1
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Li Y, Liu M, Yang C, Fu H, Wang J. Engineering microbial metabolic homeostasis for chemicals production. Crit Rev Biotechnol 2024:1-20. [PMID: 39004513 DOI: 10.1080/07388551.2024.2371465] [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: 02/06/2024] [Accepted: 06/03/2024] [Indexed: 07/16/2024]
Abstract
Microbial-based bio-refining promotes the development of a biotechnology revolution to encounter and tackle the enormous challenges in petroleum-based chemical production by biomanufacturing, biocomputing, and biosensing. Nevertheless, microbial metabolic homeostasis is often incompatible with the efficient synthesis of bioproducts mainly due to: inefficient metabolic flow, robust central metabolism, sophisticated metabolic network, and inevitable environmental perturbation. Therefore, this review systematically summarizes how to optimize microbial metabolic homeostasis by strengthening metabolic flux for improving biotransformation turnover, redirecting metabolic direction for rewiring bypass pathway, and reprogramming metabolic network for boosting substrate utilization. Future directions are also proposed for providing constructive guidance on the development of industrial biotechnology.
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Affiliation(s)
- Yang Li
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Mingxiong Liu
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Changyang Yang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Hongxin Fu
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, South China University of Technology, Guangzhou, China
| | - Jufang Wang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, South China University of Technology, Guangzhou, China
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2
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Guo L, Ouyang X, Wang W, Qiu X, Zhao YL, Xu P, Tang H. Fine-tuning an aromatic ring-hydroxylating oxygenase to degrade high molecular weight polycyclic aromatic hydrocarbon. J Biol Chem 2024; 300:107343. [PMID: 38705395 PMCID: PMC11176777 DOI: 10.1016/j.jbc.2024.107343] [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: 02/28/2024] [Revised: 04/25/2024] [Accepted: 04/29/2024] [Indexed: 05/07/2024] Open
Abstract
Rieske nonheme iron aromatic ring-hydroxylating oxygenases (RHOs) play pivotal roles in determining the substrate preferences of polycyclic aromatic hydrocarbon (PAH) degraders. However, their potential to degrade high molecular weight PAHs (HMW-PAHs) has been relatively unexplored. NarA2B2 is an RHO derived from a thermophilic Hydrogenibacillus sp. strain N12. In this study, we have identified four "hotspot" residues (V236, Y300, W316, and L375) that may hinder the catalytic capacity of NarA2B2 when it comes to HMW-PAHs. By employing structure-guided rational enzyme engineering, we successfully modified NarA2B2, resulting in NarA2B2 variants capable of catalyzing the degradation of six different types of HMW-PAHs, including pyrene, fluoranthene, chrysene, benzo[a]anthracene, benzo[b]fluoranthene, and benzo[a]pyrene. Three representative variants, NarA2B2W316I, NarA2B2Y300F-W316I, and NarA2B2V236A-W316I-L375F, not only maintain their abilities to degrade low-molecular-weight PAHs (LMW-PAHs) but also exhibited 2 to 4 times higher degradation efficiency for HMW-PAHs in comparison to another isozyme, NarAaAb. Computational analysis of the NarA2B2 variants predicts that these modifications alter the size and hydrophobicity of the active site pocket making it more suitable for HMW-PAHs. These findings provide a comprehensive understanding of the relationship between three-dimensional structure and functionality, thereby opening up possibilities for designing improved RHOs that can be more effectively used in the bioremediation of PAHs.
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Affiliation(s)
- Lihua Guo
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Xingyu Ouyang
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Weiwei Wang
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Xiaoyu Qiu
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Yi-Lei Zhao
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Ping Xu
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Hongzhi Tang
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, People's Republic of China.
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3
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Ren Y, Cheng L, Cheng Z, Liu Y, Li M, Yuan T, Shen Z. Molecular insight into the enhanced performance of CALB toward PBDF degradation. Int J Biol Macromol 2024; 262:130181. [PMID: 38360240 DOI: 10.1016/j.ijbiomac.2024.130181] [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: 09/03/2023] [Revised: 02/11/2024] [Accepted: 02/12/2024] [Indexed: 02/17/2024]
Abstract
Poly(butylene diglycolate-co-furandicarboxylate) (PBDF) is a newly developed biodegradable copolyester. Candida antarctica lipase B (CALB) has been identified as an effective catalyst for PBDF degradation. The mechanism is elucidated using a combination of molecular dynamics simulations and quantum chemistry approaches. The findings unveil a four-step catalytic reaction pathway. Furthermore, bond analysis, charge and interaction analysis are conducted to gain a more comprehensive understanding of the PBDF degradation process. Additionally, through the introduction of single-point mutations to crucial residues in CALB's active sites, two mutants, T138I and D134I, are discovered to exhibit improved catalytic efficiency. These significant findings contribute to the advancement of our comprehension concerning the molecular mechanism of underlying copolyesters degradation, while also presenting a novel approach for expediting the degradation rate by the CALB enzyme modification.
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Affiliation(s)
- Yuanyang Ren
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Luwei Cheng
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Zhiwen Cheng
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China; State Environmental Protection Key Laboratory of Environmental Health Impact Assessment of Emerging Contaminants, Shanghai 200240, China
| | - Yawei Liu
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Mingyue Li
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Tao Yuan
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China; State Environmental Protection Key Laboratory of Environmental Health Impact Assessment of Emerging Contaminants, Shanghai 200240, China.
| | - Zhemin Shen
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China; State Environmental Protection Key Laboratory of Environmental Health Impact Assessment of Emerging Contaminants, Shanghai 200240, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, China.
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4
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Ge F, Chen G, Qian M, Xu C, Liu J, Cao J, Li X, Hu D, Xu Y, Xin Y, Wang D, Zhou J, Shi H, Tan Z. Artificial Intelligence Aided Lipase Production and Engineering for Enzymatic Performance Improvement. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:14911-14930. [PMID: 37800676 DOI: 10.1021/acs.jafc.3c05029] [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: 10/07/2023]
Abstract
With the development of artificial intelligence (AI), tailoring methods for enzyme engineering have been widely expanded. Additional protocols based on optimized network models have been used to predict and optimize lipase production as well as properties, namely, catalytic activity, stability, and substrate specificity. Here, different network models and algorithms for the prediction and reforming of lipase, focusing on its modification methods and cases based on AI, are reviewed in terms of both their advantages and disadvantages. Different neural networks coupled with various algorithms are usually applied to predict the maximum yield of lipase by optimizing the external cultivations for lipase production, while one part is used to predict the molecule variations affecting the properties of lipase. However, few studies have directly utilized AI to engineer lipase by affecting the structure of the enzyme, and a set of research gaps needs to be explored. Additionally, future perspectives of AI application in enzymes, including lipase engineering, are deduced to help the redesign of enzymes and the reform of new functional biocatalysts. This review provides a new horizon for developing effective and innovative AI tools for lipase production and engineering and facilitating lipase applications in the food industry and biomass conversion.
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Affiliation(s)
- Feiyin Ge
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huai'an 223003, People's Republic of China
| | - Gang Chen
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huai'an 223003, People's Republic of China
| | - Minjing Qian
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huai'an 223003, People's Republic of China
| | - Cheng Xu
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huai'an 223003, People's Republic of China
| | - Jiao Liu
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huai'an 223003, People's Republic of China
| | - Jiaqi Cao
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huai'an 223003, People's Republic of China
| | - Xinchao Li
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huai'an 223003, People's Republic of China
| | - Die Hu
- School of Pharmacy & School of Biological and Food Engineering, Changzhou University, Changzhou 213164, People's Republic of China
| | - Yangsen Xu
- Dongtai Hanfangyuan Biotechnology Co. Ltd., Yancheng 224241, People's Republic of China
| | - Ya Xin
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huai'an 223003, People's Republic of China
| | - Dianlong Wang
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huai'an 223003, People's Republic of China
| | - Jia Zhou
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huai'an 223003, People's Republic of China
| | - Hao Shi
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huai'an 223003, People's Republic of China
| | - Zhongbiao Tan
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huai'an 223003, People's Republic of China
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5
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Zhang Q, Jin Y, Yang K, Hu S, Lv C, Huang J, Mei J, Zhao W, Mei L. Modification of the 4-Hydroxyphenylacetate-3-hydroxylase Substrate Pocket to Increase Activity towards Resveratrol. Molecules 2023; 28:5602. [PMID: 37513473 PMCID: PMC10384689 DOI: 10.3390/molecules28145602] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Revised: 07/16/2023] [Accepted: 07/20/2023] [Indexed: 07/30/2023] Open
Abstract
4-Hydroxyphenylacetate-3-hydroxylase (4HPA3H; EC 1.14.14.9) is a heterodimeric flavin-dependent monooxygenase complex that catalyzes the ortho-hydroxylation of resveratrol to produce piceatannol. Piceatannol has various health benefits and valuable applications in food, medicine, and cosmetics. Enhancing the catalytic activity of 4HPA3H toward resveratrol has the potential to benefit piceatannol production. In this study, the critical amino acid residues in the substrate pocket of 4HPA3H that affect its activity toward resveratrol were identified using semi-rational engineering. Two key amino acid sites (I157 and A211) were discovered and the simultaneous "best" mutant I157L/A211D enabled catalytic efficiency (Kcat/Km-resveratrol) to increase by a factor of 4.7-fold. Molecular dynamics simulations indicated that the increased flexibility of the 4HPA3H substrate pocket has the potential to improve the catalytic activity of the enzyme toward resveratrol. On this basis, we produced 3.78 mM piceatannol by using the mutant I157L/A211D whole cells. In this study, we successfully developed a highly active 4HPA3H variant for the hydroxylation of resveratrol to piceatannol.
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Affiliation(s)
- Qianchao Zhang
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou 310014, China
- School of Biological and Chemical Engineering, NingboTech University, Ningbo 315100, China
| | - Yuning Jin
- School of Biological and Chemical Engineering, NingboTech University, Ningbo 315100, China
| | - Kai Yang
- Department of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
| | - Sheng Hu
- School of Biological and Chemical Engineering, NingboTech University, Ningbo 315100, China
| | - Changjiang Lv
- School of Biological and Chemical Engineering, Zhejiang University of Science and Technology, Hangzhou 310023, China
| | - Jun Huang
- School of Biological and Chemical Engineering, Zhejiang University of Science and Technology, Hangzhou 310023, China
| | - Jiaqi Mei
- Hangzhou Huadong Medicine Group Co., Ltd., Hangzhou 310011, China
| | - Weirui Zhao
- School of Biological and Chemical Engineering, NingboTech University, Ningbo 315100, China
| | - Lehe Mei
- School of Biological and Chemical Engineering, NingboTech University, Ningbo 315100, China
- Department of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
- Jinhua Advanced Research Institute, Jinhua 321019, China
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6
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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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7
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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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8
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Song Z, Zhang Q, Wu W, Pu Z, Yu H. Rational design of enzyme activity and enantioselectivity. Front Bioeng Biotechnol 2023; 11:1129149. [PMID: 36761300 PMCID: PMC9902596 DOI: 10.3389/fbioe.2023.1129149] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 01/16/2023] [Indexed: 01/25/2023] Open
Abstract
The strategy of rational design to engineer enzymes is to predict the potential mutants based on the understanding of the relationships between protein structure and function, and subsequently introduce the mutations using the site-directed mutagenesis. Rational design methods are universal, relatively fast and have the potential to be developed into algorithms that can quantitatively predict the performance of the designed sequences. Compared to the protein stability, it was more challenging to design an enzyme with improved activity or selectivity, due to the complexity of enzyme molecular structure and inadequate understanding of the relationships between enzyme structures and functions. However, with the development of computational force, advanced algorithm and a deeper understanding of enzyme catalytic mechanisms, rational design could significantly simplify the process of engineering enzyme functions and the number of studies applying rational design strategy has been increasing. Here, we reviewed the recent advances of applying the rational design strategy to engineer enzyme functions including activity and enantioselectivity. Five strategies including multiple sequence alignment, strategy based on steric hindrance, strategy based on remodeling interaction network, strategy based on dynamics modification and computational protein design are discussed and the successful cases using these strategies are introduced.
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Affiliation(s)
- Zhongdi Song
- Key Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province, Interdisciplinary Research Academy, Zhejiang Shuren University, Hangzhou, China
| | - Qunfeng Zhang
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, Zhejiang, China
| | - Wenhui Wu
- ZJU-Hangzhou Global Scientific and Technological Innovation Centre, Hangzhou, Zhejiang, China
| | - Zhongji Pu
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, Zhejiang, China,ZJU-Hangzhou Global Scientific and Technological Innovation Centre, Hangzhou, Zhejiang, China
| | - Haoran Yu
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, Zhejiang, China,ZJU-Hangzhou Global Scientific and Technological Innovation Centre, Hangzhou, Zhejiang, China,*Correspondence: Haoran Yu,
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9
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Lu XF, Diao HJ, Wu ZM, Zhang ZL, Zheng RC, Zheng YG. Engineering of reaction specificity, enantioselectivity and catalytic activity of nitrilase for highly efficient synthesis of pregabalin precursor. Biotechnol Bioeng 2022; 119:2399-2412. [PMID: 35750945 DOI: 10.1002/bit.28165] [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: 03/26/2022] [Revised: 05/29/2022] [Accepted: 06/19/2022] [Indexed: 11/11/2022]
Abstract
Simultaneous evolution of multiple enzyme properties remains challenging in protein engineering. A chimeric nitrilase (BaNITM0 ) with high activity towards isobutylsuccinonitrile (IBSN) was previously constructed for biosynthesis of pregabalin precursor (S)-3-cyano-5-methylhexanoic acid ((S)-CMHA). However, BaNITM0 also catalyzed the hydration of IBSN to produce by-product (S)-3-cyano-5-methylhexanoic amide. In order to obtain industrial nitrilase with vintage performance, we carried out engineering of BaNITM0 for simultaneous evolution of reaction specificity, enantioselectivity and catalytic activity. The best variant V82L/M127I/C237S (BaNITM2 ) displayed higher enantioselectivity (E=515), increased enzyme activity (5.4-fold) and reduced amide formation (from 15.8% to 1.9 %) compared with BaNITM0 . Structure analysis and molecular dynamics simulations indicated that mutation M127I and C237S restricted the movement of E66 in the catalytic triad, resulting in decreased amide formation. Mutation V82L was incorporated to induce the reconstruction of the substrate binding region in the enzyme catalytic pocket, engendering the improvement of stereoselectivity. Enantio- and regio-selective hydrolysis of 150 g/L IBSN using 1.5 g/L E. coli cells harboring BaNITM2 as biocatalyst afforded (S)-CMHA with >99.0% ee and 45.9% conversion, which highlighted the robustness of BaNITM2 for efficient manufacturing of pregabalin. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Xia-Feng Lu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, P. R. China.,Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, 310014, P. R. China
| | - Hong-Juan Diao
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, P. R. China.,Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, 310014, P. R. China
| | - Zhe-Ming Wu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, P. R. China.,Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, 310014, P. R. China
| | - Zi-Long Zhang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, P. R. China.,Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, 310014, P. R. China
| | - Ren-Chao Zheng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, P. R. China.,Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, 310014, P. R. China
| | - Yu-Guo Zheng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, P. R. China.,Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, 310014, P. R. China
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10
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Lei J, Tang K, Zhang T, Li Y, Gao Z, Jia H. Efficient Production of 2-O-α-D-Glucosyl Glycerol Catalyzed by an Engineered Sucrose Phosphorylase from Bifidobacterium longum. Appl Biochem Biotechnol 2022; 194:5274-5291. [PMID: 35731443 DOI: 10.1007/s12010-022-03939-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/20/2022] [Indexed: 11/02/2022]
Abstract
2-O-α-D-Glucosyl glycerol (2-αGG) can be used as a multipurpose anti-aging, cell-stimulating, and skin moisturizing agent in the cosmetic industry. Sucrose phosphorylase (SPase) has been widely used in the production of 2-αGG. In this paper, the gene encoding sucrose phosphorylase from Bifidobacterium longum (BlSP) was inserted into pRSF-Duet-1 to construct the recombinant plasmid pRSF-BlSP and was functionally expressed in E. coli BL21(DE3) to be used as a biocatalyst for the synthesis of 2-αGG firstly. The mutations of BlSP were carried out based on alanine scanning, and a positive mutant G293A with a 50% increase in activity for 2-αGG production was identified. Mutant G293A has less Km and bigger kcat/Km towards glycerol than the parental BlSP. Subsequently, the production of 177.6 g/L 2-αGG was attained from 1 M sucrose and 1.2 M glycerol catalyzed by 17 mg/mL G293A mutant. This study indicated that BlSP has good potential in the production of 2-αGG.
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Affiliation(s)
- Jiping Lei
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, China
| | - Kexin Tang
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, China
| | - Ting Zhang
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, China
| | - Yan Li
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, China.
| | - Zhen Gao
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, China
| | - Honghua Jia
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, China.
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11
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Structural Basis for the Regiospecificity of a Lipase from Streptomyces sp. W007. Int J Mol Sci 2022; 23:ijms23105822. [PMID: 35628632 PMCID: PMC9146090 DOI: 10.3390/ijms23105822] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Revised: 05/17/2022] [Accepted: 05/18/2022] [Indexed: 02/01/2023] Open
Abstract
The efficiency and accuracy of the synthesis of structural lipids are closely related to the regiospecificity of lipases. Understanding the structural mechanism of their regiospecificity contributes to the regiospecific redesign of lipases for meeting the technological innovation needs. Here, we used a thermostable lipase from Streptomyces sp. W007 (MAS1), which has been recently reported to show great potential in industry, to gain an insight into the structural basis of its regiospecificity by molecular modelling and mutagenesis experiments. The results indicated that increasing the steric hindrance of the site for binding a non-reactive carbonyl group of TAGs could transform the non-specific MAS1 to a α-specific lipase, such as the mutants G40E, G40F, G40Q, G40R, G40W, G40Y, N45Y, H108W and T237Y (PSI > 80). In addition, altering the local polarity of the site as well as the conformational stability of its composing residues could also impact the regiospecificity. Our present study could not only aid the rational design of the regiospecificity of lipases, but open avenues of exploration for further industrial applications of lipases.
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12
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Construction of L-Asparaginase Stable Mutation for the Application in Food Acrylamide Mitigation. FERMENTATION 2022. [DOI: 10.3390/fermentation8050218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Acrylamide, a II A carcinogen, widely exists in fried and baked foods. L-asparaginase can inhibit acrylamide formation in foods, and enzymatic stability is the key to its application. In this study, the Escherichia coli L-asparaginase (ECA) stable variant, D60W/L211R/L310R, was obtained with molecular dynamics (MD) simulation, saturation mutation, and combinatorial mutation, the half-life of which increased to 110 min from 60 min at 50 °C. Furthermore, the working temperature (maintaining the activity above 80%) of mutation expanded from 31 °C–43 °C to 35 °C–55 °C, and the relative activity of mutation increased to 82% from 65% at a pH range of 6–10. On treating 60 U/mL and 100 U/g flour L-asparaginase stable mutant (D60W/L211R/L310R) under uncontrolled temperature and pH, the acrylamide content of potato chips and bread was reduced by 66.9% and 51.7%, which was 27% and 49.9% higher than that of the wild type, respectively. These results demonstrated that the mutation could be of great potential to reduce food acrylamide formation in practical applications.
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13
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Production of phenylpyruvic acid by engineered l-amino acid deaminase from Proteus mirabilis. Biotechnol Lett 2022; 44:635-642. [DOI: 10.1007/s10529-022-03245-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 03/07/2022] [Indexed: 12/20/2022]
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14
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β-Alanine production by L-aspartate-α-decarboxylase from Corynebacterium glutamicum and variants with reduced substrate inhibition. MOLECULAR CATALYSIS 2022. [DOI: 10.1016/j.mcat.2022.112246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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15
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Qu G, Sun Z. In Silico Prediction Methods for Site-Saturation Mutagenesis. Methods Mol Biol 2022; 2397:49-69. [PMID: 34813059 DOI: 10.1007/978-1-0716-1826-4_4] [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] [Indexed: 06/13/2023]
Abstract
Directed enzyme evolution has proven to be a powerful means to endow biocatalysts with novel catalytic repertoires. Apart from completely random gene mutagenesis, site-directed or site-saturation mutagenesis requires a semi-rational selection of the amino acid positions or the substituted residues, which can dramatically reduce the screening efforts in protein engineering. To this end, in silico prediction methods play a pivotal role in targeting site-saturation mutagenesis. In this chapter, we provide two distinct computational methods, (a) conformational dynamics-guided design and (b) protein-ligand interaction fingerprinting analysis, to identify specific positions for site-saturation mutagenesis toward manipulating substrate specificity/stereoselectivity of an alcohol dehydrogenase, and improving activity of a carboxylic acid reductase, respectively.
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Affiliation(s)
- Ge Qu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
| | - Zhoutong Sun
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.
- National Technology Innovation Center of Synthetic Biology, Tianjin, China.
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16
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Wang H, Zhang Y, Yue W, Liang J, Su W. Application of magnetic field (MF) as an effective method to improve the activity of immobilized Candida antarctica lipase B (CALB). Catal Sci Technol 2022. [DOI: 10.1039/d2cy00628f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The process of immobilized enzyme and the change mechanism of enzyme in magnetic field.
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Affiliation(s)
- Honghai Wang
- School of Chemical Engineering and Technology, Hebei University of Technology, Tianjin 300130, China
- The National and Local Joint Engineering Laboratory for Energy Conservation of Chemical Process Integration and Resources Utilization, Tianjin 300130, China
| | - Yu Zhang
- School of Chemical Engineering and Technology, Hebei University of Technology, Tianjin 300130, China
- The National and Local Joint Engineering Laboratory for Energy Conservation of Chemical Process Integration and Resources Utilization, Tianjin 300130, China
| | - Wenda Yue
- School of Chemical Engineering and Technology, Hebei University of Technology, Tianjin 300130, China
- The National and Local Joint Engineering Laboratory for Energy Conservation of Chemical Process Integration and Resources Utilization, Tianjin 300130, China
| | - Jun Liang
- School of Chemical Engineering and Technology, Hebei University of Technology, Tianjin 300130, China
- The National and Local Joint Engineering Laboratory for Energy Conservation of Chemical Process Integration and Resources Utilization, Tianjin 300130, China
| | - Weiyi Su
- School of Chemical Engineering and Technology, Hebei University of Technology, Tianjin 300130, China
- The National and Local Joint Engineering Laboratory for Energy Conservation of Chemical Process Integration and Resources Utilization, Tianjin 300130, China
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17
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Wu Y, Zhang S, Song W, Liu J, Chen X, Hu G, Zhou Y, Liu L, Wu J. Enhanced Catalytic Efficiency of L‐amino Acid Deaminase Achieved by a Shorter Hydride Transfer Distance. ChemCatChem 2021. [DOI: 10.1002/cctc.202101067] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Yaoyun Wu
- School of Pharmaceutical Science Jiangnan University Wuxi 214122 P. R. China
- State Key Laboratory of Food Science and Technology Jiangnan University Wuxi 214122 P. R. China
| | - Sheng Zhang
- Tianrui Chemical Co. Ltd Department of Chemistry Quzhou 324400 P. R. China
| | - Wei Song
- School of Pharmaceutical Science Jiangnan University Wuxi 214122 P. R. China
- State Key Laboratory of Food Science and Technology Jiangnan University Wuxi 214122 P. R. China
| | - Jia Liu
- State Key Laboratory of Food Science and Technology Jiangnan University Wuxi 214122 P. R. China
| | - Xiulai Chen
- State Key Laboratory of Food Science and Technology Jiangnan University Wuxi 214122 P. R. China
| | - Guipeng Hu
- School of Pharmaceutical Science Jiangnan University Wuxi 214122 P. R. China
- State Key Laboratory of Food Science and Technology Jiangnan University Wuxi 214122 P. R. China
| | - Yiwen Zhou
- School of Pharmaceutical Science Jiangnan University Wuxi 214122 P. R. China
| | - Liming Liu
- State Key Laboratory of Food Science and Technology Jiangnan University Wuxi 214122 P. R. China
| | - Jing Wu
- School of Pharmaceutical Science Jiangnan University Wuxi 214122 P. R. China
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18
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Diversifying Arena of Drug Synthesis: In the Realm of Lipase Mediated Waves of Biocatalysis. Catalysts 2021. [DOI: 10.3390/catal11111328] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Hydrolases, being most prominent enzymes used in industrial processes have left no stone unturned in fascinating the pharmaceutical industry. Lipases, being a part of acyl hydrolases are the ones that function similarly to esterases (except an interfacial action) wherein they generally catalyze the hydrolysis of ester bonds. Be it in terms of stereoselectivity or regioselectivity, lipases have manifested their promiscuous proficiency in rendering biocatalytic drug synthesis and intermediates thereof. Industrial utilization of lipases is prevalent since decades ago, but their distinctive catalytic competencies have rendered them suitable for maneuverability in various tides of biocatalytic industrial process development. Numbers of exquisite catalysts have been fabricated out of lipases using nanobiotechnology whereby enzyme reusability and robustness have been conferred to many of the organic synthesis procedures. This marks a considerable achievement of lipases in the second wave of biocatalysis. Furthermore, in the third wave an advent of genetic engineering has fostered an era of customized lipases for suitable needs. Be it stability or an enhanced efficacy, genetic engineering techniques have ushered an avenue for biocatalytic development of drugs and drug intermediates through greener processes using lipases. Even in the forthcoming concept of co-modular catalytic systems, lipases may be the frontiers because of their astonishing capability to act along with other enzymes. The concept may render feasibility in the development of cascade reactions in organic synthesis. An upcoming wave demands fulfilling the vision of tailored lipase whilst a far-flung exploration needs to be unveiled for various research impediments in rendering lipase as a custom fit biocatalyst in pharmaceutical industry.
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19
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Liu K, Chen X, Zhong Y, Gao C, Hu G, Liu J, Guo L, Song W, Liu L. Rational design of a highly efficient catalytic system for the production of PAPS from ATP and its application in the synthesis of chondroitin sulfate. Biotechnol Bioeng 2021; 118:4503-4515. [PMID: 34406648 DOI: 10.1002/bit.27919] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 08/09/2021] [Accepted: 08/14/2021] [Indexed: 12/19/2022]
Abstract
The compound 3'-phosphoadenosine-5'-phosphosulfate (PAPS) serves as a sulfate group donor in the production of valuable sulfated compounds. However, elevated costs and low conversion efficiency limit the industrial applicability of PAPS. Here, we designed and constructed an efficient and controllable catalytic system for the conversion of adenosine triphosphate (ATP) (disodium salt) into PAPS without inhibition from by-products. In vitro and in vivo testing in Escherichia coli identified adenosine-5'-phosphosulfate kinase from Penicillium chrysogenum (PcAPSK) as the rate-limiting enzyme. Based on analysis of the catalytic steps and molecular dynamics simulations, a mechanism-guided "ADP expulsion" strategy was developed to generate an improved PcAPSK variant (L7), with a specific activity of 48.94 U·mg-1 and 73.27-fold higher catalytic efficiency (kcat/Km) that of the wild-type enzyme. The improvement was attained chiefly by reducing the ADP-binding affinity of PcAPSK, as well as by changing the enzyme's flexibility and lid structure to a more open conformation. By introducing PcAPSK L7 in an in vivo catalytic system, 73.59 mM (37.32 g·L-1 ) PAPS was produced from 150 mM ATP in 18.5 h using a 3-L bioreactor, and achieved titer is the highest reported to date and corresponds to a 98.13% conversion rate. Then, the PAPS catalytic system was combined with the chondroitin 4-sulfotransferase using a one-pot method. Finally, chondroitin sulfate was transformed from chondroitin at a conversion rate of 98.75%. This strategy has great potential for scale biosynthesis of PAPS and chondroitin sulfate.
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Affiliation(s)
- Kaifang Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,School of Biotechnology, Jiangnan University, Wuxi, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, China
| | - Xiulai Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,School of Biotechnology, Jiangnan University, Wuxi, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, China
| | - Yunlu Zhong
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,School of Biotechnology, Jiangnan University, Wuxi, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, China
| | - Cong Gao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,School of Biotechnology, Jiangnan University, Wuxi, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, China
| | - Guipeng Hu
- International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, China.,School of Pharmaceutical Science, Jiangnan University, Wuxi, China
| | - Jia Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,School of Biotechnology, Jiangnan University, Wuxi, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, China
| | - Liang Guo
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,School of Biotechnology, Jiangnan University, Wuxi, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, China
| | - Wei Song
- International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, China.,School of Pharmaceutical Science, Jiangnan University, Wuxi, China
| | - Liming Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,School of Biotechnology, Jiangnan University, Wuxi, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, China
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20
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Shukla V, Runthala A, Rajput VS, Chandrasai PD, Tripathi A, Phulara SC. Computational and synthetic biology approaches for the biosynthesis of antiviral and anticancer terpenoids from Bacillus subtilis. Med Chem 2021; 18:307-322. [PMID: 34254925 DOI: 10.2174/1573406417666210712211557] [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: 10/09/2020] [Revised: 04/18/2021] [Accepted: 04/25/2021] [Indexed: 11/22/2022]
Abstract
Recent advancements in medicinal research have identified several antiviral and anticancer terpenoids that are usually deployed as a source of flavor, fragrances and pharmaceuticals. Under the current COVID-19 pandemic conditions, natural therapeutics with least side effects are the need of the hour to save the patients, especially, which are pre-affected with other medical complications. Although, plants are the major sources of terpenoids; however, for the environmental concerns, the global interest has shifted to the biocatalytic production of molecules from microbial sources. The gram-positive bacterium Bacillus subtilis is a suitable host in this regard due to its GRAS (generally regarded as safe) status, ease in genetic manipulations and wide industrial acceptability. The B. subtilis synthesizes its terpenoid molecules from 1-deoxy-d-xylulose-5-phosphate (DXP) pathway, a common route in almost all microbial strains. Here, we summarize the computational and synthetic biology approaches to improve the production of terpenoid-based therapeutics from B. subtilis by utilizing DXP pathway. We focus on the in-silico approaches for screening the functionally improved enzyme-variants of the two crucial enzymes namely, the DXP synthase (DXS) and farnesyl pyrophosphate synthase (FPPS). The approaches for engineering the active sites are subsequently explained. It will be helpful to construct the functionally improved enzymes for the high-yield production of terpenoid-based anticancer and antiviral metabolites, which would help to reduce the cost and improve the availability of such therapeutics for the humankind.
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Affiliation(s)
- Vibha Shukla
- Food, Drug and Chemical Toxicology Group, CSIR-Indian Institute of Toxicology Research, Vishvigyan Bhawan, 31 Mahatma Gandhi Marg, Lucknow-226001, India
| | - Ashish Runthala
- Department of Biotechnology, Koneru Lakshmaiah Education Foundation, Vaddeswaram, Guntur-522502, Andhra Pradesh, India
| | | | - Potla Durthi Chandrasai
- Department of Biotechnology, National Institute of Technology Warangal, Warangal-506004, Telangana, India
| | - Anurag Tripathi
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad- 201002, India
| | - Suresh Chandra Phulara
- Department of Biotechnology, Koneru Lakshmaiah Education Foundation, Vaddeswaram, Guntur-522502, Andhra Pradesh, India
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21
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Song W, Xu X, Gao C, Zhang Y, Wu J, Liu J, Chen X, Luo Q, Liu L. Open Gate of Corynebacterium glutamicum Threonine Deaminase for Efficient Synthesis of Bulky α-Keto Acids. ACS Catal 2020. [DOI: 10.1021/acscatal.0c01672] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Wei Song
- School of Pharmaceutical Science, Jiangnan University, Wuxi 214122, P. R. China
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, P. R. China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, P. R. China
| | - Xin Xu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, P. R. China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, P. R. China
| | - Cong Gao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, P. R. China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, P. R. China
| | - Yuxuan Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, P. R. China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, P. R. China
| | - Jing Wu
- School of Pharmaceutical Science, Jiangnan University, Wuxi 214122, P. R. China
| | - Jia Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, P. R. China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, P. R. China
| | - Xiulai Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, P. R. China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, P. R. China
| | - Qiuling Luo
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, P. R. China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, P. R. China
| | - Liming Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, P. R. China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, P. R. China
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22
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Surpeta B, Sequeiros-Borja CE, Brezovsky J. Dynamics, a Powerful Component of Current and Future in Silico Approaches for Protein Design and Engineering. Int J Mol Sci 2020; 21:E2713. [PMID: 32295283 PMCID: PMC7215530 DOI: 10.3390/ijms21082713] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 04/10/2020] [Accepted: 04/12/2020] [Indexed: 12/13/2022] Open
Abstract
Computational prediction has become an indispensable aid in the processes of engineering and designing proteins for various biotechnological applications. With the tremendous progress in more powerful computer hardware and more efficient algorithms, some of in silico tools and methods have started to apply the more realistic description of proteins as their conformational ensembles, making protein dynamics an integral part of their prediction workflows. To help protein engineers to harness benefits of considering dynamics in their designs, we surveyed new tools developed for analyses of conformational ensembles in order to select engineering hotspots and design mutations. Next, we discussed the collective evolution towards more flexible protein design methods, including ensemble-based approaches, knowledge-assisted methods, and provable algorithms. Finally, we highlighted apparent challenges that current approaches are facing and provided our perspectives on their further development.
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Affiliation(s)
- Bartłomiej Surpeta
- Laboratory of Biomolecular Interactions and Transport, Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, 61-614 Poznan, Poland; (B.S.); (C.E.S.-B.)
- International Institute of Molecular and Cell Biology in Warsaw, Ks Trojdena 4, 02-109 Warsaw, Poland
| | - Carlos Eduardo Sequeiros-Borja
- Laboratory of Biomolecular Interactions and Transport, Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, 61-614 Poznan, Poland; (B.S.); (C.E.S.-B.)
- International Institute of Molecular and Cell Biology in Warsaw, Ks Trojdena 4, 02-109 Warsaw, Poland
| | - Jan Brezovsky
- Laboratory of Biomolecular Interactions and Transport, Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, 61-614 Poznan, Poland; (B.S.); (C.E.S.-B.)
- International Institute of Molecular and Cell Biology in Warsaw, Ks Trojdena 4, 02-109 Warsaw, Poland
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23
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Xu L, Han F, Dong Z, Wei Z. Engineering Improves Enzymatic Synthesis of L-Tryptophan by Tryptophan Synthase from Escherichia coli. Microorganisms 2020; 8:microorganisms8040519. [PMID: 32260519 PMCID: PMC7232222 DOI: 10.3390/microorganisms8040519] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 04/02/2020] [Accepted: 04/03/2020] [Indexed: 11/20/2022] Open
Abstract
To improve the thermostability of tryptophan synthase, the molecular modification of tryptophan synthase was carried out by rational molecular engineering. First, B-FITTER software was used to analyze the temperature factor (B-factor) of each amino acid residue in the crystal structure of tryptophan synthase. A key amino acid residue, G395, which adversely affected the thermal stability of the enzyme, was identified, and then, a mutant library was constructed by site-specific saturation mutation. A mutant (G395S) enzyme with significantly improved thermal stability was screened from the saturated mutant library. Error-prone PCR was used to conduct a directed evolution of the mutant enzyme (G395S). Compared with the parent, the mutant enzyme (G395S /A191T) had a Km of 0.21 mM and a catalytic efficiency kcat/Km of 5.38 mM−1∙s−1, which was 4.8 times higher than that of the wild-type strain. The conditions for L-tryptophan synthesis by the mutated enzyme were a L-serine concentration of 50 mmol/L, a reaction temperature of 40 °C, pH of 8, a reaction time of 12 h, and an L-tryptophan yield of 81%. The thermal stability of the enzyme can be improved by using an appropriate rational design strategy to modify the correct site. The catalytic activity of tryptophan synthase was increased by directed evolution.
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Affiliation(s)
- Lisheng Xu
- Department of Life and Food Science, Suzhou University, Suzhou 234000, China; (F.H.); (Z.D.)
- Correspondence: ; Tel.: +86-557-287-1681
| | - Fangkai Han
- Department of Life and Food Science, Suzhou University, Suzhou 234000, China; (F.H.); (Z.D.)
| | - Zeng Dong
- Department of Life and Food Science, Suzhou University, Suzhou 234000, China; (F.H.); (Z.D.)
| | - Zhaojun Wei
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China;
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24
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Qian Y, Lu C, Liu J, Song W, Chen X, Luo Q, Liu L, Wu J. Engineering protonation conformation of
l
‐aspartate‐α‐decarboxylase to relieve mechanism‐based inactivation. Biotechnol Bioeng 2020; 117:1607-1614. [DOI: 10.1002/bit.27316] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2019] [Revised: 02/22/2020] [Accepted: 02/22/2020] [Indexed: 01/01/2023]
Affiliation(s)
- Yuanyuan Qian
- State Key Laboratory of Food Science and TechnologyJiangnan University Wuxi China
- Key Laboratory of Industrial Biotechnology, Ministry of EducationJiangnan University Wuxi China
| | - Cui Lu
- State Key Laboratory of Food Science and TechnologyJiangnan University Wuxi China
- Key Laboratory of Industrial Biotechnology, Ministry of EducationJiangnan University Wuxi China
- School of Pharmaceutical ScienceJiangnan University Wuxi China
| | - Jia Liu
- State Key Laboratory of Food Science and TechnologyJiangnan University Wuxi China
- Key Laboratory of Industrial Biotechnology, Ministry of EducationJiangnan University Wuxi China
| | - Wei Song
- State Key Laboratory of Food Science and TechnologyJiangnan University Wuxi China
- Key Laboratory of Industrial Biotechnology, Ministry of EducationJiangnan University Wuxi China
- School of Pharmaceutical ScienceJiangnan University Wuxi China
| | - Xiulai Chen
- State Key Laboratory of Food Science and TechnologyJiangnan University Wuxi China
- Key Laboratory of Industrial Biotechnology, Ministry of EducationJiangnan University Wuxi China
| | - Qiuling Luo
- State Key Laboratory of Food Science and TechnologyJiangnan University Wuxi China
- Key Laboratory of Industrial Biotechnology, Ministry of EducationJiangnan University Wuxi China
| | - Liming Liu
- State Key Laboratory of Food Science and TechnologyJiangnan University Wuxi China
- Key Laboratory of Industrial Biotechnology, Ministry of EducationJiangnan University Wuxi China
- National Engineering Laboratory for Cereal Fermentation TechnologyJiangnan University Wuxi China
| | - Jing Wu
- School of Pharmaceutical ScienceJiangnan University Wuxi China
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25
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Li X, Zhang X, Xu S, Xu M, Yang T, Wang L, Zhang H, Fang H, Osire T, Rao Z. Insight into the thermostability of thermophilic L-asparaginase and non-thermophilic L-asparaginase II through bioinformatics and structural analysis. Appl Microbiol Biotechnol 2019; 103:7055-7070. [DOI: 10.1007/s00253-019-09967-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 04/29/2019] [Accepted: 06/10/2019] [Indexed: 01/16/2023]
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26
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Liu B, Qu G, Li J, Fan W, Ma J, Xu Y, Nie Y, Sun Z. Conformational Dynamics‐Guided Loop Engineering of an Alcohol Dehydrogenase: Capture, Turnover and Enantioselective Transformation of Difficult‐to‐Reduce Ketones. Adv Synth Catal 2019. [DOI: 10.1002/adsc.201900249] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Beibei Liu
- School of Biotechnology, Key laboratory of Industrial Biotechnology, Ministry of EducationJiangnan University Wuxi 214122 People's Republic of China
- Tianjin Institute of Industrial BiotechnologyChinese Academy of Sciences 32 West 7th Avenue, Tianjin Airport Economic Area Tianjin 300308 People's Republic of China
| | - Ge Qu
- Tianjin Institute of Industrial BiotechnologyChinese Academy of Sciences 32 West 7th Avenue, Tianjin Airport Economic Area Tianjin 300308 People's Republic of China
| | - Jun‐Kuan Li
- Tianjin Institute of Industrial BiotechnologyChinese Academy of Sciences 32 West 7th Avenue, Tianjin Airport Economic Area Tianjin 300308 People's Republic of China
- Department of Chemistry, Tianjin Key Laboratory of Molecular Optoelectronic Sciences, and Tianjin Collaborative Innovation Center of Chemical Science and EngineeringTianjin University Tianjin 300072 People's Republic of China
| | - Wenchao Fan
- Tianjin Institute of Industrial BiotechnologyChinese Academy of Sciences 32 West 7th Avenue, Tianjin Airport Economic Area Tianjin 300308 People's Republic of China
| | - Jun‐An Ma
- Department of Chemistry, Tianjin Key Laboratory of Molecular Optoelectronic Sciences, and Tianjin Collaborative Innovation Center of Chemical Science and EngineeringTianjin University Tianjin 300072 People's Republic of China
| | - Yan Xu
- School of Biotechnology, Key laboratory of Industrial Biotechnology, Ministry of EducationJiangnan University Wuxi 214122 People's Republic of China
| | - Yao Nie
- School of Biotechnology, Key laboratory of Industrial Biotechnology, Ministry of EducationJiangnan University Wuxi 214122 People's Republic of China
| | - Zhoutong Sun
- Tianjin Institute of Industrial BiotechnologyChinese Academy of Sciences 32 West 7th Avenue, Tianjin Airport Economic Area Tianjin 300308 People's Republic of China
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27
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Yuan Y, Song W, Liu J, Chen X, Luo Q, Liu L. Production of α‐Ketoisocaproate and α‐Keto‐β‐Methylvalerate by Engineered L‐Amino Acid Deaminase. ChemCatChem 2019. [DOI: 10.1002/cctc.201900259] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Yuxiang Yuan
- State Key Laboratory of Food Science and TechnologyJiangnan University Wuxi 214122 P. R. China
- Key Laboratory of Industrial Biotechnology Ministry of EducationJiangnan University Wuxi 214122 P. R. China
| | - Wei Song
- State Key Laboratory of Food Science and TechnologyJiangnan University Wuxi 214122 P. R. China
- Key Laboratory of Industrial Biotechnology Ministry of EducationJiangnan University Wuxi 214122 P. R. China
| | - Jia Liu
- State Key Laboratory of Food Science and TechnologyJiangnan University Wuxi 214122 P. R. China
- Key Laboratory of Industrial Biotechnology Ministry of EducationJiangnan University Wuxi 214122 P. R. China
| | - Xiulai Chen
- State Key Laboratory of Food Science and TechnologyJiangnan University Wuxi 214122 P. R. China
- Key Laboratory of Industrial Biotechnology Ministry of EducationJiangnan University Wuxi 214122 P. R. China
| | - Qiuling Luo
- State Key Laboratory of Food Science and TechnologyJiangnan University Wuxi 214122 P. R. China
- Key Laboratory of Industrial Biotechnology Ministry of EducationJiangnan University Wuxi 214122 P. R. China
| | - Liming Liu
- State Key Laboratory of Food Science and TechnologyJiangnan University Wuxi 214122 P. R. China
- Key Laboratory of Industrial Biotechnology Ministry of EducationJiangnan University Wuxi 214122 P. R. China
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28
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Zhou J, Zhang R, Yang T, Liu Q, Zheng J, Wang F, Liu F, Xu M, Zhang X, Rao Z. Relieving Allosteric Inhibition by Designing Active Inclusion Bodies and Coating of the Inclusion Bodies with Fe3O4 Nanomaterials for Sustainable 2-Oxobutyric Acid Production. ACS Catal 2018. [DOI: 10.1021/acscatal.8b03181] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Junping Zhou
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu Province 214122, China
| | - Rongzhen Zhang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu Province 214122, China
| | - Taowei Yang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu Province 214122, China
| | - Qiaoli Liu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu Province 214122, China
| | - Junxian Zheng
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu Province 214122, China
| | - Fang Wang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu Province 214122, China
| | - Fei Liu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu Province 214122, China
| | - Meijuan Xu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu Province 214122, China
| | - Xian Zhang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu Province 214122, China
| | - Zhiming Rao
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu Province 214122, China
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29
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Maria-Solano MA, Serrano-Hervás E, Romero-Rivera A, Iglesias-Fernández J, Osuna S. Role of conformational dynamics in the evolution of novel enzyme function. Chem Commun (Camb) 2018; 54:6622-6634. [PMID: 29780987 PMCID: PMC6009289 DOI: 10.1039/c8cc02426j] [Citation(s) in RCA: 93] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 05/10/2018] [Indexed: 12/26/2022]
Abstract
The free energy landscape concept that describes enzymes as an ensemble of differently populated conformational sub-states in dynamic equilibrium is key for evaluating enzyme activity, enantioselectivity, and specificity. Mutations introduced in the enzyme sequence can alter the populations of the pre-existing conformational states, thus strongly modifying the enzyme ability to accommodate alternative substrates, revert its enantiopreferences, and even increase the activity for some residual promiscuous reactions. In this feature article, we present an overview of the current experimental and computational strategies to explore the conformational free energy landscape of enzymes. We provide a series of recent publications that highlight the key role of conformational dynamics for the enzyme evolution towards new functions and substrates, and provide some perspectives on how conformational dynamism should be considered in future computational enzyme design protocols.
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Affiliation(s)
- Miguel A. Maria-Solano
- CompBioLab Group
, Institut de Química Computacional i Catàlisi and Departament de Química
, Universitat de Girona
,
Carrer Maria Aurèlia Capmany, 69
, 17003 Girona
, Catalonia
, Spain
.
| | - Eila Serrano-Hervás
- CompBioLab Group
, Institut de Química Computacional i Catàlisi and Departament de Química
, Universitat de Girona
,
Carrer Maria Aurèlia Capmany, 69
, 17003 Girona
, Catalonia
, Spain
.
| | - Adrian Romero-Rivera
- CompBioLab Group
, Institut de Química Computacional i Catàlisi and Departament de Química
, Universitat de Girona
,
Carrer Maria Aurèlia Capmany, 69
, 17003 Girona
, Catalonia
, Spain
.
| | - Javier Iglesias-Fernández
- CompBioLab Group
, Institut de Química Computacional i Catàlisi and Departament de Química
, Universitat de Girona
,
Carrer Maria Aurèlia Capmany, 69
, 17003 Girona
, Catalonia
, Spain
.
| | - Sílvia Osuna
- CompBioLab Group
, Institut de Química Computacional i Catàlisi and Departament de Química
, Universitat de Girona
,
Carrer Maria Aurèlia Capmany, 69
, 17003 Girona
, Catalonia
, Spain
.
- ICREA
,
Pg. Lluís Companys 23
, 08010 Barcelona
, Spain
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30
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The molecular basis for lipase stereoselectivity. Appl Microbiol Biotechnol 2018; 102:3487-3495. [DOI: 10.1007/s00253-018-8858-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 02/11/2018] [Accepted: 02/12/2018] [Indexed: 01/13/2023]
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