51
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Meng D, Qiao Y, Wang X, Wen W, Zhao S. DABCO-catalyzed Knoevenagel condensation of aldehydes with ethyl cyanoacetate using hydroxy ionic liquid as a promoter. RSC Adv 2018; 8:30180-30185. [PMID: 35546849 PMCID: PMC9085423 DOI: 10.1039/c8ra06506c] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 08/14/2018] [Indexed: 11/24/2022] Open
Abstract
N-(2-Hydroxy-ethyl)-pyridinium chloride ([HyEtPy]Cl) was synthesized and explored as a novel promoter for 1,4-diazabicyclo [2.2.2] octane (DABCO)-catalyzed Knoevenagel condensation reactions, which showed better catalytic activity compared to other ionic liquid (IL) that had no hydroxyl group attached to the IL scaffold. The effect of hydrogen bond formation between the hydroxyl group of [HyEtPy]Cl and the carbonyl group of aldehyde played an important role in the Knoevenagel condensation reaction. In the [HyEtPy]Cl–H2O–DABCO composite system, Knoevenagel condensation reactions proceeded smoothly and cleanly, and the corresponding Knoevenagel condensation products were obtained in good to excellent yields in all cases examined. This protocol provides a versatile solvent–catalyst system, which has notable advantages such as being eco-friendly, ease of work-up and convenient reuse of the ionic liquid. N-(2-Hydroxy-ethyl)-pyridinium chloride ([HyEtPy]Cl) was synthesized and explored as a novel promoter for 1,4-diazabicyclo [2.2.2] octane (DABCO)-catalyzed Knoevenagel condensation reactions, excellent catalytic activity was obtained.![]()
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Affiliation(s)
- Dan Meng
- School Chemistry and Material Science
- Shanxi Normal University
- Linfen 041001
- China
| | - Yongsheng Qiao
- Department of Chemistry
- Xinzhou Teachers University
- Xinzhou 034000
- China
| | - Xin Wang
- Department of Chemistry
- Xinzhou Teachers University
- Xinzhou 034000
- China
| | - Wei Wen
- Department of Chemistry
- Xinzhou Teachers University
- Xinzhou 034000
- China
| | - Sanhu Zhao
- School Chemistry and Material Science
- Shanxi Normal University
- Linfen 041001
- China
- Department of Chemistry
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52
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Romero-Rivera A, Garcia-Borràs M, Osuna S. Role of Conformational Dynamics in the Evolution of Retro-Aldolase Activity. ACS Catal 2017; 7:8524-8532. [PMID: 29226011 PMCID: PMC5716449 DOI: 10.1021/acscatal.7b02954] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 10/19/2017] [Indexed: 12/19/2022]
Abstract
![]()
Enzymes exist as
ensembles of conformations that are important
for function. Tuning these populations of conformational states through
mutation enables evolution toward additional activities. Here we computationally
evaluate the population shifts induced by distal and active site mutations
in a family of computationally designed and experimentally optimized
retro-aldolases. The conformational landscape of these enzymes was
significantly altered during evolution, as pre-existing catalytically
active conformational substates became major states in the most evolved
variants. We further demonstrate that key residues responsible for
these substate conversions can be predicted computationally. Significantly,
the identified residues coincide with those positions mutated in the
laboratory evolution experiments. This study establishes that distal
mutations that affect enzyme catalytic activity can be predicted computationally
and thus provides the enzyme (re)design field with a rational strategy
to determine promising sites for enhancing activity through mutation.
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Affiliation(s)
- Adrian Romero-Rivera
- Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona, Carrer Maria Aurèlia Capmany 69, 17003 Girona, Spain
| | - Marc Garcia-Borràs
- Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona, Carrer Maria Aurèlia Capmany 69, 17003 Girona, Spain
- Department of Chemistry and Biochemistry, University of California, Los Angeles (UCLA), 607 Charles E. Young Drive, Los Angeles, California 90095, United States
| | - Sílvia Osuna
- Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona, Carrer Maria Aurèlia Capmany 69, 17003 Girona, Spain
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53
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Goldsmith M, Tawfik DS. Enzyme engineering: reaching the maximal catalytic efficiency peak. Curr Opin Struct Biol 2017; 47:140-150. [PMID: 29035814 DOI: 10.1016/j.sbi.2017.09.002] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Revised: 07/04/2017] [Accepted: 09/20/2017] [Indexed: 01/01/2023]
Abstract
The practical need for highly efficient enzymes presents new challenges in enzyme engineering, in particular, the need to improve catalytic turnover (kcat) or efficiency (kcat/KM) by several orders of magnitude. However, optimizing catalysis demands navigation through complex and rugged fitness landscapes, with optimization trajectories often leading to strong diminishing returns and dead-ends. When no further improvements are observed in library screens or selections, it remains unclear whether the maximal catalytic efficiency of the enzyme (the catalytic 'fitness peak') has been reached; or perhaps, an alternative combination of mutations exists that could yield additional improvements. Here, we discuss fundamental aspects of the process of catalytic optimization, and offer practical solutions with respect to overcoming optimization plateaus.
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Affiliation(s)
- Moshe Goldsmith
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel.
| | - Dan S Tawfik
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
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54
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Revisiting the Knoevenagel condensations: A universal and flexible bis-ammoniated fiber catalyst for the mild synthesis of α,β-unsaturated compounds. J IND ENG CHEM 2017. [DOI: 10.1016/j.jiec.2017.05.020] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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55
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Zeymer C, Zschoche R, Hilvert D. Optimization of Enzyme Mechanism along the Evolutionary Trajectory of a Computationally Designed (Retro-)Aldolase. J Am Chem Soc 2017; 139:12541-12549. [DOI: 10.1021/jacs.7b05796] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Cathleen Zeymer
- Laboratory of Organic Chemistry, ETH Zürich, 8093 Zürich, Switzerland
| | - Reinhard Zschoche
- Laboratory of Organic Chemistry, ETH Zürich, 8093 Zürich, Switzerland
| | - Donald Hilvert
- Laboratory of Organic Chemistry, ETH Zürich, 8093 Zürich, Switzerland
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56
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Grisewood MJ, Hernández-Lozada NJ, Thoden JB, Gifford NP, Mendez-Perez D, Schoenberger HA, Allan MF, Floy ME, Lai RY, Holden HM, Pfleger BF, Maranas CD. Computational Redesign of Acyl-ACP Thioesterase with Improved Selectivity toward Medium-Chain-Length Fatty Acids. ACS Catal 2017; 7:3837-3849. [PMID: 29375928 DOI: 10.1021/acscatal.7b00408] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Enzyme and metabolic engineering offer the potential to develop biocatalysts for converting natural resources into a wide range of chemicals. To broaden the scope of potential products beyond natural metabolites, methods of engineering enzymes to accept alternative substrates and/or perform novel chemistries must be developed. DNA synthesis can create large libraries of enzyme-coding sequences, but most biochemistries lack a simple assay to screen for promising enzyme variants. Our solution to this challenge is structure-guided mutagenesis in which optimization algorithms select the best sequences from libraries based on specified criteria (i.e. binding selectivity). Here, we demonstrate this approach by identifying medium-chain (C6-C12) acyl-ACP thioesterases through structure-guided mutagenesis. Medium-chain fatty acids, products of thioesterase-catalyzed hydrolysis, are limited in natural abundance compared to long-chain fatty acids; the limited supply leads to high costs of C6-C10 oleochemicals such as fatty alcohols, amines, and esters. Here, we applied computational tools to tune substrate binding to the highly-active 'TesA thioesterase in Escherichia coli. We used the IPRO algorithm to design thioesterase variants with enhanced C12- or C8-specificity while maintaining high activity. After four rounds of structure-guided mutagenesis, we identified three thioesterases with enhanced production of dodecanoic acid (C12) and twenty-seven thioesterases with enhanced production of octanoic acid (C8). The top variants reached up to 49% C12 and 50% C8 while exceeding native levels of total free fatty acids. A comparably sized library created by random mutagenesis failed to identify promising mutants. The chain length-preference of 'TesA and the best mutant were confirmed in vitro using acyl-CoA substrates. Molecular dynamics simulations, confirmed by resolved crystal structures, of 'TesA variants suggest that hydrophobic forces govern 'TesA substrate specificity. We expect that the design rules we uncovered and the thioesterase variants identified will be useful to metabolic engineering projects aimed at sustainable production of medium-chain oleochemicals.
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Affiliation(s)
- Matthew J. Grisewood
- Department
of Chemical Engineering, Pennsylvania State University, 158 Fenske Laboratory, University Park, Pennsylvania 16802, United States
| | - Néstor J. Hernández-Lozada
- Department
of Chemical and Biological Engineering, University of Wisconsin−Madison, 1415 Engineering Drive, Madison, Wisconsin 53706, United States
| | - James B. Thoden
- Department
of Biochemistry, University of Wisconsin−Madison, 440 Henry Mall, Madison, Wisconsin 53706, United States
| | - Nathanael P. Gifford
- Department
of Chemical Engineering, Pennsylvania State University, 158 Fenske Laboratory, University Park, Pennsylvania 16802, United States
| | - Daniel Mendez-Perez
- Department
of Chemical and Biological Engineering, University of Wisconsin−Madison, 1415 Engineering Drive, Madison, Wisconsin 53706, United States
| | - Haley A. Schoenberger
- Department
of Chemical and Biological Engineering, University of Wisconsin−Madison, 1415 Engineering Drive, Madison, Wisconsin 53706, United States
| | - Matthew F. Allan
- Department
of Chemical Engineering, Pennsylvania State University, 158 Fenske Laboratory, University Park, Pennsylvania 16802, United States
| | - Martha E. Floy
- Department
of Chemical and Biological Engineering, University of Wisconsin−Madison, 1415 Engineering Drive, Madison, Wisconsin 53706, United States
| | - Rung-Yi Lai
- Department
of Chemical and Biological Engineering, University of Wisconsin−Madison, 1415 Engineering Drive, Madison, Wisconsin 53706, United States
| | - Hazel M. Holden
- Department
of Biochemistry, University of Wisconsin−Madison, 440 Henry Mall, Madison, Wisconsin 53706, United States
| | - Brian F. Pfleger
- Department
of Chemical and Biological Engineering, University of Wisconsin−Madison, 1415 Engineering Drive, Madison, Wisconsin 53706, United States
| | - Costas D. Maranas
- Department
of Chemical Engineering, Pennsylvania State University, 158 Fenske Laboratory, University Park, Pennsylvania 16802, United States
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57
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Wang A, Fan R, Dong Y, Song Y, Zhou Y, Zheng J, Du X, Xing K, Yang Y. Novel Hydrogen-Bonding Cross-Linking Aggregation-Induced Emission: Water as a Fluorescent "Ribbon" Detected in a Wide Range. ACS APPLIED MATERIALS & INTERFACES 2017; 9:15744-15757. [PMID: 28420233 DOI: 10.1021/acsami.7b01254] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
The development of efficient sensors for detection of the water content in a wide detection range is highly desirable for balance in many industrial processes and products. Presented herein are six novel different substituted Schiff base Zn(II) complexes, which exhibit the remarkable capability to detect traces of water in a wide linear range (most can reach 0-94%, v/v), low detection limit of 0.2% (v/v), and rapid response time of 8 s in various organic solvents by virtue of an unusual water-activated hydrogen-bonding cross-linking AIE (WHCAIE) mechanism. As a proof-of-concept, the WHCAIE mechanism is explained well by single X-ray diffraction, absorption spectra, fluorescence spectra, dynamic light scattering, 1H NMR spectra, and theoretical calculations. In addition, the molecules demonstrated their application for the detection of humidity (42-80%). These Schiff base Zn(II) complexes become one of the most powerful water sensors known due to their extraordinary sensitivity, fast response, and wide detection range for water.
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Affiliation(s)
- Ani Wang
- MIIT Key Laboratory of Critical Materials Technology for New Energy Conversion and Storage, School of Chemistry and Chemical Engineering, Harbin Institute of Technology , Harbin 150001, P. R. of China
| | - Ruiqing Fan
- MIIT Key Laboratory of Critical Materials Technology for New Energy Conversion and Storage, School of Chemistry and Chemical Engineering, Harbin Institute of Technology , Harbin 150001, P. R. of China
| | - Yuwei Dong
- MIIT Key Laboratory of Critical Materials Technology for New Energy Conversion and Storage, School of Chemistry and Chemical Engineering, Harbin Institute of Technology , Harbin 150001, P. R. of China
| | - Yang Song
- MIIT Key Laboratory of Critical Materials Technology for New Energy Conversion and Storage, School of Chemistry and Chemical Engineering, Harbin Institute of Technology , Harbin 150001, P. R. of China
| | - Yuze Zhou
- MIIT Key Laboratory of Critical Materials Technology for New Energy Conversion and Storage, School of Chemistry and Chemical Engineering, Harbin Institute of Technology , Harbin 150001, P. R. of China
| | - Jianzong Zheng
- MIIT Key Laboratory of Critical Materials Technology for New Energy Conversion and Storage, School of Chemistry and Chemical Engineering, Harbin Institute of Technology , Harbin 150001, P. R. of China
| | - Xi Du
- MIIT Key Laboratory of Critical Materials Technology for New Energy Conversion and Storage, School of Chemistry and Chemical Engineering, Harbin Institute of Technology , Harbin 150001, P. R. of China
| | - Kai Xing
- MIIT Key Laboratory of Critical Materials Technology for New Energy Conversion and Storage, School of Chemistry and Chemical Engineering, Harbin Institute of Technology , Harbin 150001, P. R. of China
| | - Yulin Yang
- MIIT Key Laboratory of Critical Materials Technology for New Energy Conversion and Storage, School of Chemistry and Chemical Engineering, Harbin Institute of Technology , Harbin 150001, P. R. of China
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58
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Garrabou X, Macdonald DS, Hilvert D. Chemoselective Henry Condensations Catalyzed by Artificial Carboligases. Chemistry 2017; 23:6001-6003. [PMID: 28070900 DOI: 10.1002/chem.201605757] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Indexed: 11/08/2022]
Abstract
The promiscuity of de novo designed enzymes provides a privileged platform for diverse abiological reactions. In this work, we report the first example of a nitroolefin synthase that catalyzes the Henry condensation between aromatic aldehydes and nitromethane. Significant catalytic activity was discovered in the computationally designed and evolved carboligase RA95.5-8, and mutations around the active site were shown to improve the reaction rate, demonstrating the potential to optimize the enzyme by directed evolution. This novel nitroolefin synthase could participate in complex biological cascades, whereby the highly tunable chemoselectivity could afford useful synthetic building blocks.
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Affiliation(s)
- Xavier Garrabou
- Laboratory of Organic Chemistry, ETH Zürich, 8093, Zürich, Switzerland
| | | | - Donald Hilvert
- Laboratory of Organic Chemistry, ETH Zürich, 8093, Zürich, Switzerland
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59
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Hartley CJ, Wilding M, Scott C. Hacking nature: genetic tools for reprograming enzymes. MICROBIOLOGY AUSTRALIA 2017. [DOI: 10.1071/ma17032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Enzymes have many modern industrial applications, from biomass decomposition in the production of biofuels to highly stereospecific biotransformations in pharmaceutical manufacture. The capacity to find or engineer enzymes with activities pertinent to specific applications has been essential for the growth of a multibillion dollar enzyme industry. Over the course of the past 50–60 years our capacity to address this issue has become increasingly sophisticated, supported by innumerable advances, from early discoveries such as the co-linearity of DNA and protein sequence1 to modern computational technologies for enzyme design. The design of enzyme function is an exciting nexus of fundamental biochemical understanding and applied engineering. Herein, we will cover some of the methods used in discovery and design, including some ‘next generation’ tools.
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60
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Garrabou X, Verez R, Hilvert D. Enantiocomplementary Synthesis of γ-Nitroketones Using Designed and Evolved Carboligases. J Am Chem Soc 2016; 139:103-106. [PMID: 27992715 DOI: 10.1021/jacs.6b11928] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Artificial enzymes created by computational design and directed evolution are versatile biocatalysts whose promiscuous activities represent potentially attractive starting points for divergent evolution in the laboratory. The artificial aldolase RA95.5-8, for example, exploits amine catalysis to promote mechanistically diverse carboligations. Here we report that RA95.5-8 variants catalyze the asymmetric synthesis of γ-nitroketones via two alternative enantiocomplementary Michael-type reactions: enamine-mediated addition of acetone to nitrostyrenes, and nitroalkane addition to conjugated ketones activated as iminium ions. In addition, a cascade of three aldolase-catalyzed reactions enables one-pot assembly of γ-nitroketones from three simpler building blocks. Together, our results highlight the chemical versatility of artificial aldolases for the practical synthesis of important chiral synthons.
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Affiliation(s)
- Xavier Garrabou
- Laboratory of Organic Chemistry, ETH Zurich , 8093 Zurich, Switzerland
| | - Rebecca Verez
- Laboratory of Organic Chemistry, ETH Zurich , 8093 Zurich, Switzerland
| | - Donald Hilvert
- Laboratory of Organic Chemistry, ETH Zurich , 8093 Zurich, Switzerland
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61
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Romero-Rivera A, Garcia-Borràs M, Osuna S. Computational tools for the evaluation of laboratory-engineered biocatalysts. Chem Commun (Camb) 2016; 53:284-297. [PMID: 27812570 PMCID: PMC5310519 DOI: 10.1039/c6cc06055b] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Accepted: 09/06/2016] [Indexed: 12/18/2022]
Abstract
Biocatalysis is based on the application of natural catalysts for new purposes, for which enzymes were not designed. Although the first examples of biocatalysis were reported more than a century ago, biocatalysis was revolutionized after the discovery of an in vitro version of Darwinian evolution called Directed Evolution (DE). Despite the recent advances in the field, major challenges remain to be addressed. Currently, the best experimental approach consists of creating multiple mutations simultaneously while limiting the choices using statistical methods. Still, tens of thousands of variants need to be tested experimentally, and little information is available on how these mutations lead to enhanced enzyme proficiency. This review aims to provide a brief description of the available computational techniques to unveil the molecular basis of improved catalysis achieved by DE. An overview of the strengths and weaknesses of current computational strategies is explored with some recent representative examples. The understanding of how this powerful technique is able to obtain highly active variants is important for the future development of more robust computational methods to predict amino-acid changes needed for activity.
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Affiliation(s)
- Adrian Romero-Rivera
- Institut de Química Computacional i Catàlisi and Departament de Química Universitat de Girona, Campus Montilivi, 17071 Girona, Catalonia, Spain.
| | - Marc Garcia-Borràs
- Department of Chemistry and Biochemistry, University of California, 607 Charles E. Young Drive, Los Angeles, California 90095, USA
| | - Sílvia Osuna
- Institut de Química Computacional i Catàlisi and Departament de Química Universitat de Girona, Campus Montilivi, 17071 Girona, Catalonia, Spain.
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62
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Applied evolutionary theories for engineering of secondary metabolic pathways. Curr Opin Chem Biol 2016; 35:133-141. [PMID: 27736648 DOI: 10.1016/j.cbpa.2016.09.021] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Revised: 09/18/2016] [Accepted: 09/19/2016] [Indexed: 11/20/2022]
Abstract
An expanded definition of 'secondary metabolism' is emerging. Once the exclusive provenance of naturally occurring organisms, evolved over geological time scales, secondary metabolism increasingly encompasses molecules generated via human engineered biocatalysts and biosynthetic pathways. Many of the tools and strategies for enzyme and pathway engineering can find origins in evolutionary theories. This perspective presents an overview of selected proposed evolutionary strategies in the context of engineering secondary metabolism. In addition to the wealth of biocatalysts provided via secondary metabolic pathways, improving the understanding of biosynthetic pathway evolution will provide rich resources for methods to adapt to applied laboratory evolution.
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63
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The coming of age of de novo protein design. Nature 2016; 537:320-7. [DOI: 10.1038/nature19946] [Citation(s) in RCA: 803] [Impact Index Per Article: 100.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 07/20/2016] [Indexed: 12/24/2022]
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64
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Emergence of a catalytic tetrad during evolution of a highly active artificial aldolase. Nat Chem 2016; 9:50-56. [DOI: 10.1038/nchem.2596] [Citation(s) in RCA: 202] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Accepted: 07/12/2016] [Indexed: 12/24/2022]
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65
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Obexer R, Pott M, Zeymer C, Griffiths AD, Hilvert D. Efficient laboratory evolution of computationally designed enzymes with low starting activities using fluorescence-activated droplet sorting. Protein Eng Des Sel 2016; 29:355-66. [DOI: 10.1093/protein/gzw032] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Accepted: 06/21/2016] [Indexed: 11/14/2022] Open
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