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Hecko S, Schiefer A, Badenhorst CPS, Fink MJ, Mihovilovic MD, Bornscheuer UT, Rudroff F. Enlightening the Path to Protein Engineering: Chemoselective Turn-On Probes for High-Throughput Screening of Enzymatic Activity. Chem Rev 2023; 123:2832-2901. [PMID: 36853077 PMCID: PMC10037340 DOI: 10.1021/acs.chemrev.2c00304] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
Abstract
Many successful stories in enzyme engineering are based on the creation of randomized diversity in large mutant libraries, containing millions to billions of enzyme variants. Methods that enabled their evaluation with high throughput are dominated by spectroscopic techniques due to their high speed and sensitivity. A large proportion of studies relies on fluorogenic substrates that mimic the chemical properties of the target or coupled enzymatic assays with an optical read-out that assesses the desired catalytic efficiency indirectly. The most reliable hits, however, are achieved by screening for conversions of the starting material to the desired product. For this purpose, functional group assays offer a general approach to achieve a fast, optical read-out. They use the chemoselectivity, differences in electronic and steric properties of various functional groups, to reduce the number of false-positive results and the analytical noise stemming from enzymatic background activities. This review summarizes the developments and use of functional group probes for chemoselective derivatizations, with a clear focus on screening for enzymatic activity in protein engineering.
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Affiliation(s)
- Sebastian Hecko
- Institute of Applied Synthetic Chemistry, OC-163, TU Wien, Getreidemarkt 9, 1060 Vienna, Austria
| | - Astrid Schiefer
- Institute of Applied Synthetic Chemistry, OC-163, TU Wien, Getreidemarkt 9, 1060 Vienna, Austria
| | - Christoffel P S Badenhorst
- Institute of Biochemistry, Dept. of Biotechnology & Enzyme Catalysis, University of Greifswald, Felix-Hausdorff-Str. 4, 17489 Greifswald, Germany
| | - Michael J Fink
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford St, Cambridge, Massachusetts 02138, United States
| | - Marko D Mihovilovic
- Institute of Applied Synthetic Chemistry, OC-163, TU Wien, Getreidemarkt 9, 1060 Vienna, Austria
| | - Uwe T Bornscheuer
- Institute of Biochemistry, Dept. of Biotechnology & Enzyme Catalysis, University of Greifswald, Felix-Hausdorff-Str. 4, 17489 Greifswald, Germany
| | - Florian Rudroff
- Institute of Applied Synthetic Chemistry, OC-163, TU Wien, Getreidemarkt 9, 1060 Vienna, Austria
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Gomez de Santos P, Cañellas M, Tieves F, Younes SHH, Molina-Espeja P, Hofrichter M, Hollmann F, Guallar V, Alcalde M. Selective Synthesis of the Human Drug Metabolite 5′-Hydroxypropranolol by an Evolved Self-Sufficient Peroxygenase. ACS Catal 2018. [DOI: 10.1021/acscatal.8b01004] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
| | - Marina Cañellas
- Joint BSC-CRG-IRB Research Program in Computational Biology, Barcelona Supercomputing Center, 08034 Barcelona, Spain
| | - Florian Tieves
- Department of Biotechnology, Delft University of Technology, van der Massweg 9, 2629HZ Delft, The Netherlands
| | - Sabry H. H. Younes
- Department of Biotechnology, Delft University of Technology, van der Massweg 9, 2629HZ Delft, The Netherlands
| | | | - Martin Hofrichter
- Department of Bio- and Environmental Sciences, TU Dresden, International Institute Zittau, Mark 23, 02763 Zittau, Germany
| | - Frank Hollmann
- Department of Biotechnology, Delft University of Technology, van der Massweg 9, 2629HZ Delft, The Netherlands
| | - Victor Guallar
- Joint BSC-CRG-IRB Research Program in Computational Biology, Barcelona Supercomputing Center, 08034 Barcelona, Spain
| | - Miguel Alcalde
- Department of Biocatalysis, Institute of Catalysis, CSIC, 28049 Madrid, Spain
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Evolution of enzymes with new specificity by high-throughput screening using DmpR-based genetic circuits and multiple flow cytometry rounds. Sci Rep 2018; 8:2659. [PMID: 29422524 PMCID: PMC5805759 DOI: 10.1038/s41598-018-20943-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 01/26/2018] [Indexed: 11/12/2022] Open
Abstract
Genetic circuit-based biosensors are useful in detecting target metabolites or in vivo enzymes using transcription factors (Tx) as a molecular switch to express reporter signals, such as cellular fluorescence and antibiotic resistance. Herein, a phenol-detecting Tx (DmpR) was employed as a critical tool for enzyme engineering, specifically for the rapid analysis of numerous mutants with multiple mutations at the active site of tryptophan-indole lyase (TIL, EC 4.1.99.1). Cellular fluorescence was monitored cell-by-cell using flow cytometry to detect the creation of phenolic compounds by a new tyrosine-phenol-lyase (TPL, EC 4.1.99.2). In the TIL scaffold, target amino acids near the indole ring (Asp137, Phe304, Val394, Ile396 and His463) were mutated randomly to construct a large diversity of specificity variations. Collection of candidate positives by cell sorting using flow cytometry and subsequent shuffling of beneficial mutations identified a critical hit with four mutations (D137P, F304D, V394L, and I396R) in the TIL sequence. The variant displayed one-thirteenth the level of TPL activity, compared with native TPLs, and completely lost the original TIL activity. The findings demonstrate that hypersensitive, Tx-based biosensors could be useful critically to generate new activity from a related template, which would alleviate the current burden to high-throughput screening.
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Abstract
Knowing how protein sequence maps to function (the "fitness landscape") is critical for understanding protein evolution as well as for engineering proteins with new and useful properties. We demonstrate that the protein fitness landscape can be inferred from experimental data, using Gaussian processes, a Bayesian learning technique. Gaussian process landscapes can model various protein sequence properties, including functional status, thermostability, enzyme activity, and ligand binding affinity. Trained on experimental data, these models achieve unrivaled quantitative accuracy. Furthermore, the explicit representation of model uncertainty allows for efficient searches through the vast space of possible sequences. We develop and test two protein sequence design algorithms motivated by Bayesian decision theory. The first one identifies small sets of sequences that are informative about the landscape; the second one identifies optimized sequences by iteratively improving the Gaussian process model in regions of the landscape that are predicted to be optimized. We demonstrate the ability of Gaussian processes to guide the search through protein sequence space by designing, constructing, and testing chimeric cytochrome P450s. These algorithms allowed us to engineer active P450 enzymes that are more thermostable than any previously made by chimeragenesis, rational design, or directed evolution.
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Sawayama AM, Chen MMY, Kulanthaivel P, Kuo MS, Hemmerle H, Arnold FH. A panel of cytochrome P450 BM3 variants to produce drug metabolites and diversify lead compounds. Chemistry 2009; 15:11723-9. [PMID: 19774562 PMCID: PMC3118466 DOI: 10.1002/chem.200900643] [Citation(s) in RCA: 119] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Herein we demonstrate that a small panel of variants of cytochrome P450 BM3 from Bacillus megaterium covers the breadth of reactivity of human P450s by producing 12 of 13 mammalian metabolites for two marketed drugs, verapamil and astemizole, and one research compound. The most active enzymes support preparation of individual metabolites for preclinical bioactivity and toxicology evaluations. Underscoring their potential utility in drug lead diversification, engineered P450 BM3 variants also produce novel metabolites by catalyzing reactions at carbon centers beyond those targeted by animal and human P450s. Production of a specific metabolite can be improved by directed evolution of the enzyme catalyst. Some variants are more active on the more hydrophobic parent drug than on its metabolites, which limits production of multiply-hydroxylated species, a preference that appears to depend on the evolutionary history of the P450 variant.
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Affiliation(s)
- Andrew M. Sawayama
- Dr. A. M. Sawayama, M. M. Y. Chen, Prof. F. H. Arnold, Division of Chemistry and Chemical Engineering 210-41, California Institute of Technology, Pasadena, CA 91125-4100 (USA), Fax: (+1) 626-528-8743
| | - Michael M. Y. Chen
- Dr. A. M. Sawayama, M. M. Y. Chen, Prof. F. H. Arnold, Division of Chemistry and Chemical Engineering 210-41, California Institute of Technology, Pasadena, CA 91125-4100 (USA), Fax: (+1) 626-528-8743
| | - Palaniappan Kulanthaivel
- Dr. P. Kulanthaivel, Dr. M.-S. Kuo, Dr. H. Hemmerle, Eli Lilly & Company, Indianapolis, IN 46285 (USA)
| | - Ming-Shang Kuo
- Dr. P. Kulanthaivel, Dr. M.-S. Kuo, Dr. H. Hemmerle, Eli Lilly & Company, Indianapolis, IN 46285 (USA)
| | - Horst Hemmerle
- Dr. P. Kulanthaivel, Dr. M.-S. Kuo, Dr. H. Hemmerle, Eli Lilly & Company, Indianapolis, IN 46285 (USA)
| | - Frances H. Arnold
- Dr. A. M. Sawayama, M. M. Y. Chen, Prof. F. H. Arnold, Division of Chemistry and Chemical Engineering 210-41, California Institute of Technology, Pasadena, CA 91125-4100 (USA), Fax: (+1) 626-528-8743
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Rha E, Kim S, Choi SL, Hong SP, Sung MH, Song JJ, Lee SG. Simultaneous improvement of catalytic activity and thermal stability of tyrosine phenol-lyase by directed evolution. FEBS J 2009; 276:6187-94. [DOI: 10.1111/j.1742-4658.2009.07322.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Bloom JD, Romero PA, Lu Z, Arnold FH. Neutral genetic drift can alter promiscuous protein functions, potentially aiding functional evolution. Biol Direct 2007; 2:17. [PMID: 17598905 PMCID: PMC1914045 DOI: 10.1186/1745-6150-2-17] [Citation(s) in RCA: 132] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2007] [Accepted: 06/28/2007] [Indexed: 11/10/2022] Open
Abstract
Background Many of the mutations accumulated by naturally evolving proteins are neutral in the sense that they do not significantly alter a protein's ability to perform its primary biological function. However, new protein functions evolve when selection begins to favor other, "promiscuous" functions that are incidental to a protein's original biological role. If mutations that are neutral with respect to a protein's primary biological function cause substantial changes in promiscuous functions, these mutations could enable future functional evolution. Results Here we investigate this possibility experimentally by examining how cytochrome P450 enzymes that have evolved neutrally with respect to activity on a single substrate have changed in their abilities to catalyze reactions on five other substrates. We find that the enzymes have sometimes changed as much as four-fold in the promiscuous activities. The changes in promiscuous activities tend to increase with the number of mutations, and can be largely rationalized in terms of the chemical structures of the substrates. The activities on chemically similar substrates tend to change in a coordinated fashion, potentially providing a route for systematically predicting the change in one activity based on the measurement of several others. Conclusion Our work suggests that initially neutral genetic drift can lead to substantial changes in protein functions that are not currently under selection, in effect poising the proteins to more readily undergo functional evolution should selection favor new functions in the future. Reviewers This article was reviewed by Martijn Huynen, Fyodor Kondrashov, and Dan Tawfik (nominated by Christoph Adami).
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Affiliation(s)
- Jesse D Bloom
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Philip A Romero
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Zhongyi Lu
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Frances H Arnold
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
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Landwehr M, Carbone M, Otey CR, Li Y, Arnold FH. Diversification of catalytic function in a synthetic family of chimeric cytochrome p450s. ACTA ACUST UNITED AC 2007; 14:269-78. [PMID: 17379142 PMCID: PMC1991292 DOI: 10.1016/j.chembiol.2007.01.009] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2006] [Accepted: 01/22/2007] [Indexed: 10/23/2022]
Abstract
We report initial characterization of a synthetic family of more than 3000 cytochrome P450s made by SCHEMA recombination of 3 bacterial CYP102s. A total of 16 heme domains and their holoenzyme fusions with each of the 3 parental reductase domains were tested for activity on 11 different substrates. The results show that the chimeric enzymes have acquired significant functional diversity, including the ability to accept substrates not accepted by the parent enzymes. K-means clustering analysis of the activity data allowed the enzymes to be classified into five distinct groups based on substrate specificity. The substrates can also be grouped such that one can be a "surrogate" for others in the group. Fusion of a functional chimeric heme domain with a parental reductase domain always reconstituted a functional holoenzyme, indicating that key interdomain interactions are conserved upon reductase swapping.
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Affiliation(s)
- Marco Landwehr
- Division of Chemistry and Chemical Engineering, California Institute of Technology, mail code 210-41, Pasadena, California 91125, USA
| | - Martina Carbone
- Division of Chemistry and Chemical Engineering, California Institute of Technology, mail code 210-41, Pasadena, California 91125, USA
| | - Christopher R. Otey
- Biochemistry and Molecular Biophysics, California Institute of Technology, mail code 210-41, Pasadena, California 91125, USA
| | - Yougen Li
- Division of Chemistry and Chemical Engineering, California Institute of Technology, mail code 210-41, Pasadena, California 91125, USA
| | - Frances H. Arnold
- Division of Chemistry and Chemical Engineering, California Institute of Technology, mail code 210-41, Pasadena, California 91125, USA
- Biochemistry and Molecular Biophysics, California Institute of Technology, mail code 210-41, Pasadena, California 91125, USA
- ¶ Correspondence should be addressed to: Prof. Frances H. Arnold, Division of Chemistry and Chemical Engineering, California Institute of Technology, Mail code 210-41, Pasadena, CA 91125, Tel: (626) 395-4162, Fax: (626) 568-8743, E-mail:
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Otey CR, Landwehr M, Endelman JB, Hiraga K, Bloom JD, Arnold FH. Structure-guided recombination creates an artificial family of cytochromes P450. PLoS Biol 2006; 4:e112. [PMID: 16594730 PMCID: PMC1431580 DOI: 10.1371/journal.pbio.0040112] [Citation(s) in RCA: 115] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2005] [Accepted: 02/09/2006] [Indexed: 11/19/2022] Open
Abstract
Creating artificial protein families affords new opportunities to explore the determinants of structure and biological function free from many of the constraints of natural selection. We have created an artificial family comprising 3,000 P450 heme proteins that correctly fold and incorporate a heme cofactor by recombining three cytochromes P450 at seven crossover locations chosen to minimize structural disruption. Members of this protein family differ from any known sequence at an average of 72 and by as many as 109 amino acids. Most (>73%) of the properly folded chimeric P450 heme proteins are catalytically active peroxygenases; some are more thermostable than the parent proteins. A multiple sequence alignment of 955 chimeras, including both folded and not, is a valuable resource for sequence-structure-function studies. Logistic regression analysis of the multiple sequence alignment identifies key structural contributions to cytochrome P450 heme incorporation and peroxygenase activity and suggests possible structural differences between parents CYP102A1 and CYP102A2.
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Affiliation(s)
- Christopher R Otey
- 1Biochemistry and Molecular Biophysics, California Institute of Technology, Pasadena, California, United States of America
| | - Marco Landwehr
- 2Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, United States of America
| | - Jeffrey B Endelman
- 3Bioengineering, California Institute of Technology, Pasadena, California, United States of America
| | - Kaori Hiraga
- 2Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, United States of America
| | - Jesse D Bloom
- 2Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, United States of America
| | - Frances H Arnold
- 1Biochemistry and Molecular Biophysics, California Institute of Technology, Pasadena, California, United States of America
- 2Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, United States of America
- 3Bioengineering, California Institute of Technology, Pasadena, California, United States of America
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Bloom JD, Labthavikul ST, Otey CR, Arnold FH. Protein stability promotes evolvability. Proc Natl Acad Sci U S A 2006; 103:5869-74. [PMID: 16581913 PMCID: PMC1458665 DOI: 10.1073/pnas.0510098103] [Citation(s) in RCA: 810] [Impact Index Per Article: 45.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2005] [Indexed: 11/18/2022] Open
Abstract
The biophysical properties that enable proteins to so readily evolve to perform diverse biochemical tasks are largely unknown. Here, we show that a protein's capacity to evolve is enhanced by the mutational robustness conferred by extra stability. We use simulations with model lattice proteins to demonstrate how extra stability increases evolvability by allowing a protein to accept a wider range of beneficial mutations while still folding to its native structure. We confirm this view experimentally by mutating marginally stable and thermostable variants of cytochrome P450 BM3. Mutants of the stabilized parent were more likely to exhibit new or improved functions. Only the stabilized P450 parent could tolerate the highly destabilizing mutations needed to confer novel activities such as hydroxylating the antiinflammatory drug naproxen. Our work establishes a crucial link between protein stability and evolution. We show that we can exploit this link to discover protein functions, and we suggest how natural evolution might do the same.
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Affiliation(s)
| | | | - Christopher R. Otey
- Biochemistry and Molecular Biophysics Option, Mail Code 210-41, California Institute of Technology, Pasadena, CA 91125
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Otey CR, Bandara G, Lalonde J, Takahashi K, Arnold FH. Preparation of human metabolites of propranolol using laboratory-evolved bacterial cytochromes P450. Biotechnol Bioeng 2006; 93:494-9. [PMID: 16224788 DOI: 10.1002/bit.20744] [Citation(s) in RCA: 117] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Testing the toxicities and biological activities of the human metabolites of drugs is important for development of safe and effective pharmaceuticals. Producing these metabolites using human cytochrome P450s is difficult, however, because the human enzymes are costly, poorly stable, and slow. We have used directed evolution to generate variants of P450 BM3 from Bacillus megaterium that function via the "peroxide shunt" pathway, using hydrogen peroxide in place of the reductase domain, oxygen and NADPH. Here, we report further evolution of the P450 BM3 heme domain peroxygenase to enhance production of the authentic human metabolites of propranolol by this biocatalytic route. This system offers a versatile, cost-effective, and scaleable route to the synthesis of drug metabolites.
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Affiliation(s)
- Christopher R Otey
- Biochemistry and Molecular Biophysics, California Institute of Technology, Pasadena, 91125, USA
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