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Reetz MT. What are the Limitations of Enzymes in Synthetic Organic Chemistry? CHEM REC 2016; 16:2449-2459. [DOI: 10.1002/tcr.201600040] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Indexed: 12/31/2022]
Affiliation(s)
- Manfred T. Reetz
- Fachbereich Chemie (15) Philipps-Universität Marburg Hans-Meerwein Straße; 35032 Marburg Germany
- Max-Planck-Institut für Kohlenforschung; Kaiser-Wilhelm-Platz 1 45470 Mülheim an der Ruhr Germany
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52
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Bendl J, Stourac J, Sebestova E, Vavra O, Musil M, Brezovsky J, Damborsky J. HotSpot Wizard 2.0: automated design of site-specific mutations and smart libraries in protein engineering. Nucleic Acids Res 2016; 44:W479-87. [PMID: 27174934 PMCID: PMC4987947 DOI: 10.1093/nar/gkw416] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2016] [Accepted: 05/03/2016] [Indexed: 01/13/2023] Open
Abstract
HotSpot Wizard 2.0 is a web server for automated identification of hot spots and design of smart libraries for engineering proteins' stability, catalytic activity, substrate specificity and enantioselectivity. The server integrates sequence, structural and evolutionary information obtained from 3 databases and 20 computational tools. Users are guided through the processes of selecting hot spots using four different protein engineering strategies and optimizing the resulting library's size by narrowing down a set of substitutions at individual randomized positions. The only required input is a query protein structure. The results of the calculations are mapped onto the protein's structure and visualized with a JSmol applet. HotSpot Wizard lists annotated residues suitable for mutagenesis and can automatically design appropriate codons for each implemented strategy. Overall, HotSpot Wizard provides comprehensive annotations of protein structures and assists protein engineers with the rational design of site-specific mutations and focused libraries. It is freely available at http://loschmidt.chemi.muni.cz/hotspotwizard.
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Affiliation(s)
- Jaroslav Bendl
- Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment RECETOX, Masaryk University, 625 00 Brno, Czech Republic Department of Information Systems, Faculty of Information Technology, Brno University of Technology, 612 66 Brno, Czech Republic International Clinical Research Center, St. Anne's University Hospital Brno, Brno, Czech Republic
| | - Jan Stourac
- Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment RECETOX, Masaryk University, 625 00 Brno, Czech Republic
| | - Eva Sebestova
- Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment RECETOX, Masaryk University, 625 00 Brno, Czech Republic
| | - Ondrej Vavra
- Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment RECETOX, Masaryk University, 625 00 Brno, Czech Republic
| | - Milos Musil
- Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment RECETOX, Masaryk University, 625 00 Brno, Czech Republic Department of Information Systems, Faculty of Information Technology, Brno University of Technology, 612 66 Brno, Czech Republic
| | - Jan Brezovsky
- Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment RECETOX, Masaryk University, 625 00 Brno, Czech Republic International Clinical Research Center, St. Anne's University Hospital Brno, Brno, Czech Republic
| | - Jiri Damborsky
- Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment RECETOX, Masaryk University, 625 00 Brno, Czech Republic International Clinical Research Center, St. Anne's University Hospital Brno, Brno, Czech Republic
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Sun Z, Wikmark Y, Bäckvall JE, Reetz MT. New Concepts for Increasing the Efficiency in Directed Evolution of Stereoselective Enzymes. Chemistry 2016; 22:5046-54. [DOI: 10.1002/chem.201504406] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Indexed: 01/28/2023]
Affiliation(s)
- Zhoutong Sun
- Max-Planck-Institut für Kohlenforschung; Kaiser-Wilhelm-Platz 1 45470 Mülheim an der Ruhr Germany
- Fachbereich Chemie; Philipps-Universität Marburg; Hans-Meerwein-Strasse 4 35032 Marburg Germany
| | - Ylva Wikmark
- Department of Organic Chemistry; Arrhenius Laboratory; Stockholm University; 106 91 Stockholm Sweden
| | - Jan-E. Bäckvall
- Department of Organic Chemistry; Arrhenius Laboratory; Stockholm University; 106 91 Stockholm Sweden
| | - Manfred T. Reetz
- Max-Planck-Institut für Kohlenforschung; Kaiser-Wilhelm-Platz 1 45470 Mülheim an der Ruhr Germany
- Fachbereich Chemie; Philipps-Universität Marburg; Hans-Meerwein-Strasse 4 35032 Marburg Germany
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54
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Sun Z, Lonsdale R, Ilie A, Li G, Zhou J, Reetz MT. Catalytic Asymmetric Reduction of Difficult-to-Reduce Ketones: Triple-Code Saturation Mutagenesis of an Alcohol Dehydrogenase. ACS Catal 2016. [DOI: 10.1021/acscatal.5b02752] [Citation(s) in RCA: 93] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Zhoutong Sun
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
- Fachbereich Chemie der Philipps-Universität, Hans-Meerwein-Strasse, 35032 Marburg, Germany
| | - Richard Lonsdale
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
- Fachbereich Chemie der Philipps-Universität, Hans-Meerwein-Strasse, 35032 Marburg, Germany
| | - Adriana Ilie
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
- Fachbereich Chemie der Philipps-Universität, Hans-Meerwein-Strasse, 35032 Marburg, Germany
| | - Guangyue Li
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
- Fachbereich Chemie der Philipps-Universität, Hans-Meerwein-Strasse, 35032 Marburg, Germany
| | - Jiahai Zhou
- State Key Laboratory of Bio-organic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China
| | - Manfred T. Reetz
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
- Fachbereich Chemie der Philipps-Universität, Hans-Meerwein-Strasse, 35032 Marburg, Germany
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Sun Z, Lonsdale R, Wu L, Li G, Li A, Wang J, Zhou J, Reetz MT. Structure-Guided Triple-Code Saturation Mutagenesis: Efficient Tuning of the Stereoselectivity of an Epoxide Hydrolase. ACS Catal 2016. [DOI: 10.1021/acscatal.5b02751] [Citation(s) in RCA: 87] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Zhoutong Sun
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
- Fachbereich Chemie der Philipps-Universität, Hans-Meerwein-Strasse, 35032 Marburg, Germany
| | - Richard Lonsdale
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
- Fachbereich Chemie der Philipps-Universität, Hans-Meerwein-Strasse, 35032 Marburg, Germany
| | - Lian Wu
- State Key Laboratory of Bio-organic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China
| | - Guangyue Li
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
- Fachbereich Chemie der Philipps-Universität, Hans-Meerwein-Strasse, 35032 Marburg, Germany
| | - Aitao Li
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
- Fachbereich Chemie der Philipps-Universität, Hans-Meerwein-Strasse, 35032 Marburg, Germany
| | - Jianbo Wang
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
- Fachbereich Chemie der Philipps-Universität, Hans-Meerwein-Strasse, 35032 Marburg, Germany
| | - Jiahai Zhou
- State Key Laboratory of Bio-organic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China
| | - Manfred T. Reetz
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
- Fachbereich Chemie der Philipps-Universität, Hans-Meerwein-Strasse, 35032 Marburg, Germany
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56
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Engqvist MKM, Nielsen J. ANT: Software for Generating and Evaluating Degenerate Codons for Natural and Expanded Genetic Codes. ACS Synth Biol 2015; 4:935-8. [PMID: 25901796 DOI: 10.1021/acssynbio.5b00018] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The Ambiguous Nucleotide Tool (ANT) is a desktop application that generates and evaluates degenerate codons. Degenerate codons are used to represent DNA positions that have multiple possible nucleotide alternatives. This is useful for protein engineering and directed evolution, where primers specified with degenerate codons are used as a basis for generating libraries of protein sequences. ANT is intuitive and can be used in a graphical user interface or by interacting with the code through a defined application programming interface. ANT comes with full support for nonstandard, user-defined, or expanded genetic codes (translation tables), which is important because synthetic biology is being applied to an ever widening range of natural and engineered organisms. The Python source code for ANT is freely distributed so that it may be used without restriction, modified, and incorporated in other software or custom data pipelines.
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Affiliation(s)
- Martin K. M. Engqvist
- Department of Chemical & Biological Engineering, Chalmers University of Technology, Kemivägen 10, SE-412 96 Göteborg, Sweden
| | - Jens Nielsen
- Department of Chemical & Biological Engineering, Chalmers University of Technology, Kemivägen 10, SE-412 96 Göteborg, Sweden
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57
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Parra LP, Acevedo JP, Reetz MT. Directed evolution of phenylacetone monooxygenase as an active catalyst for the Baeyer-Villiger conversion of cyclohexanone to caprolactone. Biotechnol Bioeng 2015; 112:1354-64. [PMID: 25675885 DOI: 10.1002/bit.25564] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Accepted: 02/05/2015] [Indexed: 01/10/2023]
Abstract
Phenylacetone monooxygenase (PAMO) is an exceptionally robust Baeyer-Villiger monooxygenase, which makes it ideal for potential industrial applications. However, its substrate scope is limited, unreactive cyclohexanone being a prominent example. Such a limitation is unfortunate, because this particular transformation in an ecologically viable manner would be highly desirable, the lactone and the respective lactam being of considerable interest as monomers in polymer science. We have applied directed evolution in search of an active mutant for this valuable C-C activating reaction. Using iterative saturation mutagenesis (ISM), several active mutants were evolved, with only a minimal trade-off in terms of stability. The best mutants allow for quantitative conversion of 2 mM cyclohexanone within 1 h reaction time. In order to circumvent the NADP(+) regeneration problem, whole E. coli resting cells were successfully applied. Molecular dynamics simulations and induced fit docking throw light on the origin of enhanced PAMO activity. The PAMO mutants constitute ideal starting points for future directed evolution optimization necessary for an industrial process.
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Affiliation(s)
- Loreto P Parra
- Department of Synthetic Organic Chemistry, Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470, Mülheim an der Ruhr, Germany.,Fachbereich Chemie Philipps-Universität Marburg, Marburg, Germany.,Department of Chemical and Bioprocesses Engineering, School of Engineering, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Juan P Acevedo
- Department of Synthetic Organic Chemistry, Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470, Mülheim an der Ruhr, Germany.,Fachbereich Chemie Philipps-Universität Marburg, Marburg, Germany.,Facultad de Medicina y Facultad de Ingeniería y Ciencias Aplicadas, Universidad de los Andes, Santiago, Chile
| | - Manfred T Reetz
- Department of Synthetic Organic Chemistry, Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470, Mülheim an der Ruhr, Germany. .,Fachbereich Chemie Philipps-Universität Marburg, Marburg, Germany.
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58
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Sun Z, Lonsdale R, Kong XD, Xu JH, Zhou J, Reetz MT. Reshaping an Enzyme Binding Pocket for Enhanced and Inverted Stereoselectivity: Use of Smallest Amino Acid Alphabets in Directed Evolution. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201501809] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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59
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Sun Z, Lonsdale R, Kong XD, Xu JH, Zhou J, Reetz MT. Reshaping an Enzyme Binding Pocket for Enhanced and Inverted Stereoselectivity: Use of Smallest Amino Acid Alphabets in Directed Evolution. Angew Chem Int Ed Engl 2015; 54:12410-5. [DOI: 10.1002/anie.201501809] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Indexed: 01/06/2023]
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60
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Wang X, Lin H, Zheng Y, Feng J, Yang Z, Tang L. MDC-Analyzer-facilitated combinatorial strategy for improving the activity and stability of halohydrin dehalogenase from Agrobacterium radiobacter AD1. J Biotechnol 2015; 206:1-7. [PMID: 25896949 DOI: 10.1016/j.jbiotec.2015.04.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Revised: 04/02/2015] [Accepted: 04/08/2015] [Indexed: 01/05/2023]
Abstract
Halohydrin dehalogenase from Agrobacterium radiobacter AD1 (HheC) displays a broad substrate range with high regio- and enantioselectivity of both ring-closure and ring-opening reactions, making the enzyme a useful catalyst for the production of optically pure epoxides and β-substituted alcohols. In this study, we report a novel method using an MDC-Analyzer-facilitated combinatorial strategy to improve the activity and stability of HheC by simultaneously randomizing multiple contiguous residues. Six contiguous active-site residues, which are the hotspots for improving the activity of HheC, were simultaneously selected and randomized using the MDC-Analyzer-facilitated combinatorial strategy, resulting in a high-quality mutagenesis library. After screening a total of 1152 clones, three positive mutants were obtained, which exhibited approximately 3.5-5.9-fold higher kcat values than the wild-type HheC toward 1,3-dichloro-2-propanol (1,3-DCP). However, the inactivation half-life of the best mutant (DG9) at 55 °C decreased 9-fold compared with that of the wild-type HheC. To improve the stability of mutant DG9, seven contiguous potential surface amino acids were revealed by using the B-FITTER tool. Two charged amino acids, Glu and Lys, which are more abundant in thermophilic proteins than in their mesophilic counterparts, were selected to substitute those seven amino acids and were combined together via an MDC-Analyzer-facilitated combinatorial strategy. Two mutants displaying 1.6- and 2.3-fold higher half-life τ1/2 (55 °C) values than their DG9 template were obtained after screening only 384 clones. The results indicated that an MDC-Analyzer-facilitated combinatorial strategy represents an efficient tool for the directed evolution of functional enzymes with multiple contiguous targeting sites.
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Affiliation(s)
- Xiong Wang
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China.
| | - Hao Lin
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China.
| | - Yu Zheng
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China.
| | - Juan Feng
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China.
| | - Zujun Yang
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China.
| | - Lixia Tang
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China.
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61
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Acevedo-Rocha CG, Reetz MT. Assembly of Designed Oligonucleotides: a useful tool in synthetic biology for creating high-quality combinatorial DNA libraries. Methods Mol Biol 2015; 1179:189-206. [PMID: 25055779 DOI: 10.1007/978-1-4939-1053-3_13] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The method dubbed Assembly of Designed Oligonucleotides (ADO) is a powerful tool in synthetic biology to create combinatorial DNA libraries for gene, protein, metabolic, and genome engineering. In directed evolution of proteins, ADO benefits from using reduced amino acid alphabets for saturation mutagenesis and/or DNA shuffling, but all 20 canonical amino acids can be also used as building blocks. ADO is performed in a two-step reaction. The first involves a primer-free, polymerase cycling assembly or overlap extension PCR step using carefully designed overlapping oligonucleotides. The second step is a PCR amplification using the outer primers, resulting in a high-quality and bias-free double-stranded DNA library that can be assembled with other gene fragments and/or cloned into a suitable plasmid subsequently. The protocol can be performed in a few hours. In theory, neither the length of the DNA library nor the number of DNA changes has any limits. Furthermore, with the costs of synthetic DNA dropping every year, after an initial investment is made in the oligonucleotides, these can be exchanged for alternative ones with different sequences at any point in the process, fully exploiting the potential of creating highly diverse combinatorial libraries. In the example chosen here, we show the construction of a high-quality combinatorial ADO library targeting sixteen different codons simultaneously with nonredundant degenerate codons encoding various reduced alphabets of four amino acids along the heme region of the monooxygenase P450-BM3.
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Affiliation(s)
- Carlos G Acevedo-Rocha
- Organische Synthese, Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470, Mülheim, Germany
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62
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Yang N, Su Z, Feng X, Hu C. Theoretical Studies on the Asymmetric Baeyer-Villiger Oxidation Reaction of 4-Phenylcyclohexanone with m-Chloroperoxobenzoic Acid Catalyzed by Chiral Scandium(III)-N,N'-Dioxide Complexes. Chemistry 2015; 21:7264-77. [PMID: 25809412 DOI: 10.1002/chem.201406478] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2014] [Indexed: 11/05/2022]
Abstract
The mechanism and enantioselectivity of the asymmetric Baeyer-Villiger oxidation reaction between 4-phenylcyclohexanone and m-chloroperoxobenzoic acid (m-CPBA) catalyzed by Sc(III) -N,N'-dioxide complexes were investigated theoretically. The calculations indicated that the first step, corresponding to the addition of m-CPBA to the carbonyl group of 4-phenylcyclohexanone, is the rate-determining step (RDS) for all the pathways studied. The activation barrier of the RDS for the uncatalyzed reaction was predicted to be 189.8 kJ mol(-1) . The combination of an Sc(III) -N,N'-dioxide complex and the m-CBA molecule can construct a bifunctional catalyst in which the Lewis acidic Sc(III) center activates the carbonyl group of 4-phenylcyclohexanone while m-CBA transfers a proton, which lowers the activation barrier of the addition step (RDS) to 86.7 kJ mol(-1) . The repulsion between the m-chlorophenyl group of m-CPBA and the 2,4,6-iPr3 C6 H2 group of the N,N'-dioxide ligand, as well as the steric hindrance between the phenyl group of 4-phenylcyclohexanone and the amino acid skeleton of the N,N'-dioxide ligand, play important roles in the control of the enantioselectivity.
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Affiliation(s)
- Na Yang
- Key Laboratory of Green Chemistry & Technology, Ministry of Education, College of Chemistry, Sichuan University, Chengdu, 610064 (P. R. China)
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63
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Exploring the enantioselective mechanism of halohydrin dehalogenase from Agrobacterium radiobacter AD1 by iterative saturation mutagenesis. Appl Environ Microbiol 2015; 81:2919-26. [PMID: 25681194 DOI: 10.1128/aem.04153-14] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Halohydrin dehalogenase from Agrobacterium radiobacter AD1 (HheC) shows great potential in producing valuable chiral epoxides and β-substituted alcohols. The wild-type (WT) enzyme displays a high R-enantiopreference toward most aromatic substrates, whereas no S-selective HheC has been reported to date. To obtain more enantioselective enzymes, seven noncatalytic active-site residues were subjected to iterative saturation mutagenesis (ISM). After two rounds of screening aspects of both activity and enantioselectivity (E), three outstanding mutants (Thr134Val/Leu142Met, Leu142Phe/Asn176His, and Pro84Val/Phe86Pro/Thr134Ala/Asn176Ala mutants) with divergent enantioselectivity were obtained. The two double mutants displayed approximately 2-fold improvement in R-enantioselectivity toward 2-chloro-1-phenylethanol (2-CPE) without a significant loss of enzyme activity compared with the WT enzyme. Strikingly, the Pro84Val/Phe86Pro/Thr134Ala/Asn176Ala mutant showed an inverted enantioselectivity (from an ER of 65 [WT] to an ES of 101) and approximately 100-fold-enhanced catalytic efficiency toward (S)-2-CPE. Molecular dynamic simulation and docking analysis revealed that the phenyl side chain of (S)-2-CPE bound at a different location than that of its R-counterpart; those mutations generated extra connections for the binding of the favored enantiomer, while the eliminated connections reduced binding of the nonfavored enantiomer, all of which could contribute to the observed inverted enantiopreference.
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64
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Huang JT, Wang T, Huang SR, Li X. Reduced alphabet for protein folding prediction. Proteins 2015; 83:631-9. [PMID: 25641420 DOI: 10.1002/prot.24762] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Revised: 11/07/2014] [Accepted: 12/21/2014] [Indexed: 01/17/2023]
Abstract
What are the key building blocks that would have been needed to construct complex protein folds? This is an important issue for understanding protein folding mechanism and guiding de novo protein design. Twenty naturally occurring amino acids and eight secondary structures consist of a 28-letter alphabet to determine folding kinetics and mechanism. Here we predict folding kinetic rates of proteins from many reduced alphabets. We find that a reduced alphabet of 10 letters achieves good correlation with folding rates, close to the one achieved by full 28-letter alphabet. Many other reduced alphabets are not significantly correlated to folding rates. The finding suggests that not all amino acids and secondary structures are equally important for protein folding. The foldable sequence of a protein could be designed using at least 10 folding units, which can either promote or inhibit protein folding. Reducing alphabet cardinality without losing key folding kinetic information opens the door to potentially faster machine learning and data mining applications in protein structure prediction, sequence alignment and protein design.
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Affiliation(s)
- Jitao T Huang
- Department of Chemistry and National Laboratory of Elemento-Organic Chemistry, Nankai University, Tianjin, 300071, People's Republic of China
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65
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Jacobs TM, Yumerefendi H, Kuhlman B, Leaver-Fay A. SwiftLib: rapid degenerate-codon-library optimization through dynamic programming. Nucleic Acids Res 2014; 43:e34. [PMID: 25539925 PMCID: PMC4357694 DOI: 10.1093/nar/gku1323] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Degenerate codon (DC) libraries efficiently address the experimental library-size limitations of directed evolution by focusing diversity toward the positions and toward the amino acids (AAs) that are most likely to generate hits; however, manually constructing DC libraries is challenging, error prone and time consuming. This paper provides a dynamic programming solution to the task of finding the best DCs while keeping the size of the library beneath some given limit, improving on the existing integer-linear programming formulation. It then extends the algorithm to consider multiple DCs at each position, a heretofore unsolved problem, while adhering to a constraint on the number of primers needed to synthesize the library. In the two library-design problems examined here, the use of multiple DCs produces libraries that very nearly cover the set of desired AAs while still staying within the experimental size limits. Surprisingly, the algorithm is able to find near-perfect libraries where the ratio of amino-acid sequences to nucleic-acid sequences approaches 1; it effectively side-steps the degeneracy of the genetic code. Our algorithm is freely available through our web server and solves most design problems in about a second.
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Affiliation(s)
- Timothy M Jacobs
- Department of Biochemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Hayretin Yumerefendi
- Department of Biochemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Brian Kuhlman
- Department of Biochemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Andrew Leaver-Fay
- Department of Biochemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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66
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Yachnin BJ, McEvoy MB, MacCuish RJD, Morley KL, Lau PCK, Berghuis AM. Lactone-bound structures of cyclohexanone monooxygenase provide insight into the stereochemistry of catalysis. ACS Chem Biol 2014; 9:2843-51. [PMID: 25265531 DOI: 10.1021/cb500442e] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The Baeyer-Villiger monooxygenases (BVMOs) are microbial enzymes that catalyze the synthetically useful Baeyer-Villiger oxidation reaction. The available BVMO crystal structures all lack a substrate or product bound in a position that would determine the substrate specificity and stereospecificity of the enzyme. Here, we report two crystal structures of cyclohexanone monooxygenase (CHMO) with its product, ε-caprolactone, bound: the CHMO(Tight) and CHMO(Loose) structures. The CHMO(Tight) structure represents the enzyme state in which substrate acceptance and stereospecificity is determined, providing a foundation for engineering BVMOs with altered substrate spectra and/or stereospecificity. The CHMO(Loose) structure is the first structure where the product is solvent accessible. This structure represents the enzyme state upon binding and release of the substrate and product. In addition, the role of the invariant Arg329 in chaperoning the substrate/product during the catalytic cycle is highlighted. Overall, these data provide a structural framework for the engineering of BVMOs with altered substrate spectra and/or stereospecificity.
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Affiliation(s)
| | | | | | - Krista L. Morley
- National Research Council of Canada, 6100 Royalmount Avenue, Montreal, Quebec, Canada H4P 2R2
| | - Peter C. K. Lau
- Departments of Microbiology & Immunology and Chemistry, McGill University, 3775 University Street, Montreal, Quebec, Canada H3A 2B4
- FQRNT Center for Green Chemistry and Catalysis, Montreal, Quebec, Canada
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67
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Acevedo-Rocha CG, Agudo R, Reetz MT. Directed evolution of stereoselective enzymes based on genetic selection as opposed to screening systems. J Biotechnol 2014; 191:3-10. [DOI: 10.1016/j.jbiotec.2014.04.009] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2014] [Revised: 03/26/2014] [Accepted: 04/07/2014] [Indexed: 01/25/2023]
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68
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Zhang ZG, Lonsdale R, Sanchis J, Reetz MT. Extreme Synergistic Mutational Effects in the Directed Evolution of a Baeyer–Villiger Monooxygenase as Catalyst for Asymmetric Sulfoxidation. J Am Chem Soc 2014; 136:17262-72. [DOI: 10.1021/ja5098034] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Zhi-Gang Zhang
- Department
of Chemistry, Philipps-Universität Marburg, Hans-Meerwein
Str., 35032 Marburg, Germany
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Richard Lonsdale
- Department
of Chemistry, Philipps-Universität Marburg, Hans-Meerwein
Str., 35032 Marburg, Germany
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Joaquin Sanchis
- Monash
Institute of Pharmaceutical Sciences, Monash University, 381 Royal
Parade, Parkville, 3052
VIC, Australia
| | - Manfred T. Reetz
- Department
of Chemistry, Philipps-Universität Marburg, Hans-Meerwein
Str., 35032 Marburg, Germany
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
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69
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Functional divergence between closely related Baeyer-Villiger monooxygenases from Aspergillus flavus. ACTA ACUST UNITED AC 2014. [DOI: 10.1016/j.molcatb.2014.05.015] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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70
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Zhou L, Liu X, Ji J, Zhang Y, Wu W, Liu Y, Lin L, Feng X. Regio- and enantioselective Baeyer-Villiger oxidation: kinetic resolution of racemic 2-substituted cyclopentanones. Org Lett 2014; 16:3938-41. [PMID: 25029483 DOI: 10.1021/ol501737a] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
A kinetic resolution of racemic 2-substituted cyclopentanones via highly regio- and enantioselective Baeyer-Villiger oxidation has been successfully developed. The reaction could afford the normal 6-substituted δ-lactones in up to 98% ee and >19/1 regioselectivity. Meanwhile, the unreacted ketones were recovered in excellent ee values (up to 98%). It represents the best results of the kinetic resolution of racemic 2-substituted cyclopentanones via nonenzymic asymmetric BV oxidation.
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Affiliation(s)
- Lin Zhou
- Key Laboratory of Green Chemistry & Technology, Ministry of Education, College of Chemistry, Sichuan University , Chengdu 610064, P. R. China
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71
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MDC-Analyzer: a novel degenerate primer design tool for the construction of intelligent mutagenesis libraries with contiguous sites. Biotechniques 2014; 56:301-2, 304, 306-8, passim. [PMID: 24924390 DOI: 10.2144/000114177] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2013] [Accepted: 04/03/2014] [Indexed: 11/23/2022] Open
Abstract
Recent computational and bioinformatics advances have enabled the efficient creation of novel biocatalysts by reducing amino acid variability at hot spot regions. To further expand the utility of this strategy, we present here a tool called Multi-site Degenerate Codon Analyzer (MDC-Analyzer) for the automated design of intelligent mutagenesis libraries that can completely cover user-defined randomized sequences, especially when multiple contiguous and/or adjacent sites are targeted. By initially defining an objective function, the possible optimal degenerate PCR primer profiles could be automatically explored using the heuristic approach of Greedy Best-First-Search. Compared to the previously developed DC-Analyzer, MDC-Analyzer allows for the existence of a small amount of undesired sequences as a tradeoff between the number of degenerate primers and the encoded library size while still providing all the benefits of DC-Analyzer with the ability to randomize multiple contiguous sites. MDC-Analyzer was validated using a series of randomly generated mutation schemes and experimental case studies on the evolution of halohydrin dehalogenase, which proved that the MDC methodology is more efficient than other methods and is particularly well-suited to exploring the sequence space of proteins using data-driven protein engineering strategies.
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72
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Huang L, Ma HM, Yu HL, Xu JH. Altering the Substrate Specificity of ReductaseCgKR1 fromCandida glabrataby Protein Engineering for Bioreduction of Aromatic α-Keto Esters. Adv Synth Catal 2014. [DOI: 10.1002/adsc.201300775] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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73
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Adrio JL, Demain AL. Microbial enzymes: tools for biotechnological processes. Biomolecules 2014; 4:117-39. [PMID: 24970208 PMCID: PMC4030981 DOI: 10.3390/biom4010117] [Citation(s) in RCA: 283] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2013] [Revised: 01/02/2014] [Accepted: 01/02/2014] [Indexed: 11/29/2022] Open
Abstract
Microbial enzymes are of great importance in the development of industrial bioprocesses. Current applications are focused on many different markets including pulp and paper, leather, detergents and textiles, pharmaceuticals, chemical, food and beverages, biofuels, animal feed and personal care, among others. Today there is a need for new, improved or/and more versatile enzymes in order to develop more novel, sustainable and economically competitive production processes. Microbial diversity and modern molecular techniques, such as metagenomics and genomics, are being used to discover new microbial enzymes whose catalytic properties can be improved/modified by different strategies based on rational, semi-rational and random directed evolution. Most industrial enzymes are recombinant forms produced in bacteria and fungi.
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Affiliation(s)
- Jose L Adrio
- Neol Biosolutions SA, BIC Granada, Granada 18016, Spain.
| | - Arnold L Demain
- Research Institute for Scientists Emeriti (R.I.S.E.), Drew University, Madison, NJ 07940, USA.
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74
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Sebestova E, Bendl J, Brezovsky J, Damborsky J. Computational tools for designing smart libraries. Methods Mol Biol 2014; 1179:291-314. [PMID: 25055786 DOI: 10.1007/978-1-4939-1053-3_20] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Traditional directed evolution experiments are often time-, labor- and cost-intensive because they involve repeated rounds of random mutagenesis and the selection or screening of large mutant libraries. The efficiency of directed evolution experiments can be significantly improved by targeting mutagenesis to a limited number of hot-spot positions and/or selecting a limited set of substitutions. The design of such "smart" libraries can be greatly facilitated by in silico analyses and predictions. Here we provide an overview of computational tools applicable for (a) the identification of hot-spots for engineering enzyme properties, and (b) the evaluation of predicted hot-spots and selection of suitable amino acids for substitutions. The selected tools do not require any specific expertise and can easily be implemented by the wider scientific community.
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Affiliation(s)
- Eva Sebestova
- Loschmidt Laboratories, Masaryk University, Kamenice 5/A13, 625 00, Brno, Czech Republic
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75
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Acevedo-Rocha CG, Hoebenreich S, Reetz MT. Iterative saturation mutagenesis: a powerful approach to engineer proteins by systematically simulating Darwinian evolution. Methods Mol Biol 2014; 1179:103-28. [PMID: 25055773 DOI: 10.1007/978-1-4939-1053-3_7] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Iterative saturation mutagenesis (ISM) is a widely applicable and powerful strategy for the efficient directed evolution of enzymes. First, one or more amino acid positions from the chosen enzyme are assigned to multi-residue sites (i.e., groups of amino acids or "multisites"). Then, the residues in each multisite are mutated with a user-defined randomization scheme to all canonical amino acids or a reduced amino acid alphabet. Subsequently, the genes of chosen variants (usually the best but not necessarily) are used as templates for saturation mutagenesis at other multisites, and the process is repeated until the desired degree of biocatalyst improvement has been achieved. Addressing multisites iteratively results in a so-called ISM scheme or tree with various upward branches or pathways. The systematic character of ISM simulates in vitro the natural process of Darwinian evolution: variation (library creation), selection (library screening), and amplification (template chosen for the next round of randomization). However, the main feature of ISM that distinguishes it from other directed evolution methods is the systematic probing of a defined segment of the protein sequence space, as it has been shown that ISM is much more efficient in terms of biocatalyst optimization than random methods such as error-prone PCR. In addition, ISM trees have also shed light on the emergence of epistasis, thereby rationally improving the strategies for evolving better enzymes. ISM was developed to improve catalytic properties such as rate, substrate scope, stereo- and regioselectivity using the Combinatorial Active-site Saturation Test (CAST), as well as chemical and thermal stability employing the B-Factor Iterative Test (B-FIT). However, ISM can also be invoked to manipulate such protein properties as binding affinity among other possibilities, including protein-protein interactions. Herein, we provide general guidelines for ISM, using CAST as the case study in the quest to enhance the activity and regioselectivity of the monooxygenase P450BM3 toward testosterone.
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Affiliation(s)
- Carlos G Acevedo-Rocha
- Organische Synthese, Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470, Mülheim, Germany
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76
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Dudek HM, Fink MJ, Shivange AV, Dennig A, Mihovilovic MD, Schwaneberg U, Fraaije MW. Extending the substrate scope of a Baeyer–Villiger monooxygenase by multiple-site mutagenesis. Appl Microbiol Biotechnol 2013; 98:4009-20. [DOI: 10.1007/s00253-013-5364-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Revised: 10/25/2013] [Accepted: 10/28/2013] [Indexed: 10/26/2022]
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77
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Parra LP, Agudo R, Reetz MT. Directed Evolution by Using Iterative Saturation Mutagenesis Based on Multiresidue Sites. Chembiochem 2013; 14:2301-9. [DOI: 10.1002/cbic.201300486] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2013] [Indexed: 12/18/2022]
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78
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Improvement of biocatalysts for industrial and environmental purposes by saturation mutagenesis. Biomolecules 2013; 3:778-811. [PMID: 24970191 PMCID: PMC4030971 DOI: 10.3390/biom3040778] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2013] [Revised: 09/22/2013] [Accepted: 09/23/2013] [Indexed: 11/16/2022] Open
Abstract
Laboratory evolution techniques are becoming increasingly widespread among protein engineers for the development of novel and designed biocatalysts. The palette of different approaches ranges from complete randomized strategies to rational and structure-guided mutagenesis, with a wide variety of costs, impacts, drawbacks and relevance to biotechnology. A technique that convincingly compromises the extremes of fully randomized vs. rational mutagenesis, with a high benefit/cost ratio, is saturation mutagenesis. Here we will present and discuss this approach in its many facets, also tackling the issue of randomization, statistical evaluation of library completeness and throughput efficiency of screening methods. Successful recent applications covering different classes of enzymes will be presented referring to the literature and to research lines pursued in our group. The focus is put on saturation mutagenesis as a tool for designing novel biocatalysts specifically relevant to production of fine chemicals for improving bulk enzymes for industry and engineering technical enzymes involved in treatment of waste, detoxification and production of clean energy from renewable sources.
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79
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Bergdahl B, Sandström AG, Borgström C, Boonyawan T, van Niel EWJ, Gorwa-Grauslund MF. Engineering yeast hexokinase 2 for improved tolerance toward xylose-induced inactivation. PLoS One 2013; 8:e75055. [PMID: 24040384 PMCID: PMC3765440 DOI: 10.1371/journal.pone.0075055] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2013] [Accepted: 08/05/2013] [Indexed: 11/21/2022] Open
Abstract
Hexokinase 2 (Hxk2p) from Saccharomyces cerevisiae is a bi-functional enzyme being both a catalyst and an important regulator in the glucose repression signal. In the presence of xylose Hxk2p is irreversibly inactivated through an autophosphorylation mechanism, affecting all functions. Consequently, the regulation of genes involved in sugar transport and fermentative metabolism is impaired. The aim of the study was to obtain new Hxk2p-variants, immune to the autophosphorylation, which potentially can restore the repressive capability closer to its nominal level. In this study we constructed the first condensed, rationally designed combinatorial library targeting the active-site in Hxk2p. We combined protein engineering and genetic engineering for efficient screening and identified a variant with Phe159 changed to tyrosine. This variant had 64% higher catalytic activity in the presence of xylose compared to the wild-type and is expected to be a key component for increasing the productivity of recombinant xylose-fermenting strains for bioethanol production from lignocellulosic feedstocks.
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Affiliation(s)
- Basti Bergdahl
- Division of Applied Microbiology, Department of Chemistry, Lund University, Lund, Sweden
- * E-mail:
| | - Anders G. Sandström
- Division of Applied Microbiology, Department of Chemistry, Lund University, Lund, Sweden
| | - Celina Borgström
- Division of Applied Microbiology, Department of Chemistry, Lund University, Lund, Sweden
| | - Tarinee Boonyawan
- Division of Applied Microbiology, Department of Chemistry, Lund University, Lund, Sweden
| | - Ed W. J. van Niel
- Division of Applied Microbiology, Department of Chemistry, Lund University, Lund, Sweden
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80
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Reetz MT. Biocatalysis in organic chemistry and biotechnology: past, present, and future. J Am Chem Soc 2013; 135:12480-96. [PMID: 23930719 DOI: 10.1021/ja405051f] [Citation(s) in RCA: 522] [Impact Index Per Article: 47.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Enzymes as catalysts in synthetic organic chemistry gained importance in the latter half of the 20th century, but nevertheless suffered from two major limitations. First, many enzymes were not accessible in large enough quantities for practical applications. The advent of recombinant DNA technology changed this dramatically in the late 1970s. Second, many enzymes showed a narrow substrate scope, often poor stereo- and/or regioselectivity and/or insufficient stability under operating conditions. With the development of directed evolution beginning in the 1990s and continuing to the present day, all of these problems can be addressed and generally solved. The present Perspective focuses on these and other developments which have popularized enzymes as part of the toolkit of synthetic organic chemists and biotechnologists. Included is a discussion of the scope and limitation of cascade reactions using enzyme mixtures in vitro and of metabolic engineering of pathways in cells as factories for the production of simple compounds such as biofuels and complex natural products. Future trends and problems are also highlighted, as is the discussion concerning biocatalysis versus nonbiological catalysis in synthetic organic chemistry. This Perspective does not constitute a comprehensive review, and therefore the author apologizes to those researchers whose work is not specifically treated here.
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Affiliation(s)
- Manfred T Reetz
- Department of Chemistry, Philipps-Universität Marburg, Hans-Meerwein Strasse, 35032 Marburg, Germany.
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81
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Nov Y. Fitness loss and library size determination in saturation mutagenesis. PLoS One 2013; 8:e68069. [PMID: 23844158 PMCID: PMC3700877 DOI: 10.1371/journal.pone.0068069] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2013] [Accepted: 05/24/2013] [Indexed: 01/31/2023] Open
Abstract
Saturation mutagenesis is a widely used directed evolution technique, in which a large number of protein variants, each having random amino acids in certain predetermined positions, are screened in order to discover high-fitness variants among them. Several metrics for determining the library size (the number of variants screened) have been suggested in the literature, but none of them incorporates the actual fitness of the variants discovered in the experiment. We present the results of an extensive simulation study, which is based on probabilistic models for protein fitness landscape, and which investigates how the result of a saturation mutagenesis experiment – the fitness of the best variant discovered – varies as a function of the library size. In particular, we study the loss of fitness in the experiment: the difference between the fitness of the best variant discovered, and the fitness of the best variant in variant space. Our results are that the existing criteria for determining the library size are conservative, so smaller libraries are often satisfactory. Reducing the library size can save labor, time, and expenses in the laboratory.
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Affiliation(s)
- Yuval Nov
- Department of Statistics, University of Haifa, Haifa, Israel.
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82
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Dudek HM, Popken P, van Bloois E, Duetz WA, Fraaije MW. A generic, whole-cell-based screening method for Baeyer-Villiger monooxygenases. ACTA ACUST UNITED AC 2013; 18:678-87. [PMID: 23536548 DOI: 10.1177/1087057113480390] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Baeyer-Villiger monooxygenases (BVMOs) have been receiving increasing attention as enzymes useful for biocatalytic applications. Industrial requirements call for rapid and extensive redesign of these enzymes. In response to the need for screening large libraries of BVMO mutants, we established a generic screening method that allows screening of Escherichia coli cells expressing active BVMOs in 96-well plate format. For this, we first developed an expression system for production of phenylacetone monooxygenase (PAMO) in the periplasm of E. coli. This allows probing the enzyme for any target substrate while it is also compatible with extracellular coenzyme regeneration. For coenzyme regeneration, we used phosphite dehydrogenase, which forms phosphate upon NADPH recycling. This allowed the use of a chromogenic molybdate-based phosphate determination assay. The screening procedure was supplemented with a detection method for identification of mutant enzymes that act as NADPH oxidases, thereby excluding false-positives. The whole-cell-based screening method was validated by screening site-saturation libraries of PAMO and resulted in the identification of PAMO mutants with altered catalytic properties. This new method can be used for screening libraries of BVMOs for activity with any desired substrate and therefore is a powerful tool for engineering of these enzymes.
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Affiliation(s)
- Hanna M Dudek
- Molecular Enzymology Group, University of Groningen, Groningen, The Netherlands
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83
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Kille S, Acevedo-Rocha CG, Parra LP, Zhang ZG, Opperman DJ, Reetz MT, Acevedo JP. Reducing codon redundancy and screening effort of combinatorial protein libraries created by saturation mutagenesis. ACS Synth Biol 2013; 2:83-92. [PMID: 23656371 DOI: 10.1021/sb300037w] [Citation(s) in RCA: 199] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Saturation mutagenesis probes define sections of the vast protein sequence space. However, even if randomization is limited this way, the combinatorial numbers problem is severe. Because diversity is created at the codon level, codon redundancy is a crucial factor determining the necessary effort for library screening. Additionally, due to the probabilistic nature of the sampling process, oversampling is required to ensure library completeness as well as a high probability to encounter all unique variants. Our trick employs a special mixture of three primers, creating a degeneracy of 22 unique codons coding for the 20 canonical amino acids. Therefore, codon redundancy and subsequent screening effort is significantly reduced, and a balanced distribution of codon per amino acid is achieved, as demonstrated exemplarily for a library of cyclohexanone monooxygenase. We show that this strategy is suitable for any saturation mutagenesis methodology to generate less-redundant libraries.
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Affiliation(s)
- Sabrina Kille
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1,
45470 Mülheim an der Ruhr, Germany
- Fachbereich Chemie, Philipps-Universität Marburg, Hans-Meerwein-Straße,
35043 Marburg, Germany
| | - Carlos G. Acevedo-Rocha
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1,
45470 Mülheim an der Ruhr, Germany
- Fachbereich Chemie, Philipps-Universität Marburg, Hans-Meerwein-Straße,
35043 Marburg, Germany
| | - Loreto P. Parra
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1,
45470 Mülheim an der Ruhr, Germany
- Fachbereich Chemie, Philipps-Universität Marburg, Hans-Meerwein-Straße,
35043 Marburg, Germany
| | - Zhi-Gang Zhang
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1,
45470 Mülheim an der Ruhr, Germany
- Fachbereich Chemie, Philipps-Universität Marburg, Hans-Meerwein-Straße,
35043 Marburg, Germany
| | - Diederik J. Opperman
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1,
45470 Mülheim an der Ruhr, Germany
| | - Manfred T. Reetz
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1,
45470 Mülheim an der Ruhr, Germany
- Fachbereich Chemie, Philipps-Universität Marburg, Hans-Meerwein-Straße,
35043 Marburg, Germany
| | - Juan Pablo Acevedo
- Facultad
de Medicina y Facultad
de Ingeniería de la Universidad de los Andes, Santiago, Chile
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84
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Dror A, Fishman A. Engineering non-heme mono- and dioxygenases for biocatalysis. Comput Struct Biotechnol J 2012; 2:e201209011. [PMID: 24688652 PMCID: PMC3962191 DOI: 10.5936/csbj.201209011] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2012] [Revised: 10/02/2012] [Accepted: 10/12/2012] [Indexed: 11/25/2022] Open
Abstract
Oxygenases are ubiquitous enzymes that catalyze the introduction of one or two oxygen atoms to unreactive chemical compounds. They require reduction equivalents from NADH or NADPH and comprise metal ions, metal ion complexes, or coenzymes in their active site. Thus, for industrial purposes, oxygenases are most commonly employed using whole cell catalysis, to alleviate the need for co-factor regeneration. Biotechnological applications include bioremediation, chiral synthesis, biosensors, fine chemicals, biofuels, pharmaceuticals, food ingredients and polymers. Controlling activity and selectivity of oxygenases is therefore of great importance and of growing interest to the scientific community. This review focuses on protein engineering of non-heme monooxygenases and dioxygenases for generating improved or novel functionalities. Rational mutagenesis based on x-ray structures and sequence alignment, as well as random methods such as directed evolution, have been utilized. It is concluded that knowledge-based protein engineering accompanied with targeted libraries, is most efficient for the design and tuning of biocatalysts towards novel substrates and enhanced catalytic activity while minimizing the screening efforts.
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Affiliation(s)
- Adi Dror
- Department of Biotechnology and Food Engineering, Technion-Israel Institute of Technology, Haifa, 32000, Israel
| | - Ayelet Fishman
- Department of Biotechnology and Food Engineering, Technion-Israel Institute of Technology, Haifa, 32000, Israel
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85
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Zhou L, Liu X, Ji J, Zhang Y, Hu X, Lin L, Feng X. Enantioselective Baeyer–Villiger Oxidation: Desymmetrization of Meso Cyclic Ketones and Kinetic Resolution of Racemic 2-Arylcyclohexanones. J Am Chem Soc 2012; 134:17023-6. [DOI: 10.1021/ja309262f] [Citation(s) in RCA: 135] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Lin Zhou
- Key Laboratory of Green Chemistry & Technology, Ministry of Education, College of Chemistry, Sichuan University, Chengdu 610064, P. R. China
| | - Xiaohua Liu
- Key Laboratory of Green Chemistry & Technology, Ministry of Education, College of Chemistry, Sichuan University, Chengdu 610064, P. R. China
| | - Jie Ji
- Key Laboratory of Green Chemistry & Technology, Ministry of Education, College of Chemistry, Sichuan University, Chengdu 610064, P. R. China
| | - Yuheng Zhang
- Key Laboratory of Green Chemistry & Technology, Ministry of Education, College of Chemistry, Sichuan University, Chengdu 610064, P. R. China
| | - Xiaolei Hu
- Key Laboratory of Green Chemistry & Technology, Ministry of Education, College of Chemistry, Sichuan University, Chengdu 610064, P. R. China
| | - Lili Lin
- Key Laboratory of Green Chemistry & Technology, Ministry of Education, College of Chemistry, Sichuan University, Chengdu 610064, P. R. China
| | - Xiaoming Feng
- Key Laboratory of Green Chemistry & Technology, Ministry of Education, College of Chemistry, Sichuan University, Chengdu 610064, P. R. China
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86
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Saß S, Kadow M, Geitner K, Thompson ML, Talmann L, Böttcher D, Schmidt M, Bornscheuer UT. A high-throughput assay method to quantify Baeyer–Villiger monooxygenase activity. Tetrahedron 2012. [DOI: 10.1016/j.tet.2012.05.098] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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87
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Reetz MT. Laboratory evolution of stereoselective enzymes as a means to expand the toolbox of organic chemists. Tetrahedron 2012. [DOI: 10.1016/j.tet.2012.05.093] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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88
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Zhang ZG, Parra LP, Reetz MT. Protein Engineering of Stereoselective Baeyer-Villiger Monooxygenases. Chemistry 2012; 18:10160-72. [DOI: 10.1002/chem.201202163] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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89
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Siloto RM, Weselake RJ. Site saturation mutagenesis: Methods and applications in protein engineering. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2012. [DOI: 10.1016/j.bcab.2012.03.010] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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90
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Balke K, Kadow M, Mallin H, Sass S, Bornscheuer UT. Discovery, application and protein engineering of Baeyer-Villiger monooxygenases for organic synthesis. Org Biomol Chem 2012; 10:6249-65. [PMID: 22733152 DOI: 10.1039/c2ob25704a] [Citation(s) in RCA: 109] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Baeyer-Villiger monooxygenases (BVMOs) are useful enzymes for organic synthesis as they enable the direct and highly regio- and stereoselective oxidation of ketones to esters or lactones simply with molecular oxygen. This contribution covers novel concepts such as searching in protein sequence databases using distinct motifs to discover new Baeyer-Villiger monooxygenases as well as high-throughput assays to facilitate protein engineering in order to improve BVMOs with respect to substrate range, enantioselectivity, thermostability and other properties. Recent examples for the application of BVMOs in synthetic organic synthesis illustrate the broad potential of these biocatalysts. Furthermore, methods to facilitate the more efficient use of BVMOs in organic synthesis by applying e.g. improved cofactor regeneration, substrate feed and in situ product removal or immobilization are covered in this perspective.
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Affiliation(s)
- Kathleen Balke
- Institute of Biochemistry, Dept of Biotechnology & Enzyme Catalysis, Greifswald University, Felix-Hausdorff-Str. 4, 17487 Greifswald, Germany
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91
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Yachnin BJ, Sprules T, McEvoy MB, Lau PCK, Berghuis AM. The substrate-bound crystal structure of a Baeyer-Villiger monooxygenase exhibits a Criegee-like conformation. J Am Chem Soc 2012; 134:7788-95. [PMID: 22506764 PMCID: PMC3349289 DOI: 10.1021/ja211876p] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
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The Baeyer–Villiger monooxygenases (BVMOs) are
a family of bacterial flavoproteins that catalyze the synthetically
useful Baeyer–Villiger oxidation reaction. This involves the
conversion of ketones into esters or cyclic ketones into lactones
by introducing an oxygen atom adjacent to the carbonyl group. The
BVMOs offer exquisite regio- and enantiospecificity while acting on
a wide range of substrates. They use only NADPH and oxygen as cosubstrates,
and produce only NADP+ and water as byproducts, making
them environmentally attractive for industrial purposes. Here, we
report the first crystal structure of a BVMO, cyclohexanone monooxygenase
(CHMO) from Rhodococcus sp. HI-31 in complex with
its substrate, cyclohexanone, as well as NADP+ and FAD,
to 2.4 Å resolution. This structure shows a drastic rotation
of the NADP+ cofactor in comparison to previously reported
NADP+-bound structures, as the nicotinamide moiety is no
longer positioned above the flavin ring. Instead, the substrate, cyclohexanone,
is found at this location, in an appropriate position for the formation
of the Criegee intermediate. The rotation of NADP+ permits
the substrate to gain access to the reactive flavin peroxyanion intermediate
while preventing it from diffusing out of the active site. The structure
thus reveals the conformation of the enzyme during the key catalytic
step. CHMO is proposed to undergo a series of conformational changes
to gradually move the substrate from the solvent, via binding in a
solvent excluded pocket that dictates the enzyme’s chemospecificity,
to a location above the flavin–peroxide adduct where catalysis
occurs.
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Affiliation(s)
- Brahm J Yachnin
- Department of Biochemistry, McGill University, 3649 Promenade Sir William Osler, Bellini Pavilion, Room 466, Montreal, QC, Canada H3G 0B1
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92
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Gumulya Y, Sanchis J, Reetz MT. Many Pathways in Laboratory Evolution Can Lead to Improved Enzymes: How to Escape from Local Minima. Chembiochem 2012; 13:1060-6. [DOI: 10.1002/cbic.201100784] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2011] [Indexed: 12/29/2022]
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Leisch H, Shi R, Grosse S, Morley K, Bergeron H, Cygler M, Iwaki H, Hasegawa Y, Lau PCK. Cloning, Baeyer-Villiger biooxidations, and structures of the camphor pathway 2-oxo-Δ(3)-4,5,5-trimethylcyclopentenylacetyl-coenzyme A monooxygenase of Pseudomonas putida ATCC 17453. Appl Environ Microbiol 2012; 78:2200-12. [PMID: 22267661 PMCID: PMC3302634 DOI: 10.1128/aem.07694-11] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2011] [Accepted: 01/10/2012] [Indexed: 11/20/2022] Open
Abstract
A dimeric Baeyer-Villiger monooxygenase (BVMO) catalyzing the lactonization of 2-oxo-Δ(3)-4,5,5-trimethylcyclopentenylacetyl-coenzyme A (CoA), a key intermediate in the metabolism of camphor by Pseudomonas putida ATCC 17453, had been initially characterized in 1983 by Ougham and coworkers (H. J. Ougham, D. G. Taylor, and P. W. Trudgill, J. Bacteriol. 153:140-152, 1983). Here we cloned and overexpressed the 2-oxo-Δ(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase (OTEMO) in Escherichia coli and determined its three-dimensional structure with bound flavin adenine dinucleotide (FAD) at a 1.95-Å resolution as well as with bound FAD and NADP(+) at a 2.0-Å resolution. OTEMO represents the first homodimeric type 1 BVMO structure bound to FAD/NADP(+). A comparison of several crystal forms of OTEMO bound to FAD and NADP(+) revealed a conformational plasticity of several loop regions, some of which have been implicated in contributing to the substrate specificity profile of structurally related BVMOs. Substrate specificity studies confirmed that the 2-oxo-Δ(3)-4,5,5-trimethylcyclopentenylacetic acid coenzyme A ester is preferred over the free acid. However, the catalytic efficiency (k(cat)/K(m)) favors 2-n-hexyl cyclopentanone (4.3 × 10(5) M(-1) s(-1)) as a substrate, although its affinity (K(m) = 32 μM) was lower than that of the CoA-activated substrate (K(m) = 18 μM). In whole-cell biotransformation experiments, OTEMO showed a unique enantiocomplementarity to the action of the prototypical cyclohexanone monooxygenase (CHMO) and appeared to be particularly useful for the oxidation of 4-substituted cyclohexanones. Overall, this work extends our understanding of the molecular structure and mechanistic complexity of the type 1 family of BVMOs and expands the catalytic repertoire of one of its original members.
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Affiliation(s)
- Hannes Leisch
- Biotechnology Research Institute, National Research Council Canada, Montreal, Quebec, Canada
| | - Rong Shi
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada
| | - Stephan Grosse
- Biotechnology Research Institute, National Research Council Canada, Montreal, Quebec, Canada
| | - Krista Morley
- Biotechnology Research Institute, National Research Council Canada, Montreal, Quebec, Canada
| | - Hélène Bergeron
- Biotechnology Research Institute, National Research Council Canada, Montreal, Quebec, Canada
| | - Miroslaw Cygler
- Biotechnology Research Institute, National Research Council Canada, Montreal, Quebec, Canada
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada
| | - Hiroaki Iwaki
- Department of Life Science and Biotechnology and ORDIST, Kansai University, Suita, Osaka, Japan
| | - Yoshie Hasegawa
- Department of Life Science and Biotechnology and ORDIST, Kansai University, Suita, Osaka, Japan
| | - Peter C. K. Lau
- Biotechnology Research Institute, National Research Council Canada, Montreal, Quebec, Canada
- Departments of Chemistry and Microbiology & Immunology, McGill University, Montreal, Quebec, Canada, and FRQNT Centre in Green Chemistry and Catalysis, Montreal, Quebec, Canada
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94
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Feng X, Sanchis J, Reetz MT, Rabitz H. Enhancing the efficiency of directed evolution in focused enzyme libraries by the adaptive substituent reordering algorithm. Chemistry 2012; 18:5646-54. [PMID: 22434591 DOI: 10.1002/chem.201103811] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2011] [Indexed: 11/11/2022]
Abstract
Directed evolution is a broadly successful strategy for protein engineering in the quest to enhance the stereoselectivity, activity, and thermostability of enzymes. To increase the efficiency of directed evolution based on iterative saturation mutagenesis, the adaptive substituent reordering algorithm (ASRA) is introduced here as an alternative to traditional quantitative structure-activity relationship (QSAR) methods for identifying potential protein mutants with desired properties from minimal sampling of focused libraries. The operation of ASRA depends on identifying the underlying regularity of the protein property landscape, allowing it to make predictions without explicit knowledge of the structure-property relationships. In a proof-of-principle study, ASRA identified all or most of the best enantioselective mutants among the synthesized epoxide hydrolase from Aspergillus niger, in the absence of peptide seeds with high E-values. ASRA even revealed a laboratory error from irregularities of the reordered E-value landscape alone.
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Affiliation(s)
- Xiaojiang Feng
- Department of Chemistry, Princeton University, New Jersey 08544, USA
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95
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Sandström AG, Wikmark Y, Engström K, Nyhlén J, Bäckvall JE. Combinatorial reshaping of the Candida antarctica lipase A substrate pocket for enantioselectivity using an extremely condensed library. Proc Natl Acad Sci U S A 2012; 109:78-83. [PMID: 22178758 PMCID: PMC3252943 DOI: 10.1073/pnas.1111537108] [Citation(s) in RCA: 99] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A highly combinatorial structure-based protein engineering method for obtaining enantioselectivity is reported that results in a thorough modification of the substrate binding pocket of Candida antarctica lipase A (CALA). Nine amino acid residues surrounding the entire pocket were simultaneously mutated, contributing to a reshaping of the substrate pocket to give increased enantioselectivity and activity for a sterically demanding substrate. This approach seems to be powerful for developing enantioselectivity when a complete reshaping of the active site is required. Screening toward ibuprofen ester 1, a substrate for which previously used methods had failed, gave variants with a significantly increased enantioselectivity and activity. Wild-type CALA has a moderate activity with an E value of only 3.4 toward this substrate. The best variant had an E value of 100 and it also displayed a high activity. The variation at each mutated position was highly reduced, comprising only the wild type and an alternative residue, preferably a smaller one with similar properties. These minimal binary variations allow for an extremely condensed protein library. With this highly combinatorial method synergistic effects are accounted for and the protein fitness landscape is explored efficiently.
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Affiliation(s)
- Anders G. Sandström
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Ylva Wikmark
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Karin Engström
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Jonas Nyhlén
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Jan-E. Bäckvall
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, SE-106 91 Stockholm, Sweden
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van Beek HL, Gonzalo GD, Fraaije MW. Blending Baeyer–Villiger monooxygenases: using a robust BVMO as a scaffold for creating chimeric enzymes with novel catalytic properties. Chem Commun (Camb) 2012; 48:3288-90. [DOI: 10.1039/c2cc17656d] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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van Leeuwen JGE, Wijma HJ, Floor RJ, van der Laan JM, Janssen DB. Directed Evolution Strategies for Enantiocomplementary Haloalkane Dehalogenases: From Chemical Waste to Enantiopure Building Blocks. Chembiochem 2011; 13:137-48. [DOI: 10.1002/cbic.201100579] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2011] [Indexed: 01/06/2023]
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98
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Bornscheuer U, Kazlauskas RJ. Survey of protein engineering strategies. CURRENT PROTOCOLS IN PROTEIN SCIENCE 2011; Chapter 26:26.7.1-26.7.14. [PMID: 22045562 DOI: 10.1002/0471140864.ps2607s66] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Protein engineering is altering the structure of a protein to improve or change its properties. This unit summarizes concepts for protein engineering using rational design, directed evolution, and combinations of them. Different strategies are presented for identifying the best mutagenesis method, how to identify desired variants by screening or selection, and examples for successful applications are given. This should enable researchers to choose the most promising tools to solve their protein engineering challenges.
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Affiliation(s)
- Uwe Bornscheuer
- Department of Biotechnology and Enzyme Catalysis, Institute of Biochemistry, Greifswald University, Greifswald, Germany
| | - Romas J Kazlauskas
- Department of Biochemistry, Molecular Biology and Biophysics and the Biotechnology Institute, University of Minnesota, Saint Paul, Minnesota
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99
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Behrens GA, Hummel A, Padhi SK, Schätzle S, Bornscheuer UT. Discovery and Protein Engineering of Biocatalysts for Organic Synthesis. Adv Synth Catal 2011. [DOI: 10.1002/adsc.201100446] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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100
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