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Zhen H, Liu J, Xiong K, Zheng L, Hu Y, Li M, Jin W. Engineering a carboxypeptidase from Aspergillus oryzae M30011 to improve the terminal-specific enzymatic hydrolysis of aromatic amino acids. Process Biochem 2023. [DOI: 10.1016/j.procbio.2023.01.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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2
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Xiong K, Liu J, Wang X, Sun B, Zhang Y, Zhao Z, Pei P, Li X. Engineering a carboxypeptidase from Aspergillus niger M00988 by mutation to increase its ability in high Fischer ratio oligopeptide preparation. J Biotechnol 2021; 330:1-8. [PMID: 33647354 DOI: 10.1016/j.jbiotec.2021.02.015] [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: 09/05/2020] [Revised: 02/18/2021] [Accepted: 02/21/2021] [Indexed: 02/06/2023]
Abstract
High Fischer ratio oligopeptides have better conditioning effects on chronic diseases caused by long-term sub-health. At present, the enzymatic method for producing high Fischer ratio oligopeptides has a low yield, complicated purification, and a high cost. The use of exopeptidases with specific catalytic activity for aromatic amino acids in the preparation of high Fischer ratio oligopeptides is an important means to solve this problem. The carboxypeptidase from Aspergillus niger M00988 was cloned, which has good specificity for hydrophobic amino acids. Mutations at important substrate binding sites 135, 160, and 206 were performed to study important factors affecting the enzyme-specific recognition of aromatic groups. The results showed that the steric hindrance of amino acid residues at position 135 and the effects of positions 160 and 206 on the binding force of the enzyme to the substrate have important effects on the specific recognition of aromatic groups by the enzyme. Therefore, the S135 G, Y160S, and Y206S mutant enzymes have good application prospects in the preparation of high Fischer ratio oligopeptides with Chlorella powder. The obtained oligopeptides' Fischer ratio reached 31.45, 38.42, and 36.54, respectively. Compared with the original enzyme, the Fischer ratio increased by 2.58 %, 25.31 %, and 19.18 %, respectively.
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Affiliation(s)
- Ke Xiong
- Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology & Business University (BTBU), Beijing, 100048, China; Beijing Laboratory for Food Quality and Safety, Beijing Technology & Business University (BTBU), Beijing, 100048, China.
| | - Jiayun Liu
- Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology & Business University (BTBU), Beijing, 100048, China; Beijing Key Laboratory of Flavor Chemistry, Beijing Technology and Business University (BTBU), Beijing, 100048, China
| | - Xiaoyi Wang
- Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology & Business University (BTBU), Beijing, 100048, China; Beijing Laboratory for Food Quality and Safety, Beijing Technology & Business University (BTBU), Beijing, 100048, China
| | - Baoguo Sun
- Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology & Business University (BTBU), Beijing, 100048, China; Beijing Innovation Centre of Food Nutrition and Human, Beijing Technology & Business University (BTBU), Beijing, 100048, China
| | - Yuyu Zhang
- Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology & Business University (BTBU), Beijing, 100048, China; Beijing Laboratory for Food Quality and Safety, Beijing Technology & Business University (BTBU), Beijing, 100048, China
| | - Zhiyao Zhao
- Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology & Business University (BTBU), Beijing, 100048, China; Beijing Laboratory for Food Quality and Safety, Beijing Technology & Business University (BTBU), Beijing, 100048, China
| | - Penggang Pei
- Beijing Laboratory for Food Quality and Safety, Beijing Technology & Business University (BTBU), Beijing, 100048, China; Beijing Innovation Centre of Food Nutrition and Human, Beijing Technology & Business University (BTBU), Beijing, 100048, China
| | - Xiuyuan Li
- Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology & Business University (BTBU), Beijing, 100048, China; Beijing Key Laboratory of Flavor Chemistry, Beijing Technology and Business University (BTBU), Beijing, 100048, China
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Hou Q, Li N, Chao Y, Li S, Zhang L. Design and regulation of the surface and interfacial behavior of protein molecules. Chin J Chem Eng 2020. [DOI: 10.1016/j.cjche.2020.05.035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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4
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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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5
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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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6
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Wang DC, Li H, Xia SN, Xue YP, Zheng YG. Engineering of a keto acid reductase through reconstructing the substrate binding pocket to improve its activity. Catal Sci Technol 2019. [DOI: 10.1039/c8cy02586j] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Enzyme–substrate docking-guided point mutation of the substrate-binding pocket to generate mutant L244G/A250G/L245R with superior activity in the synthesis of (R)-2-hydroxy-4-phenylbutyric acid.
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Affiliation(s)
- Di-Chen Wang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province
- College of Biotechnology and Bioengineering
- Zhejiang University of Technology
- Hangzhou 310014
- China
| | - Heng Li
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province
- College of Biotechnology and Bioengineering
- Zhejiang University of Technology
- Hangzhou 310014
- China
| | - Shu-Ning Xia
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province
- College of Biotechnology and Bioengineering
- Zhejiang University of Technology
- Hangzhou 310014
- China
| | - Ya-Ping Xue
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province
- College of Biotechnology and Bioengineering
- Zhejiang University of Technology
- Hangzhou 310014
- China
| | - Yu-Guo Zheng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province
- College of Biotechnology and Bioengineering
- Zhejiang University of Technology
- Hangzhou 310014
- China
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7
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Ao YF, Zhang LB, Wang QQ, Wang DX, Wang MX. Biocatalytic Desymmetrization of Prochiral 3-Aryl and 3-Arylmethyl Glutaramides: Different Remote Substituent Effect on Catalytic Efficiency and Enantioselectivity. Adv Synth Catal 2018. [DOI: 10.1002/adsc.201800956] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Yu-Fei Ao
- Beijing National Laboratory for Molecular Sciences; CAS Key Laboratory of Molecular Recognition and Function; Institute of Chemistry; Chinese Academy of Sciences; Beijing 100190 People's Republic of China
| | - Li-Bin Zhang
- Beijing National Laboratory for Molecular Sciences; CAS Key Laboratory of Molecular Recognition and Function; Institute of Chemistry; Chinese Academy of Sciences; Beijing 100190 People's Republic of China
| | - Qi-Qiang Wang
- Beijing National Laboratory for Molecular Sciences; CAS Key Laboratory of Molecular Recognition and Function; Institute of Chemistry; Chinese Academy of Sciences; Beijing 100190 People's Republic of China
- University of Chinese Academy of Sciences; Beijing 100049 People's Republic of China
| | - De-Xian Wang
- Beijing National Laboratory for Molecular Sciences; CAS Key Laboratory of Molecular Recognition and Function; Institute of Chemistry; Chinese Academy of Sciences; Beijing 100190 People's Republic of China
- University of Chinese Academy of Sciences; Beijing 100049 People's Republic of China
| | - Mei-Xiang Wang
- MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology; Department of Chemistry; Tsinghua University; Beijing 100084 People's Republic of China
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Engineering the Enantioselectivity and Thermostability of a (+)-γ-Lactamase from Microbacterium hydrocarbonoxydans for Kinetic Resolution of Vince Lactam (2-Azabicyclo[2.2.1]hept-5-en-3-one). Appl Environ Microbiol 2017; 84:AEM.01780-17. [PMID: 29054871 DOI: 10.1128/aem.01780-17] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Accepted: 09/29/2017] [Indexed: 11/20/2022] Open
Abstract
To produce promising biocatalysts, natural enzymes often need to be engineered to increase their catalytic performance. In this study, the enantioselectivity and thermostability of a (+)-γ-lactamase from Microbacterium hydrocarbonoxydans as the catalyst in the kinetic resolution of Vince lactam (2-azabicyclo[2.2.1]hept-5-en-3-one) were improved. Enantiomerically pure (-)-Vince lactam is the key synthon in the synthesis of antiviral drugs, such as carbovir and abacavir, which are used to fight against HIV and hepatitis B virus. The work was initialized by using the combinatorial active-site saturation test strategy to engineer the enantioselectivity of the enzyme. The approach resulted in two mutants, Val54Ser and Val54Leu, which catalyzed the hydrolysis of Vince lactam to give (-)-Vince lactam, with 99.2% (enantiomeric ratio [E] > 200) enantiomeric excess (ee) and 99.5% ee (E > 200), respectively. To improve the thermostability of the enzyme, 11 residues with high temperature factors (B-factors) calculated by B-FITTER or high root mean square fluctuation (RMSF) values from the molecular dynamics simulation were selected. Six mutants with increased thermostability were obtained. Finally, the mutants generated with improved enantioselectivity and mutants evolved for enhanced thermostability were combined. Several variants showing (+)-selectivity (E value > 200) and improved thermostability were observed. These engineered enzymes are good candidates to serve as enantioselective catalysts for the preparation of enantiomerically pure Vince lactam.IMPORTANCE Enzymatic kinetic resolution of the racemic Vince lactam using (+)-γ-lactamase is the most often utilized means of resolving the enantiomers for the preparation of carbocyclic nucleoside compounds. The efficiency of the native enzymes could be improved by using protein engineering methods, such as directed evolution and rational design. In our study, two properties (enantioselectivity and thermostability) of a γ-lactamase identified from Microbacterium hydrocarbonoxydans were tackled using a semirational design. The protein engineering was initialized by combinatorial active-site saturation test to improve the enantioselectivity. At the same time, two strategies were applied to identify mutation candidates to enhance the thermostability based on calculations from both a static (B-FITTER based on the crystal structure) and a dynamic (root mean square fluctuation [RMSF] values based on molecular dynamics simulations) way. After combining the mutants, we successfully obtained the final mutants showing better properties in both properties. The engineered (+)-lactamase could be a candidate for the preparation of (-)-Vince lactam.
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Huo YY, Li S, Huang J, Rong Z, Wang Z, Li Z, Ji R, Kuang S, Cui HL, Li J, Xu XW. Crystal structure of Pelagibacterium halotolerans PE8: New insight into its substrate-binding pattern. Sci Rep 2017; 7:4422. [PMID: 28667306 PMCID: PMC5493697 DOI: 10.1038/s41598-017-04550-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Accepted: 05/17/2017] [Indexed: 11/16/2022] Open
Abstract
Lysophospholipase_carboxylesterase (LPCE) has highly conserved homologs in many diverse species ranging from bacteria to humans, as well as substantial biological significance and potential therapeutic implications. However, its biological function and catalytic mechanism remain minimally investigated because of the lack of structural information. Here, we report the crystal structure of a bacterial esterase PE8 belonging to the LPCE family. The crystal structure of PE8 was solved with a high resolution of 1.66 Å. Compared with other homologs in the family, significant differences were observed in the amino acid sequence, three-dimensional structure, and substrate-binding pattern. Residue Arg79 undergoes configuration switching when binding to the substrate and forms a unique wall, leading to a relatively closed cavity in the substrate-binding pocket compared with the relatively more open and longer clefts in other homologs. Moreover, the mutant Met122Ala showed much stronger substrate affinity and higher catalytic efficiency because less steric repulsion acted on the substrates. Taken together, these results showed that, in PE8, Arg79 and Met122 play important roles in substrate binding and the binding pocket shaping, respectively. Our study provides new insight into the catalytic mechanism of LPCE, which may facilitate the development of structure-based therapeutics and other biocatalytic applications.
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Affiliation(s)
- Ying-Yi Huo
- Key Laboratory of Marine Ecosystem and Biogeochemistry, Second Institute of Oceanography, State Oceanic Administration, Hangzhou, 310012, China
| | - Suhua Li
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Shanghai Engineering Research Center of Industrial Microorganisms, Fudan University, Shanghai, 200438, China
| | - Jing Huang
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Shanghai Engineering Research Center of Industrial Microorganisms, Fudan University, Shanghai, 200438, China
| | - Zhen Rong
- Key Laboratory of Marine Ecosystem and Biogeochemistry, Second Institute of Oceanography, State Oceanic Administration, Hangzhou, 310012, China
| | - Zhao Wang
- College of Food and Biological Engineering, Jiangsu University, Zhenjiang, 212013, China
| | - Zhengyang Li
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Shanghai Engineering Research Center of Industrial Microorganisms, Fudan University, Shanghai, 200438, China
| | - Rui Ji
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Shanghai Engineering Research Center of Industrial Microorganisms, Fudan University, Shanghai, 200438, China
| | - Siyun Kuang
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Shanghai Engineering Research Center of Industrial Microorganisms, Fudan University, Shanghai, 200438, China
| | - Heng-Lin Cui
- College of Food and Biological Engineering, Jiangsu University, Zhenjiang, 212013, China
| | - Jixi Li
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Shanghai Engineering Research Center of Industrial Microorganisms, Fudan University, Shanghai, 200438, China.
| | - Xue-Wei Xu
- Key Laboratory of Marine Ecosystem and Biogeochemistry, Second Institute of Oceanography, State Oceanic Administration, Hangzhou, 310012, China.
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Li A, Ye L, Yang X, Wang B, Yang C, Gu J, Yu H. Reconstruction of the Catalytic Pocket and Enzyme-Substrate Interactions To Enhance the Catalytic Efficiency of a Short-Chain Dehydrogenase/Reductase. ChemCatChem 2016. [DOI: 10.1002/cctc.201600921] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Aipeng Li
- Institute of Bioengineering, College of Chemical and Biological Engineering; Zhejiang University; 310027 Hangzhou P.R. China
| | - Lidan Ye
- Institute of Bioengineering, College of Chemical and Biological Engineering; Zhejiang University; 310027 Hangzhou P.R. China
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education; Zhejiang University; 310027 Hangzhou P.R. China
| | - Xiaohong Yang
- Institute of Bioengineering, College of Chemical and Biological Engineering; Zhejiang University; 310027 Hangzhou P.R. China
| | - Bei Wang
- College of Pharmaceutical Science; Zhejiang University of Technology; 310014 Hangzhou P.R. China
| | - Chengcheng Yang
- Institute of Bioengineering, College of Chemical and Biological Engineering; Zhejiang University; 310027 Hangzhou P.R. China
| | - Jiali Gu
- College of Life Science, Department of Materials Chemistry; Huzhou University; 313000 Huzhou P.R. China
| | - Hongwei Yu
- Institute of Bioengineering, College of Chemical and Biological Engineering; Zhejiang University; 310027 Hangzhou P.R. China
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11
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Insight into the role of halogen bond in the activity of d-mandelate dehydrogenase toward halogenated substrates. Tetrahedron Lett 2016. [DOI: 10.1016/j.tetlet.2016.03.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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12
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Li A, Ye L, Yang X, Yang C, Gu J, Yu H. Structure-guided stereoselectivity inversion of a short-chain dehydrogenase/reductase towards halogenated acetophenones. Chem Commun (Camb) 2016; 52:6284-7. [DOI: 10.1039/c6cc00051g] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The structure-guided rational design of an NADH-dependent short-chain dehydrogenase/reductase (SDR) reversed the stereoselectivity towards halogenated acetophenones from Prelog to anti-Prelog.
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Affiliation(s)
- Aipeng Li
- Institute of Bioengineering
- College of Chemical and Biological Engineering
- Zhejiang University
- Hangzhou 310027
- P. R. China
| | - Lidan Ye
- Institute of Bioengineering
- College of Chemical and Biological Engineering
- Zhejiang University
- Hangzhou 310027
- P. R. China
| | - Xiaohong Yang
- Institute of Bioengineering
- College of Chemical and Biological Engineering
- Zhejiang University
- Hangzhou 310027
- P. R. China
| | - Chengcheng Yang
- Institute of Bioengineering
- College of Chemical and Biological Engineering
- Zhejiang University
- Hangzhou 310027
- P. R. China
| | - Jiali Gu
- College of Life Science
- Department of Materials Chemistry
- Huzhou University
- Huzhou 313000
- P. R. China
| | - Hongwei Yu
- Institute of Bioengineering
- College of Chemical and Biological Engineering
- Zhejiang University
- Hangzhou 310027
- P. R. China
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Gu J, Tong H, Ye L, Yu H. The role of aromatic residue W20 in the activity and enantioselectivity control of esterase BioH toward aryl substrate. Biochem Eng J 2015. [DOI: 10.1016/j.bej.2015.05.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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14
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Gu J, Ye L, Guo F, Lv X, Lu W, Yu H. Improved apparent enantioselectivity of a hydrolase by sequential hydrolysis and racemization. Tetrahedron Lett 2015. [DOI: 10.1016/j.tetlet.2014.12.139] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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15
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Ye L, Xie W, Zhou P, Yu H. Biotechnological Production of Astaxanthin through Metabolic Engineering of Yeasts. CHEMBIOENG REVIEWS 2015. [DOI: 10.1002/cben.201400023] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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