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Fan XY, Yu Y, Yao Y, Li WD, Tao FY, Wang N. Applications of Ene-Reductases in the Synthesis of Flavors and Fragrances. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:18305-18320. [PMID: 38966982 PMCID: PMC11342376 DOI: 10.1021/acs.jafc.4c02897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 06/26/2024] [Accepted: 06/28/2024] [Indexed: 07/06/2024]
Abstract
Flavors and fragrances (F&F) are interesting organic compounds in chemistry. These compounds are widely used in the food, cosmetic, and medical industries. Enzymatic synthesis exhibits several advantages over natural extraction and chemical preparation, including a high yield, stable quality, mildness, and environmental friendliness. To date, many oxidoreductases and hydrolases have been used to biosynthesize F&F. Ene-reductases (ERs) are a class of biocatalysts that can catalyze the asymmetric reduction of α,β-unsaturated compounds and offer superior specificity and selectivity; therefore, ERs have been increasingly considered an ideal alternative to their chemical counterparts. This review summarizes the research progress on the use of ERs in F&F synthesis over the past 20 years, including the achievements of various scholars, the differences and similarities among the findings, and the discussions of future research trends related to ERs. We hope this review can inspire researchers to promote the development of biotechnology in the F&F industry.
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Affiliation(s)
- Xin-Yue Fan
- Key
Laboratory of Green Chemistry & Technology, Ministry of Education,
College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, People’s
Republic of China
| | - Yuan Yu
- Key
Laboratory of Green Chemistry & Technology, Ministry of Education,
College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, People’s
Republic of China
| | - Yao Yao
- Key
Laboratory of Green Chemistry & Technology, Ministry of Education,
College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, People’s
Republic of China
| | - Wen-Dian Li
- Harmful
Components and Tar Reduction in Cigarette Key Laboratory of Sichuan
Province, China Tobacco Sichuan Industrial
Company, Limited, Chengdu, Sichuan 610066, People’s Republic of China
- Sichuan
Sanlian New Material Company, Limited, Chengdu, Sichuan 610041, People’s Republic
of China
| | - Fei-Yan Tao
- Harmful
Components and Tar Reduction in Cigarette Key Laboratory of Sichuan
Province, China Tobacco Sichuan Industrial
Company, Limited, Chengdu, Sichuan 610066, People’s Republic of China
- Sichuan
Sanlian New Material Company, Limited, Chengdu, Sichuan 610041, People’s Republic
of China
| | - Na Wang
- Key
Laboratory of Green Chemistry & Technology, Ministry of Education,
College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, People’s
Republic of China
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2
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Anderson NT, Xie JS, Chacko AN, Liu VL, Fan KC, Mukherjee A. Rational Design of a Circularly Permuted Flavin-Based Fluorescent Protein. Chembiochem 2024; 25:e202300814. [PMID: 38356332 PMCID: PMC11065581 DOI: 10.1002/cbic.202300814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 02/12/2024] [Accepted: 02/14/2024] [Indexed: 02/16/2024]
Abstract
Flavin-based fluorescent proteins are oxygen-independent reporters that hold great promise for imaging anaerobic and hypoxic biological systems. In this study, we explored the feasibility of applying circular permutation, a valuable method for the creation of fluorescent sensors, to flavin-based fluorescent proteins. We used rational design and structural data to identify a suitable location for circular permutation in iLOV, a flavin-based reporter derived from A. thaliana. However, relocating the N- and C-termini to this position resulted in a significant reduction in fluorescence. This loss of fluorescence was reversible, however, by fusing dimerizing coiled coils at the new N- and C-termini to compensate for the increase in local chain entropy. Additionally, by inserting protease cleavage sites in circularly permuted iLOV, we developed two protease sensors and demonstrated their application in mammalian cells. In summary, our work establishes the first approach to engineer circularly permuted FbFPs optimized for high fluorescence and further showcases the utility of circularly permuted FbFPs to serve as a scaffold for sensor engineering.
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Affiliation(s)
| | - Jason S. Xie
- Department of Molecular, Cellular, and Developmental Biology
| | | | - Vannie L. Liu
- Department of Molecular, Cellular, and Developmental Biology
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3
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Coleman T, Shin J, Silberg JJ, Shamoo Y, Atkinson JT. The Biochemical Impact of Extracting an Embedded Adenylate Kinase Domain Using Circular Permutation. Biochemistry 2024; 63:599-609. [PMID: 38357768 DOI: 10.1021/acs.biochem.3c00605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2024]
Abstract
Adenylate kinases (AKs) have evolved AMP-binding and lid domains that are encoded as continuous polypeptides embedded at different locations within the discontinuous polypeptide encoding the core domain. A prior study showed that AK homologues of different stabilities consistently retain cellular activity following circular permutation that splits a region with high energetic frustration within the AMP-binding domain into discontinuous fragments. Herein, we show that mesophilic and thermophilic AKs having this topological restructuring retain activity and substrate-binding characteristics of the parental AK. While permutation decreased the activity of both AK homologues at physiological temperatures, the catalytic activity of the thermophilic AK increased upon permutation when assayed >30 °C below the melting temperature of the native AK. The thermostabilities of the permuted AKs were uniformly lower than those of native AKs, and they exhibited multiphasic unfolding transitions, unlike the native AKs, which presented cooperative thermal unfolding. In addition, proteolytic digestion revealed that permutation destabilized each AK in differing manners, and mass spectrometry suggested that the new termini within the AMP-binding domain were responsible for the increased proteolysis sensitivity. These findings illustrate how changes in contact order can be used to tune enzyme activity and alter folding dynamics in multidomain enzymes.
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Affiliation(s)
- Tom Coleman
- Department of BioSciences, Rice University, MS-140, 6100 Main Street, Houston, Texas 77005, United States
| | - John Shin
- Department of BioSciences, Rice University, MS-140, 6100 Main Street, Houston, Texas 77005, United States
| | - Jonathan J Silberg
- Department of BioSciences, Rice University, MS-140, 6100 Main Street, Houston, Texas 77005, United States
- Department of Chemical and Biomolecular Engineering, Rice University, MS-362, 6100 Main Street, Houston, Texas 77005, United States
- Department of Bioengineering, Rice University, MS-142, 6100 Main Street, Houston, Texas 77005, United States
| | - Yousif Shamoo
- Department of BioSciences, Rice University, MS-140, 6100 Main Street, Houston, Texas 77005, United States
| | - Joshua T Atkinson
- Department of BioSciences, Rice University, MS-140, 6100 Main Street, Houston, Texas 77005, United States
- Department of Physics and Astronomy, University of Southern California, Los Angeles, California 90007, United States
- Department of Civil and Environmental Engineering, Princeton University, Princeton, New Jersey 08544, United States
- Omenn-Darling Bioengineering Institute, Princeton University, Princeton, New Jersey 08544, United States
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4
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Kong J, Hu J, Li J, Zhang J, Shen Y, Yue T, Shen X, Wang Y, Li Z, Xia Y. Rethreading Design of Ratiometric roGFP2 Mimetic Peptide for Hydrogen Peroxide Sensing. Anal Chem 2023; 95:8284-8290. [PMID: 37161261 DOI: 10.1021/acs.analchem.3c00486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Reconstruction of the miniaturized peptide to mimic the tailored functions of protein has been attractive but challenging. Herein, initialized from the crystal structure of redox-sensitive green fluorescent protein-2 (roGFP2), we propose a practical approach to construct the roGFP2 mimetic peptide by rethreading the aromatic residues adjacent to the chromophore fragment. By fine-tuning the residues of peptides, a mini tetrapeptide (Cys-Phe-Phe-His) was designed, which can act as a hydrogen peroxide sensor using its ratiometric fluorescence. The roGFP2 mimetic tetrapeptide is biocompatible and photostable and has competitive fluorescent properties with roGFP2 by the virtue of its assembly induced emissions. We expand the ratiometric tetrapeptide for sensing hydrogen peroxide in acidic chambers. The results provide a promising approach for the artificial design of miniaturized peptides with the desired function.
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Affiliation(s)
- Jia Kong
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi 712100, P. R. China
| | - Jinyao Hu
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi 712100, P. R. China
| | - Jia Li
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi 712100, P. R. China
| | - Jiaxing Zhang
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, P. R. China
| | - Yuhe Shen
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, P. R. China
| | - Tianli Yue
- College of Food Science and Engineering, Northwest University, Xian, Shaanxi 710069, P. R. China
| | - Xihui Shen
- State Key Laboratory of Crop Stress Biology for Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, P. R. China
| | - Yuefei Wang
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, P. R. China
| | - Zhonghong Li
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi 712100, P. R. China
| | - Yinqiang Xia
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi 712100, P. R. China
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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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Feng J, Xue Y, Wang J, Xie X, Lu C, Chen H, Lu Y, Zhu L, Chu D, Chen X. Enhancing the asymmetric reduction activity of ene-reductases for the synthesis of a brivaracetam precursor. Process Biochem 2022. [DOI: 10.1016/j.procbio.2022.12.036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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7
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Ramos De Dios SM, Tiwari VK, McCune CD, Dhokale RA, Berkowitz DB. Biomacromolecule-Assisted Screening for Reaction Discovery and Catalyst Optimization. Chem Rev 2022; 122:13800-13880. [PMID: 35904776 DOI: 10.1021/acs.chemrev.2c00213] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Reaction discovery and catalyst screening lie at the heart of synthetic organic chemistry. While there are efforts at de novo catalyst design using computation/artificial intelligence, at its core, synthetic chemistry is an experimental science. This review overviews biomacromolecule-assisted screening methods and the follow-on elaboration of chemistry so discovered. All three types of biomacromolecules discussed─enzymes, antibodies, and nucleic acids─have been used as "sensors" to provide a readout on product chirality exploiting their native chirality. Enzymatic sensing methods yield both UV-spectrophotometric and visible, colorimetric readouts. Antibody sensors provide direct fluorescent readout upon analyte binding in some cases or provide for cat-ELISA (Enzyme-Linked ImmunoSorbent Assay)-type readouts. DNA biomacromolecule-assisted screening allows for templation to facilitate reaction discovery, driving bimolecular reactions into a pseudo-unimolecular format. In addition, the ability to use DNA-encoded libraries permits the barcoding of reactants. All three types of biomacromolecule-based screens afford high sensitivity and selectivity. Among the chemical transformations discovered by enzymatic screening methods are the first Ni(0)-mediated asymmetric allylic amination and a new thiocyanopalladation/carbocyclization transformation in which both C-SCN and C-C bonds are fashioned sequentially. Cat-ELISA screening has identified new classes of sydnone-alkyne cycloadditions, and DNA-encoded screening has been exploited to uncover interesting oxidative Pd-mediated amido-alkyne/alkene coupling reactions.
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Affiliation(s)
| | - Virendra K Tiwari
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
| | - Christopher D McCune
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
| | - Ranjeet A Dhokale
- Higuchi Biosciences Center, University of Kansas, Lawrence, Kansas 66047, United States
| | - David B Berkowitz
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
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8
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Liu G, Li S, Shi Q, Li H, Guo J, Ouyang J, Jia X, Zhang L, You S, Qin B. Engineering of Saccharomyces pastorianus old yellow enzyme 1 for the synthesis of pharmacologically active (S)-profen derivatives. MOLECULAR CATALYSIS 2021. [DOI: 10.1016/j.mcat.2021.111568] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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9
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Atkinson JT, Jones AM, Nanda V, Silberg JJ. Protein tolerance to random circular permutation correlates with thermostability and local energetics of residue-residue contacts. Protein Eng Des Sel 2019; 32:489-501. [PMID: 32626892 PMCID: PMC7462040 DOI: 10.1093/protein/gzaa012] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 04/13/2020] [Accepted: 04/15/2020] [Indexed: 01/08/2023] Open
Abstract
Adenylate kinase (AK) orthologs with a range of thermostabilities were subjected to random circular permutation, and deep mutational scanning was used to evaluate where new protein termini were nondisruptive to activity. The fraction of circularly permuted variants that retained function in each library correlated with AK thermostability. In addition, analysis of the positional tolerance to new termini, which increase local conformational flexibility, showed that bonds were either functionally sensitive to cleavage across all homologs, differentially sensitive, or uniformly tolerant. The mobile AMP-binding domain, which displays the highest calculated contact energies, presented the greatest tolerance to new termini across all AKs. In contrast, retention of function in the lid and core domains was more dependent upon AK melting temperature. These results show that family permutation profiling identifies primary structure that has been selected by evolution for dynamics that are critical to activity within an enzyme family. These findings also illustrate how deep mutational scanning can be applied to protein homologs in parallel to differentiate how topology, stability, and local energetics govern mutational tolerance.
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Affiliation(s)
- Joshua T Atkinson
- Systems, Synthetic, and Physical Biology Graduate Program, Rice University, 6100 Main Street, MS-180, Houston, TX 77005, USA
- Department of BioSciences, Rice University, 6100 Main Street, MS-140, Houston, TX 77005, USA
| | - Alicia M Jones
- Biochemistry and Cell Biology Graduate Program, Rice University, 6100 Main Street, MS-140, Houston, TX 77005, USA
| | - Vikas Nanda
- Center for Advanced Biotechnology and Medicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Jonathan J Silberg
- Department of BioSciences, Rice University, 6100 Main Street, MS-140, Houston, TX 77005, USA
- Department of Bioengineering, Rice University, 6100 Main Street, MS-142, Houston, TX 77005, USA
- Department of Chemical and Biomolecular Engineering, Rice University, 6100 Main Street, MS-362, Houston, TX 77005, USA
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10
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Toogood HS, Scrutton NS. Discovery, Characterisation, Engineering and Applications of Ene Reductases for Industrial Biocatalysis. ACS Catal 2019; 8:3532-3549. [PMID: 31157123 PMCID: PMC6542678 DOI: 10.1021/acscatal.8b00624] [Citation(s) in RCA: 158] [Impact Index Per Article: 31.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Recent studies of multiple enzyme families collectively referred to as ene-reductases (ERs) have highlighted potential industrial application of these biocatalysts in the production of fine and speciality chemicals. Processes have been developed whereby ERs contribute to synthetic routes as isolated enzymes, components of multi-enzyme cascades, and more recently in metabolic engineering and synthetic biology programmes using microbial cell factories to support chemicals production. The discovery of ERs from previously untapped sources and the expansion of directed evolution screening programmes, coupled to deeper mechanistic understanding of ER reactions, have driven their use in natural product and chemicals synthesis. Here we review developments, challenges and opportunities for the use of ERs in fine and speciality chemicals manufacture. The ER research field is rapidly expanding and the focus of this review is on developments that have emerged predominantly over the last 4 years.
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Affiliation(s)
- Helen S. Toogood
- School of Chemistry, Faculty of Science and Engineering, University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
| | - Nigel S. Scrutton
- School of Chemistry, Faculty of Science and Engineering, University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
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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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Eilenberger C, Spitz S, Bachmann BEM, Ehmoser EK, Ertl P, Rothbauer M. The Usual Suspects 2019: of Chips, Droplets, Synthesis, and Artificial Cells. MICROMACHINES 2019; 10:E285. [PMID: 31035574 PMCID: PMC6562886 DOI: 10.3390/mi10050285] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 04/24/2019] [Accepted: 04/26/2019] [Indexed: 12/03/2022]
Abstract
Synthetic biology aims to understand fundamental biological processes in more detail than possible for actual living cells. Synthetic biology can combat decomposition and build-up of artificial experimental models under precisely controlled and defined environmental and biochemical conditions. Microfluidic systems can provide the tools to improve and refine existing synthetic systems because they allow control and manipulation of liquids on a micro- and nanoscale. In addition, chip-based approaches are predisposed for synthetic biology applications since they present an opportune technological toolkit capable of fully automated high throughput and content screening under low reagent consumption. This review critically highlights the latest updates in microfluidic cell-free and cell-based protein synthesis as well as the progress on chip-based artificial cells. Even though progress is slow for microfluidic synthetic biology, microfluidic systems are valuable tools for synthetic biology and may one day help to give answers to long asked questions of fundamental cell biology and life itself.
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Affiliation(s)
- Christoph Eilenberger
- Institute of Applied Synthetic Chemistry, Institute of Chemical Technologies and Analytics, Faculty of Technical Chemistry, Vienna University of Technology, A-1060 Vienna, Austria.
| | - Sarah Spitz
- Institute of Applied Synthetic Chemistry, Institute of Chemical Technologies and Analytics, Faculty of Technical Chemistry, Vienna University of Technology, A-1060 Vienna, Austria.
| | - Barbara Eva Maria Bachmann
- Austrian Cluster for Tissue Regeneration, Vienna, Austria; Ludwig Boltzmann Institute for Experimental and Clinical Traumatology, Allgemeine Unfallversicherungsanstalt (AUVA) Research Centre, A-1200 Vienna, Austria.
| | - Eva Kathrin Ehmoser
- Institute of Synthetic Bioarchitectures, Department of Nanobiotechnology, University of Natural Resources and Life Sciences Vienna, A-1190 Vienna, Austria.
| | - Peter Ertl
- Institute of Applied Synthetic Chemistry, Institute of Chemical Technologies and Analytics, Faculty of Technical Chemistry, Vienna University of Technology, A-1060 Vienna, Austria.
| | - Mario Rothbauer
- Institute of Applied Synthetic Chemistry, Institute of Chemical Technologies and Analytics, Faculty of Technical Chemistry, Vienna University of Technology, A-1060 Vienna, Austria.
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13
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Ying X, Yu S, Huang M, Wei R, Meng S, Cheng F, Yu M, Ying M, Zhao M, Wang Z. Engineering the Enantioselectivity of Yeast Old Yellow Enzyme OYE2y in Asymmetric Reduction of ( E/ Z)-Citral to ( R)-Citronellal. Molecules 2019; 24:E1057. [PMID: 30889828 PMCID: PMC6470962 DOI: 10.3390/molecules24061057] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2019] [Revised: 03/13/2019] [Accepted: 03/14/2019] [Indexed: 11/25/2022] Open
Abstract
The members of the Old Yellow Enzyme (OYE) family are capable of catalyzing the asymmetric reduction of (E/Z)-citral to (R)-citronellal-a key intermediate in the synthesis of L-menthol. The applications of OYE-mediated biotransformation are usually hampered by its insufficient enantioselectivity and low activity. Here, the (R)-enantioselectivity of Old Yellow Enzyme from Saccharomyces cerevisiae CICC1060 (OYE2y) was enhanced through protein engineering. The single mutations of OYE2y revealed that the sites R330 and P76 could act as the enantioselectivity switch of OYE2y. Site-saturation mutagenesis was conducted to generate all possible replacements for the sites R330 and P76, yielding 17 and five variants with improved (R)-enantioselectivity in the (E/Z)-citral reduction, respectively. Among them, the variants R330H and P76C partly reversed the neral derived enantioselectivity from 32.66% e.e. (S) to 71.92% e.e. (R) and 37.50% e.e. (R), respectively. The docking analysis of OYE2y and its variants revealed that the substitutions R330H and P76C enabled neral to bind with a flipped orientation in the active site and thus reverse the enantioselectivity. Remarkably, the double substitutions of R330H/P76M, P76G/R330H, or P76S/R330H further improved (R)-enantioselectivity to >99% e.e. in the reduction of (E)-citral or (E/Z)-citral. The results demonstrated that it was feasible to alter the enantioselectivity of OYEs through engineering key residue distant from active sites, e.g., R330 in OYE2y.
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Affiliation(s)
- Xiangxian Ying
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China.
| | - Shihua Yu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China.
| | - Meijuan Huang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China.
| | - Ran Wei
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China.
| | - Shumin Meng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China.
| | - Feng Cheng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China.
| | - Meilan Yu
- College of Life Sciences, Zhejiang Sci-Tech Univeristy, Hangzhou 310018, China.
| | - Meirong Ying
- Grain and Oil Products Quality Inspection Center of Zhejiang Province, Hangzhou 310012, China.
| | - Man Zhao
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China.
| | - Zhao Wang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China.
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14
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Lee PG, Lee SH, Hong EY, Lutz S, Kim BG. Circular permutation of a bacterial tyrosinase enables efficient polyphenol-specific oxidation and quantitative preparation of orobol. Biotechnol Bioeng 2018; 116:19-27. [DOI: 10.1002/bit.26795] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 07/06/2018] [Accepted: 07/11/2018] [Indexed: 01/07/2023]
Affiliation(s)
- Pyung-Gang Lee
- School of Chemical and Biological Engineering; Seoul National University; Seoul Korea
- Institute of Molecular Biology and Genetics, Seoul National University; Seoul Korea
| | - Sang-Hyuk Lee
- School of Chemical and Biological Engineering; Seoul National University; Seoul Korea
- Institute of Molecular Biology and Genetics, Seoul National University; Seoul Korea
| | - Eun Young Hong
- School of Chemical and Biological Engineering; Seoul National University; Seoul Korea
- Institute of Molecular Biology and Genetics, Seoul National University; Seoul Korea
| | - Stefan Lutz
- Department of Chemistry; Emory University; Atlanta Georgia
| | - Byung-Gee Kim
- School of Chemical and Biological Engineering; Seoul National University; Seoul Korea
- Institute of Molecular Biology and Genetics, Seoul National University; Seoul Korea
- Bioengineering Institute, Seoul National University; Seoul Korea
- Institute of Engineering Research, Seoul National University; Seoul Korea
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15
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Gaytán P, Roldán-Salgado A, Yáñez JA, Morales-Arrieta S, Juárez-González VR. CiPerGenesis, A Mutagenesis Approach that Produces Small Libraries of Circularly Permuted Proteins Randomly Opened at a Focused Region: Testing on the Green Fluorescent Protein. ACS COMBINATORIAL SCIENCE 2018; 20:400-413. [PMID: 29812897 DOI: 10.1021/acscombsci.7b00152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Circularly permuted proteins (cpPs) represent a novel type of mutant proteins with original termini that are covalently linked through a peptide connector and opened at any other place of the polypeptide backbone to create new ends. cpPs are finding wide applications in biotechnology because their properties may be quite different from those of the parental protein. However, the actual challenge for the creation of successful cpPs is to identify those peptide bonds that can be broken to create new termini and ensure functional and well-folded cpPs. Herein, we describe CiPerGenesis, a combinatorial mutagenesis approach that uses two oligonucleotide libraries to amplify a circularized gene by PCR, starting and ending from a focused target region. This approach creates small libraries of circularly permuted genes that are easily cloned in the correct direction and frame using two different restriction sites encoded in the oligonucleotides. Once expressed, the protein libraries exhibit a unique sequence diversity, comprising cpPs that exhibit ordinary breakpoints between adjacent amino acids localized at the target region as well as cpPs with new termini containing user-defined truncations and repeats of some amino acids. CiPerGenesis was tested at the lid region G134-H148 of green fluorescent protein (GFP), revealing that the most fluorescent variants were those starting at Leu141 and ending at amino acids Tyr145, Tyr143, Glu142, Leu141, Lys140, and H139. Purification and biochemical characterization of some variants suggested a differential expression, solubility and maturation extent of the mutant proteins as the likely cause for the variability in fluorescence intensity observed in colonies.
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Affiliation(s)
- Paul Gaytán
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Avenida Universidad 2001, Cuernavaca, Morelos 62210, México
| | - Abigail Roldán-Salgado
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Avenida Universidad 2001, Cuernavaca, Morelos 62210, México
| | - Jorge A. Yáñez
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Avenida Universidad 2001, Cuernavaca, Morelos 62210, México
| | - Sandra Morales-Arrieta
- Departamento de Ingeniería en Biotecnología, Universidad Politécnica del Estado de Morelos, Boulevard Cuauhnáhuac No. 566, Col. Lomas del Texcal, Jiutepec, Morelos 62550, México
| | - Víctor R. Juárez-González
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Avenida Universidad 2001, Cuernavaca, Morelos 62210, México
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16
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Diefenbach XW, Farasat I, Guetschow ED, Welch CJ, Kennedy RT, Sun S, Moore JC. Enabling Biocatalysis by High-Throughput Protein Engineering Using Droplet Microfluidics Coupled to Mass Spectrometry. ACS OMEGA 2018; 3:1498-1508. [PMID: 30023807 PMCID: PMC6044804 DOI: 10.1021/acsomega.7b01973] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Accepted: 01/18/2018] [Indexed: 05/24/2023]
Abstract
Directed Evolution is a key technology driving the utility of biocatalysis in pharmaceutical synthesis. Conventional approaches to Directed Evolution are conducted using bacterial cells expressing enzymes in microplates, with catalyzed reactions measured by HPLC, high-performance liquid chromatography-mass spectrometry (HPLC-MS), or optical detectors, which require either long cycle times or tailor-made substrates. To better fit modern, fast-paced process chemistry development where solutions are rapidly needed for new substrates, droplet microfluidics interfaced with electrospray ionization (ESI)-MS provides a label-free high-throughput screening platform. To apply this method to industrial enzyme screening and to explore potential approaches that may further improve the overall throughput, we optimized the existing droplet-MS methods. Carryover between droplets, traditionally a significant issue, was reduced to undetectable level by replacing the stainless steel ESI needle with a Teflon needle within a capillary electrophoresis (CE)-MS source. Throughput was improved to 3 Hz with a wide range of droplet sizes (10-50 nL) by tuning the sheath flow within the CE-MS source. The optimized method was demonstrated by screening reactions using two different transaminase libraries. Good correlations (r2 ∼ 0.95) were found between the droplet-MS and LC-MS methods, with 100% match on hit variants. We further explored the capability of the system by performing in vitro transcription-translation inside the droplets and directly analyzing the intact reaction mixture droplets by MS. The synthesized protein attained comparable activity to the protein standard, and the complex samples appeared well tolerated by the MS. The success of the above applications indicates that the MS analysis of the microfluidic droplets is an available option for considerably accelerating the screening of enzyme evolution libraries.
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Affiliation(s)
- Xue W. Diefenbach
- Merck
Research Laboratory, Merck & Co., Inc., 126 E Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Iman Farasat
- Merck
Research Laboratory, Merck & Co., Inc., 126 E Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Erik D. Guetschow
- Merck
Research Laboratory, Merck & Co., Inc., 126 E Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Christopher J. Welch
- Merck
Research Laboratory, Merck & Co., Inc., 126 E Lincoln Avenue, Rahway, New Jersey 07065, United States
- Welch
Innovation, LLC., Cranbury, New Jersey 08512, United States
| | - Robert T. Kennedy
- Department
of Chemistry, University of Michigan, 930 N University Avenue, Ann Arbor, Michigan 48109, United States
| | - Shuwen Sun
- Merck
Research Laboratory, Merck & Co., Inc., 126 E Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Jeffrey C. Moore
- Merck
Research Laboratory, Merck & Co., Inc., 126 E Lincoln Avenue, Rahway, New Jersey 07065, United States
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17
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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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18
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Fink MJ, Syrén PO. Redesign of water networks for efficient biocatalysis. Curr Opin Chem Biol 2017; 37:107-114. [DOI: 10.1016/j.cbpa.2017.02.013] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Revised: 02/01/2017] [Accepted: 02/08/2017] [Indexed: 01/28/2023]
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19
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Yachnin BJ, Khare SD. Engineering carboxypeptidase G2 circular permutations for the design of an autoinhibited enzyme. Protein Eng Des Sel 2017; 30:321-331. [PMID: 28160000 PMCID: PMC6283397 DOI: 10.1093/protein/gzx005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Revised: 01/11/2017] [Accepted: 01/18/2017] [Indexed: 11/14/2022] Open
Abstract
Carboxypeptidase G2 (CPG2) is an Food and Drug Administration (FDA)-approved enzyme drug used to treat methotrexate (MTX) toxicity in cancer patients receiving MTX treatment. It has also been used in directed enzyme-prodrug chemotherapy, but this strategy has been hampered by off-site activation of the prodrug by the circulating enzyme. The development of a tumor protease activatable CPG2, which could be achieved using a circular permutation of CPG2 fused to an inactivating 'prodomain', would aid in these applications. We report the development of a protease accessibility-based screen to identify candidate sites for circular permutation in proximity of the CPG2 active site. The resulting six circular permutants showed similar expression, structure, thermal stability, and, in four cases, activity levels compared to the wild-type enzyme. We rationalize these results based on structural models of the permutants obtained using the Rosetta software. We developed a cell growth-based selection system, and demonstrated that when fused to periplasm-directing signal peptides, one of our circular permutants confers MTX resistance in Escherichia coli with equal efficiency as the wild-type enzyme. As the permutants have similar properties to wild-type CPG2, these enzymes are promising starting points for the development of autoinhibited, protease-activatable zymogen forms of CPG2 for use in therapeutic contexts.
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Affiliation(s)
- Brahm J. Yachnin
- Department of Chemistry & Chemical Biology and the Center for Integrative Proteomics, Rutgers University, Piscataway, NJ 08854, USA
| | - Sagar D. Khare
- Department of Chemistry & Chemical Biology and the Center for Integrative Proteomics, Rutgers University, Piscataway, NJ 08854, USA
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20
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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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21
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Joo JC, Khusnutdinova AN, Flick R, Kim T, Bornscheuer UT, Yakunin AF, Mahadevan R. Alkene hydrogenation activity of enoate reductases for an environmentally benign biosynthesis of adipic acid. Chem Sci 2017; 8:1406-1413. [PMID: 28616142 PMCID: PMC5460604 DOI: 10.1039/c6sc02842j] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Accepted: 10/08/2016] [Indexed: 12/26/2022] Open
Abstract
Adipic acid, a precursor for Nylon-6,6 polymer, is one of the most important commodity chemicals, which is currently produced from petroleum. The biosynthesis of adipic acid from glucose still remains challenging due to the absence of biocatalysts required for the hydrogenation of unsaturated six-carbon dicarboxylic acids to adipic acid. Here, we demonstrate the first enzymatic hydrogenation of 2-hexenedioic acid and muconic acid to adipic acid using enoate reductases (ERs). ERs can hydrogenate 2-hexenedioic acid and muconic acid producing adipic acid with a high conversion rate and yield in vivo and in vitro. Purified ERs exhibit a broad substrate spectrum including aromatic and aliphatic 2-enoates and a significant oxygen tolerance. The discovery of the hydrogenation activity of ERs contributes to an understanding of the catalytic mechanism of these poorly characterized enzymes and enables the environmentally benign biosynthesis of adipic acid and other chemicals from renewable resources.
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Affiliation(s)
- Jeong Chan Joo
- Center for Bio-based Chemistry , Division of Convergence Chemistry , Korea Research Institute of Chemical Technology , 141 Gajeong-ro, Yuseong-gu , Daejeon 34114 , Republic of Korea .
| | - Anna N Khusnutdinova
- Department of Chemical Engineering and Applied Chemistry , University of Toronto , 200 College Street , ON M5S 3E5 , Canada . ;
| | - Robert Flick
- Department of Chemical Engineering and Applied Chemistry , University of Toronto , 200 College Street , ON M5S 3E5 , Canada . ;
| | - Taeho Kim
- Department of Chemical Engineering and Applied Chemistry , University of Toronto , 200 College Street , ON M5S 3E5 , Canada . ;
| | - Uwe T Bornscheuer
- Institute of Biochemistry , Department of Biotechnology & Enzyme Catalysis , Greifswald University , Felix-Hausdorff-Strasse 4 , 17487 Greifswald , Germany
| | - Alexander F Yakunin
- Department of Chemical Engineering and Applied Chemistry , University of Toronto , 200 College Street , ON M5S 3E5 , Canada . ;
| | - Radhakrishnan Mahadevan
- Department of Chemical Engineering and Applied Chemistry , University of Toronto , 200 College Street , ON M5S 3E5 , Canada . ;
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22
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23
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Pandey N, Kuypers BE, Nassif B, Thomas EE, Alnahhas RN, Segatori L, Silberg JJ. Tolerance of a Knotted Near-Infrared Fluorescent Protein to Random Circular Permutation. Biochemistry 2016; 55:3763-73. [PMID: 27304983 DOI: 10.1021/acs.biochem.6b00258] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Bacteriophytochrome photoreceptors (BphP) are knotted proteins that have been developed as near-infrared fluorescent protein (iRFP) reporters of gene expression. To explore how rearrangements in the peptides that interlace into the knot within the BphP photosensory core affect folding, we subjected iRFPs to random circular permutation using an improved transposase mutagenesis strategy and screened for variants that fluoresce. We identified 27 circularly permuted iRFPs that display biliverdin-dependent fluorescence in Escherichia coli. The variants with the brightest whole cell fluorescence initiated translation at residues near the domain linker and knot tails, although fluorescent variants that initiated translation within the PAS and GAF domains were discovered. Circularly permuted iRFPs retained sufficient cofactor affinity to fluoresce in tissue culture without the addition of biliverdin, and one variant displayed enhanced fluorescence when expressed in bacteria and tissue culture. This variant displayed a quantum yield similar to that of iRFPs but exhibited increased resistance to chemical denaturation, suggesting that the observed increase in the magnitude of the signal arose from more efficient protein maturation. These results show how the contact order of a knotted BphP can be altered without disrupting chromophore binding and fluorescence, an important step toward the creation of near-infrared biosensors with expanded chemical sensing functions for in vivo imaging.
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Affiliation(s)
- Naresh Pandey
- Department of Biosciences, Rice University , Houston, Texas 77005, United States.,Biochemistry and Cell Biology Graduate Program, Rice University , Houston, Texas 77005, United States
| | - Brianna E Kuypers
- Systems, Synthetic, and Physical Biology Graduate Program, Rice University , Houston, Texas 77005, United States.,Department of Chemical and Biomolecular Engineering, Rice University , Houston, Texas 77005, United States
| | - Barbara Nassif
- Department of Biosciences, Rice University , Houston, Texas 77005, United States
| | - Emily E Thomas
- Department of Biosciences, Rice University , Houston, Texas 77005, United States.,Biochemistry and Cell Biology Graduate Program, Rice University , Houston, Texas 77005, United States
| | - Razan N Alnahhas
- Department of Biosciences, Rice University , Houston, Texas 77005, United States.,Biochemistry and Cell Biology Graduate Program, Rice University , Houston, Texas 77005, United States
| | - Laura Segatori
- Department of Biosciences, Rice University , Houston, Texas 77005, United States.,Department of Chemical and Biomolecular Engineering, Rice University , Houston, Texas 77005, United States.,Department of Bioengineering, Rice University , Houston, Texas 77005, United States
| | - Jonathan J Silberg
- Department of Biosciences, Rice University , Houston, Texas 77005, United States.,Department of Bioengineering, Rice University , Houston, Texas 77005, United States
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24
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Protein rethreading: A novel approach to protein design. Sci Rep 2016; 6:26847. [PMID: 27229326 PMCID: PMC4882587 DOI: 10.1038/srep26847] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Accepted: 05/04/2016] [Indexed: 12/29/2022] Open
Abstract
Protein engineering is an important tool for the design of proteins with novel and desirable features. Templates from the protein databank (PDB) are often used as initial models that can be modified to introduce new properties. We examine whether it is possible to reconnect a protein in a manner that generates a new topology yet preserves its structural integrity. Here, we describe the rethreading of dihydrofolate reductase (DHFR) from E. coli (wtDHFR). The rethreading process involved the removal of three native loops, and the introduction of three new loops with alternate connections. The structure of the rethreaded DHFR (rDHFR-1) was determined to 1.6 Å, demonstrating the success of the rethreading process. Both wtDHFR and rDHFR-1 exhibited similar affinities towards methotrexate. However, rDHFR-1 showed no reducing activity towards dihydrofolate, and exhibited about ~6-fold lower affinity towards NADPH than wtDHFR. This work demonstrates that protein rethreading can be a powerful tool for the design of a large array of proteins with novel structures and topologies, and that by careful rearrangement of a protein sequence, the sequence to structure relationship can be expanded substantially.
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25
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Jones AM, Mehta MM, Thomas EE, Atkinson JT, Segall-Shapiro TH, Liu S, Silberg JJ. The Structure of a Thermophilic Kinase Shapes Fitness upon Random Circular Permutation. ACS Synth Biol 2016; 5:415-25. [PMID: 26976658 DOI: 10.1021/acssynbio.5b00305] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Proteins can be engineered for synthetic biology through circular permutation, a sequence rearrangement in which native protein termini become linked and new termini are created elsewhere through backbone fission. However, it remains challenging to anticipate a protein's functional tolerance to circular permutation. Here, we describe new transposons for creating libraries of randomly circularly permuted proteins that minimize peptide additions at their termini, and we use transposase mutagenesis to study the tolerance of a thermophilic adenylate kinase (AK) to circular permutation. We find that libraries expressing permuted AKs with either short or long peptides amended to their N-terminus yield distinct sets of active variants and present evidence that this trend arises because permuted protein expression varies across libraries. Mapping all sites that tolerate backbone cleavage onto AK structure reveals that the largest contiguous regions of sequence that lack cleavage sites are proximal to the phosphotransfer site. A comparison of our results with a range of structure-derived parameters further showed that retention of function correlates to the strongest extent with the distance to the phosphotransfer site, amino acid variability in an AK family sequence alignment, and residue-level deviations in superimposed AK structures. Our work illustrates how permuted protein libraries can be created with minimal peptide additions using transposase mutagenesis, and it reveals a challenge of maintaining consistent expression across permuted variants in a library that minimizes peptide additions. Furthermore, these findings provide a basis for interpreting responses of thermophilic phosphotransferases to circular permutation by calibrating how different structure-derived parameters relate to retention of function in a cellular selection.
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Affiliation(s)
- Alicia M. Jones
- Department
of Biosciences, Rice University, MS-140, 6100 Main Street, Houston, Texas 77005, United States
| | - Manan M. Mehta
- Medical
Scientist Training Program, Northwestern University, 303 East
Chicago Avenue, Morton 1-670, Chicago, Illinois 60611, United States
| | - Emily E. Thomas
- Department
of Biosciences, Rice University, MS-140, 6100 Main Street, Houston, Texas 77005, United States
| | - Joshua T. Atkinson
- Systems,
Synthetic, and Physical Biology Graduate Program, Rice University, 6100
Main MS-180, Houston, Texas 77005, United States
| | - Thomas H. Segall-Shapiro
- Department
of Biological Engineering, Synthetic Biology Center, Massachusetts Institute of Technology, 500 Technology Square, NE47-257, Cambridge, Massachusetts 02139, United States
| | - Shirley Liu
- Department
of Biosciences, Rice University, MS-140, 6100 Main Street, Houston, Texas 77005, United States
| | - Jonathan J. Silberg
- Department
of Biosciences, Rice University, MS-140, 6100 Main Street, Houston, Texas 77005, United States
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26
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Karim AS, Jewett MC. A cell-free framework for rapid biosynthetic pathway prototyping and enzyme discovery. Metab Eng 2016; 36:116-126. [PMID: 26996382 DOI: 10.1016/j.ymben.2016.03.002] [Citation(s) in RCA: 149] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Revised: 02/12/2016] [Accepted: 03/10/2016] [Indexed: 10/22/2022]
Abstract
Speeding up design-build-test (DBT) cycles is a fundamental challenge facing biochemical engineering. To address this challenge, we report a new cell-free protein synthesis driven metabolic engineering (CFPS-ME) framework for rapid biosynthetic pathway prototyping. In our framework, cell-free cocktails for synthesizing target small molecules are assembled in a mix-and-match fashion from crude cell lysates either containing selectively enriched pathway enzymes from heterologous overexpression or directly producing pathway enzymes in lysates by CFPS. As a model, we apply our approach to n-butanol biosynthesis showing that Escherichia coli lysates support a highly active 17-step CoA-dependent n-butanol pathway in vitro. The elevated degree of flexibility in the cell-free environment allows us to manipulate physiochemical conditions, access enzymatic nodes, discover new enzymes, and prototype enzyme sets with linear DNA templates to study pathway performance. We anticipate that CFPS-ME will facilitate efforts to define, manipulate, and understand metabolic pathways for accelerated DBT cycles without the need to reengineer organisms.
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Affiliation(s)
- Ashty S Karim
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Tech E-136, Evanston, IL 60208, USA; Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA
| | - Michael C Jewett
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Tech E-136, Evanston, IL 60208, USA; Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA; Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL 60611, USA; Simpson Querrey Institute, Northwestern University, Chicago, IL 60611, USA.
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27
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Kries H, Niquille DL, Hilvert D. A subdomain swap strategy for reengineering nonribosomal peptides. ACTA ACUST UNITED AC 2016; 22:640-8. [PMID: 26000750 DOI: 10.1016/j.chembiol.2015.04.015] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Revised: 03/31/2015] [Accepted: 04/15/2015] [Indexed: 11/24/2022]
Abstract
Nonribosomal peptide synthetases (NRPSs) protect microorganisms from environmental threats by producing diverse siderophores, antibiotics, and other peptide natural products. Their modular molecular structure is also attractive from the standpoint of biosynthetic engineering. Here we evaluate a methodology for swapping module specificities of these mega-enzymes that takes advantage of flavodoxin-like subdomains involved in substrate recognition. Nine subdomains encoding diverse specificities were transplanted into the Phe-specific GrsA initiation module of gramicidin S synthetase. All chimeras could be purified as soluble protein. One construct based on a Val-specific subdomain showed sizable adenylation activity and functioned as a Val-Pro diketopiperazine synthetase upon addition of the proline-specific GrsB1 module. These results suggest that subdomain swapping could be a viable alternative to previous NRPS design approaches targeting binding pockets, domains, or entire modules. The short length of the swapped sequence stretch may facilitate straightforward exploitation of the wealth of existing NRPS modules for combinatorial biosynthesis.
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Affiliation(s)
- Hajo Kries
- Laboratory of Organic Chemistry, ETH Zurich, 8093 Zürich, Switzerland
| | - David L Niquille
- Laboratory of Organic Chemistry, ETH Zurich, 8093 Zürich, Switzerland
| | - Donald Hilvert
- Laboratory of Organic Chemistry, ETH Zurich, 8093 Zürich, Switzerland.
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28
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Quertinmont LT, Orru R, Lutz S. RApid Parallel Protein EvaluatoR (RAPPER), from gene to enzyme function in one day. Chem Commun (Camb) 2015; 51:122-4. [PMID: 25384037 DOI: 10.1039/c4cc08240k] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Cell-free transcription-translation systems offer an effective and versatile platform to explore the impact of genetic variations on protein function. We have developed a protocol for preparing linear, mutagenic DNA templates for direct use in the PURE system, enabling the fast and semi-quantitative evaluation of amino acid variations on catalytic activity and stereo-selectivity in native and engineered variants of Old Yellow Enzyme.
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Affiliation(s)
- L T Quertinmont
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, GA 30322, USA.
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29
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Martínez Cuesta S, Rahman SA, Furnham N, Thornton JM. The Classification and Evolution of Enzyme Function. Biophys J 2015; 109:1082-6. [PMID: 25986631 DOI: 10.1016/j.bpj.2015.04.020] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Revised: 04/16/2015] [Accepted: 04/17/2015] [Indexed: 11/30/2022] Open
Abstract
Enzymes are the proteins responsible for the catalysis of life. Enzymes sharing a common ancestor as defined by sequence and structure similarity are grouped into families and superfamilies. The molecular function of enzymes is defined as their ability to catalyze biochemical reactions; it is manually classified by the Enzyme Commission and robust approaches to quantitatively compare catalytic reactions are just beginning to appear. Here, we present an overview of studies at the interface of the evolution and function of enzymes.
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Affiliation(s)
- Sergio Martínez Cuesta
- European Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Syed Asad Rahman
- European Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Nicholas Furnham
- Department of Pathogen Molecular Biology, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Janet M Thornton
- European Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom.
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30
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Brenna E, Crotti M, Gatti FG, Monti D, Parmeggiani F, Powell RW, Santangelo S, Stewart JD. Opposite Enantioselectivity in the Bioreduction of (Z
)-β-Aryl-β-cyanoacrylates Mediated by the Tryptophan 116 Mutants of Old Yellow Enzyme 1: Synthetic Approach to (R
)- and (S
)-β-Aryl-γ-lactams. Adv Synth Catal 2015. [DOI: 10.1002/adsc.201500206] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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31
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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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Currin A, Swainston N, Day PJ, Kell DB. Synthetic biology for the directed evolution of protein biocatalysts: navigating sequence space intelligently. Chem Soc Rev 2015; 44:1172-239. [PMID: 25503938 PMCID: PMC4349129 DOI: 10.1039/c4cs00351a] [Citation(s) in RCA: 251] [Impact Index Per Article: 27.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Indexed: 12/21/2022]
Abstract
The amino acid sequence of a protein affects both its structure and its function. Thus, the ability to modify the sequence, and hence the structure and activity, of individual proteins in a systematic way, opens up many opportunities, both scientifically and (as we focus on here) for exploitation in biocatalysis. Modern methods of synthetic biology, whereby increasingly large sequences of DNA can be synthesised de novo, allow an unprecedented ability to engineer proteins with novel functions. However, the number of possible proteins is far too large to test individually, so we need means for navigating the 'search space' of possible protein sequences efficiently and reliably in order to find desirable activities and other properties. Enzymologists distinguish binding (Kd) and catalytic (kcat) steps. In a similar way, judicious strategies have blended design (for binding, specificity and active site modelling) with the more empirical methods of classical directed evolution (DE) for improving kcat (where natural evolution rarely seeks the highest values), especially with regard to residues distant from the active site and where the functional linkages underpinning enzyme dynamics are both unknown and hard to predict. Epistasis (where the 'best' amino acid at one site depends on that or those at others) is a notable feature of directed evolution. The aim of this review is to highlight some of the approaches that are being developed to allow us to use directed evolution to improve enzyme properties, often dramatically. We note that directed evolution differs in a number of ways from natural evolution, including in particular the available mechanisms and the likely selection pressures. Thus, we stress the opportunities afforded by techniques that enable one to map sequence to (structure and) activity in silico, as an effective means of modelling and exploring protein landscapes. Because known landscapes may be assessed and reasoned about as a whole, simultaneously, this offers opportunities for protein improvement not readily available to natural evolution on rapid timescales. Intelligent landscape navigation, informed by sequence-activity relationships and coupled to the emerging methods of synthetic biology, offers scope for the development of novel biocatalysts that are both highly active and robust.
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Affiliation(s)
- Andrew Currin
- Manchester Institute of Biotechnology , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK . ; http://dbkgroup.org/; @dbkell ; Tel: +44 (0)161 306 4492
- School of Chemistry , The University of Manchester , Manchester M13 9PL , UK
- Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM) , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK
| | - Neil Swainston
- Manchester Institute of Biotechnology , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK . ; http://dbkgroup.org/; @dbkell ; Tel: +44 (0)161 306 4492
- Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM) , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK
- School of Computer Science , The University of Manchester , Manchester M13 9PL , UK
| | - Philip J. Day
- Manchester Institute of Biotechnology , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK . ; http://dbkgroup.org/; @dbkell ; Tel: +44 (0)161 306 4492
- Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM) , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK
- Faculty of Medical and Human Sciences , The University of Manchester , Manchester M13 9PT , UK
| | - Douglas B. Kell
- Manchester Institute of Biotechnology , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK . ; http://dbkgroup.org/; @dbkell ; Tel: +44 (0)161 306 4492
- School of Chemistry , The University of Manchester , Manchester M13 9PL , UK
- Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM) , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK
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33
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Panigrahi K, Applegate GA, Malik G, Berkowitz DB. Combining a Clostridial enzyme exhibiting unusual active site plasticity with a remarkably facile sigmatropic rearrangement: rapid, stereocontrolled entry into densely functionalized fluorinated phosphonates for chemical biology. J Am Chem Soc 2015; 137:3600-9. [PMID: 25719907 DOI: 10.1021/jacs.5b00022] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Described is an efficient stereocontrolled route into valuable, densely functionalized fluorinated phosphonates that takes advantage of (i) a Clostridial enzyme to set the absolute stereochemistry and (ii) a new [3,3]-sigmatropic rearrangement of the thiono-Claisen variety that is among the fastest sigmatropic rearrangements yet reported. Here, a pronounced rate enhancement is achieved by distal fluorination. This rearrangement is completely stereoretentive, parlaying the enzymatically established β-C-O stereochemistry in the substrate into the δ-C-S stereochemistry in the product. The final products are of interest to chemical biology, with a platform for Zn-aminopeptidase A inhibitors being constructed here. The enzyme, Clostridium acetobutylicum (CaADH), recently expressed by our group, reduces a spectrum of γ,δ-unsaturated β-keto-α,α-difluorophosphonate esters (93-99% ee; 10 examples). The resultant β-hydroxy-α,α-difluorophosphonates possess the "L"-stereochemistry, opposite to that previously observed for the CaADH-reduction of ω-keto carboxylate esters ("D"), indicating an unusual active site plasticity. For the thiono-Claisen rearrangement, a notable structure-reactivity relationship is observed. Measured rate constants vary by over 3 orders of magnitude, depending upon thiono-ester structure. Temperature-dependent kinetics reveal an unusually favorable entropy of activation (ΔS(‡) = 14.5 ± 0.6 e.u.). Most notably, a 400-fold rate enhancement is seen upon fluorination of the distal arene ring, arising from favorable enthalpic (ΔΔH(‡) = -2.3 kcal/mol) and entropic (ΔΔS(‡) = 4 e.u., i.e. 1.2 kcal/mol at rt) contributions. The unusual active site plasticity seen here is expected to drive structural biology studies on CaADH, while the exceptionally facile sigmatropic rearrangement is expected to drive computational studies to elucidate its underlying entropic and enthalpic basis.
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Affiliation(s)
- Kaushik Panigrahi
- Department of Chemistry, University of Nebraska, Lincoln, Nebraska 68588-0304, United States
| | - Gregory A Applegate
- Department of Chemistry, University of Nebraska, Lincoln, Nebraska 68588-0304, United States
| | - Guillaume Malik
- Department of Chemistry, University of Nebraska, Lincoln, Nebraska 68588-0304, United States
| | - David B Berkowitz
- Department of Chemistry, University of Nebraska, Lincoln, Nebraska 68588-0304, United States
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34
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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
![]()
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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35
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Engineering strictosidine synthase: Rational design of a small, focused circular permutation library of the β-propeller fold enzyme. Bioorg Med Chem 2014; 22:5633-7. [DOI: 10.1016/j.bmc.2014.06.023] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Revised: 06/09/2014] [Accepted: 06/11/2014] [Indexed: 12/23/2022]
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36
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Patterson-Orazem A, Sullivan B, Stewart JD. Pichia stipitis OYE 2.6 variants with improved catalytic efficiencies from site-saturation mutagenesis libraries. Bioorg Med Chem 2014; 22:5628-32. [PMID: 25087048 DOI: 10.1016/j.bmc.2014.07.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2014] [Revised: 06/23/2014] [Accepted: 07/01/2014] [Indexed: 01/25/2023]
Abstract
An earlier directed evolution project using alkene reductase OYE 2.6 from Pichia stipitis yielded 13 active site variants with improved properties toward three homologous Baylis-Hillman adducts. Here, we probed the generality of these improvements by testing the wild-type and all 13 variants against a panel of 16 structurally-diverse electron-deficient alkenes. Several substrates were sterically demanding, and as hoped, creating additional active site volume yielded better conversions for these alkenes. The most impressive improvement was found for 2-butylidenecyclohexanone. The wild-type provided less than 20% conversion after 24h; a triple mutant afforded more than 60% conversion in the same time period. Moreover, even wild-type OYE 2.6 can reduce cyclohexenones with very bulky 4-substituents efficiently.
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Affiliation(s)
| | - Bradford Sullivan
- Department of Chemistry, University of Florida, 126 Sisler Hall, Gainesville, FL 32611, USA
| | - Jon D Stewart
- Department of Chemistry, University of Florida, 126 Sisler Hall, Gainesville, FL 32611, USA.
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37
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Walton AZ, Sullivan B, Patterson-Orazem AC, Stewart JD. Residues Controlling Facial Selectivity in an Alkene Reductase and Semirational Alterations to Create Stereocomplementary Variants. ACS Catal 2014; 4:2307-2318. [PMID: 25068071 PMCID: PMC4105185 DOI: 10.1021/cs500429k] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Revised: 05/22/2014] [Indexed: 01/07/2023]
Abstract
![]()
A systematic
saturation mutagenesis campaign was carried out on
an alkene reductase from Pichia stipitis (OYE 2.6) to develop variants with reversed stereoselectivities.
Wild-type OYE 2.6 reduces three representative Baylis–Hillman
adducts to the corresponding S products with almost
complete stereoselectivities and good catalytic efficiencies. We created
and screened 13 first-generation, site-saturation mutagenesis libraries,
targeting residues found near the bound substrate. One variant (Tyr78Trp)
showed high R selectivity
toward one of the three substrates, but no change (cyclohexenone derivative)
and no catalytic activity (acrylate derivative) for the other two.
Subsequent rounds of mutagenesis retained the Tyr78Trp mutation and
explored other residues that impacted stereoselectivity when altered
in a wild-type background. These efforts yielded double and triple
mutants that possessed inverted stereoselectivities for two of the
three substrates (conversions >99% and at least 91% ee (R)). To understand the reasons underlying the stereochemical
changes,
we solved crystal structures of two key mutants: Tyr78Trp and Tyr78Trp/Ile113Cys,
the latter with substrate partially occupying the active site. By
combining these experimental data with modeling studies, we have proposed
a rationale that explains the impacts of the most useful mutations.
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Affiliation(s)
- Adam Z. Walton
- Department of Chemistry, 126 Sisler Hall, University of Florida, Gainesville, Florida 32611 United States
| | - Bradford Sullivan
- Department of Chemistry, 126 Sisler Hall, University of Florida, Gainesville, Florida 32611 United States
| | - Athéna C. Patterson-Orazem
- Department of Chemistry, 126 Sisler Hall, University of Florida, Gainesville, Florida 32611 United States
| | - Jon D. Stewart
- Department of Chemistry, 126 Sisler Hall, University of Florida, Gainesville, Florida 32611 United States
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38
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Toogood HS, Scrutton NS. New developments in 'ene'-reductase catalysed biological hydrogenations. Curr Opin Chem Biol 2014; 19:107-15. [PMID: 24608082 DOI: 10.1016/j.cbpa.2014.01.019] [Citation(s) in RCA: 98] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2013] [Revised: 12/13/2013] [Accepted: 01/30/2014] [Indexed: 01/07/2023]
Abstract
Asymmetric biocatalytic hydrogenations are important reactions performed primarily by members of the Old Yellow Enzyme family. These reactions have great potential in the chemosynthesis of a variety of industrially useful synthons due to the generation of up to two stereogenic centres. In this review, additional enzyme classes capable of asymmetric hydrogenations will be discussed, as will examples of multienzyme cascading reactions. New and improved technology that enhances the commercial viability of biotransformations are included, such as the nicotinamide coenzyme-independent reactions. This review will focus on progress in this field within the last two years, with emphasis on industrial applications of this technology.
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Affiliation(s)
- Helen S Toogood
- Manchester Institute of Biotechnology, Faculty of Life Sciences, University of Manchester, 131 Princess Street, Manchester M1 7DN, 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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39
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Ni Y, Yu HL, Lin GQ, Xu JH. An ene reductase from Clavispora lusitaniae for asymmetric reduction of activated alkenes. Enzyme Microb Technol 2014; 56:40-5. [PMID: 24564901 DOI: 10.1016/j.enzmictec.2013.12.016] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2013] [Revised: 12/09/2013] [Accepted: 12/30/2013] [Indexed: 01/15/2023]
Abstract
A putative ene reductase gene from Clavispora lusitaniae was heterologously overexpressed in Escherichia coli, and the encoded protein (ClER) was purified and characterized for its biocatalytic properties. This NADPH-dependent flavoprotein was identified with reduction activities toward a diverse range of activated alkenes including conjugated enones, enals, maleimide derivative and α,β-unsaturated carboxylic esters. The purified ClER exhibited a relatively high activity of 7.3 U mg(prot)⁻¹ for ketoisophorone while a remarkable catalytic efficiency (k(cat)/K(m)=810 s⁻¹ mM⁻¹) was obtained for 2-methyl-cinnamaldehyde due to the high affinity. A series of prochiral activated alkenes were stereoselectively reduced by ClER furnishing the corresponding saturated products in up to 99% ee. The practical applicability of ClER was further evaluated for the production of (R)-levodione, a valuable chiral compound, from ketoisophorone. Using the crude enzyme of ClER and glucose dehydrogenase (GDH), 500 mM of ketoisophorone was efficiently converted to (R)-levodione with excellent stereoselectivity (98% ee) within 1h. All these positive features demonstrate a high synthetic potential of ClER in the asymmetric reduction of activated alkenes.
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Affiliation(s)
- Yan Ni
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Hui-Lei Yu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Guo-Qiang Lin
- Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China
| | - Jian-He Xu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China.
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40
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Abstract
Protein engineering by random circular permutation is an effective tool for tailoring protein topology with potential functional benefits including improved catalytic activity. This method involves covalently connecting the native protein termini with a peptide linker and cleaving a peptide bond elsewhere in the polypeptide sequence. Termini relocation can impact protein ternary and quaternary structure and translate into functional enhancements due to changes in protein conformation and flexibility. As the effects of new termini in specific protein locations are difficult to predict, the preparation of a library constituting all possible permutation sites is an effective search strategy for identifying variants with novel properties.
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Affiliation(s)
- Stefan Lutz
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, GA, USA,
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