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Niu J, Ma B, Shen J, Chi H, Zhou H, Lu Z, Lu F, Zhu P. Structure-Guided Steric Hindrance Engineering of Devosia Strain A6-243 Quinone-Dependent Dehydrogenase to Enhance Its Catalytic Efficiency. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:549-558. [PMID: 38153089 DOI: 10.1021/acs.jafc.3c07179] [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: 12/29/2023]
Abstract
Deoxynivalenol (DON), the most widely distributed mycotoxin worldwide, causes severe health risks for humans and animals. Quinone-dependent dehydrogenase derived from Devosia strain A6-243 (DADH) can degrade DON into less toxic 3-keto-DON and then aldo-keto reductase AKR13B3 can reduce 3-keto-DON into relatively nontoxic 3-epi-DON. However, the poor catalytic efficiency of DADH made it unsuitable for practical applications, and it has become the rate-limiting step of the two-step enzymatic cascade catalysis. Here, structure-guided steric hindrance engineering was employed to enhance the catalytic efficiency of DADH. After the steric hindrance engineering, the best mutant, V429G/N431V/T432V/L434V/F537A (M5-1), showed an 18.17-fold increase in specific activity and an 11.04-fold increase in catalytic efficiency (kcat/Km) compared with that of wild-type DADH. Structure-based computational analysis provided information on the increased catalytic efficiency in the directions that attenuated steric hindrance, which was attributed to the reshaped substrate-binding pocket with an expanded catalytic binding cavity and a favorable attack distance. Tunnel analysis suggested that reshaping the active cavity by mutation might alter the shape and size of the enzyme tunnels or form one new enzyme tunnel, which might contribute to the improved catalytic efficiency of M5-1. These findings provide a promising strategy to enhance the catalytic efficiency by steric hindrance engineering.
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Affiliation(s)
- Jiafeng Niu
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Bin Ma
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Juan Shen
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Huibing Chi
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Huimin Zhou
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhaoxin Lu
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Fengxia Lu
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Ping Zhu
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
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Chi H, Zhu X, Shen J, Lu Z, Lu F, Lyu Y, Zhu P. Thermostability enhancement and insight of L-asparaginase from Mycobacterium sp. via consensus-guided engineering. Appl Microbiol Biotechnol 2023; 107:2321-2333. [PMID: 36843197 DOI: 10.1007/s00253-023-12443-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Revised: 02/06/2023] [Accepted: 02/13/2023] [Indexed: 02/28/2023]
Abstract
Acrylamide alleviation in food has represented as a critical issue due to its neurotoxic effect on human health. L-Asparaginase (ASNase, EC 3.5.1.1) is considered a potential additive for acrylamide alleviation in food. However, low thermal stability hinders the application of ASNase in thermal food processing. To obtain highly thermal stable ASNase for its industrial application, a consensus-guided approach combined with site-directed saturation mutation (SSM) was firstly reported to engineer the thermostability of Mycobacterium gordonae L-asparaginase (GmASNase). The key residues Gly97, Asn159, and Glu249 were identified for improving thermostability. The combinatorial triple mutant G97T/N159Y/E249Q (TYQ) displayed significantly superior thermostability with half-life values of 61.65 ± 8.69 min at 50 °C and 5.12 ± 1.66 min at 55 °C, whereas the wild-type was completely inactive at these conditions. Moreover, its Tm value increased by 8.59 °C from parent wild-type. Interestingly, TYQ still maintained excellent catalytic efficiency and specific activity. Further molecular dynamics and structure analysis revealed that the additional hydrogen bonds, increased hydrophobic interactions, and favorable electrostatic potential were essential for TYQ being in a more rigid state for thermostability enhancement. These results suggested that our strategy was an efficient engineering approach for improving fundamental properties of GmASNase and offering GmASNase as a potential agent for efficient acrylamide mitigation in food industry. KEY POINTS: • The thermostability of GmASNase was firstly improved by consensus-guided engineering. • The half-life and Tm value of triple mutant TYQ were significantly increased. • Insight on improved thermostability of TYQ was revealed by MD and structure analysis.
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Affiliation(s)
- Huibing Chi
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xiaoyu Zhu
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Juan Shen
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zhaoxin Lu
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Fengxia Lu
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yunbin Lyu
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Ping Zhu
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China.
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Chi H, Wang Y, Xia B, Zhou Y, Lu Z, Lu F, Zhu P. Enhanced Thermostability and Molecular Insights for l-Asparaginase from Bacillus licheniformis via Structure- and Computation-Based Rational Design. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:14499-14509. [PMID: 36341695 DOI: 10.1021/acs.jafc.2c05712] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
l-Asparaginase has gained much attention for effectively treating acute lymphoblastic leukemia (ALL) and mitigating carcinogenic acrylamide in fried foods. Due to high-dose dependence for clinical treatment and low mitigation efficiency for thermal food processes caused by poor thermal stability, a method to achieve thermostable l-asparaginase has become a critical bottleneck. In this study, a rational design including free energy combined with structural and conservative analyses was applied to engineer the thermostability of l-asparaginase from Bacillus licheniformis (BlAsnase). Two enhanced thermostability mutants D172W and E207A were screened out by site-directed saturation mutagenesis. The double mutant D172W/E207A exhibited highly remarkable thermostability with a 65.8-fold longer half-life at 55 °C and 5 °C higher optimum reaction temperature and melting temperature (Tm) than those of wild-type BlAsnase. Further, secondary structure, sequence, molecular dynamics (MD), and 3D-structure analysis revealed that the excellent thermostability of the mutant D172W/E207A was on account of increased hydrophobicity and decreased flexibility, highly rigid structure, hydrophobic interactions, and favorable electrostatic potential. As the first report of rationally designing l-asparaginase with improved thermostability from B. licheniformis, this study offers a facile and efficient process to improve the thermostability of l-asparaginase for industrial applications.
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Affiliation(s)
- Huibing Chi
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing210095, China
| | - Yilian Wang
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing210095, China
| | - Bingjie Xia
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing210095, China
| | - Yawen Zhou
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing210095, China
| | - Zhaoxin Lu
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing210095, China
| | - Fengxia Lu
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing210095, China
| | - Ping Zhu
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing210095, China
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“Nonpolarity paving” in substrate tunnel of a Limnobacter sp. Phenylacetone monooxygenase for efficient single whole-cell synthesis of esomeprazole. Bioorg Chem 2022; 125:105867. [DOI: 10.1016/j.bioorg.2022.105867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 05/04/2022] [Accepted: 05/06/2022] [Indexed: 11/18/2022]
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Wamser N, Wu H, Buono F, Brundage A, Ricci F, Lorenz JC, Wang J, Haddad N, Paolillo J, Leung JC, Lee H, Hossain A. Discovery and Process Development of a Scalable Biocatalytic Kinetic Resolution toward Synthesis of a Sterically Hindered Chiral Ketone. Org Process Res Dev 2022. [DOI: 10.1021/acs.oprd.2c00067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Nicole Wamser
- Boehringer Ingelheim Pharmaceuticals Inc., 900 Ridgebury Road, P.O. Box 368, Ridgefield, Connecticut 06877, United States
| | - Hao Wu
- Boehringer Ingelheim Pharmaceuticals Inc., 900 Ridgebury Road, P.O. Box 368, Ridgefield, Connecticut 06877, United States
| | - Frederic Buono
- Boehringer Ingelheim Pharmaceuticals Inc., 900 Ridgebury Road, P.O. Box 368, Ridgefield, Connecticut 06877, United States
| | - Anthony Brundage
- Boehringer Ingelheim Pharmaceuticals Inc., 900 Ridgebury Road, P.O. Box 368, Ridgefield, Connecticut 06877, United States
| | - Francesco Ricci
- Boehringer Ingelheim Pharmaceuticals Inc., 900 Ridgebury Road, P.O. Box 368, Ridgefield, Connecticut 06877, United States
| | - Jon C. Lorenz
- Boehringer Ingelheim Pharmaceuticals Inc., 900 Ridgebury Road, P.O. Box 368, Ridgefield, Connecticut 06877, United States
| | - Jun Wang
- Boehringer Ingelheim Pharmaceuticals Inc., 900 Ridgebury Road, P.O. Box 368, Ridgefield, Connecticut 06877, United States
| | - Nizar Haddad
- Boehringer Ingelheim Pharmaceuticals Inc., 900 Ridgebury Road, P.O. Box 368, Ridgefield, Connecticut 06877, United States
| | - Joshua Paolillo
- Boehringer Ingelheim Pharmaceuticals Inc., 900 Ridgebury Road, P.O. Box 368, Ridgefield, Connecticut 06877, United States
| | - Joyce C. Leung
- Boehringer Ingelheim Pharmaceuticals Inc., 900 Ridgebury Road, P.O. Box 368, Ridgefield, Connecticut 06877, United States
| | - Heewon Lee
- Boehringer Ingelheim Pharmaceuticals Inc., 900 Ridgebury Road, P.O. Box 368, Ridgefield, Connecticut 06877, United States
| | - Azad Hossain
- Boehringer Ingelheim Pharmaceuticals Inc., 900 Ridgebury Road, P.O. Box 368, Ridgefield, Connecticut 06877, United States
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Efficient Synthesis of cis-4-Propylcyclohexanol Using a Mutant Alcohol Dehydrogenase Coupled with Glucose Dehydrogenase. Catalysts 2022. [DOI: 10.3390/catal12040406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/10/2022] Open
Abstract
cis-4-Propylcyclohexanol is an important intermediate for synthesizing trans-2-(4-propylcyclohexyl)-1,3-propanediol, which is widely used in the manufacture of liquid crystal displays. In this study, cis-4-propylcyclohexanol was prepared using a mutant alcohol dehydrogenase from Lactobacillus kefir (LK-TADH, A94T/F147L/L199H/A202L) coupled with glucose dehydrogenase. Using the optimal catalytic conditions, 125 g/L (250 g) of 4-propylcyclohexanone was completely transformed after 5 h, and 225.8 g of cis-4-propylcyclohexanol (cis/trans ratio of 99.5:0.5) was obtained through extraction and rotary evaporation at a yield of 90.32%. This study reports a potential method for the green production of cis-4-propylcyclohexanol as the key intermediate of trans-2-(4-propylcyclohexyl)-1,3-propanediol at an industrial level.
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Li SF, Xie JY, Qiu S, Xu SY, Cheng F, Wang YJ, Zheng YG. Semirational engineering of an aldo-keto reductase KmAKR for overcoming trade-offs between catalytic activity and thermostability. Biotechnol Bioeng 2021; 118:4441-4452. [PMID: 34374988 DOI: 10.1002/bit.27913] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 07/30/2021] [Accepted: 08/01/2021] [Indexed: 01/05/2023]
Abstract
Enzyme engineering usually generates trade-offs between activity, stability, and selectivity. Herein, we report semirational engineering of an aldo-keto reductase (AKR) KmAKR for simultaneously enhancing its thermostability and catalytic activity. Previously, we constructed KmAKRM9 (W297H/Y296W/K29H/Y28A/T63M/A30P/T302S/N109K/S196C), which showed outstanding activity towards t-butyl 6-chloro-(3R,5S)-dihydroxyhexanoate ((3R,5S)-CDHH), and t-butyl 6-cyano-(3R,5R)-dihydroxyhexanoate, the key chiral building blocks of rosuvastatin and atorvastatin. Under the guidance of computer-aided design including consensus residues analysis and molecular dynamics (MD) simulations, K164, S182, S232, and Q266 were dug out for their thermostability conferring roles, generating the "best" mutant KmAKRM13 (W297H/Y296W/K29H/Y28A/T63M/A30P/T302S/N109K/S196C/K164E/S232A/S182H/Q266D). The Tm and T50 15 values of KmAKRM13 were 10.4 and 6.1°C higher than that of KmAKRM9 , respectively. Moreover, it displayed a significantly elevated organic solvent tolerance over KmAKRM9 . Structural analysis indicated that stabilization of the α-helixes mainly contributed to thermostability enhancement. Under the optimized conditions, KmAKRM13 completely asymmetrically reduced 400 g/l t-butyl 6-chloro-(5S)-hydroxy-3-oxohexanoate ((5S)-CHOH) in 8.0 h at a high substrate to catalyst ratio (S/C) of 106.7 g/g, giving diastereomerically pure (3R,5S)-CDHH (>99.5% d.e.P ) with a space-time yield (STY) of 449.2 g/l·d.
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Affiliation(s)
- Shu-Fang Li
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China.,Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, China.,The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, China
| | - Jian-Yong Xie
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China.,Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, China.,The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, China
| | - Shuai Qiu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China.,Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, China.,The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, China
| | - Shen-Yuan Xu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China.,Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, China.,The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, China
| | - Feng Cheng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China.,Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, China.,The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, China
| | - Ya-Jun Wang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China.,Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, China.,The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, China
| | - Yu-Guo Zheng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China.,Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, China.,The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, China
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