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Liu M, Li Q, Liu X, Zhang P, Zhang H. Improved thermostability of type I pullulanase from Bacillus thermoliquefaciens by error-prone PCR. Enzyme Microb Technol 2023; 169:110290. [PMID: 37473696 DOI: 10.1016/j.enzmictec.2023.110290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 06/23/2023] [Accepted: 07/12/2023] [Indexed: 07/22/2023]
Abstract
Pullulanase (PulB) is a starch-debranching enzyme. In order to improve its catalytic performance, random mutagenesis was performed on the pullulanase gene derived from Bacillus thermoliquefaciens. Two rounds of error-prone PCR were carried out. Mutant T252S was screened in the first round of error-prone library, which had the highest catalytic activity. During the second round of mutations, mutant enzyme G250P/T252S/G253T/N255K was screened, which had further improved catalytic activity and the best thermostability. Compared with the parent enzyme, the specific activity of mutant enzyme G250P/T252S/G253T/N255K increased by 1.9 times, Km decreased by 22.7 %, kcat increased by 28.7 %, and kcat/Km increased by 68.4 %. The thermostability of the mutant enzyme improved significantly, showing that the half-life at 60 °C was extended to 7.5 h, which was 87.5 % higher than that of the parent enzyme. The mutation sites in these two rounds were concentrated in the 250-255 regions, indicating that this region was an important region affecting the catalytic activity and Thermostability. The reasons for the change of enzymtic properties was also preliminarily analyzed through three-dimensional simulation.
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Affiliation(s)
- Mengmeng Liu
- School of Life Sciences, Henan University, Kaifeng 475004, China; Engineering Research Center for Applied Microbiology of Henan Province, Kaifeng 475004, China
| | - Qiu Li
- School of Life Sciences, Henan University, Kaifeng 475004, China; Engineering Research Center for Applied Microbiology of Henan Province, Kaifeng 475004, China
| | - Xiaoxiao Liu
- School of Life Sciences, Henan University, Kaifeng 475004, China; Engineering Research Center for Applied Microbiology of Henan Province, Kaifeng 475004, China
| | - Pengpai Zhang
- School of Life Sciences, Henan University, Kaifeng 475004, China; Engineering Research Center for Applied Microbiology of Henan Province, Kaifeng 475004, China.
| | - Haiyan Zhang
- School of Life Sciences, Henan University, Kaifeng 475004, China; Engineering Research Center for Applied Microbiology of Henan Province, Kaifeng 475004, China.
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2
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Liu C, Wang G, Han X, Cao L, Wang K, Lin H, Sui J. Heterologous expression and activity verification of ornithine decarboxylase from a wild strain of Shewanella xiamenensis. Front Microbiol 2022; 13:1100889. [PMID: 36605515 PMCID: PMC9808388 DOI: 10.3389/fmicb.2022.1100889] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 12/05/2022] [Indexed: 01/07/2023] Open
Abstract
Shewanella xiamenensis is widely found in spoilage fish, shrimp and other seafoods. Under suitable conditions, ornithine can be synthesized into putrescine, which may spoil food or endanger health. Our research used a wild strain of Shewanella xiamenensis isolated from "Yi Lu Xian" salted fish (a salting method for sea bass) as a research object. According to the database of National Center of Biotechnology Information (NCBI), the target ornithine decarboxylase (ODC) gene SpeF was successfully amplified using the wild strain of Shewanella xiamenensis as the template. Sequencing alignment showed that the SpeF of the wild strain had more than 98% homology compared with the standard strain. The amino acid substitution occurred in the residues of 343, 618, 705, and 708 in the wild strain. After optimizing the expression conditions, a heterologous expression system of ODC was constructed to achieve a high yield of expression. The amount of 253.38 mg of ODC per liter of LB broth was finally expressed. High performance liquid chromatography (HPLC) and subsequent ODC activity verification experiments showed that hetero-expressed ODC showed a certain enzyme activity for about 11.91 ± 0.38 U/mg. Our study gives a new way to the development of a low-cost and high-yield strategy to produce ODC, providing experimental materials for further research and elimination of putrescine in food hazards.
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3
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Liu CY, Cecylia Severin L, Lyu CJ, Zhu WL, Wang HP, Jiang CJ, Mei LH, Liu HG, Huang J. Improving thermostability of (R)-selective amine transaminase from Aspergillus terreus by evolutionary coupling saturation mutagenesis. Biochem Eng J 2021. [DOI: 10.1016/j.bej.2021.107926] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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4
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Kubyshkin V, Davis R, Budisa N. Biochemistry of fluoroprolines: the prospect of making fluorine a bioelement. Beilstein J Org Chem 2021; 17:439-460. [PMID: 33727970 PMCID: PMC7934785 DOI: 10.3762/bjoc.17.40] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 01/22/2021] [Indexed: 12/12/2022] Open
Abstract
Due to the heterocyclic structure and distinct conformational profile, proline is unique in the repertoire of the 20 amino acids coded into proteins. Here, we summarize the biochemical work on the replacement of proline with (4R)- and (4S)-fluoroproline as well as 4,4-difluoroproline in proteins done mainly in the last two decades. We first recapitulate the complex position and biochemical fate of proline in the biochemistry of a cell, discuss the physicochemical properties of fluoroprolines, and overview the attempts to use these amino acids as proline replacements in studies of protein production and folding. Fluorinated proline replacements are able to elevate the protein expression speed and yields and improve the thermodynamic and kinetic folding profiles of individual proteins. In this context, fluoroprolines can be viewed as useful tools in the biotechnological toolbox. As a prospect, we envision that proteome-wide proline-to-fluoroproline substitutions could be possible. We suggest a hypothetical scenario for the use of laboratory evolutionary methods with fluoroprolines as a suitable vehicle to introduce fluorine into living cells. This approach may enable creation of synthetic cells endowed with artificial biodiversity, containing fluorine as a bioelement.
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Affiliation(s)
- Vladimir Kubyshkin
- Department of Chemistry, University of Manitoba, 144 Dysart Rd., Winnipeg, R3T 2N2, Canada
| | - Rebecca Davis
- Department of Chemistry, University of Manitoba, 144 Dysart Rd., Winnipeg, R3T 2N2, Canada
| | - Nediljko Budisa
- Department of Chemistry, University of Manitoba, 144 Dysart Rd., Winnipeg, R3T 2N2, Canada.,Institute of Chemistry, Technical University of Berlin, Müller-Breslau-Str. 10, 10623 Berlin, Germany
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5
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Fang R, Chandra Syahputra J, Airhunmwunde O, Wu Y, Lv C, Huang J, Xiao G, Chen Q. Improving the enzyme property of ornithine transcarbamylase from Lactobacillus brevis through site-directed mutation. Lebensm Wiss Technol 2020. [DOI: 10.1016/j.lwt.2020.109953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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6
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Markova K, Chmelova K, Marques SM, Carpentier P, Bednar D, Damborsky J, Marek M. Decoding the intricate network of molecular interactions of a hyperstable engineered biocatalyst. Chem Sci 2020; 11:11162-11178. [PMID: 34094357 PMCID: PMC8162949 DOI: 10.1039/d0sc03367g] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 09/10/2020] [Indexed: 12/01/2022] Open
Abstract
Computational design of protein catalysts with enhanced stabilities for use in research and enzyme technologies is a challenging task. Using force-field calculations and phylogenetic analysis, we previously designed the haloalkane dehalogenase DhaA115 which contains 11 mutations that confer upon it outstanding thermostability (T m = 73.5 °C; ΔT m > 23 °C). An understanding of the structural basis of this hyperstabilization is required in order to develop computer algorithms and predictive tools. Here, we report X-ray structures of DhaA115 at 1.55 Å and 1.6 Å resolutions and their molecular dynamics trajectories, which unravel the intricate network of interactions that reinforce the αβα-sandwich architecture. Unexpectedly, mutations toward bulky aromatic amino acids at the protein surface triggered long-distance (∼27 Å) backbone changes due to cooperative effects. These cooperative interactions produced an unprecedented double-lock system that: (i) induced backbone changes, (ii) closed the molecular gates to the active site, (iii) reduced the volumes of the main and slot access tunnels, and (iv) occluded the active site. Despite these spatial restrictions, experimental tracing of the access tunnels using krypton derivative crystals demonstrates that transport of ligands is still effective. Our findings highlight key thermostabilization effects and provide a structural basis for designing new thermostable protein catalysts.
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Affiliation(s)
- Klara Markova
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University Kamenice 5 625 00 Brno Czech Republic
- International Clinical Research Center, St. Anne's University Hospital Brno Pekarska 53 656 91 Brno Czech Republic
| | - Klaudia Chmelova
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University Kamenice 5 625 00 Brno Czech Republic
- International Clinical Research Center, St. Anne's University Hospital Brno Pekarska 53 656 91 Brno Czech Republic
| | - Sérgio M Marques
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University Kamenice 5 625 00 Brno Czech Republic
- International Clinical Research Center, St. Anne's University Hospital Brno Pekarska 53 656 91 Brno Czech Republic
| | - Philippe Carpentier
- Université Grenoble Alpes, CNRS, CEA, Interdisciplinary Research Institute of Grenoble (IRIG), Laboratoire Chimie et Biologie des Métaux (LCBM) 17 Avenue des Martyrs 38054 Grenoble France
- European Synchrotron Radiation Facility (ESRF) 71 Avenue des Martyrs 38043 Grenoble France
| | - David Bednar
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University Kamenice 5 625 00 Brno Czech Republic
- International Clinical Research Center, St. Anne's University Hospital Brno Pekarska 53 656 91 Brno Czech Republic
| | - Jiri Damborsky
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University Kamenice 5 625 00 Brno Czech Republic
- International Clinical Research Center, St. Anne's University Hospital Brno Pekarska 53 656 91 Brno Czech Republic
| | - Martin Marek
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University Kamenice 5 625 00 Brno Czech Republic
- International Clinical Research Center, St. Anne's University Hospital Brno Pekarska 53 656 91 Brno Czech Republic
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7
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Improving the catalytic thermostability of Bacillus altitudinis W3 ω-transaminase by proline substitutions. 3 Biotech 2020; 10:323. [PMID: 32656056 DOI: 10.1007/s13205-020-02321-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 06/24/2020] [Indexed: 01/10/2023] Open
Abstract
As a green biocatalyst, transaminase with high thermostability can be better employed to synthesize many pharmaceutical intermediates in industry. To improve the thermostability of (R)-selective amine transaminase from Bacillus altitudinis W3, related mutation sites were determined by multiple amino acid sequence alignment between wild-type ω-transaminase and four potential thermophilic ω-transaminases, followed by replacement of the related amino acid residues with proline by site-directed mutagenesis. Three stabilized mutants (D192P, T237P, and D192P/T237P) showing the highest stability were obtained and used for further analysis. Comparison with the wild-type enzyme revealed that the double mutant D192P/T237P exhibited the largest shift in thermostability, with a 2.5-fold improvement of t 1/2 at 40 °C, and a 6.3 °C increase in T 50 15, and a 5 °C higher optimal catalytic temperature. Additionally, this mutant exhibited an increase in catalytic efficiency (k cat/K m) relative to the wild-type enzyme. Modeling analysis indicated that the improved thermostability of the mutants could be associated with newly formed hydrophobic interactions and hydrogen bonds. This study shown that proline substitutions guided by sequence alignment to improve the thermostability of (R)-selective amine transaminase was effective and this method can also be used to engineering other enzymes.
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8
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Mate DM, Rivera NR, Sanchez‐Freire E, Ayala JA, Berenguer J, Hidalgo A. Thermostability enhancement of the
Pseudomonas fluorescens
esterase I by in vivo folding selection in
Thermus thermophilus. Biotechnol Bioeng 2019; 117:30-38. [DOI: 10.1002/bit.27170] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 09/06/2019] [Accepted: 09/08/2019] [Indexed: 12/26/2022]
Affiliation(s)
- Diana M. Mate
- Department of Molecular Biology, Center of Molecular Biology “Severo Ochoa” (UAM‐CSIC)Autonomous University of Madrid Madrid Spain
| | - Noé R. Rivera
- Department of Molecular Biology, Center of Molecular Biology “Severo Ochoa” (UAM‐CSIC)Autonomous University of Madrid Madrid Spain
- Department of Biochemistry, Faculty of MedicineUniversity of El Salvador San Salvador El Salvador
| | - Esther Sanchez‐Freire
- Department of Molecular Biology, Center of Molecular Biology “Severo Ochoa” (UAM‐CSIC)Autonomous University of Madrid Madrid Spain
| | - Juan A. Ayala
- Consejo Superior de Investigaciones CientíficasCenter of Molecular Biology “Severo Ochoa” (UAM‐CSIC) Madrid Spain
| | - José Berenguer
- Department of Molecular Biology, Center of Molecular Biology “Severo Ochoa” (UAM‐CSIC)Autonomous University of Madrid Madrid Spain
| | - Aurelio Hidalgo
- Department of Molecular Biology, Center of Molecular Biology “Severo Ochoa” (UAM‐CSIC)Autonomous University of Madrid Madrid Spain
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Guo Y, Tu T, Zheng J, Bai Y, Huang H, Su X, Wang Y, Wang Y, Yao B, Luo H. Improvement of BsAPA Aspartic Protease Thermostability via Autocatalysis-Resistant Mutation. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:10505-10512. [PMID: 31462045 DOI: 10.1021/acs.jafc.9b03959] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
An aspartic protease gene (Bsapa) was cloned from Bispora sp. MEY-1 and expressed in Pichia pastoris. The recombinant BsAPA showed maximal activity at pH 3.0 and 75 °C and remained stable at 70 °C and below, indicating the thermostable nature of BsAPA. However, heat inactivation still limits the application of BsAPA. To further improve its thermostability, an autocatalysis site (L205-F206) in BsAPA was identified and three mutants (F193W, K204P, and A371V) were generated based on the analysis of the structure neighboring the autocatalysis site. These mutants have improved thermostability, and their half-life at 75 °C increased by 0.5-, 0.2-, and 0.3-fold, respectively. A triple-site mutant (F193W/K204P/A371V) was generated, with 1.5-fold increased half-life at 80 and a 10.7 °C increased Tm, compared with those of the wild-type. These results indicate that autocatalysis of aspartic protease reduces enzyme thermostability. Furthermore, site-directed mutagenesis at regions near the autocatalysis site is an efficient approach to improve aspartic protease thermostability.
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Affiliation(s)
- Yujie Guo
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute , Chinese Academy of Agricultural Sciences , No. 18 12 Zhongguancun South Street , Beijing 100081 , P. R. China
| | - Tao Tu
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute , Chinese Academy of Agricultural Sciences , No. 18 12 Zhongguancun South Street , Beijing 100081 , P. R. China
| | - Jie Zheng
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute , Chinese Academy of Agricultural Sciences , No. 18 12 Zhongguancun South Street , Beijing 100081 , P. R. China
| | - Yingguo Bai
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute , Chinese Academy of Agricultural Sciences , No. 18 12 Zhongguancun South Street , Beijing 100081 , P. R. China
| | - Huoqing Huang
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute , Chinese Academy of Agricultural Sciences , No. 18 12 Zhongguancun South Street , Beijing 100081 , P. R. China
| | - Xiaoyun Su
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute , Chinese Academy of Agricultural Sciences , No. 18 12 Zhongguancun South Street , Beijing 100081 , P. R. China
| | - Yuan Wang
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute , Chinese Academy of Agricultural Sciences , No. 18 12 Zhongguancun South Street , Beijing 100081 , P. R. China
| | - Yaru Wang
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute , Chinese Academy of Agricultural Sciences , No. 18 12 Zhongguancun South Street , Beijing 100081 , P. R. China
| | - Bin Yao
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute , Chinese Academy of Agricultural Sciences , No. 18 12 Zhongguancun South Street , Beijing 100081 , P. R. China
| | - Huiying Luo
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute , Chinese Academy of Agricultural Sciences , No. 18 12 Zhongguancun South Street , Beijing 100081 , P. R. China
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10
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Bownik A, Szabelak A, Kulińska M, Wałęka M. Effects of L-proline on swimming parameters of Daphnia magna subjected to heat stress. J Therm Biol 2019; 84:154-163. [PMID: 31466748 DOI: 10.1016/j.jtherbio.2019.06.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 05/27/2019] [Accepted: 06/30/2019] [Indexed: 01/19/2023]
Abstract
L-proline (L-PROL) is an essential amino acid, a constituent of many proteins and the osmoprotective molecule produced and accumulated in higher plants and some freshwater microalgae in response to various environmental stressors. Knowledge on thermoprotective effects of this amino acid on freshwater invertebrates is very scarce. Therefore the aim of our study was to determine the effect of L-PROL at concentrations: 10 mg/L, 20 mg/L and 50 mg/L on swimming behavior (immobilization, swimming track density, swimming speed, turning ability) of Daphnia magna subjected to temperatures: 22 °C, 35 °C and 38 °C. We found that L-PROL elevated all the measured swimming parameters at 22 °C when compared to the untreated crustaceans. Furthermore, L-PROL alleviated heat-induced inhibition of these parameters in the experimental animals subjected to 35 °C. The results suggest that L-PROL stimulates swimming performance and alleviates alterations of swimming parameters induced by heat stress in D. magna. Moreover, these findings may support the hypothesis that in natural conditions, L-PROL may protect crustaceans against thermal stress.
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Affiliation(s)
- Adam Bownik
- Department of Hydrobiology and Protection of Ecosystems, University of Life Sciences in Lublin, Dobrzańskiego 37, 20-262, Lublin, Poland.
| | - Aleksandra Szabelak
- Department of Hydrobiology and Protection of Ecosystems, University of Life Sciences in Lublin, Dobrzańskiego 37, 20-262, Lublin, Poland
| | - Magdalena Kulińska
- Department of Hydrobiology and Protection of Ecosystems, University of Life Sciences in Lublin, Dobrzańskiego 37, 20-262, Lublin, Poland
| | - Monika Wałęka
- Department of Hydrobiology and Protection of Ecosystems, University of Life Sciences in Lublin, Dobrzańskiego 37, 20-262, Lublin, Poland
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11
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Sun Z, Liu Q, Qu G, Feng Y, Reetz MT. Utility of B-Factors in Protein Science: Interpreting Rigidity, Flexibility, and Internal Motion and Engineering Thermostability. Chem Rev 2019; 119:1626-1665. [PMID: 30698416 DOI: 10.1021/acs.chemrev.8b00290] [Citation(s) in RCA: 275] [Impact Index Per Article: 55.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Zhoutong Sun
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West Seventh Avenue, Tianjin Airport Economic Area, Tianjin 300308, China
| | - Qian Liu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Ge Qu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West Seventh Avenue, Tianjin Airport Economic Area, Tianjin 300308, China
| | - Yan Feng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Manfred T. Reetz
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West Seventh Avenue, Tianjin Airport Economic Area, Tianjin 300308, China
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
- Chemistry Department, Philipps-University, Hans-Meerwein-Strasse 4, 35032 Marburg, Germany
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12
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Han B, Hou Y, Jiang T, Lv B, Zhao L, Feng X, Li C. Computation-Aided Rational Deletion of C-Terminal Region Improved the Stability, Activity, and Expression Level of GH2 β-Glucuronidase. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2018; 66:11380-11389. [PMID: 30296070 DOI: 10.1021/acs.jafc.8b03449] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
In this study, computation-aided design on the basis of structural analysis was employed to rationally identify a highly dynamic C-terminal region that regulates the stability, expression level, and activity of a GH2 fungal glucuronidase from Aspergillus oryzae Li-3 (PGUS). Then, four mutants with a precisely truncated C-terminal region in different lengths were constructed; among them, mutant D591-604 with a 3.8-fold increase in half-life at 65 °C and a 6.8 kJ/mol increase in Gibbs free energy showed obviously improved kinetic and thermodynamic stability in comparison to PGUS. Mutants D590-604 and D591-604 both showed approximately 2.4-fold increases in the catalytic efficiency kcat/ Km and 1.8-fold increases in the expression level. Additionally, the expression level of PGUS was doubled through a C-terminal region swap with bacterial GUS from E. coli (EGUS). Finally, the robust PGUS mutants D590-604 and D591-604 were applied in the preparation of glycyrrhetinic acid with 4.0- and 4.4-fold increases in concentration through glycyrrhizin hydrolysis by a fed-batch process.
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Affiliation(s)
- Beijia Han
- Institute for Synthetic Biosystem/Department of Biochemical Engineering, School of Chemistry and Chemical Engineering , Beijing Institute of Technology , Beijing 100081 , People's Republic of China
| | - Yuhui Hou
- Institute for Synthetic Biosystem/Department of Biochemical Engineering, School of Chemistry and Chemical Engineering , Beijing Institute of Technology , Beijing 100081 , People's Republic of China
| | - Tian Jiang
- Institute for Synthetic Biosystem/Department of Biochemical Engineering, School of Chemistry and Chemical Engineering , Beijing Institute of Technology , Beijing 100081 , People's Republic of China
| | - Bo Lv
- Institute for Synthetic Biosystem/Department of Biochemical Engineering, School of Chemistry and Chemical Engineering , Beijing Institute of Technology , Beijing 100081 , People's Republic of China
| | - Lina Zhao
- Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety , Institute of High Energy Physics, Chinese Academy of Sciences , Beijing 100049 , People's Republic of China
| | - Xudong Feng
- Institute for Synthetic Biosystem/Department of Biochemical Engineering, School of Chemistry and Chemical Engineering , Beijing Institute of Technology , Beijing 100081 , People's Republic of China
| | - Chun Li
- Institute for Synthetic Biosystem/Department of Biochemical Engineering, School of Chemistry and Chemical Engineering , Beijing Institute of Technology , Beijing 100081 , People's Republic of China
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13
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Abstract
Amide rotation of peptidyl-prolyl fragments is an important factor in backbone structure organization of proteins. Computational studies have indicated that this rotation preferentially proceeds through a defined transition-state structure (syn/exo). Here, we complement the computational findings by determining the amide bond rotation barriers for derivatives of the two symmetric proline analogues, meso and racemic pyrrolidine-2,5-dicarboxylic acids. The rotations around these residues represent syn/exo-syn/exo and anti/endo-syn/exo hybrid transition states for the meso and racemic diastereomer, respectively. The rotation barriers are lower for the former rotation by about 9 kJ mol-1 (aqueous medium), suggesting a strong preference for the syn/exo (clockwise) rotation over the anti/endo (anticlockwise) rotation. The results show that both hybrid rotation processes are enthalpically driven but respond differently to solvent polarity changes due to the different transition state dipole-dipole interactions.
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Affiliation(s)
- Vladimir Kubyshkin
- Biocatalysis Group, Institute of Chemistry, Technical University of Berlin, Müller-Breslau-Str. 10, Berlin 10623, Germany.
| | - Nediljko Budisa
- Biocatalysis Group, Institute of Chemistry, Technical University of Berlin, Müller-Breslau-Str. 10, Berlin 10623, Germany.
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14
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Jones BJ, Lim HY, Huang J, Kazlauskas RJ. Comparison of Five Protein Engineering Strategies for Stabilizing an α/β-Hydrolase. Biochemistry 2017; 56:6521-6532. [PMID: 29087185 DOI: 10.1021/acs.biochem.7b00571] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A review of the previous stabilization of α/β-hydrolase fold enzymes revealed many different strategies, but no comparison of strategies on the same enzyme. For this reason, we compared five strategies to identify stabilizing mutations in a model α/β-hydrolase fold enzyme, salicylic acid binding protein 2, to reversible denaturation by urea and to irreversible denaturation by heat. The five strategies included one location agnostic approach (random mutagenesis using error-prone polymerase chain reaction), two structure-based approaches [computational design (Rosetta, FoldX) and mutation of flexible regions], and two sequence-based approaches (addition of proline at locations where a more stable homologue has proline and mutation to consensus). All strategies identified stabilizing mutations, but the best balance of success rate, degree of stabilization, and ease of implementation was mutation to consensus. A web-based automated program that predicts substitutions needed to mutate to consensus is available at http://kazlab.umn.edu .
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Affiliation(s)
- Bryan J Jones
- Department of Biochemistry, Molecular Biology & Biophysics and The Biotechnology Institute, University of Minnesota , 1479 Gortner Avenue, Saint Paul, Minnesota 55108, United States
| | - Huey Yee Lim
- Department of Biochemistry, Molecular Biology & Biophysics and The Biotechnology Institute, University of Minnesota , 1479 Gortner Avenue, Saint Paul, Minnesota 55108, United States
| | - Jun Huang
- Department of Biochemistry, Molecular Biology & Biophysics and The Biotechnology Institute, University of Minnesota , 1479 Gortner Avenue, Saint Paul, Minnesota 55108, United States.,School of Biological and Chemical Engineering, Zhejiang University of Science and Technology , Hangzhou 310023, People's Republic of China
| | - Romas J Kazlauskas
- Department of Biochemistry, Molecular Biology & Biophysics and The Biotechnology Institute, University of Minnesota , 1479 Gortner Avenue, Saint Paul, Minnesota 55108, United States
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15
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Hu S, Zhang X, Lu Y, Lin YC, Xie DF, Fang H, Huang J, Mei LH. Cloning, expression and characterization of an aspartate aminotransferase gene from Lactobacillus brevis CGMCC 1306. BIOTECHNOL BIOTEC EQ 2017. [DOI: 10.1080/13102818.2017.1304181] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Affiliation(s)
- Sheng Hu
- School of Biological and Chemical Engineering, Ningbo Institute of Technology, Zhejiang University, Ningbo, P.R. China
| | - Xiang Zhang
- School of Biological and Chemical Engineering, Zhejiang University of Science and Technology, Hangzhou, P.R. China
| | - Yi Lu
- School of Biological and Chemical Engineering, Zhejiang University of Science and Technology, Hangzhou, P.R. China
| | - Yue-Cheng Lin
- School of Biological and Chemical Engineering, Zhejiang University of Science and Technology, Hangzhou, P.R. China
| | - Dong-Fang Xie
- School of Biological and Chemical Engineering, Zhejiang University of Science and Technology, Hangzhou, P.R. China
| | - Hui Fang
- School of Biological and Chemical Engineering, Zhejiang University of Science and Technology, Hangzhou, P.R. China
| | - Jun Huang
- School of Biological and Chemical Engineering, Zhejiang University of Science and Technology, Hangzhou, P.R. China
| | - Le-He Mei
- School of Biological and Chemical Engineering, Ningbo Institute of Technology, Zhejiang University, Ningbo, P.R. China
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Huang J, Xie DF, Feng Y. Engineering thermostable (R)-selective amine transaminase from Aspergillus terreus through in silico design employing B-factor and folding free energy calculations. Biochem Biophys Res Commun 2016; 483:397-402. [PMID: 28017723 DOI: 10.1016/j.bbrc.2016.12.131] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2016] [Accepted: 12/20/2016] [Indexed: 11/26/2022]
Abstract
Amine transaminases have recently gained a lot of attention for the synthesis of chiral amines. Using (R)-selective amine transaminase from Aspergillus terreus (AT-ATA) as a transaminase model, in silico design was applied employing B-factor and folding free energy (ΔΔGfold) calculations. Mutation sites were selected by targeting flexible regions with the greatest B-factors, and were substituted with amino acids that were determined by folding free energy calculations (ΔΔGfold < 0) to be more rigid than the original ones. By site-directed mutagenesis, we obtained four stabilized mutants (T130M, T130F, E133F and D134L) with improved stability from 19 candidates. Compared to the wild type, the best single mutant (T130M) showed an increase in thermal stability with a nearly 2.2-fold improvement of half-life (t1/2) at 40 °C and a 3.5 °C higher T1/210 min. The optimum catalytic temperature of T130F was increased by 10 °C. In addition, the T130M/E133F double mutant displayed the largest shift in thermostability with 3.3-fold improvement of t1/2 at 40 °C and a 5.0 °C higher T1/210 min. Modeling analysis showed that new hydrophobic interactions and hydrogen bonds might contribute to the observed thermostability improvement.
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Affiliation(s)
- Jun Huang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China; School of Biological and Chemical Engineering, Zhejiang University of Science and Technology, Hangzhou 310023, China.
| | - Dong-Fang Xie
- School of Biological and Chemical Engineering, Zhejiang University of Science and Technology, Hangzhou 310023, China
| | - Yan Feng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
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