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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: 65] [Impact Index Per Article: 6.5] [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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Zilly FE, Acevedo JP, Augustyniak W, Deege A, Häusig UW, Reetz MT. Berichtigung: Tuning a P450 Enzyme for Methane Oxidation. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201309655] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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103
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Zilly FE, Acevedo JP, Augustyniak W, Deege A, Häusig UW, Reetz MT. Corrigendum: Tuning a P450 Enzyme for Methane Oxidation. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/anie.201309655] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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104
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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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105
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Augustyniak W, Wienk H, Boelens R, Reetz MT. ¹H, ¹³C and ¹⁵N resonance assignments of wild-type Bacillus subtilis Lipase A and its mutant evolved towards thermostability. BIOMOLECULAR NMR ASSIGNMENTS 2013; 7:249-252. [PMID: 22996591 DOI: 10.1007/s12104-012-9420-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2012] [Accepted: 09/05/2012] [Indexed: 06/01/2023]
Abstract
Previously, we evolved Lipase A from Bacillus subtilis towards increased thermostability. The resulting mutant retains significant catalytic activity upon heating above 60 °C (and up to 100 °C) and cooling down, whereas wild-type lipase precipitates irreversibly and does not show significant activity in these conditions. Kinetic thermostability of proteins has not been characterized well on the molecular structure level so far, therefore our aim is to study it using NMR spectroscopy. Here, nearly complete (1)H, (13)C and (15)N resonance assignments are reported for wild-type and mutant Lipase A. Chemical shifts were used to predict secondary structure elements of both Lipase A variants.
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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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Polyak I, Reetz MT, Thiel W. Quantum Mechanical/Molecular Mechanical Study on the Enantioselectivity of the Enzymatic Baeyer–Villiger Reaction of 4-Hydroxycyclohexanone. J Phys Chem B 2013; 117:4993-5001. [DOI: 10.1021/jp4018019] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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108
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Roiban GD, Reetz MT. Enzympromiskuität: ein P450-Enzym als Carbentransferkatalysator. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201301083] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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109
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Roiban GD, Reetz MT. Enzyme promiscuity: using a P450 enzyme as a carbene transfer catalyst. Angew Chem Int Ed Engl 2013; 52:5439-40. [PMID: 23592495 DOI: 10.1002/anie.201301083] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2013] [Indexed: 11/10/2022]
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110
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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: 192] [Impact Index Per Article: 17.5] [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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Reetz MT. The Importance of Additive and Non-Additive Mutational Effects in Protein Engineering. Angew Chem Int Ed Engl 2013; 52:2658-66. [DOI: 10.1002/anie.201207842] [Citation(s) in RCA: 132] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2012] [Revised: 12/19/2012] [Indexed: 01/01/2023]
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112
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Wu Q, Soni P, Reetz MT. Laboratory Evolution of Enantiocomplementary Candida antarctica Lipase B Mutants with Broad Substrate Scope. J Am Chem Soc 2013; 135:1872-81. [DOI: 10.1021/ja310455t] [Citation(s) in RCA: 115] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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113
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Zhang ZG, Roiban GD, Acevedo JP, Polyak I, Reetz MT. A New Type of Stereoselectivity in Baeyer-Villiger Reactions: Access toE- andZ-Olefins. Adv Synth Catal 2013. [DOI: 10.1002/adsc.201200759] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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Abstract
Lipases can be efficiently entrapped in the pores of hydrophobic silicates by a simple and cheap sol-gel process in which a mixture of a hydrophobic alkylsilane RSi(OCH3)3 and Si(OCH3)4 is hydrolyzed under basic conditions in the presence of the enzyme. Additives such as isopropanol, polyvinyl alcohol, cyclodextrins, ionic liquids or surfactants enhance the efficiency of this type of lipase-immobilization. The main area of application of these heterogeneous biocatalysts concerns esterification or transesterification in organic solvents, ionic liquids, or supercritical carbon dioxide. Rate enhancements (relative to the traditional use of lipase powders) of several orders of magnitude have been observed, in addition to higher thermal stability. The lipase-immobilizates are particularly useful in the kinetic resolution of chiral esters, enantioselectivity often being higher than what is observed when using the commercial forms of these lipases (powder or classical immobilizates). Thus, due to the low price of sol-gel entrapment, the excellent performance of the lipase-immobilizates, and the ready recyclability, the method is industrially viable.
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Cesarini S, Bofill C, Pastor FJ, Reetz MT, Diaz P. A thermostable variant of P. aeruginosa cold-adapted LipC obtained by rational design and saturation mutagenesis. Process Biochem 2012. [DOI: 10.1016/j.procbio.2012.07.023] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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116
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Agudo R, Roiban GD, Reetz MT. Induced Axial Chirality in Biocatalytic Asymmetric Ketone Reduction. J Am Chem Soc 2012; 135:1665-8. [DOI: 10.1021/ja3092517] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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117
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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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118
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Mitchell EA, Peschiulli A, Lefevre N, Meerpoel L, Maes BUW, Pacchioni G, Mastalerz M, Patra A, Scherf U, Bozzini B, Abyaneh MK, Amati M, Gianoncelli A, Gregoratti L, Kaulich B, Kiskinova M, Zhang ZG, Parra LP, Reetz MT, Loh CCJ, Enders D, Hisaki I, Sasaki T, Tohnai N, Miyata M, Mazzoni R, Salmi M, Zanotti V. Cover Picture: Direct α-Functionalization of Saturated Cyclic Amines / Two-Dimensional Oxides: Multifunctional Materials for Advanced Technologies / Permanent Porous Materials from Discrete Organic Molecules-Towards Ultra-High Surface Areas / Fluorescent. Chemistry 2012. [DOI: 10.1002/chem.201290140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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119
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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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120
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Agudo R, Roiban GD, Reetz MT. Cover Picture: Achieving Regio- and Enantioselectivity of P450-Catalyzed Oxidative CH Activation of Small Functionalized Molecules by Structure-Guided Directed Evolution (ChemBioChem 10/2012). Chembiochem 2012. [DOI: 10.1002/cbic.201290038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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121
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Agudo R, Roiban GD, Reetz MT. Achieving regio- and enantioselectivity of P450-catalyzed oxidative CH activation of small functionalized molecules by structure-guided directed evolution. Chembiochem 2012; 13:1465-73. [PMID: 22711296 DOI: 10.1002/cbic.201200244] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2012] [Indexed: 11/08/2022]
Abstract
Directed evolution of the monooxygenase P450-BM3 utilizing iterative saturation mutagenesis at and near the binding site enables a high degree of both regio- and enantioselectivity in the oxidative hydroxylation of cyclohexene-1-carboxylic acid methyl ester. Wild-type P450-BM3 is 84% regioselective for the allylic 3-position with 34% enantioselectivity in favor of the R alcohol. Mutants enabling R selectivity (>95% ee) or S selectivity (>95% ee) were evolved, while reducing other oxidation products and thus maximizing regioselectivity to >93%. Control of the substrate-to-enzyme ratio is necessary for obtaining optimal and reproducible enantioselectivities, an observation which is important in future protein engineering of these mono-oxygenases. An E. coli strain capable of NADPH regeneration was also engineered, simplifying directed evolution of P450 enzymes in general. These synthetic results set the stage for subsequent stereoselective and stereospecific chemical transformations to form more complex compounds, thereby illustrating the viability of combining genetically altered enzymes as catalysts in organic chemistry with traditional chemical methods.
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Reetz MT. Artificial Metalloenzymes as Catalysts in Stereoselective Diels-Alder Reactions. CHEM REC 2012; 12:391-406. [DOI: 10.1002/tcr.201100043] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2011] [Indexed: 11/05/2022]
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123
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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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124
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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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Augustyniak W, Brzezinska AA, Pijning T, Wienk H, Boelens R, Dijkstra BW, Reetz MT. Biophysical characterization of mutants of Bacillus subtilis lipase evolved for thermostability: factors contributing to increased activity retention. Protein Sci 2012; 21:487-97. [PMID: 22267088 DOI: 10.1002/pro.2031] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2011] [Revised: 12/14/2011] [Accepted: 01/08/2012] [Indexed: 11/10/2022]
Abstract
Previously, Lipase A from Bacillus subtilis was subjected to in vitro directed evolution using iterative saturation mutagenesis, with randomization sites chosen on the basis of the highest B-factors available from the crystal structure of the wild-type (WT) enzyme. This provided mutants that, unlike WT enzyme, retained a large part of their activity after heating above 65 °C and cooling down. Here, we subjected the three best mutants along with the WT enzyme to biophysical and biochemical characterization. Combining thermal inactivation profiles, circular dichroism, X-ray structure analyses and NMR experiments revealed that mutations of surface amino acid residues counteract the tendency of Lipase A to undergo precipitation under thermal stress. Reduced precipitation of the unfolding intermediates rather than increased conformational stability of the evolved mutants seems to be responsible for the activity retention.
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