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Cen YK, Zhang L, Jiang Y, Meng XF, Li Y, Xiang C, Xue YP, Zheng YG. Not exclusively the activity, but the sweet spot: a dehydrogenase point mutation synergistically boosts activity, substrate tolerance, thermal stability and yield. Org Biomol Chem 2024; 22:3009-3018. [PMID: 38529785 DOI: 10.1039/d4ob00211c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/27/2024]
Abstract
Catalytic activity is undoubtedly a key focus in enzyme engineering. The complicated reaction conditions hinder some enzymes from industrialization even though they have relatively promising activity. This has occurred to some dehydrogenases. Hydroxysteroid dehydrogenases (HSDHs) specifically catalyze the conversion between hydroxyl and keto groups, and hold immense potential in the synthesis of steroid medicines. We underscored the importance of 7α-HSDH activity, and analyzed the overall robustness and underlying mechanisms. Employing a high-throughput screening approach, we comprehensively assessed a mutation library, and obtained a mutant with enhanced enzymatic activity and overall stability/tolerance. The superior mutant (I201M) was identified to harbor improved thermal stability, substrate susceptibility, cofactor affinity, as well as the yield. This mutant displayed a 1.88-fold increase in enzymatic activity, a 1.37-fold improvement in substrate tolerance, and a 1.45-fold increase in thermal stability when compared with the wild type (WT) enzyme. The I201M mutant showed a 2.25-fold increase in the kcat/KM ratio (indicative of a stronger binding affinity for the cofactor). This mutant did not exhibit the highest enzyme activity compared with all the tested mutants, but these improved characteristics contributed synergistically to the highest yield. When a substrate at 100 mM was present, the 24 h yield by I201M reached 89.7%, significantly higher than the 61.2% yield elicited by the WT enzyme. This is the first report revealing enhancement of the catalytic efficiency, cofactor affinity, substrate tolerance, and thermal stability of NAD(H)-dependent 7α-HSDH through a single-point mutation. The mutated enzyme reached the highest enzymatic activity of 7α-HSDH ever reported. High enzymatic activity is undoubtedly crucial for enabling the industrialization of an enzyme. Our findings demonstrated that, when compared with other mutants boasting even higher enzymatic activity, mutants with excellent overall robustness were superior for industrial applications. This principle was exemplified by highly active enzymes such as 7α-HSDH.
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Affiliation(s)
- Yu-Ke Cen
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China.
- Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou 310014, China
- National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou 310014, P. R. China
| | - Lin Zhang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China.
- Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou 310014, China
- National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou 310014, P. R. China
| | - Yue Jiang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China.
- Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou 310014, China
- National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou 310014, P. R. China
| | - Xiang-Fu Meng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China.
- Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou 310014, China
- National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou 310014, P. R. China
| | - Yuan Li
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China.
- Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou 310014, China
- National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou 310014, P. R. China
| | - Chao Xiang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China.
- Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou 310014, China
- National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou 310014, P. R. China
| | - Ya-Ping Xue
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China.
- Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou 310014, China
- National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, 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, China.
- Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou 310014, China
- National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou 310014, P. R. China
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2
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Li Q, Wang H, Zhang W, Wang W, Ren X, Wu M, Shi G. Structure-Guided Evolution Modulate Alcohol Oxidase to Improve Ethanol Oxidation Performance. Appl Biochem Biotechnol 2024; 196:1948-1965. [PMID: 37453026 DOI: 10.1007/s12010-023-04626-3] [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] [Accepted: 07/01/2023] [Indexed: 07/18/2023]
Abstract
A high ethanol usage of alcohol oxidase (AOX) was required in industry. In this study, a "expand substrate pocket" strategy achieved a high activity AOX from Hansenula polymorpha (H. polymorpha) by Phe to Val residue (F/V) site-directed mutation to enlarge ethanol channel. Although H. Polymorpha AOX (HpAOX) possessed respectively 71.3% and 76.1% similarity with AOX (PpAOX) from Pichia pastoris (P. pastoris) in DNA and protein sequences, their active site structures including catalytic site and substrate channel were similar according to computer-aided analysis. After 3D structure analysis, Phe99 residue of their substrate channels was the most important residue to impact enzyme activity because of its large aromatic side chains. F99V mutation of HpAOX (HpAOXF99V) was designed and executed based on the enzyme catalytic mechanism and molecular computation in order to allow more larger size ethanol into active site. The highest enzyme activity of the fourth strains of HpAOXF99V mutant strain exhibited 12.06-folds increase than that of the host GS115 strain. Furthermore, kinetic studies indicated that the HpAOXF99V significantly promoted catalytic efficiency of ethanol than HpAOX, including Km, Vmax, kcat and kcat/Km. We also provided a new insight that the cofactor FAD irritated both active AOX octamer biosynthesis production and enzyme-catalysed ability due to help enzyme assembly and redox potential.
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Affiliation(s)
- Qian Li
- School of Chemistry and Biological Engineering, Department of Biological Science and Engineering, University of Science and Technology Beijing, Beijing, China
| | - Haiou Wang
- School of Chemistry and Biological Engineering, Department of Biological Science and Engineering, University of Science and Technology Beijing, Beijing, China.
| | - Wenxiao Zhang
- School of Chemistry and Biological Engineering, Department of Biological Science and Engineering, University of Science and Technology Beijing, Beijing, China
| | - Wenxuan Wang
- School of Chemistry and Biological Engineering, Department of Biological Science and Engineering, University of Science and Technology Beijing, Beijing, China
| | - Xiaoyu Ren
- School of Chemistry and Biological Engineering, Department of Biological Science and Engineering, University of Science and Technology Beijing, Beijing, China
| | - Mengyao Wu
- School of Chemistry and Biological Engineering, Department of Biological Science and Engineering, University of Science and Technology Beijing, Beijing, China
| | - Guoqing Shi
- School of Chemistry and Biological Engineering, Department of Biological Science and Engineering, University of Science and Technology Beijing, Beijing, China
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3
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Shanbhag AP. Stairway to Stereoisomers: Engineering Short- and Medium-Chain Ketoreductases To Produce Chiral Alcohols. Chembiochem 2023; 24:e202200687. [PMID: 36640298 DOI: 10.1002/cbic.202200687] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 01/14/2023] [Accepted: 01/14/2023] [Indexed: 01/15/2023]
Abstract
The short- and medium-chain dehydrogenase/reductase superfamilies are responsible for most chiral alcohol production in laboratories and industries. In nature, they participate in diverse roles such as detoxification, housekeeping, secondary metabolite production, and catalysis of several chemicals with commercial and environmental significance. As a result, they are used in industries to create biopolymers, active pharmaceutical intermediates (APIs), and are also used as components of modular enzymes like polyketide synthases for fabricating bioactive molecules. Consequently, random, semi-rational and rational engineering have helped transform these enzymes into product-oriented efficient catalysts. The rise of newer synthetic chemicals and their enantiopure counterparts has proved challenging, and engineering them has been the subject of numerous studies. However, they are frequently limited to the synthesis of a single chiral alcohol. The study attempts to defragment and describe hotspots of engineering short- and medium-chain dehydrogenases/reductases for the production of chiral synthons.
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Affiliation(s)
- Anirudh P Shanbhag
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, Kolkata, 700009, India.,Bugworks Research India Pvt. Ltd., C-CAMP, National Centre for Biological Sciences (NCBS-TIFR), Bellary Road, Bangalore, 560003, India
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4
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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] [Grants] [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
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5
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Wang Z, Zhou H, Yu H, Pu Z, Xu J, Zhang H, Wu J, Yang L. Computational Redesign of the Substrate Binding Pocket of Glutamate Dehydrogenase for Efficient Synthesis of Noncanonical l-Amino Acids. ACS Catal 2022. [DOI: 10.1021/acscatal.2c04636] [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)
- Ziyuan Wang
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, NO.38 Zhe-da Road, Hangzhou, Zhejiang, 310027, China
| | - Haisheng Zhou
- ZJU-Hangzhou Global Scientific and Technological Innovation Centre, NO.733 Jianshe 3rd Road, Xiaoshan District, Hangzhou, Zhejiang, 311200, China
| | - Haoran Yu
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, NO.38 Zhe-da Road, Hangzhou, Zhejiang, 310027, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Centre, NO.733 Jianshe 3rd Road, Xiaoshan District, Hangzhou, Zhejiang, 311200, China
| | - Zhongji Pu
- ZJU-Hangzhou Global Scientific and Technological Innovation Centre, NO.733 Jianshe 3rd Road, Xiaoshan District, Hangzhou, Zhejiang, 311200, China
| | - Jinling Xu
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, NO.38 Zhe-da Road, Hangzhou, Zhejiang, 310027, China
| | - Hongyu Zhang
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, NO.38 Zhe-da Road, Hangzhou, Zhejiang, 310027, China
| | - Jianping Wu
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, NO.38 Zhe-da Road, Hangzhou, Zhejiang, 310027, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Centre, NO.733 Jianshe 3rd Road, Xiaoshan District, Hangzhou, Zhejiang, 311200, China
| | - Lirong Yang
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, NO.38 Zhe-da Road, Hangzhou, Zhejiang, 310027, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Centre, NO.733 Jianshe 3rd Road, Xiaoshan District, Hangzhou, Zhejiang, 311200, China
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6
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Dai L, Li H, Huang JW, Hu Y, He M, Yang Y, Min J, Guo RT, Chen CC. Structure-based rational design of a short-chain dehydrogenase/reductase for improving activity toward mycotoxin patulin. Int J Biol Macromol 2022; 222:421-428. [PMID: 36176222 DOI: 10.1016/j.ijbiomac.2022.09.121] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Revised: 09/09/2022] [Accepted: 09/13/2022] [Indexed: 11/05/2022]
Abstract
Patulin is a fatal mycotoxin that is widely detected in drinking water and fruit-derived products contaminated by diverse filamentous fungi. CgSDR from Candida guilliermondii represents the first NADPH-dependent short-chain dehydrogenase/reductase that catalyzes the reduction of patulin to the nontoxic E-ascladiol. To elucidate the catalytic mechanism of CgSDR, we solved its crystal structure in complex with cofactor and substrate. Structural analyses indicate that patulin is situated in a hydrophobic pocket adjacent to the cofactor, with the hemiacetal ring orienting toward the nicotinamide moiety of NADPH. In addition, we conducted structure-guided engineering to modify substrate-binding residue V187 and obtained variant V187F, V187K and V187W, whose catalytic activity was elevated by 3.9-, 2.2- and 1.7-fold, respectively. The crystal structures of CgSDR variants suggest that introducing additional aromatic stacking or hydrogen-bonding interactions to bind the lactone ring of patulin might account for the observed enhanced activity. These results illustrate the catalytic mechanism of SDR-mediated patulin detoxification for the first time and provide the upgraded variants that exhibit tremendous potentials in industrial applications.
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Affiliation(s)
- Longhai Dai
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Hongshan Laboratory, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, 430062, PR China
| | - Hao Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Hongshan Laboratory, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, 430062, PR China
| | - Jian-Wen Huang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Hongshan Laboratory, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, 430062, PR China
| | - Yumei Hu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Hongshan Laboratory, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, 430062, PR China
| | - Min He
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Hongshan Laboratory, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, 430062, PR China
| | - Yu Yang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Hongshan Laboratory, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, 430062, PR China
| | - Jian Min
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Hongshan Laboratory, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, 430062, PR China
| | - Rey-Ting Guo
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Hongshan Laboratory, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, 430062, PR China.
| | - Chun-Chi Chen
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Hongshan Laboratory, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, 430062, PR China.
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7
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Chen X, Duez Q, Tripodi GL, Gilissen PJ, Piperoudis D, Tinnemans P, Elemans JAAW, Roithová J, Nolte RJM. Mechanistic Studies on the Epoxidation of Alkenes by Macrocyclic Manganese Porphyrin Catalysts. European J Org Chem 2022; 2022:e202200280. [PMID: 36249861 PMCID: PMC9541230 DOI: 10.1002/ejoc.202200280] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 04/21/2022] [Indexed: 11/08/2022]
Abstract
Macrocyclic metal porphyrin complexes can act as shape-selective catalysts mimicking the action of enzymes. To achieve enzyme-like reactivity, a mechanistic understanding of the reaction at the molecular level is needed. We report a mechanistic study of alkene epoxidation by the oxidant iodosylbenzene, mediated by an achiral and a chiral manganese(V)oxo porphyrin cage complex. Both complexes convert a great variety of alkenes into epoxides in yields varying between 20-88 %. We monitored the process of the formation of the manganese(V)oxo complexes by oxygen transfer from iodosylbenzene to manganese(III) complexes and their reactivity by ion mobility mass spectrometry. The results show that in the case of the achiral cage complex the initial iodosylbenzene adduct is formed on the inside of the cage and in the case of the chiral one on the outside of the cage. Its decomposition leads to a manganese complex with the oxo ligand on either the inside or outside of the cage. These experimental results are confirmed by DFT calculations. The oxo ligand on the outside of the cage reacts faster with a substrate molecule than the oxo ligand on the inside. The results indicate how the catalytic activity of the macrocyclic porphyrin complex can be tuned and explain why the chiral porphyrin complex does not catalyze the enantioselective epoxidation of alkenes.
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Affiliation(s)
- Xiaofei Chen
- Radboud UniversityInstitute for Molecules and MaterialsHeyendaalseweg 1356525 AJNijmegenThe Netherlands
| | - Quentin Duez
- Radboud UniversityInstitute for Molecules and MaterialsHeyendaalseweg 1356525 AJNijmegenThe Netherlands
| | - Guilherme L. Tripodi
- Radboud UniversityInstitute for Molecules and MaterialsHeyendaalseweg 1356525 AJNijmegenThe Netherlands
| | - Pieter J. Gilissen
- Radboud UniversityInstitute for Molecules and MaterialsHeyendaalseweg 1356525 AJNijmegenThe Netherlands
| | - Dimitrios Piperoudis
- Radboud UniversityInstitute for Molecules and MaterialsHeyendaalseweg 1356525 AJNijmegenThe Netherlands
| | - Paul Tinnemans
- Radboud UniversityInstitute for Molecules and MaterialsHeyendaalseweg 1356525 AJNijmegenThe Netherlands
| | - Johannes A. A. W. Elemans
- Radboud UniversityInstitute for Molecules and MaterialsHeyendaalseweg 1356525 AJNijmegenThe Netherlands
| | - Jana Roithová
- Radboud UniversityInstitute for Molecules and MaterialsHeyendaalseweg 1356525 AJNijmegenThe Netherlands
| | - Roeland J. M. Nolte
- Radboud UniversityInstitute for Molecules and MaterialsHeyendaalseweg 1356525 AJNijmegenThe Netherlands
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8
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Zhu Q, Yuan Y, Yan B, Zhou J, Zuo J, Bai L. A new biomimetic nanozyme of hemin/graphdiyne oxide with superior peroxidase-like activity for colorimetric bioassays. Analyst 2021; 146:7284-7293. [PMID: 34749389 DOI: 10.1039/d1an01456k] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Graphdiyne oxide (GDYO) is a novel type of two-dimensional carbon allotrope nanomaterial consisting of a large conjugated system and excellent chemical stability. To date, application of GDYO as a nanozyme in biosensing has been rarely reported. In this study, a novel ultrasensitive colorimetric bioassay was constructed using a hemin/GDYO nanocomposite (H/GDYO) as a new nanozyme with superior peroxidase-like activity for the detection of H2O2 and glucose. It was discovered that H/GDYO exhibited 6-fold higher peroxidase-like activity than pure hemin. Catalytic kinetic analysis showed that H/GDYO had a much higher affinity for H2O2 and glucose than that of hemin. The designed colorimetric bioassay displayed excellent sensitivity for H2O2 and glucose detection with a wide linear range of 0.015-0.5 mM and 0.1-10 mM, respectively, while the limit of detection (LOD) was as low as 4.39 μM and 38 μM, respectively. Moreover, it was successfully applied for the analysis of H2O2 in milk and glucose in real human serum samples with acceptable recoveries. Importantly, the developed colorimetric bioassay shows good agreement with the results obtained from a commercial blood glucose meter. We believe that the proposed method could provide a promising prospect for medical diagnosis and biotechnology.
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Affiliation(s)
- Qiqi Zhu
- Chongqing Research Center for Pharmaceutical Engineering, College of Pharmacy, Chongqing Medical University, Chongqing 400016, PR China.
| | - Yonghua Yuan
- Research Center for Pharmacodynamic Evaluation Engineering Technology of Chongqing, College of Pharmacy, Chongqing Medical University, Chongqing 400016, PR China
| | - Bin Yan
- The Eighth Middle School of Chongqing, Chongqing 400030, PR China
| | - Jing Zhou
- Chongqing Research Center for Pharmaceutical Engineering, College of Pharmacy, Chongqing Medical University, Chongqing 400016, PR China.
| | - Jianli Zuo
- Research Center for Pharmacodynamic Evaluation Engineering Technology of Chongqing, College of Pharmacy, Chongqing Medical University, Chongqing 400016, PR China
| | - Lijuan Bai
- Chongqing Research Center for Pharmaceutical Engineering, College of Pharmacy, Chongqing Medical University, Chongqing 400016, PR China.
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9
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Cheng F, Zhai QY, Gao XF, Liu HT, Qiu S, Wang YJ, Zheng YG. Tuning enzymatic properties by protein engineering toward catalytic tetrad of carbonyl reductase. Biotechnol Bioeng 2021; 118:4643-4654. [PMID: 34436762 DOI: 10.1002/bit.27925] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Revised: 08/03/2021] [Accepted: 08/22/2021] [Indexed: 01/20/2023]
Abstract
Enzyme engineering toward catalytic-tetrad residues usually results in activity loss. Unexpectedly, we found that a directed evolution campaign yielded a beneficial residue A100 in KmCR (a carbonyl reductase from Kluyveromyces marxianus ZJB14056), which is a residue of catalytic tetrad and conserved according to multiple sequence alignment. Inspired by this finding, we performed saturation mutagenesis on all the four residues of catalytic tetrad of KmCR. A number of variants with improved enzymatic activities were obtained. Among them, the variant KmCR_A100S exhibited increased catalytic efficiency (kcat /KM = 47.3 s-1 ·mM-1 ), improved stereoselectivity (from moderate selectivity (deP = 66.7%) to strict (S)-selectivity (deP > 99.5%)), and extended substrate scope, compared to those of KmCR_WT. In silico analysis showed that a relay system was rebuilt in KmCR via the beneficial residue S100. Furthermore, comparison of 11 protein engineering campaigns indicated that the beneficial position is easily overlooked due to the long distance (>10 Å) from ketone substrates. Since CRs share similar catalytic mechanism, the knowledge gained from this study has universal significance to CR engineering.
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Affiliation(s)
- 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
| | - Qiu-Yao Zhai
- 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
| | - Xiao-Fan Gao
- 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
| | - Hua-Tao Liu
- 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
| | - 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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10
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Efficient synthesis of bepotastine and cloperastine intermediates using engineered alcohol dehydrogenase with a hydrophobic pocket. Appl Microbiol Biotechnol 2021; 105:5873-5882. [PMID: 34342711 DOI: 10.1007/s00253-021-11413-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 05/12/2021] [Accepted: 06/11/2021] [Indexed: 10/20/2022]
Abstract
(S)-4-Chlorophenylpyridylmethanol and (R)-4-chlorobenzhydrol are key pharmaceutical intermediates for the synthesis of bepotastine and cloperastine, respectively. However, the biocatalytic approach to prepare these bulky diaryl ketones remains challenging because of the low activity of naturally occurring alcohol dehydrogenases (ADH). In the present study, ADH seq5, which has an adequate binding pocket volume and accepts bulky diaryl ketones, was further engineered with a binding pocket of increased hydrophobicity. Based on molecular simulation and binding free energy analyses, a small mutation library was constructed, and mutant seq5-D150I with a threefold increase in kcat and a low Km was obtained successfully. The comparison of kinetic parameters, binding free energy, docking conformation, and critical catalytic distances calculated by molecular dynamic simulations revealed the source of increased activity. To develop a practical approach with seq5-D150I, reaction conditions including pH, temperature, buffer, and metal ions were optimised and applied to synthesise (S)-4-chlorophenylpyridylmethanol and (R)-4-chlorobenzhydrol with high enantiomeric excess. The space-time yields for (S)-4-chlorophenylpyridylmethanol and (R)-4-chlorobenzhydrol increased dramatically to as high as 263.4 g∙L-1 day-1 and 150 g∙L-1 day-1, respectively, which, to our knowledge, is the highest reported yield to date. These results show that the biocatalytic approach with seq5-D150I may be practical for future industrial applications.Key points An alcohol dehydrogenase was engineered based on binding free energy analysis. The mutant seq5-D150I obtained a threefold increase in kcat and a low Km. Two important pharmaceutical intermediates were obtained with high space-time yield.
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11
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Pinto ÉSM, Feltes BC, Pedebos C, Dorn M. Modifying the catalytic preference of alpha-amylase toward n-alkanes for bioremediation purposes using in silico strategies. J Comput Chem 2021; 42:1540-1551. [PMID: 34018199 DOI: 10.1002/jcc.26562] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 04/30/2021] [Accepted: 05/04/2021] [Indexed: 11/08/2022]
Abstract
Since the beginning of oil exploration, whole ecosystems have been affected by accidents and bad practices involving petroleum compounds. In this sense, bioremediation stands out as the cheapest and most eco-friendly alternatives to reverse the damage done in oil-impacted areas. However, more efforts must be made to engineer enzymes that could be used in the bioremediation process. Interestingly, a recent work described that α-amylase, one of the most evolutionary conserved enzymes, was able to promiscuously degrade n-alkanes, a class of molecules abundant in the petroleum admixture. Considering that α-amylase is expressed in almost all known organisms, and employed in numerous biotechnological processes, using it can be a great leap toward more efficient applications of enzyme or microorganism-consortia bioremediation approaches. In this work, we employed a strict computational approach to design new α-amylase mutants with potentially enhanced catalytic efficiency toward n-alkanes. Using in silico techniques, such as molecular docking, molecular dynamics, metadynamics, and residue-residue interaction networks, we generated mutants potentially more efficient for degrading n-alkanes, L183Y, and N314A. Our results indicate that the new mutants have an increased binding rate for tetradecane, the longest n-alkane previously tested, which can reside in the catalytic center for more extended periods. Additionally, molecular dynamics and network analysis showed that the new mutations have no negative impact on protein structure than the WT. Our results aid in solidifying this enzyme as one more tool in the petroleum bioremediation toolbox.
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Affiliation(s)
| | - Bruno César Feltes
- Department of Genetics, Federal University of Rio Grande do Sul, Porto Alegre, Brazil.,Department of Biophysics, Federal University of Rio Grande do Sul, Porto Alegre, Brazil.,Institute of Informatics, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
| | - Conrado Pedebos
- School of Chemistry, University of Southampton, Southampton, UK
| | - Márcio Dorn
- Center of Biotechnology, Federal University of Rio Grande do Sul, Porto Alegre, Brazil.,Institute of Informatics, Federal University of Rio Grande do Sul, Porto Alegre, Brazil.,National Institute of Forensic Science and Technology, Porto Alegre, Brazil
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12
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Liu Z, Zhang R, Zhang W, Xu Y. Ile258Met mutation of Brucella melitensis 7α-hydroxysteroid dehydrogenase significantly enhances catalytic efficiency, cofactor affinity, and thermostability. Appl Microbiol Biotechnol 2021; 105:3573-3586. [PMID: 33937927 DOI: 10.1007/s00253-021-11299-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 03/25/2021] [Accepted: 04/17/2021] [Indexed: 12/20/2022]
Abstract
NAD(H)-dependent 7α-hydroxysteroid dehydrogenase catalyzes the oxidation of chenodeoxycholic acid to 7-oxolithocholic acid. Here, we designed mutations of Ile258 adjacent to the catalytic pocket of Brucella melitensis 7α-hydroxysteroid dehydrogenase. The I258M variant gave a 4.7-fold higher kcat, but 4.5-fold lower KM, compared with the wild type, resulting in a 21.8-fold higher kcat/KM value for chenodeoxycholic acid oxidation. It presented a 2.0-fold lower KM value with NAD+, suggesting stronger binding to the cofactor. I258M produced 7-oxolithocholic acid in the highest yield of 92.3% in 2 h, whereas the wild-type gave 88.4% in 12 h. The I258M mutation increased the half-life from 20.8 to 31.1 h at 30 °C. Molecular dynamics simulations indicated increased interactions and a modified tunnel improved the catalytic efficiency, and enhanced rigidity at three regions around the ligand-binding pocket increased the enzyme thermostability. This is the first report about significantly improved catalytic efficiency, cofactor affinity, and enzyme thermostability through single site-mutation of Brucella melitensis 7α-hydroxysteroid dehydrogenase. KEY POINTS: • Sequence and structure analysis guided the site mutation design. • Thermostability, catalytic efficiency and 7-oxo-LCA production were determined. • MD simulation was performed to indicate the improvement by I258M mutation.
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Affiliation(s)
- Zhiyong Liu
- Key Laboratory of Industrial Biotechnology of Ministry of Education & School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, People's Republic of China
| | - Rongzhen Zhang
- Key Laboratory of Industrial Biotechnology of Ministry of Education & School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, People's Republic of China.
| | - Wenchi Zhang
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Yan Xu
- Key Laboratory of Industrial Biotechnology of Ministry of Education & School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, People's Republic of China
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13
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Li A, Wang T, Tian Q, Yang X, Yin D, Qin Y, Zhang L. Single-Point Mutant Inverts the Stereoselectivity of a Carbonyl Reductase toward β-Ketoesters with Enhanced Activity. Chemistry 2021; 27:6283-6294. [PMID: 33475219 DOI: 10.1002/chem.202005195] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 12/29/2020] [Indexed: 01/06/2023]
Abstract
Enzyme stereoselectivity control is still a major challenge. To gain insight into the molecular basis of enzyme stereo-recognition and expand the source of antiPrelog carbonyl reductase toward β-ketoesters, rational enzyme design aiming at stereoselectivity inversion was performed. The designed variant Q139G switched the enzyme stereoselectivity toward β-ketoesters from Prelog to antiPrelog, providing corresponding alcohols in high enantiomeric purity (89.1-99.1 % ee). More importantly, the well-known trade-off between stereoselectivity and activity was not found. Q139G exhibited higher catalytic activity than the wildtype enzyme, the enhancement of the catalytic efficiency (kcat /Km ) varied from 1.1- to 27.1-fold. Interestingly, the mutant Q139G did not lead to reversed stereoselectivity toward aromatic ketones. Analysis of enzyme-substrate complexes showed that the structural flexibility of β-ketoesters and a newly formed cave together facilitated the formation of the antiPrelog-preferred conformation. In contrast, the relatively large and rigid structure of the aromatic ketones prevents them from forming the antiPrelog-preferred conformation.
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Affiliation(s)
- Aipeng Li
- School of Life Sciences, Northwestern Polytechnical University, 710072, Xi'an, China.,Research & Development Institute in Shenzhen, Northwestern Polytechnical University, 518057, Shenzhen, China
| | - Ting Wang
- School of Life Sciences, Northwestern Polytechnical University, 710072, Xi'an, China.,Research & Development Institute in Shenzhen, Northwestern Polytechnical University, 518057, Shenzhen, China
| | - Qing Tian
- School of Life Sciences, Northwestern Polytechnical University, 710072, Xi'an, China.,Research & Development Institute in Shenzhen, Northwestern Polytechnical University, 518057, Shenzhen, China
| | - Xiaohong Yang
- Department of Chemistry, University of California, One Shields Avenue, Davis, California, 95616, United States
| | - Dongming Yin
- School of Life Sciences, Northwestern Polytechnical University, 710072, Xi'an, China.,Research & Development Institute in Shenzhen, Northwestern Polytechnical University, 518057, Shenzhen, China
| | - Yong Qin
- School of Life Sciences, Northwestern Polytechnical University, 710072, Xi'an, China
| | - Lianbing Zhang
- School of Life Sciences, Northwestern Polytechnical University, 710072, Xi'an, China.,Research & Development Institute in Shenzhen, Northwestern Polytechnical University, 518057, Shenzhen, China
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14
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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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15
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Li H, Zhang W, Jiang X, Wang H, Wang Q, Wang J, Jia X, Qin B, You S. Development of an Enzymatic Process for the Synthesis of the Key Intermediate of Telotristat Ethyl. Adv Synth Catal 2020. [DOI: 10.1002/adsc.202001110] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Hengyu Li
- School of Life Sciences and Biopharmaceutical Sciences Shenyang Pharmaceutical University 103 Wenhua Road, Shenhe Shenyang 110016 People's Republic of China
| | - Wenhe Zhang
- School of Life Sciences and Biopharmaceutical Sciences Shenyang Pharmaceutical University 103 Wenhua Road, Shenhe Shenyang 110016 People's Republic of China
| | - Xianyan Jiang
- School of Life Sciences and Biopharmaceutical Sciences Shenyang Pharmaceutical University 103 Wenhua Road, Shenhe Shenyang 110016 People's Republic of China
| | - Huibin Wang
- School of Life Sciences and Biopharmaceutical Sciences Shenyang Pharmaceutical University 103 Wenhua Road, Shenhe Shenyang 110016 People's Republic of China
| | - Qi Wang
- School of Pharmaceutical Engineering Shenyang Pharmaceutical University 103 Wenhua Road, Shenhe Shenyang 110016 People's Republic of China
| | - Jiajun Wang
- School of Life Sciences and Biopharmaceutical Sciences Shenyang Pharmaceutical University 103 Wenhua Road, Shenhe Shenyang 110016 People's Republic of China
| | - Xian Jia
- School of Pharmaceutical Engineering Shenyang Pharmaceutical University 103 Wenhua Road, Shenhe Shenyang 110016 People's Republic of China
| | - Bin Qin
- Wuya College of Innovation Shenyang Pharmaceutical University 103 Wenhua Road, Shenhe Shenyang 110016 People's Republic of China
| | - Song You
- School of Life Sciences and Biopharmaceutical Sciences Shenyang Pharmaceutical University 103 Wenhua Road, Shenhe Shenyang 110016 People's Republic of China
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16
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Redesign of a short-chain dehydrogenase/reductase for asymmetric synthesis of ethyl (R)-2-hydroxy-4-phenylbutanoate based on per-residue free energy decomposition and sequence conservatism analysis. GREEN SYNTHESIS AND CATALYSIS 2020. [DOI: 10.1016/j.gresc.2020.09.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
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17
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Wang Y, Wang W, Gu Z, Miao X, Huang Q, Chang B. Temperature-responsive iron nanozymes based on poly( N-vinylcaprolactam) with multi-enzyme activity. RSC Adv 2020; 10:39954-39966. [PMID: 35515401 PMCID: PMC9057499 DOI: 10.1039/d0ra07226e] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 09/28/2020] [Indexed: 11/21/2022] Open
Abstract
Iron (Fe)-based nanozymes are widely applied in the biomedical field due to their enzyme-like catalytic activity. Herein, Fe(ii)-based coordination polymer nanohydrogels (FeCPNGs) have been conveniently prepared as a new type of nanozyme by the chelation reaction between ferrous iron and polymer nanohydrogels. The P(VCL-co-NMAM) nanohydrogels prepared by a reflux precipitation polymerization method using N-vinylcaprolactam (VCL) and N-methylol acrylamide (NMAM) as monomers and N,N-methylenebisacrylamide (MBA) as a crosslinker were esterified using P2O5 and then chelated with Fe(ii) ions to form nanozymes with peroxidase and superoxide dismutase (SOD) activity. It was found by dynamic light scattering (DLS) and transmission electron microscopy (TEM) that the nanohydrogels prepared with a monomer concentration of 4% and mass ratio of 1 : 1 (VCL : NMAM) had more uniform particle size, better dispersion and a distinct temperature response. The results of Fourier transform infrared (FTIR), DLS, TEM, X-ray powder diffraction (XRD) and X-ray photoelectron spectroscopy (XPS) indicated the successful preparation of the esterified nanohydrogel and FeCPNGs. Of particular importance is that such FeCPNGs can functionally mimic two antioxidant enzymes (peroxidase and superoxide dismutase) by UV analysis of catalytic oxidation between 3,3,5,5-tetramethylbenzidine (TMB) and H2O2 and the kit analysis of SOD-like activity.
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Affiliation(s)
- Yang Wang
- Department of Medical Technology, Suzhou Chien-shiung Institute of Technology Taicang 215411 Jiangsu Province P. R. China
| | - Wei Wang
- Nhwa Pharma. Corporation Xuzhou 221000 Jiangsu Province P. R.China
| | - Zhun Gu
- Department of Medical Technology, Suzhou Chien-shiung Institute of Technology Taicang 215411 Jiangsu Province P. R. China
| | - Xiangyang Miao
- Department of Medical Technology, Suzhou Chien-shiung Institute of Technology Taicang 215411 Jiangsu Province P. R. China
| | - Qiuyan Huang
- Department of Medical Technology, Suzhou Chien-shiung Institute of Technology Taicang 215411 Jiangsu Province P. R. China
| | - Baisong Chang
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, Wuhan University of Technology Wuhan 430070 P. R. China
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18
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Rational design of the carbonyl reductase EbSDR8 for efficient biosynthesis of enantiopure (R)-3-chloro-1-phenyl-1-propanol. Appl Microbiol Biotechnol 2020; 104:9219-9228. [PMID: 32954455 DOI: 10.1007/s00253-020-10904-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 09/01/2020] [Accepted: 09/10/2020] [Indexed: 10/23/2022]
Abstract
(R)-3-Chloro-1-phenyl-1-propanol ((R)-CPPO) is an important chiral intermediate for antidepressants. For its efficient biosynthesis, the carbonyl reductase EbSDR8 was engineered to asymmetrically reduce the unnatural substrate 3-chloro-1-phenyl-1-propanone (3-CPP) at high concentrations. Molecular docking and molecular dynamics simulations of the resulting mutants suggested enlarged substrate binding pocket and more reasonable interactions between the enzyme and the substrate or cofactor as the reasons for the enhanced catalytic activity and thus the remarkably improved conversion of high-concentration 3-CPP. Using the best mutant EbSDR8G94A/L153I/Y188A/Y202M as the whole-cell biocatalyst, reduction of 3-CPP (1.0 M) was conducted using 100% isopropanol as both the solvent and co-substrate for NADH regeneration, delivering (R)-CPPO with ˃ 99% eep and 95.5% conversion. This result suggests EbSDR8G94A/L153I/Y188A/Y202M as a potential biocatalyst for green production of (R)-CPPO at the industrial scale. KEY POINTS: • Rational design of EbSDR8 by modulating steric hindrance and molecular interactions; • Non-aqueous biocatalysis using isopropanol as both the solvent and co-substrate; • Whole-cell catalyzed production of 161 g/L enantiopure (R)-CPPO from 1.0 M of 3-CPP. Graphical Abstract.
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19
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Cui X, Li Z. High production of glutathione by in vitro enzymatic cascade after thermostability enhancement. AIChE J 2020. [DOI: 10.1002/aic.17055] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Xiangwei Cui
- State Key Laboratory of Bioreactor Engineering East China University of Science and Technology Shanghai China
| | - Zhimin Li
- State Key Laboratory of Bioreactor Engineering East China University of Science and Technology Shanghai China
- Shanghai Collaborative Innovation Center for Biomanufacturing Technology East China University of Science and Technology Shanghai China
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20
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Roth S, Stockinger P, Steff J, Steimle S, Sautner V, Tittmann K, Pleiss J, Müller M. Crossing the Border: From Keto- to Imine Reduction in Short-Chain Dehydrogenases/Reductases. Chembiochem 2020; 21:2615-2619. [PMID: 32315494 PMCID: PMC7540013 DOI: 10.1002/cbic.202000233] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Indexed: 11/10/2022]
Abstract
The family of NAD(P)H-dependent short-chain dehydrogenases/reductases (SDRs) comprises numerous biocatalysts capable of C=O or C=C reduction. The highly homologous noroxomaritidine reductase (NR) from Narcissus sp. aff. pseudonarcissus and Zt_SDR from Zephyranthes treatiae, however, are SDRs with an extended imine substrate scope. Comparison with a similar SDR from Asparagus officinalis (Ao_SDR) exhibiting keto-reducing activity, yet negligible imine-reducing capability, and mining the Short-Chain Dehydrogenase/Reductase Engineering Database indicated that NR and Zt_SDR possess a unique active-site composition among SDRs. Adapting the active site of Ao_SDR accordingly improved its imine-reducing capability. By applying the same strategy, an unrelated SDR from Methylobacterium sp. 77 (M77_SDR) with distinct keto-reducing activity was engineered into a promiscuous enzyme with imine-reducing activity, thereby confirming that the ability to reduce imines can be rationally introduced into members of the "classical" SDR enzyme family. Thus, members of the SDR family could be a promising starting point for protein approaches to generate new imine-reducing enzymes.
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Affiliation(s)
- Sebastian Roth
- Institute of Pharmaceutical SciencesUniversity of FreiburgAlbertstrasse 2579104FreiburgGermany
| | - Peter Stockinger
- Institute of Biochemistry and Technical BiochemistryUniversity of StuttgartAllmandring 3170569StuttgartGermany
| | - Jakob Steff
- Institute of Pharmaceutical SciencesUniversity of FreiburgAlbertstrasse 2579104FreiburgGermany
| | - Simon Steimle
- Institute of Pharmaceutical SciencesUniversity of FreiburgAlbertstrasse 2579104FreiburgGermany
| | - Viktor Sautner
- Department of Molecular EnzymologyUniversity of GöttingenJulia-Lermontowa-Weg 337077GöttingenGermany
| | - Kai Tittmann
- Department of Molecular EnzymologyUniversity of GöttingenJulia-Lermontowa-Weg 337077GöttingenGermany
| | - Jürgen Pleiss
- Institute of Biochemistry and Technical BiochemistryUniversity of StuttgartAllmandring 3170569StuttgartGermany
| | - Michael Müller
- Institute of Pharmaceutical SciencesUniversity of FreiburgAlbertstrasse 2579104FreiburgGermany
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21
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Enzymatic synthesis of an orlistat intermediate using a mutant short-chain dehydrogenase from Novosphingobium aromaticivorans. Process Biochem 2020. [DOI: 10.1016/j.procbio.2020.02.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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22
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Wei P, Chao P, Wang YY, Li DL, Zou QJ, Zong MH, Lou WY. Marked improvement in the asymmetric reduction of 2-hydroxyacetophenone with mut-AcCR in a biphasic system. MOLECULAR CATALYSIS 2020. [DOI: 10.1016/j.mcat.2020.110903] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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23
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Efficient biosynthesis of (R)-2-chloro-1-(2, 4-dichlorophenyl) ethanol using a mutant short-chain dehydrogenase from Novosphingobium aromaticivorans. Tetrahedron Lett 2020. [DOI: 10.1016/j.tetlet.2020.151914] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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24
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Li A, Li X, Pang W, Tian Q, Wang T, Zhang L. Fine-tuning of the substrate binding mode to enhance the catalytic efficiency of an ortho-haloacetophenone-specific carbonyl reductase. Catal Sci Technol 2020. [DOI: 10.1039/c9cy02335f] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Fine-tuning of the substrate binding mode was successfully applied for enhancing the catalytic efficiency of an ortho-haloacetophenone-specific carbonyl reductase.
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Affiliation(s)
- Aipeng Li
- Research & Development Institute in Shenzhen
- Northwestern Polytechnical University
- 518057 Shenzhen
- China
- School of Life Sciences
| | - Xue Li
- School of Life Sciences
- Northwestern Polytechnical University
- 710072 Xi'an
- China
| | - Wei Pang
- School of Life Sciences
- Northwestern Polytechnical University
- 710072 Xi'an
- China
| | - Qing Tian
- School of Life Sciences
- Northwestern Polytechnical University
- 710072 Xi'an
- China
| | - Ting Wang
- School of Life Sciences
- Northwestern Polytechnical University
- 710072 Xi'an
- China
| | - Lianbing Zhang
- Research & Development Institute in Shenzhen
- Northwestern Polytechnical University
- 518057 Shenzhen
- China
- School of Life Sciences
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25
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Su BM, Shao ZH, Li AP, Naeem M, Lin J, Ye LD, Yu HW. Rational Design of Dehydrogenase/Reductases Based on Comparative Structural Analysis of Prereaction-State and Free-State Simulations for Efficient Asymmetric Reduction of Bulky Aryl Ketones. ACS Catal 2019. [DOI: 10.1021/acscatal.9b04778] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Bing-Mei Su
- College of Chemical Engineering, Fuzhou University, Fuzhou 350116, China
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
| | - Ze-Hui Shao
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou 310027, China
| | - Ai-Peng Li
- School of Life Sciences, Northwestern Polytechnical University, Xi’an 710072, China
| | - Muhammad Naeem
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
| | - Juan Lin
- College of Chemical Engineering, Fuzhou University, Fuzhou 350116, China
- College of Biological Science and Engineering, Fuzhou University, Fuzhou 350116, China
| | - Li-Dan Ye
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
| | - Hong-Wei Yu
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
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Marine Collagen Peptides Promote Cell Proliferation of NIH-3T3 Fibroblasts via NF-κB Signaling Pathway. Molecules 2019; 24:molecules24224201. [PMID: 31752414 PMCID: PMC6891425 DOI: 10.3390/molecules24224201] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 11/13/2019] [Accepted: 11/18/2019] [Indexed: 02/07/2023] Open
Abstract
Marine collagen peptides (MCPs) with the ability to promote cell proliferation and migration were obtained from the skin of Nibea japonica. The purpose of MCPs isolation was an attempt to convert the by-products of the marine product processing industry to high value-added items. MCPs were observed to contain many polypeptides with molecular weights ≤ 10 kDa and most amino acid residues were hydrophilic. MCPs (0.25–10 mg/mL) also exhibited 2, 2-diphenyl-1-picrylhydrazyl (DPPH), hydroxyl, superoxide anion, and 2′-azino-bis-3-ethylbenzothiazoline-6-sulfonic acid (ABTS) radical scavenging activities. Furthermore, MCPs promoted the proliferation of NIH-3T3 cells. In vitro scratch assays indicated that MCPs significantly enhanced the scratch closure rate and promoted the migration of NIH-3T3 cells. To further determine the signaling mechanism of MCPs, western blotting was used to study the expression levels of nuclear factor kappa-B (NF-κB) p65, IκB kinase α (IKKα), and IκB kinase β (IKKβ) proteins of the NF-κB signaling pathway. Our results indicated protein levels of NF-κB p65, IKKα and IKKβ increased in MCPs-treated NIH-3T3 cells. In addition, MCPs increased the expression of epidermal growth factor (EGF), fibroblast growth factor (FGF), vascular endothelial growth factor (VEGF), and transforming growth factor (TGF-β) in NIH-3T3 cells. Therefore, MCPs, a by-product of N. japonica, exhibited potential wound healing abilities in vitro.
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Chen N, Chen Y, Tang Y, Zhao Q, Liu C, Niu W, Huang P, Yu F, Yang Z, Ding G. Efficient synthesis of (S)-2-chloro-1-(2, 4-dichlorophenyl) ethanol using a tetrad mutant alcohol dehydrogenase from Lactobacillus kefir. Process Biochem 2019. [DOI: 10.1016/j.procbio.2019.07.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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Li A, Yuchi Q, Li X, Pang W, Li B, Xue F, Zhang L. Discovery of a novel ortho-haloacetophenones-specific carbonyl reductase from Bacillus aryabhattai and insight into the molecular basis for its catalytic performance. Int J Biol Macromol 2019; 138:781-790. [PMID: 31351953 DOI: 10.1016/j.ijbiomac.2019.07.153] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 07/23/2019] [Accepted: 07/24/2019] [Indexed: 12/25/2022]
Abstract
To exploit robust biocatalysts for chiral 1-(2-halophenyl)ethanols synthesis, an ortho-haloacetophenones-specific carbonyl reductase (BaSDR1) gene from Bacillus aryabhattai was cloned and expressed in Escherichia coli. The impressive properties regarding BaSDR1 application include preference for NADH as coenzyme, noticeable tolerance against high cosubstrate concentration, and remarkable catalytic performance over a broad pH range from 5.0 to 10.0. The optimal temperature was 35 °C, with a half-life of 3.1 h at 35 °C and 0.75 h at 45 °C, respectively. Notably, BaSDR1 displayed excellent catalytic performance toward various ortho-haloacetophenones, providing chiral 1-(2-halophenyl)ethanols with 99% ee for all the substrates tested. Most importantly, the docking results indicated that the enzyme-substrate interactions and the steric hindrance of halogen atoms act in a push-pull manner in regulating enzyme catalytic ability. These results provide valuable clues for the structure-function relationships of BaSDR1 and the role of halogen groups in catalytic performance, and offer important reference for protein engineering and mining of functional compounds.
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Affiliation(s)
- Aipeng Li
- School of Life Sciences, Northwestern Polytechnical University, 710072 Xi'an, China; Research & Development Institute of Northwestern Polytechnical University in Shenzhen, 518057 Shenzhen, China
| | - Qingxiao Yuchi
- School of Life Sciences, Northwestern Polytechnical University, 710072 Xi'an, China
| | - Xue Li
- School of Life Sciences, Northwestern Polytechnical University, 710072 Xi'an, China
| | - Wei Pang
- School of Life Sciences, Northwestern Polytechnical University, 710072 Xi'an, China
| | - Bin Li
- School of Life Sciences, Northwestern Polytechnical University, 710072 Xi'an, China
| | - Feng Xue
- School of Marine and Bioengineering, Yancheng Institute of Technology, 224051 Yancheng, China.
| | - Lianbing Zhang
- School of Life Sciences, Northwestern Polytechnical University, 710072 Xi'an, China.
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Shen S, Zhang X, Li Z. Development of an engineered carbamoyl phosphate synthetase with released sensitivity to feedback inhibition by site-directed mutation and casting error-prone PCR. Enzyme Microb Technol 2019; 129:109354. [PMID: 31307577 DOI: 10.1016/j.enzmictec.2019.05.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 04/30/2019] [Accepted: 05/26/2019] [Indexed: 12/26/2022]
Abstract
Carbamoyl phosphate synthetase (CPS) is a key enzyme in both pyrimidine and arginine biosynthesis. However, it is inhibited strongly by uridine monophosphate (UMP), which is an intermediate of the de-novo synthesis of pyrimidine nucleoside. In this study, the native carbamoyl phosphate synthetase, from Escherichia coli, was evolved by site-directed mutation and casting error-prone PCR. Compared with the wild-type, the variant N1015 F had released sensitivity to UMP and exhibited 100% of the initial activity in the presence of UMP. Variant K1006A exhibited 0.14-fold improvement in initial activity and kept above 65% of relative activity under the saturated concentration of inhibitor. Structure analysis of variants demonstrated that the reduced sensitivity to inhibitor was largely attributed to the decreased hydrogen bonds, which could reduce the binding affinity with UMP. Also, Phe with large side chain could narrow the binding pocket and generate more steric hindrance. Based on the results in this study, N1015F was an ideal alternative catalyst for the wild-type CPS for pyrimidine biosynthesis.
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Affiliation(s)
- Su Shen
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Xing Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Zhimin Li
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China; Shanghai Collaborative Innovation Center for Biomanufacturing Technology, 130 Meilong Road, Shanghai 200237, China.
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30
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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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31
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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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32
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Gong XM, Qin Z, Li FL, Zeng BB, Zheng GW, Xu JH. Development of an Engineered Ketoreductase with Simultaneously Improved Thermostability and Activity for Making a Bulky Atorvastatin Precursor. ACS Catal 2018. [DOI: 10.1021/acscatal.8b03382] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Xu-Min Gong
- State Key Laboratory of Bioreactor Engineering and Shanghai Collaborative Innovation Center for Biomanufacturing, East China University of Science and Technology, Shanghai 200237, China
| | - Zhen Qin
- State Key Laboratory of Bioreactor Engineering and R&D Center of Separation and Extraction Technology in Fermentation Industry, East China University of Science and Technology, Shanghai 200237, China
| | - Fu-Long Li
- State Key Laboratory of Bioreactor Engineering and Shanghai Collaborative Innovation Center for Biomanufacturing, East China University of Science and Technology, Shanghai 200237, China
| | - Bu-Bing Zeng
- Shanghai Key Laboratory of New Drug Design, East China University of Science and Technology, Shanghai 200237, China
| | - Gao-Wei Zheng
- State Key Laboratory of Bioreactor Engineering and Shanghai Collaborative Innovation Center for Biomanufacturing, East China University of Science and Technology, Shanghai 200237, China
| | - Jian-He Xu
- State Key Laboratory of Bioreactor Engineering and Shanghai Collaborative Innovation Center for Biomanufacturing, East China University of Science and Technology, Shanghai 200237, 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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Directed Evolution of Recombinant C-Terminal Truncated Staphylococcus epidermidis Lipase AT2 for the Enhancement of Thermostability. Int J Mol Sci 2017; 18:ijms18112202. [PMID: 29113034 PMCID: PMC5713198 DOI: 10.3390/ijms18112202] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2017] [Revised: 10/09/2017] [Accepted: 10/12/2017] [Indexed: 11/17/2022] Open
Abstract
In the industrial processes, lipases are expected to operate at temperatures above 45 °C and could retain activity in organic solvents. Hence, a C-terminal truncated lipase from Staphylococcus epidermis AT2 (rT-M386) was engineered by directed evolution. A mutant with glycine-to-cysteine substitution (G210C) demonstrated a remarkable improvement of thermostability, whereby the mutation enhanced the activity five-fold when compared to the rT-M386 at 50 °C. The rT-M386 and G210C lipases were purified concurrently using GST-affinity chromatography. The biochemical and biophysical properties of both enzymes were investigated. The G210C lipase showed a higher optimum temperature (45 °C) and displayed a more prolonged half-life in the range of 40-60 °C as compared to rT-M386. Both lipases exhibited optimal activity and stability at pH 8. The G210C showed the highest stability in the presence of polar organic solvents at 50 °C compared to the rT-M386. Denatured protein analysis presented a significant change in the molecular ellipticity value above 60 °C, which verified the experimental result on the temperature and thermostability profile of G210C.
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35
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Is literature data useful for identifying enzyme catalysts for new substrates? A case study on reduction of 1-aryl-2-alkanoates. Bioorg Chem 2017; 74:260-271. [DOI: 10.1016/j.bioorg.2017.08.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 08/16/2017] [Accepted: 08/17/2017] [Indexed: 01/04/2023]
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