, 361021, Xiamen, China
- Fujian Provincial Key Laboratory of Food Microbiology and Enzyme Engineering, 361021, Xiamen, China
- Research Center of Food Biotechnology of Xiamen City, 361021, Xiamen, China
| | - Qingbiao Li
- College of Ocean Food and Biological Engineering, Jimei University, 361021, Xiamen, China
- Fujian Provincial Key Laboratory of Food Microbiology and Enzyme Engineering, 361021, Xiamen, China
- Research Center of Food Biotechnology of Xiamen City, 361021, Xiamen, China
| | - Yanbing Zhu
- College of Ocean Food and Biological Engineering, Jimei University, 361021, Xiamen, China.
- Fujian Provincial Key Laboratory of Food Microbiology and Enzyme Engineering, 361021, Xiamen, China.
- Research Center of Food Biotechnology of Xiamen City, 361021, Xiamen, China.
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19
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Xiang X, Zhu E, Xiong D, Wen Y, Xing Y, Yue L, He S, Han N, Huang Z. Improving the Thermostability of Thermomyces lanuginosus Lipase by Restricting the Flexibility of N-Terminus and C-Terminus Simultaneously via the 25-Loop Substitutions. Int J Mol Sci 2023; 24:16562. [PMID: 38068886 PMCID: PMC10706272 DOI: 10.3390/ijms242316562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 11/17/2023] [Accepted: 11/20/2023] [Indexed: 12/18/2023] Open
Abstract
(1) Lipases are catalysts widely applied in industrial fields. To sustain the harsh treatments in industries, optimizing lipase activities and thermal stability is necessary to reduce production loss. (2) The thermostability of Thermomyces lanuginosus lipase (TLL) was evaluated via B-factor analysis and consensus-sequence substitutions. Five single-point variants (K24S, D27N, D27R, P29S, and A30P) with improved thermostability were constructed via site-directed mutagenesis. (3) The optimal reaction temperatures of all the five variants displayed 5 °C improvement compared with TLL. Four variants, except D27N, showed enhanced residual activities at 80 °C. The melting temperatures of three variants (D27R, P29S, and A30P) were significantly increased. The molecular dynamics simulations indicated that the 25-loop (residues 24-30) in the N-terminus of the five variants generated more hydrogen bonds with surrounding amino acids; hydrogen bond pair D254-I255 preserved in the C-terminus of the variants also contributes to the improved thermostability. Furthermore, the newly formed salt-bridge interaction (R27…E56) in D27R was identified as a crucial determinant for thermostability. (4) Our study discovered that substituting residues from the 25-loop will enhance the stability of the N-terminus and C-terminus simultaneously, restrict the most flexible regions of TLL, and result in improved thermostability.
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Affiliation(s)
- Xia Xiang
- School of Life Sciences, Yunnan Normal University, Kunming 650500, China
| | - Enheng Zhu
- School of Life Sciences, Yunnan Normal University, Kunming 650500, China
| | - Diao Xiong
- School of Life Sciences, Yunnan Normal University, Kunming 650500, China
| | - Yin Wen
- School of Life Sciences, Yunnan Normal University, Kunming 650500, China
| | - Yu Xing
- School of Life Sciences, Yunnan Normal University, Kunming 650500, China
| | - Lirong Yue
- School of Life Sciences, Yunnan Normal University, Kunming 650500, China
| | - Shuang He
- School of Life Sciences, Yunnan Normal University, Kunming 650500, China
| | - Nanyu Han
- School of Life Sciences, Yunnan Normal University, Kunming 650500, China
- Engineering Research Center of Sustainable and Utilization of Biomass Energy, Ministry of Education, Yunnan Normal University, Kunming 650500, China
- Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Yunnan Normal University, Kunming 650500, China
- Key Laboratory of Enzyme Engineering, Yunnan Normal University, Kunming 650500, China
| | - Zunxi Huang
- School of Life Sciences, Yunnan Normal University, Kunming 650500, China
- Engineering Research Center of Sustainable and Utilization of Biomass Energy, Ministry of Education, Yunnan Normal University, Kunming 650500, China
- Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Yunnan Normal University, Kunming 650500, China
- Key Laboratory of Enzyme Engineering, Yunnan Normal University, Kunming 650500, China
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20
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Zhang B, Chi H, Shen J, Tao Y, Lu Z, Lu F, Zhu P. Improved catalytic performance and molecular insight for lipoxygenase from Enterovibrio norvegicus via directed evolution. Front Bioeng Biotechnol 2023; 11:1305582. [PMID: 38047284 PMCID: PMC10690365 DOI: 10.3389/fbioe.2023.1305582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Accepted: 11/06/2023] [Indexed: 12/05/2023] Open
Abstract
Lipoxygenase (LOX) holds significant promise for food and pharmaceutical industries. However, albeit its application has been hampered by low catalytic activity and suboptimal thermostability. To address the drawbacks, a directed evolution strategy was explored to enhance the catalytic activity and thermostability of LOX from Enterovibrio norvegicus (EnLOX) for the first time. After two rounds of error-prone polymerase chain reaction (error-prone PCR) and one generations of sequential DNA shuffling, all of four different mutants showed a significant increase in the specific activity of EnLOX, ranging from 132.07 ± 9.34 to 330.17 ± 18.54 U/mg. Among these mutants, D95E/T99A/A121H/S142N/N444W/S613G (EAHNWG) exhibited the highest specific activity, which was 8.25-fold higher than the wild-type enzyme (WT). Meanwhile, the catalytic efficiency (K cat /K m) of EAHNWG was also improved, which was 13.61 ± 1.67 s-1 μM-1, in comparison to that of WT (4.83 ± 0.38 s-1 μM-1). In addition, mutant EAHNWG had a satisfied thermostability with the t 1/2,50 °C value of 6.44 ± 0.24 h, which was 0.4 h longer than that of the WT. Furthermore, the molecular dynamics simulation and structural analysis demonstrated that the reduction of hydrogen bonds number, the enhancement of hydrophobic interactions in the catalytic pocket, and the improvement of flexibility of the lid domain facilitated structural stability and the strength of substrate binding capacity for improved thermal stability and catalytic efficiency of mutant LOX after directed evolution. Overall, these results could provide the guidance for further enzymatic modification of LOX with high catalytic performance for industrial application.
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Affiliation(s)
| | | | | | | | | | - Fengxia Lu
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Ping Zhu
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, China
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21
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Xu L, Pan F, Li Y, Liu H, Wang C. Characterization and Molecular Dynamics Simulation of a Lipase Capable of Improving the Functional Characteristics of an Egg-Yolk-Contaminated Liquid Egg White. Foods 2023; 12:4098. [PMID: 38002155 PMCID: PMC10670289 DOI: 10.3390/foods12224098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 11/02/2023] [Accepted: 11/06/2023] [Indexed: 11/26/2023] Open
Abstract
Lipase has great application potential in hydrolyzing residual yolk lipid in egg white liquid to restore its functional properties. In this study, a lipase gene from Bacillus subtilis was expressed in E. coli BL21 (DE3) and named Lip-IM. Results showed that although Lip-IM has stronger specificity for medium- and short-chain substrates than long-chain substrates (C16, C18), due to its excellent enzyme activity, it also has strong hydrolysis activity for long-chain substrates and maintained over 80% activity at 4-20 °C, but significantly reduced when the temperature exceeds 40 °C. The addition of 0.5% Lip-IM enhanced foaming ability by 26% (from 475 to 501%) and reduced liquid precipitation rate by 9% (from 57 to 48%). Furthermore, molecular dynamics (MD) simulations were run to investigate the conformational stability of Lip-IM at different temperatures. Results showed that Lip-IM maintained a stable conformation within the temperature range of 277-303 K. Fluctuations in the flexible area and backbone movement of proteins were identified as the main reasons for its poor thermal stability.
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Affiliation(s)
- Linlin Xu
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology & Business University (BTBU), Beijing 100048, China; (L.X.); (H.L.)
| | - Fei Pan
- State Key Laboratory of Resource Insects, Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing 100093, China;
| | - Yingnan Li
- Ministry of Education Key Laboratory of Industrial Biotechnology, School of Biotechnology, Jiangnan University, Wuxi 214122, China;
| | - Huiqian Liu
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology & Business University (BTBU), Beijing 100048, China; (L.X.); (H.L.)
| | - Chengtao Wang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology & Business University (BTBU), Beijing 100048, China; (L.X.); (H.L.)
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22
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Ma Z, Mu K, Zhu J, Xiao M, Wang L, Jiang X. Molecular dynamics simulations identify the topological weak spots of a protease CN2S8A. J Mol Graph Model 2023; 124:108571. [PMID: 37487372 DOI: 10.1016/j.jmgm.2023.108571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 07/06/2023] [Accepted: 07/19/2023] [Indexed: 07/26/2023]
Abstract
Thermophilic enzymes are highly desired in industrial applications due to their efficient catalytic activity at high temperature. However, most enzymes exhibit inferior thermostability and it remains challenging to identify the optimal sites for designing mutations to improve protein stability. To tackle this issue, we integrated topological analysis and all-atom molecular dynamics simulations to efficiently pinpoint the thermally-unstable regions in protein structures. Using a protease CN2S8A as the model, we analyzed the intramolecular hydrogen bonding interactions between adjacent secondary structure elements, and then identified the topological weak spots of CN2S8A where weak hydrogen bonding interactions were formed. To examine the role of these sites in protein structural stability, we designed three virtual mutations at different weak spots and characterized the effects of these mutations on the structural properties of CN2S8A. The results showed that all three mutations increased the protein structural stability. In conclusion, these findings provide a novel method to identify the topological weak spots of proteins, with implications in the rational design of biocatalysts with superior thermostability.
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Affiliation(s)
- Zhenyu Ma
- National Glycoengineering Research Center, Shandong University, Qingdao, 266237, China
| | - Kaijie Mu
- Biomedicine Discovery Institute, Monash University, Melbourne, 3500, Australia
| | - Jingyi Zhu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Min Xiao
- National Glycoengineering Research Center, Shandong University, Qingdao, 266237, China
| | - Lushan Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Xukai Jiang
- National Glycoengineering Research Center, Shandong University, Qingdao, 266237, China.
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23
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Malbranke C, Rostain W, Depardieu F, Cocco S, Monasson R, Bikard D. Computational design of novel Cas9 PAM-interacting domains using evolution-based modelling and structural quality assessment. PLoS Comput Biol 2023; 19:e1011621. [PMID: 37976326 PMCID: PMC10729993 DOI: 10.1371/journal.pcbi.1011621] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 12/19/2023] [Accepted: 10/19/2023] [Indexed: 11/19/2023] Open
Abstract
We present here an approach to protein design that combines (i) scarce functional information such as experimental data (ii) evolutionary information learned from a natural sequence variants and (iii) physics-grounded modeling. Using a Restricted Boltzmann Machine (RBM), we learn a sequence model of a protein family. We use semi-supervision to leverage available functional information during the RBM training. We then propose a strategy to explore the protein representation space that can be informed by external models such as an empirical force-field method (FoldX). Our approach is applied to a domain of the Cas9 protein responsible for recognition of a short DNA motif. We experimentally assess the functionality of 71 variants generated to explore a range of RBM and FoldX energies. Sequences with as many as 50 differences (20% of the protein domain) to the wild-type retained functionality. Overall, 21/71 sequences designed with our method were functional. Interestingly, 6/71 sequences showed an improved activity in comparison with the original wild-type protein sequence. These results demonstrate the interest in further exploring the synergies between machine-learning of protein sequence representations and physics grounded modeling strategies informed by structural information.
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Affiliation(s)
- Cyril Malbranke
- Laboratory of Physics of the Ecole Normale Superieure, PSL Research, CNRS UMR 8023, Sorbonne Université, Paris, France
- Institut Pasteur, Université Paris Cité, CNRS UMR 6047, Synthetic Biology, Paris, France
| | - William Rostain
- Institut Pasteur, Université Paris Cité, CNRS UMR 6047, Synthetic Biology, Paris, France
| | - Florence Depardieu
- Institut Pasteur, Université Paris Cité, CNRS UMR 6047, Synthetic Biology, Paris, France
| | - Simona Cocco
- Laboratory of Physics of the Ecole Normale Superieure, PSL Research, CNRS UMR 8023, Sorbonne Université, Paris, France
| | - Rémi Monasson
- Laboratory of Physics of the Ecole Normale Superieure, PSL Research, CNRS UMR 8023, Sorbonne Université, Paris, France
| | - David Bikard
- Institut Pasteur, Université Paris Cité, CNRS UMR 6047, Synthetic Biology, Paris, France
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24
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Wu C, Yu X, Zheng P, Chen P, Wu D. Rational Redesign of Chitosanase to Enhance Thermostability and Catalytic Activity to Produce Chitooligosaccharides with a Relatively High Degree of Polymerization. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:15213-15223. [PMID: 37793074 DOI: 10.1021/acs.jafc.3c04542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/06/2023]
Abstract
Chitooligosaccharides (hdpCOS) with a high degree of polymerization (hdp, DP 4-10) generally have greater biological activities than those of low-DP (ldp, DP 2-3) COS. Chitosanase from Bacillus amyloliquefaciens KCP2 (Csn46) can degrade chitosan to more hdpCOS at high temperature (70 °C), but low thermal stability at this temperature makes it unsuitable for industrial application; the wild-type enzyme can only produce COS (DP 2-4) at lower temperatures. Several thermostable mutants were obtained by modifying chitosanase using a comprehensive strategy based on a computer-aided mutant design. A combination of four beneficial single-point mutations (A129L/T175 V/K70T/D34G) to Csn46 was selected to obtain a markedly improved mutant, Mut4, with a half-life at 60 °C extended from 34.31 to 690.80 min, and the specific activity increased from 1671.73 to 3528.77 U/mg. Mut4 produced COS with DPs of 2-4 and 2-7 at 60 and 70 °C, respectively. Therefore, Mut4 has the potential to be applied to the industrial-scale preparation of hdpCOS with high biological activity.
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Affiliation(s)
- Changyun Wu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China
| | - Xiaowei Yu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China
| | - Pu Zheng
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China
| | - Pengcheng Chen
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China
| | - Dan Wu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China
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25
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Sardiña-Peña AJ, Mesa-Ramos L, Iglesias-Figueroa BF, Ballinas-Casarrubias L, Siqueiros-Cendón TS, Espinoza-Sánchez EA, Flores-Holguín NR, Arévalo-Gallegos S, Rascón-Cruz Q. Analyzing Current Trends and Possible Strategies to Improve Sucrose Isomerases' Thermostability. Int J Mol Sci 2023; 24:14513. [PMID: 37833959 PMCID: PMC10572972 DOI: 10.3390/ijms241914513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 09/10/2023] [Accepted: 09/10/2023] [Indexed: 10/15/2023] Open
Abstract
Due to their ability to produce isomaltulose, sucrose isomerases are enzymes that have caught the attention of researchers and entrepreneurs since the 1950s. However, their low activity and stability at temperatures above 40 °C have been a bottleneck for their industrial application. Specifically, the instability of these enzymes has been a challenge when it comes to their use for the synthesis and manufacturing of chemicals on a practical scale. This is because industrial processes often require biocatalysts that can withstand harsh reaction conditions, like high temperatures. Since the 1980s, there have been significant advancements in the thermal stabilization engineering of enzymes. Based on the literature from the past few decades and the latest achievements in protein engineering, this article systematically describes the strategies used to enhance the thermal stability of sucrose isomerases. Additionally, from a theoretical perspective, we discuss other potential mechanisms that could be used for this purpose.
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Affiliation(s)
- Amado Javier Sardiña-Peña
- Laboratorio de Biotecnología I, Facultad de Ciencias Químicas, Universidad Autónoma de Chihuahua, Circuito Universitarios s/n Nuevo Campus Universitario, Chihuahua 31125, Mexico; (A.J.S.-P.); (B.F.I.-F.); (L.B.-C.); (T.S.S.-C.); (E.A.E.-S.); (S.A.-G.)
| | - Liber Mesa-Ramos
- Laboratorio de Microbiología III, Facultad de Ciencias Químicas, Universidad Autónoma de Chihuahua, Circuito Universitarios s/n Nuevo Campus Universitario, Chihuahua 31125, Mexico;
| | - Blanca Flor Iglesias-Figueroa
- Laboratorio de Biotecnología I, Facultad de Ciencias Químicas, Universidad Autónoma de Chihuahua, Circuito Universitarios s/n Nuevo Campus Universitario, Chihuahua 31125, Mexico; (A.J.S.-P.); (B.F.I.-F.); (L.B.-C.); (T.S.S.-C.); (E.A.E.-S.); (S.A.-G.)
| | - Lourdes Ballinas-Casarrubias
- Laboratorio de Biotecnología I, Facultad de Ciencias Químicas, Universidad Autónoma de Chihuahua, Circuito Universitarios s/n Nuevo Campus Universitario, Chihuahua 31125, Mexico; (A.J.S.-P.); (B.F.I.-F.); (L.B.-C.); (T.S.S.-C.); (E.A.E.-S.); (S.A.-G.)
| | - Tania Samanta Siqueiros-Cendón
- Laboratorio de Biotecnología I, Facultad de Ciencias Químicas, Universidad Autónoma de Chihuahua, Circuito Universitarios s/n Nuevo Campus Universitario, Chihuahua 31125, Mexico; (A.J.S.-P.); (B.F.I.-F.); (L.B.-C.); (T.S.S.-C.); (E.A.E.-S.); (S.A.-G.)
| | - Edward Alexander Espinoza-Sánchez
- Laboratorio de Biotecnología I, Facultad de Ciencias Químicas, Universidad Autónoma de Chihuahua, Circuito Universitarios s/n Nuevo Campus Universitario, Chihuahua 31125, Mexico; (A.J.S.-P.); (B.F.I.-F.); (L.B.-C.); (T.S.S.-C.); (E.A.E.-S.); (S.A.-G.)
| | - Norma Rosario Flores-Holguín
- Laboratorio Virtual NANOCOSMOS, Departamento de Medio Ambiente y Energía, Centro de Investigación en Materiales Avanzados, Chihuahua 31136, Mexico;
| | - Sigifredo Arévalo-Gallegos
- Laboratorio de Biotecnología I, Facultad de Ciencias Químicas, Universidad Autónoma de Chihuahua, Circuito Universitarios s/n Nuevo Campus Universitario, Chihuahua 31125, Mexico; (A.J.S.-P.); (B.F.I.-F.); (L.B.-C.); (T.S.S.-C.); (E.A.E.-S.); (S.A.-G.)
| | - Quintín Rascón-Cruz
- Laboratorio de Biotecnología I, Facultad de Ciencias Químicas, Universidad Autónoma de Chihuahua, Circuito Universitarios s/n Nuevo Campus Universitario, Chihuahua 31125, Mexico; (A.J.S.-P.); (B.F.I.-F.); (L.B.-C.); (T.S.S.-C.); (E.A.E.-S.); (S.A.-G.)
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26
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Ming Y, Zhang H, Zhao Z, Zhang Z, Wang H, Liang Z. Enhancing the thermostability of carboxypeptidase A by a multiple computer-aided rational design based on amino acids preferences at β-turns. Int J Biol Macromol 2023; 245:125447. [PMID: 37330104 DOI: 10.1016/j.ijbiomac.2023.125447] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 05/27/2023] [Accepted: 06/14/2023] [Indexed: 06/19/2023]
Abstract
Carboxypeptidase A (CPA) with efficient hydrolysis ability has shown vital potential in food and biological fields. In addition, it is also the earliest discovered enzyme with Ochratoxin A (OTA) degradation activity. Thermostability plays an imperative role to catalyze the reactions at high temperatures in industry, but the poor thermostability of CPA restricts its industrial application. In order to improve the thermostability of CPA, flexible loops were predicted through molecular dynamics (MD) simulation. Based on the amino acid preferences at β-turns, three ΔΔG-based computational programs (Rosetta, FoldX and PoPMuSiC) were employed to screen three variants from plentiful candidates and MD simulations were then used to verify two potential variants with enhanced thermostability (R124K and S134P). Results showed that compared to the wild-type CPA, the variants S134P and R124K exhibited rise of 4.2 min and 7.4 min in half-life (t1/2) at 45 °C, 3 °C and 4.1 °C in the half inactivation temperature (T5010), in addition to increase by 1.9 °C and 1.2 °C in the melting temperature (Tm), respectively. The mechanism responsible for the enhanced thermostability was elucidated through the comprehensive analysis of molecular structure. This study shows that the thermostability of CPA can be improved by the multiple computer-aided rational design based on amino acid preferences at β-turns, broadening its industrial applicability of OTA degradation and providing a valuable strategy for the protein engineering of mycotoxin degrading enzymes.
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Affiliation(s)
- Yue Ming
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Haoxiang Zhang
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Zitong Zhao
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Zhenzhen Zhang
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Honglei Wang
- Yantai Institute of China Agricultural University, Yantai 264670, China
| | - Zhihong Liang
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China; Beijing Laboratory for Food Quality and Safety, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China; The Supervision, Inspection and Testing Center of Genetically Modified Organisms, Ministry of Agriculture, Beijing 100083, China.
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27
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Huang Z, Ni D, Chen Z, Zhu Y, Zhang W, Mu W. Application of molecular dynamics simulation in the field of food enzymes: improving the thermal-stability and catalytic ability. Crit Rev Food Sci Nutr 2023:1-13. [PMID: 37485919 DOI: 10.1080/10408398.2023.2238054] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/25/2023]
Abstract
Enzymes can produce high-quality food with low pollution, high function, high acceptability, and medical aid. However, most enzymes, in their native form, do not meet the industrial requirements. Sequence-based and structure-based methods are the two main strategies used for enzyme modification. Molecular Dynamics (MD) simulation is a sufficiently comprehensive technology, from a molecular perspective, which has been widely used for structure information analysis and enzyme modification. In this review, we summarize the progress and development of MD simulation, particularly for software, force fields, and a standard procedure. Subsequently, we review the application of MD simulation in various food enzymes for thermostability and catalytic improvement was reviewed in depth. Finally, the limitations and prospects of MD simulation in food enzyme modification research are discussed. This review highlights the significance of MD simulation and its prospects in food enzyme modification.
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Affiliation(s)
- Zhaolin Huang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
| | - Dawei Ni
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
| | - Ziwei Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
| | - Yingying Zhu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
| | - Wenli Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
| | - Wanmeng Mu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
- International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, Jiangsu, China
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28
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Jia DX, Yu H, Wang F, Jin LQ, Liu ZQ, Zheng YG. Computer-aided design of novel cellobiose 2-epimerase for efficient synthesis of lactulose using lactose. Bioprocess Biosyst Eng 2023:10.1007/s00449-023-02896-z. [PMID: 37450268 DOI: 10.1007/s00449-023-02896-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 06/16/2023] [Indexed: 07/18/2023]
Abstract
Cellobiose 2-epimerase (CE) is ideally suited to synthesize lactulose from lactose, but the poor thermostability and catalytic efficiency restrict enzymatic application. Herein, a non-characterized CE originating from Caldicellulosiruptor morganii (CmCE) was discovered in the NCBI database. Then, a smart mutation library was constructed based on FoldX ΔΔG calculation and modeling structure analysis, from which a positive mutant D226G located within the α8/α9 loop exhibited longer half-lives at 65-75 °C as well as lower Km and higher kcat/Km values compared with CmCE. Molecular modeling demonstrated that the improvement of D226G was largely attributed to the rigidification of the flexible loop, the compactness of the catalysis pocket and the increment of substrate-binding capability. Finally, the yield of synthesizing lactulose catalyzed by D226G reached 45.5%, higher than the 35.9% achieved with CmCE. The disclosed effect of the flexible loop on enzymatic stability and catalysis provides insight to redesign efficient CEs to biosynthesize lactulose.
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Affiliation(s)
- Dong-Xu Jia
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, 18 Chaowang Road, Hangzhou, 310014, People's Republic of China
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, 18 Chaowang Road, Hangzhou, 310014, People's Republic of China
| | - Hai Yu
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, 18 Chaowang Road, Hangzhou, 310014, People's Republic of China
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, 18 Chaowang Road, Hangzhou, 310014, People's Republic of China
| | - Fan Wang
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, 18 Chaowang Road, Hangzhou, 310014, People's Republic of China
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, 18 Chaowang Road, Hangzhou, 310014, People's Republic of China
| | - Li-Qun Jin
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, 18 Chaowang Road, Hangzhou, 310014, People's Republic of China
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, 18 Chaowang Road, Hangzhou, 310014, People's Republic of China
| | - Zhi-Qiang Liu
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, 18 Chaowang Road, Hangzhou, 310014, People's Republic of China.
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, 18 Chaowang Road, Hangzhou, 310014, People's Republic of China.
| | - Yu-Guo Zheng
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, 18 Chaowang Road, Hangzhou, 310014, People's Republic of China
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, 18 Chaowang Road, Hangzhou, 310014, People's Republic of China
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29
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Sardiña-Peña AJ, Ballinas-Casarrubias L, Siqueiros-Cendón TS, Espinoza-Sánchez EA, Flores-Holguín NR, Iglesias-Figueroa BF, Rascón-Cruz Q. Thermostability improvement of sucrose isomerase PalI NX-5: a comprehensive strategy. Biotechnol Lett 2023:10.1007/s10529-023-03388-6. [PMID: 37199887 DOI: 10.1007/s10529-023-03388-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 03/29/2023] [Accepted: 04/27/2023] [Indexed: 05/19/2023]
Abstract
OBJECTIVE To increase the thermal stability of sucrose isomerase from Erwinia rhapontici NX-5, we designed a comprehensive strategy that combines different thermostabilizing elements. RESULTS We identified 19 high B value amino acid residues for site-directed mutagenesis. An in silico evaluation of the influence of post-translational modifications on the thermostability was also carried out. The sucrose isomerase variants were expressed in Pichia pastoris X33. Thus, for the first time, we report the expression and characterization of glycosylated sucrose isomerases. The designed mutants K174Q, L202E and K174Q/L202E, showed an increase in their optimal temperature of 5 °C, while their half-lives increased 2.21, 1.73 and 2.89 times, respectively. The mutants showed an increase in activity of 20.3% up to 25.3%. The Km values for the K174Q, L202E, and K174Q/L202E mutants decreased by 5.1%, 7.9%, and 9.4%, respectively; furthermore, the catalytic efficiency increased by up to 16%. CONCLUSIONS With the comprehensive strategy followed, we successfully obtain engineered mutants more suitable for industrial applications than their counterparts: native (this research) and wild-type from E. rhapontici NX-5, without compromising the catalytic activity of the molecule.
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Affiliation(s)
- A J Sardiña-Peña
- Laboratorio de Biotecnología I, Facultad de Ciencias Químicas, Universidad Autónoma de Chihuahua, Circuito Universitarios s/n Nuevo Campus Universitario, C. P. 31125, Chihuahua, México
| | - L Ballinas-Casarrubias
- Laboratorio de Química Analítica III, Facultad de Ciencias Químicas, Universidad Autónoma de Chihuahua, Circuito Universitarios s/n Nuevo Campus Universitario, C. P. 31125, Chihuahua, México
| | - T S Siqueiros-Cendón
- Laboratorio de Biotecnología I, Facultad de Ciencias Químicas, Universidad Autónoma de Chihuahua, Circuito Universitarios s/n Nuevo Campus Universitario, C. P. 31125, Chihuahua, México
| | - E A Espinoza-Sánchez
- Laboratorio de Biotecnología I, Facultad de Ciencias Químicas, Universidad Autónoma de Chihuahua, Circuito Universitarios s/n Nuevo Campus Universitario, C. P. 31125, Chihuahua, México
| | - N R Flores-Holguín
- Laboratorio Virtual NANOCOSMOS, Departamento de Medio Ambiente y Energía, Centro de Investigación en Materiales Avanzados, Chihuahua, México
| | - B F Iglesias-Figueroa
- Laboratorio de Biotecnología I, Facultad de Ciencias Químicas, Universidad Autónoma de Chihuahua, Circuito Universitarios s/n Nuevo Campus Universitario, C. P. 31125, Chihuahua, México
| | - Q Rascón-Cruz
- Laboratorio de Biotecnología I, Facultad de Ciencias Químicas, Universidad Autónoma de Chihuahua, Circuito Universitarios s/n Nuevo Campus Universitario, C. P. 31125, Chihuahua, México.
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30
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Li B, Sun Y, Zhu X, Qian S, Pu J, Guo Y, Wu H, Zhang L, Xin Y. Aggregation Interface and Rigid Spots Sustain the Stable Framework of a Thermophilic N-Demethylase. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:5614-5629. [PMID: 37000489 DOI: 10.1021/acs.jafc.3c00877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Enzymes from thermophilic microorganisms usually show high thermostability, which is of great potential in industrial application; to understand the structural logic of these enzymes is helpful for the construction of robust biocatalysts. In this study, based on the crystal structure of an N-demethylase─TrSOX─with outstanding thermostability from Thermomicrobium roseum, substitutions were introduced on the aggregation interface and rigid spots to reduce the aggregation ratio and the rigidity. Four substitutions on the aggregation interface─V162S, M308S, F170S, and V306S─considerably reduced the thermostability and slightly enhanced the catalytic efficiency. In addition, the thermostable framework was considerably disrupted in several multiple P → G substitutions in several local motifs (P129G/P134G, P237G/P259G, and P259G/P276G). These structural fluctuations were in good accordance with whole-structure or partial root-mean-square deviation, radius of gyration H-bonds, and solvent-accessible surface area values in molecular dynamics simulation. Furthermore, these key spots were introduced into an unstable homolog from Bacillus sp., resulting in a dramatical increase in the half-life at 60 °C from <10 to 1440 min. These results could help understand the natural stable framework of thermophilic enzymes, which could be references for the construction of robust enzymes in industrial applications.
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Affiliation(s)
- Bingjie Li
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, P.R. China
| | - Yuqian Sun
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, P.R. China
| | - Xinyi Zhu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, P.R. China
| | - Siyu Qian
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, P.R. China
| | - Jiayang Pu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, P.R. China
| | - Yuwen Guo
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, P.R. China
| | - Haobo Wu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, P.R. China
| | - Liang Zhang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, P.R. China
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, National Engineering Research Center for Cereal Fermentation and Food Bio Manufacturing, Jiangnan University, Wuxi 214122, Jiangsu, P.R. China
| | - Yu Xin
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, P.R. China
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, National Engineering Research Center for Cereal Fermentation and Food Bio Manufacturing, Jiangnan University, Wuxi 214122, Jiangsu, P.R. China
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31
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Chi H, Zhu X, Shen J, Lu Z, Lu F, Lyu Y, Zhu P. Thermostability enhancement and insight of L-asparaginase from Mycobacterium sp. via consensus-guided engineering. Appl Microbiol Biotechnol 2023; 107:2321-2333. [PMID: 36843197 DOI: 10.1007/s00253-023-12443-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Revised: 02/06/2023] [Accepted: 02/13/2023] [Indexed: 02/28/2023]
Abstract
Acrylamide alleviation in food has represented as a critical issue due to its neurotoxic effect on human health. L-Asparaginase (ASNase, EC 3.5.1.1) is considered a potential additive for acrylamide alleviation in food. However, low thermal stability hinders the application of ASNase in thermal food processing. To obtain highly thermal stable ASNase for its industrial application, a consensus-guided approach combined with site-directed saturation mutation (SSM) was firstly reported to engineer the thermostability of Mycobacterium gordonae L-asparaginase (GmASNase). The key residues Gly97, Asn159, and Glu249 were identified for improving thermostability. The combinatorial triple mutant G97T/N159Y/E249Q (TYQ) displayed significantly superior thermostability with half-life values of 61.65 ± 8.69 min at 50 °C and 5.12 ± 1.66 min at 55 °C, whereas the wild-type was completely inactive at these conditions. Moreover, its Tm value increased by 8.59 °C from parent wild-type. Interestingly, TYQ still maintained excellent catalytic efficiency and specific activity. Further molecular dynamics and structure analysis revealed that the additional hydrogen bonds, increased hydrophobic interactions, and favorable electrostatic potential were essential for TYQ being in a more rigid state for thermostability enhancement. These results suggested that our strategy was an efficient engineering approach for improving fundamental properties of GmASNase and offering GmASNase as a potential agent for efficient acrylamide mitigation in food industry. KEY POINTS: • The thermostability of GmASNase was firstly improved by consensus-guided engineering. • The half-life and Tm value of triple mutant TYQ were significantly increased. • Insight on improved thermostability of TYQ was revealed by MD and structure analysis.
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Affiliation(s)
- Huibing Chi
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xiaoyu Zhu
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Juan Shen
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zhaoxin Lu
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Fengxia Lu
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yunbin Lyu
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Ping Zhu
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China.
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32
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Zhu W, Qin L, Xu Y, Lu H, Wu Q, Li W, Zhang C, Li X. Three Molecular Modification Strategies to Improve the Thermostability of Xylanase XynA from Streptomyces rameus L2001. Foods 2023; 12:foods12040879. [PMID: 36832954 PMCID: PMC9957083 DOI: 10.3390/foods12040879] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 02/07/2023] [Accepted: 02/13/2023] [Indexed: 02/22/2023] Open
Abstract
Glycoside hydrolase family 11 (GH11) xylanases are the preferred candidates for the production of functional oligosaccharides. However, the low thermostability of natural GH11 xylanases limits their industrial applications. In this study, we investigated the following three strategies to modify the thermostability of xylanase XynA from Streptomyces rameus L2001 mutation to reduce surface entropy, intramolecular disulfide bond construction, and molecular cyclization. Changes in the thermostability of XynA mutants were analyzed using molecular simulations. All mutants showed improved thermostability and catalytic efficiency compared with XynA, except for molecular cyclization. The residual activities of high-entropy amino acid-replacement mutants Q24A and K104A increased from 18.70% to more than 41.23% when kept at 65 °C for 30 min. The catalytic efficiencies of Q24A and K143A increased to 129.99 and 92.26 mL/s/mg, respectively, compared with XynA (62.97 mL/s/mg) when using beechwood xylan as the substrate. The mutant enzyme with disulfide bonds formed between Val3 and Thr30 increased the t1/260 °C by 13.33-fold and the catalytic efficiency by 1.80-fold compared with the wild-type XynA. The high thermostabilities and hydrolytic activities of XynA mutants will be useful for enzymatic production of functional xylo-oligosaccharides.
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Affiliation(s)
- Weijia Zhu
- School of Food and Health, Beijing Technology and Business University (BTBU), Beijing 100048, China
| | - Liqin Qin
- School of Food and Health, Beijing Technology and Business University (BTBU), Beijing 100048, China
| | - Youqiang Xu
- School of Food and Health, Beijing Technology and Business University (BTBU), Beijing 100048, China
| | - Hongyun Lu
- School of Food and Health, Beijing Technology and Business University (BTBU), Beijing 100048, China
| | - Qiuhua Wu
- School of Food and Health, Beijing Technology and Business University (BTBU), Beijing 100048, China
| | - Weiwei Li
- Key Laboratory of Brewing Microbiome and Enzymatic Molecular Engineering, China General Chamber of Commerce, Beijing 100048, China
- Key Laboratory of Brewing Molecular Engineering of China Light Industry, Beijing Technology and Business University, Beijing 100048, China
| | - Chengnan Zhang
- Key Laboratory of Brewing Microbiome and Enzymatic Molecular Engineering, China General Chamber of Commerce, Beijing 100048, China
- Key Laboratory of Brewing Molecular Engineering of China Light Industry, Beijing Technology and Business University, Beijing 100048, China
| | - Xiuting Li
- School of Food and Health, Beijing Technology and Business University (BTBU), Beijing 100048, China
- Key Laboratory of Brewing Microbiome and Enzymatic Molecular Engineering, China General Chamber of Commerce, Beijing 100048, China
- Key Laboratory of Brewing Molecular Engineering of China Light Industry, Beijing Technology and Business University, Beijing 100048, China
- Correspondence:
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Ali S, Khan SA, Hamayun M, Lee IJ. The Recent Advances in the Utility of Microbial Lipases: A Review. Microorganisms 2023; 11:microorganisms11020510. [PMID: 36838475 PMCID: PMC9959473 DOI: 10.3390/microorganisms11020510] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 02/06/2023] [Accepted: 02/06/2023] [Indexed: 02/19/2023] Open
Abstract
Lipases are versatile biocatalysts and are used in different bioconversion reactions. Microbial lipases are currently attracting a great amount of attention due to the rapid advancement of enzyme technology and its practical application in a variety of industrial processes. The current review provides updated information on the different sources of microbial lipases, such as fungi, bacteria, and yeast, their classical and modern purification techniques, including precipitation and chromatographic separation, the immunopurification technique, the reversed micellar system, aqueous two-phase system (ATPS), aqueous two-phase flotation (ATPF), and the use of microbial lipases in different industries, e.g., the food, textile, leather, cosmetics, paper, and detergent industries. Furthermore, the article provides a critical analysis of lipase-producing microbes, distinguished from the previously published reviews, and illustrates the use of lipases in biosensors, biodiesel production, and tea processing, and their role in bioremediation and racemization.
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Affiliation(s)
- Sajid Ali
- Department of Horticulture and Life Science, Yeungnam University, Gyeongsan 38541, Republic of Korea
| | - Sumera Afzal Khan
- Centre of Biotechnology and Microbiology, University of Peshawar, Peshawar 25120, Pakistan
| | - Muhammad Hamayun
- Department of Botany, Garden Campus, Abdul Wali Khan University Mardan, Mardan 23200, Pakistan
- Correspondence: (M.H.); (I.-J.L.)
| | - In-Jung Lee
- Department of Applied Biosciences, Kyungpook National University, Daegu 41566, Republic of Korea
- Correspondence: (M.H.); (I.-J.L.)
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34
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Alteration of Chain-Length Selectivity and Thermostability of Rhizopus oryzae Lipase via Virtual Saturation Mutagenesis Coupled with Disulfide Bond Design. Appl Environ Microbiol 2023; 89:e0187822. [PMID: 36602359 PMCID: PMC9888275 DOI: 10.1128/aem.01878-22] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Rhizopus oryzae lipase (ROL) is one of the most important enzymes used in the food, biofuel, and pharmaceutical industries. However, the highly demanding conditions of industrial processes can reduce its stability and activity. To seek a feasible method to improve both the catalytic activity and the thermostability of this lipase, first, the structure of ROL was divided into catalytic and noncatalytic regions by identifying critical amino acids in the crevice-like binding pocket. Second, a mutant screening library aimed at improvement of ROL catalytic performance by virtual saturation mutagenesis of residues in the catalytic region was constructed based on Rosetta's Cartesian_ddg protocol. A double mutant, E265V/S267W (with an E-to-V change at residue 265 and an S-to-W change at residue 267), with markedly improved catalytic activity toward diverse chain-length fatty acid esters was identified. Then, computational design of disulfide bonds was conducted for the noncatalytic amino acids of E265V/S267W, and two potential disulfide bonds, S61C-S115C and E190C-E238C, were identified as candidates. Experimental data validated that the variant E265V/S267W/S61C-S115C/E190C-E238C had superior stability, with an increase of 8.5°C in the melting temperature and a half-life of 31.7 min at 60°C, 4.2-fold longer than that of the wild-type enzyme. Moreover, the variant improved the lipase activity toward five 4-nitrophenyl esters by 1.5 to 3.8 times, exhibiting a potential to modify the catalytic efficiency. IMPORTANCE Rhizopus oryzae lipase (ROL) is very attractive in biotechnology and industry as a safe and environmentally friendly biocatalyst. Functional expression of ROL in Escherichia coli facilitates effective high-throughput screening for positive variants. This work highlights a method to improve both selectivity and thermostability based on a combination of virtual saturation mutagenesis in the substrate pocket and disulfide bond prediction in the noncatalytic region. Using the method, ROL thermostability and activity to diverse 4-nitrophenyl esters could be substantially improved. The strategy of rational introduction of multiple mutations in different functional domains of the enzyme is a great prospect in the modification of biocatalysts.
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35
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Genomic analysis of Paenibacillus sp. MDMC362 from the Merzouga desert leads to the identification of a potentially thermostable catalase. Antonie Van Leeuwenhoek 2023; 116:21-38. [PMID: 36383330 DOI: 10.1007/s10482-022-01793-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 11/01/2022] [Indexed: 11/17/2022]
Abstract
Microorganisms in hot deserts face heat and other environmental conditions, such as desiccation, UV radiation, or low nutrient availability. Therefore, this hostile environment harbour microorganisms with acquired characteristics related to survival in their habitat, which can be exploited in biotechnology. In this work, the genome of Paenibacillus sp. MDMC362 isolated from the Merzouga desert in Morocco was sequenced to understand its survival strategy's genetic basis; and to evaluate the thermostability of a catalase extracted from genomic annotation files using molecular dynamics. Paenibacillus sp. MDMC362 genome was rich in genetic elements involved in the fight against different stresses, notably temperature stress, UV radiations, osmotic stress, carbon starvation, and oxidative stress. Indeed, we could identify genes of the operons groES-groEL and hrcA-grpE-dnaK and those involved in the different stages of sporulation, which can help the bacteria to survive the high temperatures imposed by a desertic environment. We also observed the genetic components of the UvrABC system and additional mechanisms involved in DNA repair, which help overcome UV radiation damage. Other genes have been identified in the genome, like those coding for ectoine and proline, that aids fight osmotic stress and desiccation. Catalase thermostability investigation using molecular dynamics showed that the protein reached stability and conserved its compactness at temperatures up to 373.15 K. These results suggest a potential thermostability of the enzyme. Since the studied protein is a core protein, thermostability could be conserved among Paenibacillus sp. MDMC362 closely related strains; however, bacteria from harsh environments may have a slight advantage regarding protein stability.
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36
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Chi H, Wang Y, Xia B, Zhou Y, Lu Z, Lu F, Zhu P. Enhanced Thermostability and Molecular Insights for l-Asparaginase from Bacillus licheniformis via Structure- and Computation-Based Rational Design. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:14499-14509. [PMID: 36341695 DOI: 10.1021/acs.jafc.2c05712] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
l-Asparaginase has gained much attention for effectively treating acute lymphoblastic leukemia (ALL) and mitigating carcinogenic acrylamide in fried foods. Due to high-dose dependence for clinical treatment and low mitigation efficiency for thermal food processes caused by poor thermal stability, a method to achieve thermostable l-asparaginase has become a critical bottleneck. In this study, a rational design including free energy combined with structural and conservative analyses was applied to engineer the thermostability of l-asparaginase from Bacillus licheniformis (BlAsnase). Two enhanced thermostability mutants D172W and E207A were screened out by site-directed saturation mutagenesis. The double mutant D172W/E207A exhibited highly remarkable thermostability with a 65.8-fold longer half-life at 55 °C and 5 °C higher optimum reaction temperature and melting temperature (Tm) than those of wild-type BlAsnase. Further, secondary structure, sequence, molecular dynamics (MD), and 3D-structure analysis revealed that the excellent thermostability of the mutant D172W/E207A was on account of increased hydrophobicity and decreased flexibility, highly rigid structure, hydrophobic interactions, and favorable electrostatic potential. As the first report of rationally designing l-asparaginase with improved thermostability from B. licheniformis, this study offers a facile and efficient process to improve the thermostability of l-asparaginase for industrial applications.
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Affiliation(s)
- Huibing Chi
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing210095, China
| | - Yilian Wang
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing210095, China
| | - Bingjie Xia
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing210095, China
| | - Yawen Zhou
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing210095, China
| | - Zhaoxin Lu
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing210095, China
| | - Fengxia Lu
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing210095, China
| | - Ping Zhu
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing210095, China
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37
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Fang Y, Liu F, Shi Y, Yang T, Liang C, Xin Y, Gu Z, Shi G, Zhang L. Hotspots and Mechanisms of Action of the Thermostable Framework of a Microbial Thermolipase. ACS Synth Biol 2022; 11:3460-3470. [PMID: 36173803 DOI: 10.1021/acssynbio.2c00360] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The lipase TrLipB from Thermomicrobium roseum is highly thermostable. However, its thermostable skeleton and mechanism of action should be investigated for industrial applications. Toward this, TrLipB was crystallized using the hanging-drop vapor diffusion method and subjected to X-ray diffraction at 2.0 Å resolution in this study. The rigid sites, such as the prolines on the relatively flexible loops on the enzyme surface, were scanned. Soft substitutions of these sites were designed using both molecular dynamics (MD) simulation and site-directed mutagenesis. The thermostability of several substitutions decreased markedly, while the catalytic efficiencies of the P9G, P127G, P194G, and P300G mutants reduced substantially; additionally, the thermostable framework of the double mutant, P194G/P300G, was considerably perturbed. However, the substitutions on the lid of the enzyme, including P49G and P48G, promoted the catalytic efficiency to approximately 150% and slightly enhanced the thermostability below 80 °C. In MD simulations, the P100G, P194G, P100G/P194G, P194G/P300G, and P100G/P194G/P300G mutants showed high B-factors and RMSD values, whereas the secondary structures, radius of gyration, H-bonds, and solvent accessible surface areas of these mutants were markedly affected. Our observations will assist in understanding the natural framework of a stable lipase, which might contribute to its industrial applications.
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Affiliation(s)
- Yakun Fang
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi, Jiangsu 214122, P.R. China.,Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, Wuxi, Jiangsu 214122, P.R. China
| | - Fan Liu
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi, Jiangsu 214122, P.R. China.,Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, Wuxi, Jiangsu 214122, P.R. China
| | - Yi Shi
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi, Jiangsu 214122, P.R. China.,Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, Wuxi, Jiangsu 214122, P.R. China
| | - Ting Yang
- Wuxi Food Safety Inspection and Test Center, Technology Innovation Center of Special Food for State Market Regulation, Wuxi, Jiangsu 214122, P.R. China
| | - Chaojuan Liang
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi, Jiangsu 214122, P.R. China.,Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, Wuxi, Jiangsu 214122, P.R. China
| | - Yu Xin
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi, Jiangsu 214122, P.R. China.,Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, Wuxi, Jiangsu 214122, P.R. China
| | - Zhenghua Gu
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi, Jiangsu 214122, P.R. China.,Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, Wuxi, Jiangsu 214122, P.R. China
| | - Guiyang Shi
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi, Jiangsu 214122, P.R. China.,Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, Wuxi, Jiangsu 214122, P.R. China
| | - Liang Zhang
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi, Jiangsu 214122, P.R. China.,Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, Wuxi, Jiangsu 214122, P.R. China
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38
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Improving Both the Thermostability and Catalytic Efficiency of Phospholipase D from Moritella sp. JT01 through Disulfide Bond Engineering Strategy. Int J Mol Sci 2022; 23:ijms231911319. [PMID: 36232620 PMCID: PMC9570233 DOI: 10.3390/ijms231911319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Revised: 09/11/2022] [Accepted: 09/21/2022] [Indexed: 11/21/2022] Open
Abstract
Mining of Phospholipase D (PLD) with high activity and stability has attracted strong interest for investigation. A novel PLD from marine Moritella sp. JT01 (MsPLD) was biochemically and structurally characterized in our previous study; however, the short half-life time (t1/2) under its optimum reaction temperature seriously hampered its further applications. Herein, the disulfide bond engineering strategy was applied to improve its thermostability. Compared with wild-type MsPLD, mutant S148C-T206C/D225C-A328C with the addition of two disulfide bonds exhibited a 3.1-fold t1/2 at 35 °C and a 5.7 °C increase in melting temperature (Tm). Unexpectedly, its specific activity and catalytic efficiency (kcat/Km) also increased by 22.7% and 36.5%, respectively. The enhanced activity might be attributed to an increase in the activation entropy by displacing more water molecules by the transition state. The results of molecular dynamics simulations (MD) revealed that the introduction of double disulfide bonds rigidified the global structure of the mutant, which might cause the enhanced thermostability. Finally, the synthesis capacity of the mutant to synthesize phosphatidic acid (PA) was evaluated. The conversion rate of PA reached about 80% after 6 h reaction with wild-type MsPLD but reached 78% after 2 h with mutant S148C-T206C/D225C-A328C, which significantly reduced the time needed for the reaction to reach equilibrium. The present results pave the way for further application of MsPLD in the food and pharmaceutical industries.
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39
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Cui X, Yuan X, Li S, Hu X, Zhao J, Zhang G. Simultaneously improving the specific activity and thermostability of α-amylase BLA by rational design. Bioprocess Biosyst Eng 2022; 45:1839-1848. [PMID: 36136173 DOI: 10.1007/s00449-022-02790-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 09/10/2022] [Indexed: 11/02/2022]
Abstract
Higher activity and alkaline α-amylases are desired for textile desizing and detergent additive. Here, rational design was used to improve the specific activity and thermostability of the α-amylase BLA from Bacillus licheniformis. Seventeen mutants of BLA were designed based on sequence consensus analysis and folding free energy calculation, and characterized by measuring their respective activity and thermostability at pH 8.5. Among them, mutant Q360C exhibited nearly threefold improved activity than that of wild-type and retained a higher residual activity (75% vs 59% for wild-type) after preincubation at 70 ℃ for 30 min. The modeled structures and molecular dynamics simulations analysis demonstrated that the enhanced hydrophobic interaction near residue 360 and reduced disturbance to the conformation of catalytic residues are the possible reasons for the improved thermostability and activity of Q360C. The results suggest that 360th of BLA may act as a hotspot for engineering other enzymes in the GH13 superfamily.
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Affiliation(s)
- Xin Cui
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China.,State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062, Hubei, China
| | - Xin Yuan
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062, Hubei, China
| | - Shunyi Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062, Hubei, China
| | - Xinlin Hu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062, Hubei, China
| | - Jing Zhao
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062, Hubei, China.
| | - Guimin Zhang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China. .,State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062, Hubei, China.
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40
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Pak MA, Ivankov DN. Best templates outperform homology models in predicting the impact of mutations on protein stability. Bioinformatics 2022; 38:4312-4320. [PMID: 35894930 DOI: 10.1093/bioinformatics/btac515] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 05/31/2022] [Indexed: 12/24/2022] Open
Abstract
MOTIVATION Prediction of protein stability change upon mutation (ΔΔG) is crucial for facilitating protein engineering and understanding of protein folding principles. Robust prediction of protein folding free energy change requires the knowledge of protein three-dimensional (3D) structure. In case, protein 3D structure is not available, one can predict the structure from protein sequence; however, the perspectives of ΔΔG predictions for predicted protein structures are unknown. The accuracy of using 3D structures of the best templates for the ΔΔG prediction is also unclear. RESULTS To investigate these questions, we used a representative set of seven diverse and accurate publicly available tools (FoldX, Eris, Rosetta, DDGun, ACDC-NN, ThermoNet and DynaMut) for stability change prediction combined with AlphaFold or I-Tasser for protein 3D structure prediction. We found that best templates perform consistently better than (or similar to) homology models for all ΔΔG predictors. Our findings imply using the best template structure for the prediction of protein stability change upon mutation if the protein 3D structure is not available. AVAILABILITY AND IMPLEMENTATION The data are available at https://github.com/ivankovlab/template-vs-model. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Marina A Pak
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow 121205, Russia
| | - Dmitry N Ivankov
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow 121205, Russia
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41
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Zhu E, Xiang X, Wan S, Miao H, Han N, Huang Z. Discovery of the Key Mutation Site Influencing the Thermostability of Thermomyces lanuginosus Lipase by Rosetta Design Programs. Int J Mol Sci 2022; 23:ijms23168963. [PMID: 36012226 PMCID: PMC9408933 DOI: 10.3390/ijms23168963] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 08/04/2022] [Accepted: 08/10/2022] [Indexed: 11/16/2022] Open
Abstract
Lipases are remarkable biocatalysts and are broadly applied in many industry fields because of their versatile catalytic capabilities. Considering the harsh biotechnological treatment of industrial processes, the activities of lipase products are required to be maintained under extreme conditions. In our current study, Gibbs free energy calculations were performed to predict potent thermostable Thermomyces lanuginosus lipase (TLL) variants by Rosetta design programs. The calculating results suggest that engineering on R209 may greatly influence TLL thermostability. Accordingly, ten TLL mutants substituted R209 were generated and verified. We demonstrate that three out of ten mutants (R209H, R209M, and R209I) exhibit increased optimum reaction temperatures, melting temperatures, and thermal tolerances. Based on molecular dynamics simulation analysis, we show that the stable hydrogen bonding interaction between H198 and N247 stabilizes the local configuration of the 250-loop in the three R209 mutants, which may further contribute to higher rigidity and improved enzymatic thermostability. Our study provides novel insights into a single residue, R209, and the 250-loop, which were reported for the first time in modulating the thermostability of TLL. Additionally, the resultant R209 variants generated in this study might be promising candidates for future-industrial applications.
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Affiliation(s)
- Enheng Zhu
- School of Life Sciences, Yunnan Normal University, Kunming 650500, China
| | - Xia Xiang
- School of Life Sciences, Yunnan Normal University, Kunming 650500, China
| | - Sidi Wan
- School of Life Sciences, Yunnan Normal University, Kunming 650500, China
| | - Huabiao Miao
- School of Life Sciences, Yunnan Normal University, Kunming 650500, China
| | - Nanyu Han
- School of Life Sciences, Yunnan Normal University, Kunming 650500, China
- Engineering Research Center of Sustainable and Utilization of Biomass Energy, Ministry of Education, Yunnan Normal University, Kunming 650500, China
- Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Yunnan Normal University, Kunming 650500, China
- Key Laboratory of Enzyme Engineering, Yunnan Normal University, Kunming 650500, China
- Correspondence: (N.H.); (Z.H.)
| | - Zunxi Huang
- School of Life Sciences, Yunnan Normal University, Kunming 650500, China
- Engineering Research Center of Sustainable and Utilization of Biomass Energy, Ministry of Education, Yunnan Normal University, Kunming 650500, China
- Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Yunnan Normal University, Kunming 650500, China
- Key Laboratory of Enzyme Engineering, Yunnan Normal University, Kunming 650500, China
- Correspondence: (N.H.); (Z.H.)
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42
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Hu M, Liu F, Wang Z, Shao M, Xu M, Yang T, Zhang R, Zhang X, Rao Z. Sustainable isomaltulose production in Corynebacterium glutamicum by engineering the thermostability of sucrose isomerase coupled with one-step simplified cell immobilization. Front Microbiol 2022; 13:979079. [PMID: 36033839 PMCID: PMC9399683 DOI: 10.3389/fmicb.2022.979079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 07/20/2022] [Indexed: 11/26/2022] Open
Abstract
Sucrose isomerase (SI), catalyzing sucrose to isomaltulose, has been widely used in isomaltulose production, but its poor thermostability is still resisted in sustainable batches production. Here, protein engineering and one-step immobilized cell strategy were simultaneously coupled to maintain steady state for long-term operational stabilities. First, rational design of Pantoea dispersa SI (PdSI) for improving its thermostability by predicting and substituting the unstable amino acid residues was investigated using computational analysis. After screening mutagenesis library, two single mutants (PdSIV280L and PdSIS499F) displayed favorable characteristics on thermostability, and further study found that the double mutant PdSIV280L/S499F could stabilize PdSIWT better. Compared with PdSIWT, PdSIV280L/S499F displayed a 3.2°C-higher T m , and showed a ninefold prolonged half-life at 45°C. Subsequently, a one-step simplified immobilization method was developed for encapsulation of PdSIV280L/S499F in food-grade Corynebacterium glutamicum cells to further enhance the recyclability of isomaltulose production. Recombinant cells expressing combinatorial mutant (RCSI2) were successfully immobilized in 2.5% sodium alginate without prior permeabilization. The immobilized RCSI2 showed that the maximum yield of isomaltulose by batch conversion reached to 453.0 g/L isomaltulose with a productivity of 41.2 g/l/h from 500.0 g/L sucrose solution, and the conversion rate remained 83.2% after 26 repeated batches.
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Affiliation(s)
| | | | | | | | | | | | | | - Xian Zhang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Zhiming Rao
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
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43
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Tong L, Zheng J, Wang X, Wang X, Huang H, Yang H, Tu T, Wang Y, Bai Y, Yao B, Luo H, Qin X. Improvement of thermostability and catalytic efficiency of glucoamylase from Talaromyces leycettanus JCM12802 via site-directed mutagenesis to enhance industrial saccharification applications. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:202. [PMID: 34656167 PMCID: PMC8520190 DOI: 10.1186/s13068-021-02052-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 10/02/2021] [Indexed: 05/25/2023]
Abstract
BACKGROUND Glucoamylase is an important industrial enzyme in the saccharification of starch into glucose. However, its poor thermostability and low catalytic efficiency limit its industrial saccharification applications. Therefore, improving these properties of glucoamylase is of great significance for saccharification in the starch industry. RESULTS In this study, a novel glucoamylase-encoding gene TlGa15B from the thermophilic fungus Talaromyces leycettanus JCM12802 was cloned and expressed in Pichia pastoris. The optimal temperature and pH of recombinant TlGa15B were 65 ℃ and 4.5, respectively. TlGa15B exhibited excellent thermostability at 60 ℃. To further improve thermostability without losing catalytic efficiency, TlGa15B-GA1 and TlGa15B-GA2 were designed by introducing disulfide bonds and optimizing residual charge-charge interactions in a region distant from the catalytic center. Compared with TlGa15B, mutants showed improved optimal temperature, melting temperature, specific activity, and catalytic efficiency. The mechanism underlying these improvements was elucidated through molecular dynamics simulation and dynamics cross-correlation matrices analysis. Besides, the performance of TlGa15B-GA2 was the same as that of the commercial glucoamylase during saccharification. CONCLUSIONS We provide an effective strategy to simultaneously improve both thermostability and catalytic efficiency of glucoamylase. The excellent thermostability and high catalytic efficiency of TlGa15B-GA2 make it a good candidate for industrial saccharification applications.
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Affiliation(s)
- Lige Tong
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Jie Zheng
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Xiao Wang
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Xiaolu Wang
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Huoqing Huang
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Haomeng Yang
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Tao Tu
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Yuan Wang
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Yingguo Bai
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Bin Yao
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Huiying Luo
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Xing Qin
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
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Enhanced Thermostability of Pseudomonas nitroreducens Isoeugenol Monooxygenase by the Combinatorial Strategy of Surface Residue Replacement and Consensus Mutagenesis. Catalysts 2021. [DOI: 10.3390/catal11101199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Vanillin has many applications in industries. Isoeugenol monooxygenase (IEM) can catalyze the oxidation of isoeugenol to vanillin in the presence of oxygen under mild conditions. However, the low thermal stability of IEM limits its practical application in the biosynthesis of natural vanillin. Herein, two rational strategies were combined to improve the thermostability of IEM from Pseudomonas nitroreducens Jin1. Two variants (K83R and K95R) with better thermostability and one mutant (G398A) with higher activity were identified from twenty candidates based on the Surface Residue Replacement method. According to the Consensus Mutagenesis method, one mutant (I352R) with better thermostability and another mutant (L273F) with higher activity were also identified from nine candidates. After combinatorial mutation, a triple mutant K83R/K95R/L273F with the best thermostability and catalytic efficiency was generated. Compared with the wild-type IEM, the thermal inactivation half-lives (t1/2) of K83R/K95R/L273F at 25 °C, 30 °C, and 35 °C increased 2.9-fold, 11.9-fold, and 24.7-fold, respectively. Simultaneously, it also exhibited a 4.8-fold increase in kcat, leading to a 1.2-fold increase in catalytic efficiency (kcat/Km). When the whole cell of K83R/K95R/L273F was applied to the biotransformation of isoeugenol on preparative scale, the vanillin concentration reached 240.1 mM with space-time yield of 109.6 g/L/d, and vanillin was achieved in 77.6% isolated yield and >99% purity.
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45
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Recent Advances in Feedstock and Lipase Research and Development towards Commercialization of Enzymatic Biodiesel. Processes (Basel) 2021. [DOI: 10.3390/pr9101743] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Biodiesel is a biodegradable, renewable, and carbon-neutral alternative to petroleum diesel that can contribute to the global effort of minimizing the use of fossil fuels and meeting the ever-growing energy demands and stringent environmental constraints. The aim of this work was to (1) review the recent progress in feedstock development, including first, second, third, and fourth-generation feedstocks for biodiesel production; (2) discuss recent progress in lipase research and development as one of the key factors for establishing a cost-competitive biodiesel process in terms of enzyme sources, properties, immobilization, and transesterification efficiency; and (3) provide an update of the current challenges and opportunities for biodiesel commercialization from techno-economic and social perspectives. Related biodiesel producers, markets, challenges, and opportunities for biodiesel commercialization, including environmental considerations, are critically discussed.
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Development of thermostable sucrose phosphorylase by semi-rational design for efficient biosynthesis of alpha-D-glucosylglycerol. Appl Microbiol Biotechnol 2021; 105:7309-7319. [PMID: 34542685 PMCID: PMC8494705 DOI: 10.1007/s00253-021-11551-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Revised: 08/03/2021] [Accepted: 08/24/2021] [Indexed: 12/03/2022]
Abstract
Abstract Sucrose phosphorylase (SPase) can specifically catalyze transglycosylation reactions and can be used to enzymatically synthesize α-D-glycosides. However, the low thermostability of SPase has been a bottleneck for its industrial application. In this study, a SPase gene from Leuconostoc mesenteroides ATCC 12,291 (LmSPase) was synthesized with optimized codons and overexpressed successfully in Escherichia coli. A semi-rational design strategy that combined the FireProt (a web server designing thermostable proteins), structure–function analysis, and molecular dynamic simulations was used to improve the thermostability of LmSPase. Finally, one single-point mutation T219L and a combination mutation I31F/T219L/T263L/S360A (Mut4) with improved thermostability were obtained. The half-lives at 50 °C of T219L and Mut4 both increased approximately two-fold compared to that of wild-type LmSPase (WT). Furthermore, the two variants T219L and Mut4 were used to produce α-D-glucosylglycerol (αGG) from sucrose and glycerol by incubating with 40 U/mL crude extracts at 37 °C for 60 h and achieved the product concentration of 193.2 ± 12.9 g/L and 195.8 ± 13.1 g/L, respectively, which were approximately 1.3-fold higher than that of WT (150.4 ± 10.0 g/L). This study provides an effective strategy for improving the thermostability of an industrial enzyme. Key points • Predicted potential hotspot residues directing the thermostability of LmSPase by semi-rational design • Screened two positive variants with higher thermostability and higher activity • Synthesized α-D-glucosylglycerol to a high level by two screened positive variants Supplementary Information The online version contains supplementary material available at 10.1007/s00253-021-11551-0.
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47
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Yao W, Liu K, Liu H, Jiang Y, Wang R, Wang W, Wang T. A Valuable Product of Microbial Cell Factories: Microbial Lipase. Front Microbiol 2021; 12:743377. [PMID: 34616387 PMCID: PMC8489457 DOI: 10.3389/fmicb.2021.743377] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Accepted: 08/26/2021] [Indexed: 11/13/2022] Open
Abstract
As a powerful factory, microbial cells produce a variety of enzymes, such as lipase. Lipase has a wide range of actions and participates in multiple reactions, and they can catalyze the hydrolysis of triacylglycerol into its component free fatty acids and glycerol backbone. Lipase exists widely in nature, most prominently in plants, animals and microorganisms, among which microorganisms are the most important source of lipase. Microbial lipases have been adapted for numerous industrial applications due to their substrate specificity, heterogeneous patterns of expression and versatility (i.e., capacity to catalyze reactions at the extremes of pH and temperature as well as in the presence of metal ions and organic solvents). Now they have been introduced into applications involving the production and processing of food, pharmaceutics, paper making, detergents, biodiesel fuels, and so on. In this mini-review, we will focus on the most up-to-date research on microbial lipases and their commercial and industrial applications. We will also discuss and predict future applications of these important technologies.
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Affiliation(s)
- Wentao Yao
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Qilu University of Technology (Shandong Academy of Sciences), Jinan, China
- Key Laboratory of Shandong Microbial Engineering, College of Bioengineering, QiLu University of Technology (Shandong Academy of Sciences), Jinan, China
| | - Kaiquan Liu
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Qilu University of Technology (Shandong Academy of Sciences), Jinan, China
- Key Laboratory of Shandong Microbial Engineering, College of Bioengineering, QiLu University of Technology (Shandong Academy of Sciences), Jinan, China
| | - Hongling Liu
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Qilu University of Technology (Shandong Academy of Sciences), Jinan, China
- Key Laboratory of Shandong Microbial Engineering, College of Bioengineering, QiLu University of Technology (Shandong Academy of Sciences), Jinan, China
| | - Yi Jiang
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Qilu University of Technology (Shandong Academy of Sciences), Jinan, China
- Key Laboratory of Shandong Microbial Engineering, College of Bioengineering, QiLu University of Technology (Shandong Academy of Sciences), Jinan, China
| | - Ruiming Wang
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Qilu University of Technology (Shandong Academy of Sciences), Jinan, China
- Key Laboratory of Shandong Microbial Engineering, College of Bioengineering, QiLu University of Technology (Shandong Academy of Sciences), Jinan, China
| | - Wei Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Tengfei Wang
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Qilu University of Technology (Shandong Academy of Sciences), Jinan, China
- Key Laboratory of Shandong Microbial Engineering, College of Bioengineering, QiLu University of Technology (Shandong Academy of Sciences), Jinan, China
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Thermostable lipases and their dynamics of improved enzymatic properties. Appl Microbiol Biotechnol 2021; 105:7069-7094. [PMID: 34487207 DOI: 10.1007/s00253-021-11520-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 07/29/2021] [Accepted: 07/31/2021] [Indexed: 10/20/2022]
Abstract
Thermal stability is one of the most desirable characteristics in the search for novel lipases. The search for thermophilic microorganisms for synthesising functional enzyme biocatalysts with the ability to withstand high temperature, and capacity to maintain their native state in extreme conditions opens up new opportunities for their biotechnological applications. Thermophilic organisms are one of the most favoured organisms, whose distinctive characteristics are extremely related to their cellular constituent particularly biologically active proteins. Modifications on the enzyme structure are critical in optimizing the stability of enzyme to thermophilic conditions. Thermostable lipases are one of the most favourable enzymes used in food industries, pharmaceutical field, and actively been studied as potential biocatalyst in biodiesel production and other biotechnology application. Particularly, there is a trade-off between the use of enzymes in high concentration of organic solvents and product generation. Enhancement of the enzyme stability needs to be achieved for them to maintain their enzymatic activity regardless the environment. Various approaches on protein modification applied since decades ago conveyed a better understanding on how to improve the enzymatic properties in thermophilic bacteria. In fact, preliminary approach using advanced computational analysis is practically conducted before any modification is being performed experimentally. Apart from that, isolation of novel extremozymes from various microorganisms are offering great frontier in explaining the crucial native interaction within the molecules which could help in protein engineering. In this review, the thermostability prospect of lipases and the utility of protein engineering insights into achieving functional industrial usefulness at their high temperature habitat are highlighted. Similarly, the underlying thermodynamic and structural basis that defines the forces that stabilize these thermostable lipase is discussed. KEY POINTS: • The dynamics of lipases contributes to their non-covalent interactions and structural stability. • Thermostability can be enhanced by well-established genetic tools for improved kinetic efficiency. • Molecular dynamics greatly provides structure-function insights on thermodynamics of lipase.
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Wu H, Chen Q, Zhang W, Mu W. Overview of strategies for developing high thermostability industrial enzymes: Discovery, mechanism, modification and challenges. Crit Rev Food Sci Nutr 2021; 63:2057-2073. [PMID: 34445912 DOI: 10.1080/10408398.2021.1970508] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Biocatalysts such as enzymes are environmentally friendly and have substrate specificity, which are preferred in the production of various industrial products. However, the strict reaction conditions in industry including high temperature, organic solvents, strong acids and bases and other harsh environments often destabilize enzymes, and thus substantially compromise their catalytic functions, and greatly restrict their applications in food, pharmaceutical, textile, bio-refining and feed industries. Therefore, developing industrial enzymes with high thermostability becomes very important in industry as thermozymes have more advantages under high temperature. Discovering new thermostable enzymes using genome sequencing, metagenomics and sample isolation from extreme environments, or performing molecular modification of the existing enzymes with poor thermostability using emerging protein engineering technology have become an effective means of obtaining thermozymes. Based on the thermozymes as biocatalytic chips in industry, this review systematically analyzes the ways to discover thermostable enzymes from extreme environment, clarifies various interaction forces that will affect thermal stability of enzymes, and proposes different strategies to improve enzymes' thermostability. Furthermore, latest development in the thermal stability modification of industrial enzymes through rational design strategies is comprehensively introduced from structure-activity relationship point of view. Challenges and future research perspectives are put forward as well.
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Affiliation(s)
- Hao Wu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
| | - Qiuming Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
| | - Wenli Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
| | - Wanmeng Mu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, Jiangsu, China
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50
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Zhao P, Ren SM, Liu F, Zheng YC, Xu N, Pan J, Yu HL, Xu JH. Protein engineering of thioether monooxygenase to improve its thermostability for enzymatic synthesis of chiral sulfoxide. MOLECULAR CATALYSIS 2021. [DOI: 10.1016/j.mcat.2021.111625] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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