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Liang C, Duan X, Gao H, Shahab M, Zheng G. Chemoenzymatic synthesis of (1R,3R)-3-hydroxycyclopentanemethanol: An intermediate of carbocyclic-ddA. J Biosci Bioeng 2024; 138:111-117. [PMID: 38824112 DOI: 10.1016/j.jbiosc.2024.05.002] [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] [Received: 03/13/2024] [Revised: 04/30/2024] [Accepted: 05/07/2024] [Indexed: 06/03/2024]
Abstract
The synthesis of carbocyclic-ddA, a potent antiviral agent against hepatitis B, relies significantly on (1R,3R)-3-hydroxycyclopentanemethanol as a key intermediate. To effectively produce this intermediate, our study employed a chemoenzymatic approach. The selection of appropriate biocatalysts was based on substrate similarity, leading us to adopt the CrS enoate reductase derived from Thermus scotoductus SA-01. Additionally, we developed an enzymatic system for NADH regeneration, utilising formate dehydrogenase from Candida boidinii. This system facilitated the efficient catalysis of (S)-4-(hydroxymethyl)cyclopent-2-enone, resulting in the formation of (3R)-3-(hydroxymethyl) cyclopentanone. Furthermore, we successfully cloned, expressed, purified, and characterized the CrS enzyme in Escherichia coli. Optimal reaction conditions were determined, revealing that the highest activity occurred at 45 °C and pH 8.0. By employing 5 mM (S)-4-(hydroxymethyl)cyclopent-2-enone, 0.05 mM FMN, 0.2 mM NADH, 10 μM CrS, 40 μM formic acid dehydrogenase, and 40 mM sodium formate, complete conversion was achieved within 45 min at 35 °C and pH 7.0. Subsequently, (1R,3R)-3-hydroxycyclopentanemethanol was obtained through a simple three-step chemical conversion process. This study not only presents an effective method for synthesizing the crucial intermediate but also highlights the importance of biocatalysts and enzymatic systems in chemoenzymatic synthesis approaches.
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Affiliation(s)
- Chaoqun Liang
- State Key Laboratory of Chemical Resources Engineering, Beijing University of Chemical Technology, Beijing 100029, China; Bontac Bio-Engineering (Shenzhen) Co., Ltd., Shenzhen, Guangdong 518107, China
| | - Xiuyuan Duan
- State Key Laboratory of Chemical Resources Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Hanzi Gao
- State Key Laboratory of Chemical Resources Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Muhammad Shahab
- State Key Laboratory of Chemical Resources Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Guojun Zheng
- State Key Laboratory of Chemical Resources Engineering, Beijing University of Chemical Technology, Beijing 100029, China.
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2
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Wu S, Ma X, Yan H. Identification and characterization of an ene-reductase from Corynebacterium casei. Int J Biol Macromol 2024; 264:130427. [PMID: 38428763 DOI: 10.1016/j.ijbiomac.2024.130427] [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] [Received: 10/22/2023] [Revised: 02/12/2024] [Accepted: 02/22/2024] [Indexed: 03/03/2024]
Abstract
The asymmetric reduction of α, β-unsaturated compounds conjugated with electron-withdrawing group by ene-reductases (ERs) is a valuable method for the synthesis of enantiopure chiral compounds. This study introduced an ER from Corynebacterium casei (CcER) which was heterologously expressed in Escherichia coli BL21(DE3), and the purified recombinant CcER was characterized for its biocatalytic properties. CcER exhibited the highest specific activity at 40 °C and pH 6.5, and showcased appreciable stability below 40 °C over a pH range of 6.0-7.0. The enzyme displayed high resistance to methanol. CcER accepted NADH or NADPH as a cofactor and exhibited a broad substrate spectrum towards α, β-unsaturated compounds. It achieved complete conversion of 2-cyclohexen-1-one and good performance for stereoselective reduction of (R)-carvone (conversion 98 %, diastereoselectivity 96 %). This study highlights the robustness and potential of CcER.
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Affiliation(s)
- Shijin Wu
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Xiaojing Ma
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Hongde Yan
- College of Pharmaceutical Engineering and Biotechnology, Zhejiang Pharmaceutical University, Ningbo, China.
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3
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Yu T, Boob AG, Singh N, Su Y, Zhao H. In vitro continuous protein evolution empowered by machine learning and automation. Cell Syst 2023; 14:633-644. [PMID: 37224814 DOI: 10.1016/j.cels.2023.04.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Revised: 11/19/2022] [Accepted: 04/20/2023] [Indexed: 05/26/2023]
Abstract
Directed evolution has become one of the most successful and powerful tools for protein engineering. However, the efforts required for designing, constructing, and screening a large library of variants can be laborious, time-consuming, and costly. With the recent advent of machine learning (ML) in the directed evolution of proteins, researchers can now evaluate variants in silico and guide a more efficient directed evolution campaign. Furthermore, recent advancements in laboratory automation have enabled the rapid execution of long, complex experiments for high-throughput data acquisition in both industrial and academic settings, thus providing the means to collect a large quantity of data required to develop ML models for protein engineering. In this perspective, we propose a closed-loop in vitro continuous protein evolution framework that leverages the best of both worlds, ML and automation, and provide a brief overview of the recent developments in the field.
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Affiliation(s)
- Tianhao Yu
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Carl R. Woese Institute for Genomic Biology, Urbana, IL, USA; NSF Molecule Maker Lab Institute, Urbana, IL, USA
| | - Aashutosh Girish Boob
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Carl R. Woese Institute for Genomic Biology, Urbana, IL, USA; DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Nilmani Singh
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Yufeng Su
- NSF Molecule Maker Lab Institute, Urbana, IL, USA; Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Huimin Zhao
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Carl R. Woese Institute for Genomic Biology, Urbana, IL, USA; NSF Molecule Maker Lab Institute, Urbana, IL, USA; DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
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4
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Engineering of an ene-reductase for producing the key intermediate of antiepileptic drug Brivaracetam. Appl Microbiol Biotechnol 2023; 107:1649-1661. [PMID: 36710288 DOI: 10.1007/s00253-023-12389-4] [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: 10/27/2022] [Revised: 01/12/2023] [Accepted: 01/15/2023] [Indexed: 01/31/2023]
Abstract
(R)-4-Propyldihydrofuran-2(3H)-one (R-PDFO) is the key chiral intermediate for the antiepileptic drug Brivaracetam. Lacking a simple and economical method to approaching R-PDFO, the production of R-PDFO also remains environmentally unfriendly. Here, we developed a straightforward bioreduction way from easily synthesized 4-propylfuran-2(5H)-one (PFO) using ene-reductases. After screened with 27 ene-reductases, E116 stood out with 25.7% yield and 97% ee (R) as the starting enzyme. To improve the catalytic efficiency of E116, several rounds of directed evolution were first carried out. Through rational design, alanine scanning and random mutagenesis, engineered ene-reductase E116-M3 was obtained, with a 2.63-fold improvement in yields over WT, a 12.6-fold improvement in kcat/Km over WT, and stereoselectivity increased to 99% (R). To further improve the yield of R-PDFO, the reaction conditions were then optimized. The catalytic activity of the optimized reaction system was increased again by 2.3 times and the turnover number (TON) of E116-M3 reached 705. Subsequently, whole cells harboring E116-M3 were also shown to have similar capabilities of synthesizing R-PDFO. Finally, E116-M3 was employed in the 50-mL-scale synthesis of R-PDFO under 20 mM of PFO loading to achieve 81% isolated yield and 99% ee. In conclusion, this new approach of engineered ene-reductase catalyzing the asymmetric reduction of PFO could be a green alternative for the efficient synthesis of R-PDFO. KEY POINTS: • An ene-reductase library was first used to screen the bioreduction of PFO. • Rational design contributed to the enhanced R-stereoselectivity of PFO reduction. • E116-M3 was obtained with high activity and stereoselectivity for R-PDFO.
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5
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Van Galen CJ, Pauszek RF, Koder RL, Stanley RJ. Flavin Charge Redistribution upon Optical Excitation Is Independent of Solvent Polarity. J Phys Chem B 2023; 127:661-672. [PMID: 36649202 DOI: 10.1021/acs.jpcb.2c07266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Flavin absorption spectra encode molecular details of the flavin's local environment through coupling of local electric fields with the chromophore's charge redistribution upon optical excitation. Translating experimentally measured field-tuned transition energies to local electric field magnitudes and directions across a wide range of field magnitudes requires that the charge redistribution be independent of the local field. We have measured the charge redistribution upon optical excitation of the derivatized flavin TPARF in the non-hydrogen-bonding, nonpolar solvent toluene, with and without a tridentate hydrogen-bonding ligand, DBAP, using electronic Stark spectroscopy. These measurements were interpreted using TD-DFT finite field and difference density calculations. In comparing our present results to previous Stark spectroscopic analyses of flavin in more polar solvents, we conclude that flavin charge redistribution upon optical excitation is independent of solvent polarity, indicating that dependence of flavin transition energies on local field magnitude is linear with local field magnitude.
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Affiliation(s)
- Cornelius J Van Galen
- Department of Chemistry, Temple University, 1901 N. 13th St., 250B Beury Hall, Philadelphia, Pennsylvania19122, United States
| | - Raymond F Pauszek
- Department of Chemistry, Temple University, 1901 N. 13th St., 250B Beury Hall, Philadelphia, Pennsylvania19122, United States
| | - Ronald L Koder
- Department of Physics, The City College of New York, 1.308 CDI Bldg., 85 St. Nicholas Terrace, New York, New York10031, United States
| | - Robert J Stanley
- Department of Chemistry, Temple University, 1901 N. 13th St., 250B Beury Hall, Philadelphia, Pennsylvania19122, United States
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6
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Wu S, Wang B, Yan H. Semi-rational protein engineering of a novel ene-reductase from Galdieria sulphuraria for asymmetric reduction of (R)-carvone and ketoisophorone. Biotechnol Appl Biochem 2022; 70:697-706. [PMID: 35906824 DOI: 10.1002/bab.2391] [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: 02/01/2022] [Accepted: 07/17/2022] [Indexed: 11/10/2022]
Abstract
Asymmetric reduction of (R)-carvone and ketoisophorone by an engineered ene-reductase from Galdieria sulphuraria (GsOYE) combined with glucose dehydrogenase for NADPH regeneration were studied. A semi-rational protein engineering was used to enhance the activity and selectivity of GsOYE. Upon the sequence alignment and molecular docking results, two amino acid residues at positions 66 and 270 were selected as saturation mutation sites. Finally, a single substitution variant of GsOYE-N270A with complete conversion (100%) and diastereoselectivity (dep >99%) for reduction of (R)-carvone and a double substitution variant GsOYE-Y66P/N270H with improved stereoselectivity for reduction of ketoisophorone were obtained. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Shijin Wu
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Bijiao Wang
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Hongde Yan
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China.,School of Chemistry and Pharmaceutical Engineering, Chongqing Industry Polytechnic College, Chongqing, China
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7
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Engineering the Activity of Old Yellow Enzyme NemR-PS for Efficient Reduction of (E/Z)-Citral to (S)-Citronellol. Catalysts 2022. [DOI: 10.3390/catal12060631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The cascade catalysis of old yellow enzyme, alcohol dehydrogenase and glucose dehydrogenase has become a promising approach for one pot, two-step reduction of (E/Z)-citral to (S)-citronellol, serving as a chiral alcohol with rose fragrance. During the multi-enzymatic cascade catalysis, old yellow enzyme is responsible for the reduction of the conjugated C=C and the introduction of the chiral center, requiring high activity and (S)-enantioselectiviy. Herein, to improve the activity of the old yellow enzyme from Providencia stuartii (NemR-PS) with strict (S)-enantioselectivity, the semi-rational design on its substrate binding pocket was performed through a combination of homology modeling, molecular docking analysis, alanine scanning and iterative saturation mutagenesis. The NemR-PS variant D275G/F351A with improved activity was obtained and then purified for characterization, obeying the substrate inhibition kinetics. Compared with the wild type, the parameters Ki and Kcat/Km were increased from 39.79 mM and 2.09 s−1mM−1 to 128.50 mM and 5.01 s−1mM−1, respectively. Moreover, the variant D275G/F351A maintained strict (S)-enantioselectivity, avoiding the trade-off effect between activity and enantioselectivity. Either the enzyme NemR-PS or the variant D275G/F351A was co-expressed with alcohol dehydrogenase from Yokenella sp. WZY002 (YsADH) and glucose dehydrogenase from Bacillus megaterium (BmGDHM6). In contrast to the whole-cell biocatalyst co-expressing NemR-PS, that co-expressing the variant D275G/F351A shortened the reaction time from 36 h to 12 h in the reduction of 400 mM (E/Z)-citral. In the manner of substrate constant feeding, the accumulated product concentration reached up to 500 mM and completely eliminate the residual intermediate and by-product, suggesting the effectiveness of protein engineering and substrate engineering to improve catalytic efficiency.
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8
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Old yellow enzymes: structures and structure-guided engineering for stereocomplementary bioreduction. Appl Microbiol Biotechnol 2020; 104:8155-8170. [PMID: 32830294 DOI: 10.1007/s00253-020-10845-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 08/07/2020] [Accepted: 08/17/2020] [Indexed: 10/23/2022]
Abstract
Since the first discovery of old yellow enzyme 1 (OYE1) from Saccharomyces pastorianus in 1932, biocatalytic asymmetric reduction of activated alkenes by OYEs has become a valuable reaction in organic synthesis. To access stereocomplementary C=C-bond bioreduction, the mining of novel OYEs and especially the protein engineering of existing OYEs have been performed, which successfully achieved the stereocomplementary reduction in several cases and further raise the potential of applications. In this review, we analyzed the structures, active sites, and substrate recognition of OYEs, which are the bases for their substrate specificity and stereospecificity. Sequence similarity network of OYEs superfamily was also constructed to investigate the scope of characterized OYEs. The structure-guided engineering to switch the stereoselectivity of OYEs and thus access stereocomplementary bioreduction over the last decade (2009-2020) was then reviewed and discussed, which might give new insights into the mining and engineering of related biocatalysts. KEY POINTS: • The sequence similarity network of OYEs superfamily was constructed and annotated. • The structures and active sites of OYEs from different classes were compared. • "Left/right" binding mode was used to explain the stereopreferences of OYEs. • Structure-guided engineering of OYEs to switch their stereoselectivity was reviewed.
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9
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Abstract
Ene-reductases (ERs) belonging to the old yellow enzyme (OYE) family have been thoroughly investigated for the stereospecific reduction of activated prochiral C=C double bonds. In this work, OYE3 was immobilized both by covalent binding on glyoxyl-agarose (OYE3-GA), and by affinity-based adsorption on EziGTM particles (OYE3-EziG). The immobilized OYE3-GA was demonstrated to be active (activity recovery = 52%) and to retain almost 100% of its activity under the enzymatic assay conditions (50 mM phosphate buffer pH 7, 28 °C) for six days, whereas the activity of the non-immobilized enzyme dropped to 50% after two days. In the case of EziGTM, the highest activity recovery (54%) was achieved by using the most hydrophilic carrier (EziGTM Opal) that was selected for the full characterization of this type of enzyme preparation (stability, recycling, re-use, enzyme leakage). OYE3-EziG was slightly less stable than OYE3-GA under the same experimental conditions. OYE3-GA could be recycled and re-used for up to 12 reaction cycles in the bioreduction of α-methyl-trans-cinnamaldehyde; after 12 runs, the highest conversion achieved was 40%. In the case of the co-immobilized OYE3/GDH-EziG, the conversion dropped to 56% after two reaction cycles. No enzyme leakage was detected over 48 h for both OYE3-GA and OYE3/GDH-EziG (50 mM phosphate buffer pH 7, 28 °C). These seed results pave the way for a true optimization of the immobilization of OYE3, as well as for the use of immobilized OYE3 for preparative applications both in batch and continuous flow conditions.
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10
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Smaligo AJ, Swain M, Quintana JC, Tan MF, Kim DA, Kwon O. Hydrodealkenylative C(sp 3)-C(sp 2) bond fragmentation. Science 2019; 364:681-685. [PMID: 31097667 DOI: 10.1126/science.aaw4212] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 03/14/2019] [Indexed: 12/19/2022]
Abstract
Chemical synthesis typically relies on reactions that generate complexity through elaboration of simple starting materials. Less common are deconstructive strategies toward complexity-particularly those involving carbon-carbon bond scission. Here, we introduce one such transformation: the hydrodealkenylative cleavage of C(sp3)-C(sp2) bonds, conducted below room temperature, using ozone, an iron salt, and a hydrogen atom donor. These reactions are performed in nonanhydrous solvents and open to the air; reach completion within 30 minutes; and deliver their products in high yields, even on decagram scales. We have used this broadly functionality tolerant transformation to produce desirable synthetic intermediates, many of which are optically active, from abundantly available terpenes and terpenoid-derived precursors. We have also applied it in the formal total syntheses of complex molecules.
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Affiliation(s)
- Andrew J Smaligo
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Manisha Swain
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Jason C Quintana
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Mikayla F Tan
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Danielle A Kim
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Ohyun Kwon
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA.
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11
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Iorgu AI, Hedison TM, Hay S, Scrutton NS. Selectivity through discriminatory induced fit enables switching of NAD(P)H coenzyme specificity in Old Yellow Enzyme ene-reductases. FEBS J 2019; 286:3117-3128. [PMID: 31033202 PMCID: PMC6767020 DOI: 10.1111/febs.14862] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 03/22/2019] [Accepted: 04/24/2019] [Indexed: 11/30/2022]
Abstract
Most ene‐reductases belong to the Old Yellow Enzyme (OYE) family of flavin‐dependent oxidoreductases. OYEs use nicotinamide coenzymes as hydride donors to catalyze the reduction of alkenes that contain an electron‐withdrawing group. There have been many investigations of the structures and catalytic mechanisms of OYEs. However, the origin of coenzyme specificity in the OYE family is unknown. Structural NMR and X‐ray crystallographic data were used to rationally design variants of two OYEs, pentaerythritol tetranitrate reductase (PETNR) and morphinone reductase (MR), to discover the basis of coenzyme selectivity. PETNR has dual‐specificity and reacts with NADH and NADPH; MR accepts only NADH as hydride donor. Variants of a β‐hairpin motif in an active site loop of both these enzymes were studied using stopped‐flow spectroscopy. Specific attention was placed on the potential role of arginine residues within the β‐hairpin motif. Mutagenesis demonstrated that Arg130 governs the preference of PETNR for NADPH, and that Arg142 interacts with the coenzyme pyrophosphate group. These observations were used to switch coenzyme specificity in MR by replacing either Glu134 or Leu146 with arginine residues. These variants had increased (~15‐fold) affinity for NADH. Mutagenesis enabled MR to accept NADPH as a hydride donor, with E134R MR showing a significant (55‐fold) increase in efficiency in the reductive half‐reaction, when compared to the essentially unreactive wild‐type enzyme. Insight into the question of coenzyme selectivity in OYEs has therefore been addressed through rational redesign. This should enable coenzyme selectivity to be improved and switched in other OYEs.
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Affiliation(s)
- Andreea I Iorgu
- Manchester Institute of Biotechnology and School of Chemistry, Faculty of Science and Engineering, The University of Manchester, UK
| | - Tobias M Hedison
- Manchester Institute of Biotechnology and School of Chemistry, Faculty of Science and Engineering, The University of Manchester, UK
| | - Sam Hay
- Manchester Institute of Biotechnology and School of Chemistry, Faculty of Science and Engineering, The University of Manchester, UK
| | - Nigel S Scrutton
- Manchester Institute of Biotechnology and School of Chemistry, Faculty of Science and Engineering, The University of Manchester, UK
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12
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Iorgu AI, Cliff MJ, Waltho JP, Scrutton NS, Hay S. Isotopically labeled flavoenzymes and their uses in probing reaction mechanisms. Methods Enzymol 2019; 620:145-166. [PMID: 31072485 DOI: 10.1016/bs.mie.2019.03.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The incorporation of stable isotopes into proteins is beneficial or essential for a range of experiments, including NMR, neutron scattering and reflectometry, proteomic mass spectrometry, vibrational spectroscopy and "heavy" enzyme kinetic isotope effect (KIE) measurements. Here, we present detailed protocols for the stable isotopic labeling of pentaerythritol tetranitrate reductase (PETNR) via recombinant expression in E. coli. PETNR is an ene-reductase belonging to the Old Yellow Enzyme (OYE) family of flavoenzymes, and is regarded as a model system for studying hydride transfer reactions. Included is a discussion of how efficient back-exchange of amide protons in the protein core can be achieved and how the intrinsic flavin mononucleotide (FMN) cofactor can be exchanged, allowing the production of isotopologues with differentially labeled protein and cofactor. In addition to a thorough description of labeling strategies, we briefly exemplify how data analysis and interpretation of "heavy" enzyme KIEs can be performed.
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Affiliation(s)
- Andreea I Iorgu
- Manchester Institute of Biotechnology and School of Chemistry, The University of Manchester, Manchester, United Kingdom
| | - Matthew J Cliff
- Manchester Institute of Biotechnology and School of Chemistry, The University of Manchester, Manchester, United Kingdom
| | - Jonathan P Waltho
- Manchester Institute of Biotechnology and School of Chemistry, The University of Manchester, Manchester, United Kingdom
| | - Nigel S Scrutton
- Manchester Institute of Biotechnology and School of Chemistry, The University of Manchester, Manchester, United Kingdom
| | - Sam Hay
- Manchester Institute of Biotechnology and School of Chemistry, The University of Manchester, Manchester, United Kingdom.
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13
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Ascue Avalos GA, Toogood HS, Tait S, Messiha HL, Scrutton NS. From Bugs to Bioplastics: Total (+)-Dihydrocarvide Biosynthesis by Engineered Escherichia coli. Chembiochem 2019; 20:785-792. [PMID: 30431225 PMCID: PMC6850611 DOI: 10.1002/cbic.201800606] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Indexed: 11/15/2022]
Abstract
The monoterpenoid lactone derivative (+)-dihydrocarvide ((+)-DHCD) can be polymerised to form shape-memory polymers. Synthetic biology routes from simple, inexpensive carbon sources are an attractive, alternative route over chemical synthesis from (R)-carvone. We have demonstrated a proof-of-principle in vivo approach for the complete biosynthesis of (+)-DHCD from glucose in Escherichia coli (6.6 mg L-1 ). The pathway is based on the Mentha spicata route to (R)-carvone, with the addition of an 'ene'-reductase and Baeyer-Villiger cyclohexanone monooxygenase. Co-expression with a limonene synthesis pathway enzyme enables complete biocatalytic production within one microbial chassis. (+)-DHCD was successfully produced by screening multiple homologues of the pathway genes, combined with expression optimisation by selective promoter and/or ribosomal binding-site screening. This study demonstrates the potential application of synthetic biology approaches in the development of truly sustainable and renewable bioplastic monomers.
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Affiliation(s)
- Gabriel A. Ascue Avalos
- School of ChemistryFaculty of Science and EngineeringUniversity of Manchester131 Princess StreetManchesterM1 7DNUK
| | - Helen S. Toogood
- School of ChemistryFaculty of Science and EngineeringUniversity of Manchester131 Princess StreetManchesterM1 7DNUK
| | - Shirley Tait
- School of ChemistryFaculty of Science and EngineeringUniversity of Manchester131 Princess StreetManchesterM1 7DNUK
| | - Hanan L. Messiha
- School of ChemistryFaculty of Science and EngineeringUniversity of Manchester131 Princess StreetManchesterM1 7DNUK
| | - Nigel S. Scrutton
- School of ChemistryFaculty of Science and EngineeringUniversity of Manchester131 Princess StreetManchesterM1 7DNUK
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14
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Powell, III RW, Buteler MP, Lenka S, Crotti M, Santangelo S, Burg MJ, Bruner S, Brenna E, Roitberg AE, Stewart JD. Investigating Saccharomyces cerevisiae alkene reductase OYE 3 by substrate profiling, X-ray crystallography and computational methods. Catal Sci Technol 2018. [DOI: 10.1039/c8cy00440d] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Saccharomyces cerevisiae OYE 3 and OYE 1 share 80% sequence identity, but sometimes differ in stereoselectivities.
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Affiliation(s)
| | - M. Pilar Buteler
- Department of Chemistry
- 126 Sisler Hall
- University of Florida
- Gainesville
- USA
| | - Sunidhi Lenka
- Department of Chemistry
- 126 Sisler Hall
- University of Florida
- Gainesville
- USA
| | - Michele Crotti
- Dipartimento di Chimica
- Materiali ed Ingegneria Chimica “Giulio Natta” Politecnico di Milano
- Milano
- Italy
| | - Sara Santangelo
- Dipartimento di Chimica
- Materiali ed Ingegneria Chimica “Giulio Natta” Politecnico di Milano
- Milano
- Italy
| | - Matthew J. Burg
- Department of Chemistry
- 126 Sisler Hall
- University of Florida
- Gainesville
- USA
| | - Steven Bruner
- Department of Chemistry
- 126 Sisler Hall
- University of Florida
- Gainesville
- USA
| | - Elisabetta Brenna
- Dipartimento di Chimica
- Materiali ed Ingegneria Chimica “Giulio Natta” Politecnico di Milano
- Milano
- Italy
| | - Adrian E. Roitberg
- Department of Chemistry
- 126 Sisler Hall
- University of Florida
- Gainesville
- USA
| | - Jon D. Stewart
- Department of Chemistry
- 126 Sisler Hall
- University of Florida
- Gainesville
- USA
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15
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Mordaka PM, Hall SJ, Minton N, Stephens G. Recombinant expression and characterisation of the oxygen-sensitive 2-enoate reductase from Clostridium sporogenes. MICROBIOLOGY-SGM 2017; 164:122-132. [PMID: 29111967 PMCID: PMC5882074 DOI: 10.1099/mic.0.000568] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
‘Ene’-reductases have attracted significant attention for the preparation of chemical intermediates and biologically active products. To date, research has been focussed primarily on Old Yellow Enzyme-like proteins, due to their ease of handling, whereas 2-enoate reductases from clostridia have received much less attention, because of their oxygen sensitivity and a lack of suitable expression systems. A hypothetical 2-enoate reductase gene, fldZ, was identified in Clostridium sporogenes DSM 795. The encoded protein shares a high degree of homology to clostridial FMN- and FAD-dependent 2-enoate reductases, including the cinnamic acid reductase proposed to be involved in amino acid metabolism in proteolytic clostridia. The gene was cloned and overexpressed in Escherichia coli. Successful expression depended on the use of strictly anaerobic conditions for both growth and enzyme preparation, since FldZ was oxygen-sensitive. The enzyme reduced aromatic enoates, such as cinnamic acid or p-coumaric acid, but not short chain unsaturated aliphatic acids. The β,β-disubstituted nitroalkene, (E)-1-nitro-2-phenylpropene, was reduced to enantiopure (R)-1-nitro-2-phenylpropane with a yield of 90 %. By contrast, the α,β-disubstituted nitroalkene, (E)-2-nitro-1-phenylpropene, was reduced with a moderate yield of 56 % and poor enantioselectivity (16 % ee for (S)-2-nitro-1-phenylpropane). The availability of an expression system for this recombinant clostridial 2-enoate reductase will facilitate future characterisation of this unusual class of ‘ene’-reductases, and expand the biocatalytic toolbox available for enantioselective hydrogenation of carbon-carbon double bonds.
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Affiliation(s)
- Pawel M Mordaka
- Bioprocess, Environmental and Chemical Technologies Research Group, Faculty of Engineering, University of Nottingham, University Park, Nottingham NG7 2RD, UK.,Present address: Centre for Synthetic Biology and Innovation, Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | - Stephen J Hall
- Bioprocess, Environmental and Chemical Technologies Research Group, Faculty of Engineering, University of Nottingham, University Park, Nottingham NG7 2RD, UK
| | - Nigel Minton
- Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Life Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK
| | - Gill Stephens
- Bioprocess, Environmental and Chemical Technologies Research Group, Faculty of Engineering, University of Nottingham, University Park, Nottingham NG7 2RD, UK
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16
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Brenna E, Crotti M, Gatti FG, Monti D, Parmeggiani F, Santangelo S. Asymmetric Bioreduction of β-Acylaminonitroalkenes: Easy Access to Chiral Building Blocks with Two Vicinal Nitrogen-Containing Functional Groups. ChemCatChem 2017. [DOI: 10.1002/cctc.201700063] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Elisabetta Brenna
- Dipartimento di Chimica; Materiali ed Ingegneria Chimica “Giulio Natta”; Politecnico di Milano; Via Mancinelli 7, I- 20131 Milano Italy
- Istituto di Chimica del Riconoscimento Molecolare; C.N.R.; Via Mario Bianco 9, I- 20131 Milano Italy
| | - Michele Crotti
- Dipartimento di Chimica; Materiali ed Ingegneria Chimica “Giulio Natta”; Politecnico di Milano; Via Mancinelli 7, I- 20131 Milano Italy
| | - Francesco G. Gatti
- Dipartimento di Chimica; Materiali ed Ingegneria Chimica “Giulio Natta”; Politecnico di Milano; Via Mancinelli 7, I- 20131 Milano Italy
| | - Daniela Monti
- Istituto di Chimica del Riconoscimento Molecolare; C.N.R.; Via Mario Bianco 9, I- 20131 Milano Italy
| | - Fabio Parmeggiani
- Dipartimento di Chimica; Materiali ed Ingegneria Chimica “Giulio Natta”; Politecnico di Milano; Via Mancinelli 7, I- 20131 Milano Italy
| | - Sara Santangelo
- Dipartimento di Chimica; Materiali ed Ingegneria Chimica “Giulio Natta”; Politecnico di Milano; Via Mancinelli 7, I- 20131 Milano Italy
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17
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Waller J, Toogood HS, Karuppiah V, Rattray NJW, Mansell DJ, Leys D, Gardiner JM, Fryszkowska A, Ahmed ST, Bandichhor R, Reddy GP, Scrutton NS. Structural insights into the ene-reductase synthesis of profens. Org Biomol Chem 2017; 15:4440-4448. [PMID: 28485453 DOI: 10.1039/c7ob00163k] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Reduction of double bonds of α,β-unsaturated carboxylic acids and esters by ene-reductases remains challenging and it typically requires activation by a second electron-withdrawing moiety, such as a halide or second carboxylate group. We showed that profen precursors, 2-arylpropenoic acids and their esters, were efficiently reduced by Old Yellow Enzymes (OYEs). The XenA and GYE enzymes showed activity towards acids, while a wider range of enzymes were active towards the equivalent methyl esters. Comparative co-crystal structural analysis of profen-bound OYEs highlighted key interactions important in determining substrate binding in a catalytically active conformation. The general utility of ene reductases for the synthesis of (R)-profens was established and this work will now drive future mutagenesis studies to screen for the production of pharmaceutically-active (S)-profens.
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Affiliation(s)
- J Waller
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
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18
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Nett N, Duewel S, Richter AA, Hoebenreich S. Revealing Additional Stereocomplementary Pairs of Old Yellow Enzymes by Rational Transfer of Engineered Residues. Chembiochem 2017; 18:685-691. [PMID: 28107586 DOI: 10.1002/cbic.201600688] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Indexed: 01/01/2023]
Abstract
Every year numerous protein engineering and directed evolution studies are published, increasing the knowledge that could be used by protein engineers. Here we test a protein engineering strategy that allows quick access to improved biocatalysts with very little screening effort. Conceptually it is assumed that engineered residues previously identified by rational and random methods induce similar improvements when transferred to family members. In an application to ene-reductases from the Old Yellow Enzyme (OYE) family, the newly created variants were tested with three compounds, revealing more stereocomplementary OYE pairs with potent turnover frequencies (up to 660 h-1 ) and excellent stereoselectivities (up to >99 %). Although systematic prediction of absolute enantioselectivity of OYE variants remains a challenge, "scaffold sampling" was confirmed as a promising addition to protein engineers' collection of strategies.
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Affiliation(s)
- Nathalie Nett
- Department of Chemistry, Philipps-Universität Marburg, Hans-Meerwein-Strasse 4, 35032, Marburg, Germany
| | - Sabine Duewel
- Department of Chemistry, Philipps-Universität Marburg, Hans-Meerwein-Strasse 4, 35032, Marburg, Germany
| | - Alexandra Annelis Richter
- Department of Chemistry, Philipps-Universität Marburg, Hans-Meerwein-Strasse 4, 35032, Marburg, Germany
| | - Sabrina Hoebenreich
- Department of Chemistry, Philipps-Universität Marburg, Hans-Meerwein-Strasse 4, 35032, Marburg, Germany
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19
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20
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Peers MK, Toogood HS, Heyes DJ, Mansell D, Coe BJ, Scrutton NS. Light-driven biocatalytic reduction of α,β-unsaturated compounds by ene reductases employing transition metal complexes as photosensitizers. Catal Sci Technol 2016; 6:169-177. [PMID: 27019691 PMCID: PMC4786955 DOI: 10.1039/c5cy01642h] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2015] [Accepted: 10/16/2015] [Indexed: 11/25/2022]
Abstract
Efficient and cost effective nicotinamide cofactor regeneration is essential for industrial-scale bio-hydrogenations employing flavin-containing biocatalysts such as the Old Yellow Enzymes. A direct flavin regeneration system using visible light to initiate a photoredox cycle and drive biocatalysis is described, and shown to be effective in driving biocatalytic activated alkene reduction. Using Ru(ii) or Ir(iii) complexes as photosensitizers, coupled with an electron transfer mediator (methyl viologen) and sacrificial electron donor (triethanolamine) drives catalytic turnover of two Old Yellow Enzymes with multiple oxidative substrates. Therefore, there is great potential in the development of light-driven biocatalytic systems, providing an alternative to the reliance on enzyme-based cofactor regeneration systems.
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Affiliation(s)
- Martyn K Peers
- Manchester Institute of Biotechnology , Faculty of Life Sciences , University of Manchester , 131 Princess Street , Manchester , M1 7DN , UK .
| | - Helen S Toogood
- Manchester Institute of Biotechnology , Faculty of Life Sciences , University of Manchester , 131 Princess Street , Manchester , M1 7DN , UK .
| | - Derren J Heyes
- Manchester Institute of Biotechnology , Faculty of Life Sciences , University of Manchester , 131 Princess Street , Manchester , M1 7DN , UK .
| | - David Mansell
- Manchester Institute of Biotechnology , Faculty of Life Sciences , University of Manchester , 131 Princess Street , Manchester , M1 7DN , UK .
| | - Benjamin J Coe
- School of Chemistry , University of Manchester , Oxford Road , Manchester , M13 9PL , UK
| | - Nigel S Scrutton
- Manchester Institute of Biotechnology , Faculty of Life Sciences , University of Manchester , 131 Princess Street , Manchester , M1 7DN , UK .
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21
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Bertolotti M, Brenna E, Crotti M, Gatti FG, Monti D, Parmeggiani F, Santangelo S. Substrate Scope Evaluation of the Enantioselective Reduction of β-Alkyl-β-arylnitroalkenes by Old Yellow Enzymes 1-3 for Organic Synthesis Applications. ChemCatChem 2015. [DOI: 10.1002/cctc.201500958] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Mattia Bertolotti
- Dipartimento di Chimica; Materiali ed Ingegneria Chimica “Giulio Natta” Politecnico di Milano; Via Mancinelli 7 20131 Milano Italy
| | - Elisabetta Brenna
- Dipartimento di Chimica; Materiali ed Ingegneria Chimica “Giulio Natta” Politecnico di Milano; Via Mancinelli 7 20131 Milano Italy
- Istituto di Chimica del Riconoscimento Molecolare; C.N.R.; Via Mario Bianco, 9 20131 Milano Italy
| | - Michele Crotti
- Dipartimento di Chimica; Materiali ed Ingegneria Chimica “Giulio Natta” Politecnico di Milano; Via Mancinelli 7 20131 Milano Italy
| | - Francesco G. Gatti
- Dipartimento di Chimica; Materiali ed Ingegneria Chimica “Giulio Natta” Politecnico di Milano; Via Mancinelli 7 20131 Milano Italy
| | - Daniela Monti
- Istituto di Chimica del Riconoscimento Molecolare; C.N.R.; Via Mario Bianco, 9 20131 Milano Italy
| | - Fabio Parmeggiani
- Dipartimento di Chimica; Materiali ed Ingegneria Chimica “Giulio Natta” Politecnico di Milano; Via Mancinelli 7 20131 Milano Italy
| | - Sara Santangelo
- Dipartimento di Chimica; Materiali ed Ingegneria Chimica “Giulio Natta” Politecnico di Milano; Via Mancinelli 7 20131 Milano Italy
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22
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Forchin MC, Crotti M, Gatti FG, Parmeggiani F, Brenna E, Monti D. A Rapid and High-Throughput Assay for the Estimation of Conversions of Ene-Reductase-Catalysed Reactions. Chembiochem 2015; 16:1571-3. [PMID: 26033160 DOI: 10.1002/cbic.201500219] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Indexed: 11/10/2022]
Abstract
A fast and sensitive colorimetric assay (FRED, fast and reliable ene-reductases detection) that allows the estimation of levels of conversion of ene-reductase (ER)-catalysed reactions has been developed. The activated olefin is reduced by ER at the expense of NAD(P)H cofactor, whose regeneration is carried out in situ by the glucose/glucose dehydrogenase system. Subsequently, the consumption of the co-substrate glucose is determined colorimetrically by a multienzymatic system. The FRED assay offers a wide range of possible applications, from enzyme fingerprinting and kinetic analysis, to primary screening of enzyme libraries and optimisation of ERs' performances under different reaction conditions.
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Affiliation(s)
- Maria Chiara Forchin
- Istituto di Chimica del Riconoscimento Molecolare, CNR, Via Mario Bianco 9, 20131 Milano (Italy)
| | - Michele Crotti
- Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, Via Mancinelli 7, 20131 Milano (Italy)
| | - Francesco G Gatti
- Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, Via Mancinelli 7, 20131 Milano (Italy)
| | - Fabio Parmeggiani
- Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, Via Mancinelli 7, 20131 Milano (Italy).
| | - Elisabetta Brenna
- Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, Via Mancinelli 7, 20131 Milano (Italy)
| | - Daniela Monti
- Istituto di Chimica del Riconoscimento Molecolare, CNR, Via Mario Bianco 9, 20131 Milano (Italy).
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23
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Applications of protein engineering to members of the old yellow enzyme family. Biotechnol Adv 2015; 33:624-31. [PMID: 25940546 DOI: 10.1016/j.biotechadv.2015.04.011] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Revised: 04/24/2015] [Accepted: 04/25/2015] [Indexed: 01/28/2023]
Abstract
In the 20 years since Massey's initial report in 1995, interest in using alkene reductases to prepare chiral intermediates for synthesis has grown rapidly. While native alkene reductases often show very high stereoselectivities toward favorable substrates, these enzymes have somewhat size-restricted active sites that limit their substrate ranges to small alkenes. In addition, most alkene reductases have the same stereoselectivities, which makes it difficult to access the "other" product enantiomers. Protein engineering strategies have been used to address both of these issues and good progress has been made in several cases. This review summarizes published examples through late 2014 and focuses on studies of six enzymes: Saccharomyces pastorianus OYE 1, tomato OPR1, Zymomonas mobilis NCR, Enterobacter cloacae PB2 PETN reductase, Bacillus subtilis YqjM and Pichia stipitis OYE 2.6.
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24
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Daugherty AB, Horton JR, Cheng X, Lutz S. STRUCTURAL AND FUNCTIONAL CONSEQUENCES OF CIRCULAR PERMUTATION ON THE ACTIVE SITE OF OLD YELLOW ENZYME. ACS Catal 2015; 5:892-899. [PMID: 25692074 PMCID: PMC4327928 DOI: 10.1021/cs501702k] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
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Circular
permutation of the NADPH-dependent oxidoreductase
Old Yellow Enzyme from Saccharomyces pastorianus (OYE1) can significantly enhance the enzyme’s catalytic performance.
Termini relocation into four regions of the protein (sectors I–IV)
near the active site has proven effective in altering enzyme function.
To better understand the structural consequences and rationalize the
observed functional gains in these OYE1 variants, we selected representatives
from sectors I–III for further characterization by biophysical
methods and X-ray crystallography. These investigations not only show
trends in enzyme stability and quaternary structure as a function
of termini location but also provide a possible explanation for the
catalytic gains in our top-performing OYE variant (new N-terminus
at residue 303; sector III). Crystallographic analysis indicates that
termini relocation into sector III affects the loop β6 region
(amino acid positions: 290–310) of OYE1, which forms a lid
over the active site. Peptide backbone cleavage greatly enhances local
flexibility, effectively converting the loop into a tether and consequently
increasing the environmental exposure of the active site. Interestingly,
such an active site remodeling does not negatively impact the enzyme’s
activity and stereoselectivity; neither does it perturb the conformation
of other key active site residues with the exception of Y375. These
observations were confirmed in truncation experiments, deleting all
residues of the loop β6 region in our OYE variant. Intrigued
by the finding that circular permutation leaves most of the key catalytic
residues unchanged, we also tested OYE permutants for possible additive
or synergistic effects of amino acid substitutions. Distinct functional
changes in these OYE variants were detected upon mutations at W116,
known in native OYE1 to cause inversion of diastereoselectivity for
(S)-carvone reduction. Our findings demonstrate the
contribution of loop β6 toward determining the stereoselectivity
of OYE1, an important insight for future OYE engineering efforts.
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Affiliation(s)
- Ashley B. Daugherty
- Department
of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, Georgia 30322. United States
| | - John R. Horton
- Department
of Biochemistry, Emory University, 1510 Clifton Rd., Atlanta, Georgia 30322, United States
| | - Xiaodong Cheng
- Department
of Biochemistry, Emory University, 1510 Clifton Rd., Atlanta, Georgia 30322, United States
| | - Stefan Lutz
- Department
of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, Georgia 30322. United States
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25
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Hickling C, Toogood HS, Saiani A, Scrutton NS, Miller AF. Nanofibrillar Peptide hydrogels for the immobilization of biocatalysts for chemical transformations. Macromol Rapid Commun 2014; 35:868-74. [PMID: 24604676 PMCID: PMC4316184 DOI: 10.1002/marc.201400027] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Indexed: 01/12/2023]
Abstract
Enzymes are attractive, "green" alternatives to chemical catalysts within the industrial sector, but their robustness to environmental conditions needs optimizing. Here, an enzyme is tagged chemically and recombinantly with a self-assembling peptide that allows the conjugate to spontaneously assemble with pure peptide to form β-sheet-rich nanofibers decorated with tethered enzyme. Above a critical concentration, these fibers entangle and form a 3D hydrogel. The immobilized enzyme catalyzes chemical transformations and critically its stability is increased significantly where it retains activity after exposure to high temperatures (90 °C) and long storage times (up to 12 months).
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Affiliation(s)
- Christopher Hickling
- School of Chemical Engineering and Analytical Science, Manchester Institute of Biotechnology, University of Manchester131 Princess Street, Manchester, M1, 7DN, UK
| | - Helen S Toogood
- Manchester Institute of Biotechnology, Faculty of Life Sciences131 Princess Street, Manchester, M1, 7DN, UK
| | - Alberto Saiani
- Manchester Institute of Biotechnology, School of Materials, University of ManchesterManchester, M1, 3 9PL, UK
| | - Nigel S Scrutton
- Manchester Institute of Biotechnology, Faculty of Life Sciences131 Princess Street, Manchester, M1, 7DN, UK
| | - Aline F Miller
- School of Chemical Engineering and Analytical Science, Manchester Institute of Biotechnology, University of Manchester131 Princess Street, Manchester, M1, 7DN, UK
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26
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Pompeu YA, Sullivan B, Stewart JD. X-ray Crystallography Reveals How Subtle Changes Control the Orientation of Substrate Binding in an Alkene Reductase. ACS Catal 2013. [DOI: 10.1021/cs400622e] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yuri A. Pompeu
- Department
of Chemistry, University of Florida, 126 Sisler Hall, Gainesville, Florida 32611, United States
| | - Bradford Sullivan
- Department
of Chemistry, University of Florida, 126 Sisler Hall, Gainesville, Florida 32611, United States
| | - Jon D. Stewart
- Department
of Chemistry, University of Florida, 126 Sisler Hall, Gainesville, Florida 32611, United States
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27
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Daugherty AB, Govindarajan S, Lutz S. Improved biocatalysts from a synthetic circular permutation library of the flavin-dependent oxidoreductase old yellow enzyme. J Am Chem Soc 2013; 135:14425-32. [PMID: 23987134 DOI: 10.1021/ja4074886] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Members of the old yellow enzyme (OYE) family are widely used, effective biocatalysts for the stereoselective trans-hydrogenation of activated alkenes. To further expand their substrate scope and improve catalytic performance, we have applied a protein engineering strategy called circular permutation (CP) to enhance the function of OYE1 from Saccharomyces pastorianus. CP can influence a biocatalyst's function by altering protein backbone flexibility and active site accessibility, both critical performance features because the catalytic cycle for OYE1 is thought to involve rate-limiting conformational changes. To explore the impact of CP throughout the OYE1 protein sequence, we implemented a highly efficient approach for cell-free cpOYE library preparation by combining whole-gene synthesis with in vitro transcription/translation. The versatility of such an ex vivo system was further demonstrated by the rapid and reliable functional evaluation of library members under variable environmental conditions with three reference substrates ketoisophorone, cinnamaldehyde, and (S)-carvone. Library analysis identified over 70 functional OYE1 variants with several biocatalysts exhibiting over an order of magnitude improved catalytic activity. Although catalytic gains of individual cpOYE library members vary by substrate, the locations of new protein termini in functional variants for all tested substates fall within the same four distinct loop/lid regions near the active site. Our findings demonstrate the importance of these structural elements in enzyme function and support the hypothesis of conformational flexibility as a limiting factor for catalysis in wild type OYE.
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Affiliation(s)
- Ashley B Daugherty
- Department of Chemistry, Emory University , 1515 Dickey Drive, Atlanta, Georgia 30084, United States
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28
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Feng J, Liu H, Yang X, Gao A, Liao J, Feng L, Pu J, Xie Y, Long G, Li Y, Liao F. Comparison of activity indexes for recognizing enzyme mutants of higher activity with uricase as model. Chem Cent J 2013; 7:69. [PMID: 23594729 PMCID: PMC3637054 DOI: 10.1186/1752-153x-7-69] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2012] [Accepted: 03/06/2013] [Indexed: 11/13/2022] Open
Abstract
Background For screening a library of enzyme mutants, an efficient and cost-effective method for reliable assay of enzyme activity and a decision method for safe recognition of mutants of higher activity are needed. The comparison of activity concentrations of mutants in lysates of transformed Escherichia coli cells against a threshold is unsafe to recognize mutants of higher activity due to variations of both expression levels of mutant proteins and lysis efficiency of transformed cells. Hence, by a spectrophotometric method after verification to measure uricase activity, specific activity calculated from the level of total proteins in a lysate was tested for recognizing a mutant of higher activity. Results During uricase reaction, the intermediate 5-hydroxyisourate interferes with the assay of uric acid absorbance, but the measurement of absorbance at 293 nm in alkaline borate buffer was reliable for measuring uricase initial rates within a reasonable range. The level of total proteins in a lysate was determined by the Bradford assay. Polyacrylamide gel electrophoresis analysis supported different relative abundance of uricase mutant proteins in their lysates; activity concentrations of uricase in such lysates positively correlated with levels of total proteins. Receiver-operation-curve analysis of activity concentration or specific activity yielded area-under-the-curve close to 1.00 for recognizing a mutant with > 200% improvement of activity. For a mutant with just about 80% improvement of activity, receiver-operation-curve analysis of specific activity gave area-under-the-curve close to 1.00 while the analysis of activity concentration gave smaller area-under-the-curve. With the mean plus 1.4-fold of the standard deviation of specific activity of a starting material as the threshold, uricase mutants whose activities were improved by more than 80% were recognized with higher sensitivity and specificity. Conclusion Specific activity calculated from the level of total proteins is a favorable index for recognizing an enzyme mutant with small improvement of activity.
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Affiliation(s)
- Juan Feng
- Unit for Analytical Probes and Protein Biotechnology, Key Laboratory of Clinical Laboratory Diagnostics of the Education Ministry, College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, China.
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29
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Mansell DJ, Toogood HS, Waller J, Hughes JMX, Levy CW, Gardiner JM, Scrutton NS. Biocatalytic Asymmetric Alkene Reduction: Crystal Structure and Characterization of a Double Bond Reductase from Nicotiana tabacum. ACS Catal 2013; 3:370-379. [PMID: 27547488 PMCID: PMC4990313 DOI: 10.1021/cs300709m] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2012] [Revised: 01/18/2013] [Indexed: 02/08/2023]
Abstract
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The application of biocatalysis for the asymmetric reduction
of
activated C=C is a powerful tool for the manufacture of high-value
chemical commodities. The biocatalytic potential of “-ene”
reductases from the Old Yellow Enzyme (OYE) family of oxidoreductases
is well-known; however, the specificity of these enzymes toward mainly
small molecule substrates has highlighted the need to discover “-ene”
reductases from different enzymatic classes to broaden industrial
applicability. Here, we describe the characterization of a flavin-free
double bond reductase from Nicotiana tabacum (NtDBR), which belongs to the leukotriene B4 dehydrogenase
(LTD) subfamily of the zinc-independent, medium chain dehydrogenase/reductase
superfamily of enzymes. Using steady-state kinetics and biotransformation
reactions, we have demonstrated the regio- and stereospecificity of
NtDBR against a variety of α,β-unsaturated activated alkenes.
In addition to catalyzing the reduction of typical LTD substrates
and several classical OYE-like substrates, NtDBR also exhibited complementary
activity by reducing non-OYE substrates (i.e., reducing the exocyclic
C=C double bond of (R)-pulegone) and in some
cases showing an opposite stereopreference in comparison with the
OYE family member pentaerythritol tetranitrate (PETN) reductase. This
serves to augment classical OYE “-ene” reductase activity
and, coupled with its aerobic stability, emphasizes the potential
industrial value of NtDBR. Furthermore, we also report the X-ray crystal
structures of the holo-, binary NADP(H)-bound, and ternary [NADP+ and 4-hydroxy-3-methoxycinnamaldehyde (9a)-bound]
NtDBR complexes. These will underpin structure-driven site-saturated
mutagenesis studies aimed at enhancing the reactivity, stereochemistry,
and specificity of this enzyme.
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Affiliation(s)
- David J. Mansell
- Manchester
Institute of Biotechnology, ⊥School of Chemistry, and ‡Faculty of Life Sciences, University of Manchester, Manchester,
U.K
| | - Helen S. Toogood
- Manchester
Institute of Biotechnology, ⊥School of Chemistry, and ‡Faculty of Life Sciences, University of Manchester, Manchester,
U.K
| | - John Waller
- Manchester
Institute of Biotechnology, ⊥School of Chemistry, and ‡Faculty of Life Sciences, University of Manchester, Manchester,
U.K
| | - John M. X. Hughes
- Manchester
Institute of Biotechnology, ⊥School of Chemistry, and ‡Faculty of Life Sciences, University of Manchester, Manchester,
U.K
| | - Colin W. Levy
- Manchester
Institute of Biotechnology, ⊥School of Chemistry, and ‡Faculty of Life Sciences, University of Manchester, Manchester,
U.K
| | - John M. Gardiner
- Manchester
Institute of Biotechnology, ⊥School of Chemistry, and ‡Faculty of Life Sciences, University of Manchester, Manchester,
U.K
| | - Nigel S. Scrutton
- Manchester
Institute of Biotechnology, ⊥School of Chemistry, and ‡Faculty of Life Sciences, University of Manchester, Manchester,
U.K
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Fisher K, Mohr S, Mansell D, Goddard NJ, Fielden PR, Scrutton NS. Electro-enzymatic viologen-mediated substrate reduction using pentaerythritol tetranitrate reductase and a parallel, segmented fluid flow system. Catal Sci Technol 2013. [DOI: 10.1039/c3cy20720j] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Paul CE, Gargiulo S, Opperman DJ, Lavandera I, Gotor-Fernández V, Gotor V, Taglieber A, Arends IWCE, Hollmann F. Mimicking nature: synthetic nicotinamide cofactors for C═C bioreduction using enoate reductases. Org Lett 2012; 15:180-3. [PMID: 23256747 DOI: 10.1021/ol303240a] [Citation(s) in RCA: 135] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A series of synthetic nicotinamide cofactors were synthesized to replace natural nicotinamide cofactors and promote enoate reductase (ER) catalyzed reactions without compromising the activity or stereoselectivity of the bioreduction process. Conversions and enantioselectivities of >99% were obtained for C═C bioreductions, and the process was successfully upscaled. Furthermore, high chemoselectivity was observed when employing these nicotinamide cofactor mimics (mNADs) with crude extracts in ER-catalyzed reactions.
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Affiliation(s)
- Caroline E Paul
- Department of Biotechnology, Delft University of Technology, Julianalaan 136, 2628BL Delft, The Netherlands
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Fryszkowska A, Toogood HS, Mansell D, Stephens G, Gardiner JM, Scrutton NS. A surprising observation that oxygen can affect the product enantiopurity of an enzyme-catalysed reaction. FEBS J 2012; 279:4160-71. [PMID: 22978386 DOI: 10.1111/febs.12008] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2012] [Revised: 08/28/2012] [Accepted: 09/11/2012] [Indexed: 01/05/2023]
Abstract
Enzymes are natural catalysts, controlling reactions with typically high stereospecificity and enantiospecificity in substrate selection and/or product formation. This makes them useful in the synthesis of industrially relevant compounds, particularly where highly enantiopure products are required. The flavoprotein pentaerythritol tetranitrate (PETN) reductase is a member of the Old Yellow Enzyme family, and catalyses the asymmetric reduction of β-alkyl-β-arylnitroalkenes. Under aerobic conditions, it additionally undergoes futile cycles of NAD(P)H reduction of flavin, followed by reoxidation by oxygen, which generates the reactive oxygen species (ROS) hydrogen peroxide and superoxide. Prior studies have shown that not all reactions catalysed by PETN reductase yield enantiopure products, such as the reduction of (E)-2-phenyl-1-nitroprop-1-ene (PNE) to produce (S)-2-phenyl-1-nitropropane (PNA) with variable enantiomeric excess (ee). Recent independent studies of (E)-PNE reduction by PETN reductase showed that the major product formed could be switched to (R)-PNA, depending on the reaction conditions. We investigated this phenomenon, and found that the presence of oxygen and ROS influenced the overall product enantiopurity. Anaerobic reactions produced consistently higher nitroalkane (S)-PNA product yields than aerobic reactions (64% versus 28%). The presence of oxygen dramatically increased the preference for (R)-PNA formation (up to 52% ee). Conversely, the presence of the ROS superoxide and hydrogen peroxide switched the preference to (S)-PNA product formation. Given that oxygen has no role in the natural catalytic cycle, these findings demonstrate a remarkable ability to manipulate product enantiopurity of this enzyme-catalysed reaction by simple manipulation of reaction conditions. Potential mechanisms of this unusual behaviour are discussed.
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Affiliation(s)
- Anna Fryszkowska
- Manchester Interdisciplinary Biocentre and School of Chemistry, University of Manchester, UK
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Pompeu YA, Sullivan B, Walton AZ, Stewart JD. Structural and Catalytic Characterization of Pichia stipitis OYE 2.6, a Useful Biocatalyst for Asymmetric Alkene Reductions. Adv Synth Catal 2012. [DOI: 10.1002/adsc.201200213] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Xiang J, Sun EX, Lian CX, Yuan WC, Zhu J, Wang Q, Deng J. The highly chemoselective transfer hydrogenation of the carbon–carbon double bond of conjugated nitroalkenes by a rhodium complex. Tetrahedron 2012. [DOI: 10.1016/j.tet.2012.04.028] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Ema T, Nakano Y, Yoshida D, Kamata S, Sakai T. Redesign of enzyme for improving catalytic activity and enantioselectivity toward poor substrates: manipulation of the transition state. Org Biomol Chem 2012; 10:6299-308. [DOI: 10.1039/c2ob25614b] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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Bernard J, van Heerden E, Arends IWCE, Opperman DJ, Hollmann F. Chemoenzymatic Reduction of Conjugated CC Double Bonds. ChemCatChem 2011. [DOI: 10.1002/cctc.201100312] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Behrens GA, Hummel A, Padhi SK, Schätzle S, Bornscheuer UT. Discovery and Protein Engineering of Biocatalysts for Organic Synthesis. Adv Synth Catal 2011. [DOI: 10.1002/adsc.201100446] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Toogood HS, Fryszkowska A, Hulley M, Sakuma M, Mansell D, Stephens GM, Gardiner JM, Scrutton NS. A Site-Saturated Mutagenesis Study of Pentaerythritol Tetranitrate Reductase Reveals that Residues 181 and 184 Influence Ligand Binding, Stereochemistry and Reactivity. Chembiochem 2011; 12:738-49. [DOI: 10.1002/cbic.201000662] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2010] [Indexed: 11/09/2022]
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Fryszkowska A, Toogood H, Sakuma M, Stephens GM, Gardiner JM, Scrutton NS. Active site modifications in pentaerythritol tetranitrate reductase can lead to improved product enantiopurity, decreased by-product formation and altered stereochemical outcome in reactions with α,β-unsaturated nitroolefins. Catal Sci Technol 2011. [DOI: 10.1039/c0cy00092b] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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