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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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Nazarian Z, Arab SS. Discovery of carboxylesterases via metagenomics: Putative enzymes that contribute to chemical kinetic resolution. Process Biochem 2022. [DOI: 10.1016/j.procbio.2022.07.025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Tang CD, Zhang X, Shi HL, Liu XX, Wang HY, Lu YF, Zhang SP, Kan YC, Yao LG. Improving catalytic activity of Lactobacillus harbinensis -mandelate dehydrogenase toward -o-chloromandelic acid by laboratory evolution. MOLECULAR CATALYSIS 2022. [DOI: 10.1016/j.mcat.2022.112700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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Directed evolution of formate dehydrogenase and its application in the biosynthesis of L-phenylglycine from phenylglyoxylic acid. MOLECULAR CATALYSIS 2021. [DOI: 10.1016/j.mcat.2021.111666] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Wang HY, Xie YL, Shi X, Shi HL, Xu JH, Tang CD, Yao LG, Kan YC. Directed evolution of a D-mandelate dehydrogenase toward D-o-chloromandelic acid and insight into the molecular basis for its catalytic performance. Biochem Eng J 2021. [DOI: 10.1016/j.bej.2020.107863] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Tang CD, Shi HL, Jia YY, Li X, Wang LF, Xu JH, Yao LG, Kan YC. High level and enantioselective production of L-phenylglycine from racemic mandelic acid by engineered Escherichia coli using response surface methodology. Enzyme Microb Technol 2020; 136:109513. [PMID: 32331718 DOI: 10.1016/j.enzmictec.2020.109513] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2019] [Revised: 01/11/2020] [Accepted: 01/17/2020] [Indexed: 12/12/2022]
Abstract
L-Phenylglycine (L-PHG) is a member of unnatural amino acids, and becoming more and more important as intermediate for pharmaceuticals, food additives and agrochemicals. However, the existing synthetic methods for L-PHG mainly rely on toxic cyanide chemistry and multistep processes. To provide green, safe and high enantioselective alternatives, we envisaged cascade biocatalysis for the one-pot synthesis of L-PHG from racemic mandelic acid. A engineered E. coli strain was established to co-express mandelate racemase, D-mandelate dehydrogenase and L-leucine dehydrogenase and catalyze a 3-step reaction in one pot, enantioselectively transforming racemic mandelic acid to give L-PHG (e.e. >99 %). After the conditions for biosynthesis of L-PHG optimized by response surface methodology, the yield and space-time yield of L-PHG can reach 87.89 % and 79.70 g·L-1·d-1, which was obviously improved. The high-yielding and enantioselective synthetic methods use cheap and green reagents, and E. coli whole-cell catalysts, thus providing green and useful alternative methods for manufacturing L-PHG.
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Affiliation(s)
- Cun-Duo Tang
- Henan Provincial Engineering Laboratory of Insect Bio-Reactor and Henan Key Laboratory of Ecological Security for Water Source Region of Mid-Line of South-to-North, Nanyang Normal University, 1638 Wolong Road, Nanyang, Henan, 473061, People's Republic of China
| | - Hong-Ling Shi
- Henan Provincial Engineering Laboratory of Insect Bio-Reactor and Henan Key Laboratory of Ecological Security for Water Source Region of Mid-Line of South-to-North, Nanyang Normal University, 1638 Wolong Road, Nanyang, Henan, 473061, People's Republic of China
| | - Yuan-Yuan Jia
- Henan Provincial Engineering Laboratory of Insect Bio-Reactor and Henan Key Laboratory of Ecological Security for Water Source Region of Mid-Line of South-to-North, Nanyang Normal University, 1638 Wolong Road, Nanyang, Henan, 473061, People's Republic of China
| | - Xiang Li
- Henan Provincial Engineering Laboratory of Insect Bio-Reactor and Henan Key Laboratory of Ecological Security for Water Source Region of Mid-Line of South-to-North, Nanyang Normal University, 1638 Wolong Road, Nanyang, Henan, 473061, People's Republic of China
| | - Lin-Feng Wang
- State Key Laboratory of Automotive Biofuel Technology, 1 Tianguan Avenue, Nanyang, Henan, 473000, People's Republic of China
| | - Jian-He Xu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, People's Republic of China.
| | - Lun-Guang Yao
- Henan Provincial Engineering Laboratory of Insect Bio-Reactor and Henan Key Laboratory of Ecological Security for Water Source Region of Mid-Line of South-to-North, Nanyang Normal University, 1638 Wolong Road, Nanyang, Henan, 473061, People's Republic of China.
| | - Yun-Chao Kan
- Henan Provincial Engineering Laboratory of Insect Bio-Reactor and Henan Key Laboratory of Ecological Security for Water Source Region of Mid-Line of South-to-North, Nanyang Normal University, 1638 Wolong Road, Nanyang, Henan, 473061, People's Republic of China.
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Xue F, Zhang LH, Xu Q. Significant improvement of the enantioselectivity of a halohydrin dehalogenase for asymmetric epoxide ring opening reactions by protein engineering. Appl Microbiol Biotechnol 2020; 104:2067-2077. [DOI: 10.1007/s00253-020-10356-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 12/15/2019] [Accepted: 01/05/2020] [Indexed: 02/03/2023]
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Wu X, Yang S, Yu H, Ye L, Su B, Shao Z. Improved enantioselectivity of E. coli BioH in kinetic resolution of methyl ( S)-3-cyclohexene-1-carboxylate by combinatorial modulation of steric and aromatic interactions. Biosci Biotechnol Biochem 2019; 83:1263-1269. [PMID: 30938230 DOI: 10.1080/09168451.2019.1597620] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
As a chiral precursor for the important anticoagulant Edoxaban, enantioselective synthesis of (S)-3-cyclohexene-1-carboxylic acid is of great significance. The complicated procedures and generation of massive solid waste discourage its chemical synthesis, and the alternative biocatalysis route calls for an enzyme capable of asymmetric hydrolysis of racemic methyl-3-cyclohexene-1-carboxylate. To this end, we engineered the E. coli esterase BioH for improved S-enantioselectivity via rational design. By combinatorial modulation of steric and aromatic interactions, a positive mutant Mu3 (L24A/W81A/L209A) with relatively high S-selectivity in hydrolyzing racemic methyl-3-cyclohexene-1-carboxylate was obtained, improving the enantiomeric excess from 32.3% (the wild type) to 70.9%. Molecular dynamics simulation was conducted for both (R)- or (S)- complexes of the wild type and Mu3 to provide hints for the mechanism behind the increased S-selectivity. Moreover, the reaction conditions of Mu3 in methyl-3-cyclohexene-1-carboxylate hydrolysis was optimized to improve the conversion rate to 2 folds.
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Affiliation(s)
- Xiafen Wu
- a College of Pharmaceutical Science , Zhejiang University of Technology , Hangzhou , PR China
| | - Shengli Yang
- a College of Pharmaceutical Science , Zhejiang University of Technology , Hangzhou , PR China
| | - Hongwei Yu
- b Institute of Bioengineering, College of Chemical and Biological Engineering , Zhejiang University , Hangzhou , PR China
| | - Lidan Ye
- b Institute of Bioengineering, College of Chemical and Biological Engineering , Zhejiang University , Hangzhou , PR China
| | - Bingmei Su
- c Fujian Key Laboratory of Marine Enzyme Engineering, College of Biological Science and Engineering , Fuzhou University , Fuzhou , PR China
| | - Zehui Shao
- a College of Pharmaceutical Science , Zhejiang University of Technology , Hangzhou , PR China
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Directed evolution of mandelate racemase by a novel high-throughput screening method. Appl Microbiol Biotechnol 2016; 101:1063-1072. [DOI: 10.1007/s00253-016-7790-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Revised: 07/24/2016] [Accepted: 08/03/2016] [Indexed: 12/30/2022]
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