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Van Tassel L, Moilanen A, Ruddock LW. Efficient production of wild-type lipase B from Candida antarctica in the cytoplasm of Escherichia coli. Protein Expr Purif 2020; 165:105498. [DOI: 10.1016/j.pep.2019.105498] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 09/04/2019] [Accepted: 09/11/2019] [Indexed: 10/26/2022]
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2
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Santos YLDL, Chew-Fajardo YL, Brault G, Doucet N. Dissecting the evolvability landscape of the CalB active site toward aromatic substrates. Sci Rep 2019; 9:15588. [PMID: 31666622 PMCID: PMC6821916 DOI: 10.1038/s41598-019-51940-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Accepted: 10/07/2019] [Indexed: 01/17/2023] Open
Abstract
A key event in the directed evolution of enzymes is the systematic use of mutagenesis and selection, a process that can give rise to mutant libraries containing millions of protein variants. To this day, the functional analysis and identification of active variants among such high numbers of mutational possibilities is not a trivial task. Here, we describe a combinatorial semi-rational approach to partly overcome this challenge and help design smaller and smarter mutant libraries. By adapting a liquid medium transesterification assay in organic solvent conditions with a combination of virtual docking, iterative saturation mutagenesis, and residue interaction network (RIN) analysis, we engineered lipase B from P. antarctica (CalB) to improve enzyme recognition and activity against the bulky aromatic substrates and flavoring agents methyl cinnamate and methyl salicylate. Substrate-imprinted docking was used to target active-site positions involved in enzyme-substrate and enzyme-product complexes, in addition to identifying 'hot spots' most likely to yield active variants. This iterative semi-rational design strategy allowed selection of CalB variants exhibiting increased activity in just two rounds of site-saturation mutagenesis. Beneficial replacements were observed by screening only 0.308% of the theoretical library size, illustrating how semi-rational approaches with targeted diversity can quickly facilitate the discovery of improved activity variants relevant to a number of biotechnological applications.
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Affiliation(s)
- Yossef López de Los Santos
- Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique (INRS), Université du Québec, 531 Boulevard des Prairies, Laval, QC, H7V 1B7, Canada
| | - Ying Lian Chew-Fajardo
- Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique (INRS), Université du Québec, 531 Boulevard des Prairies, Laval, QC, H7V 1B7, Canada
| | - Guillaume Brault
- Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique (INRS), Université du Québec, 531 Boulevard des Prairies, Laval, QC, H7V 1B7, Canada
| | - Nicolas Doucet
- Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique (INRS), Université du Québec, 531 Boulevard des Prairies, Laval, QC, H7V 1B7, Canada.
- PROTEO, the Québec Network for Research on Protein Function, Engineering, and Applications, 1045 Avenue de la Médecine, Université Laval, Quebec City, QC, G1V 0A6, Canada.
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3
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da Silva TS, Campos SK, de Oliveira AR, Piovan L. An unexpected inversion of CAL-B enantiopreference based on substrate engineering of 2-bromoesters: Effect of (R)-1-phenylethyl moiety. ACTA ACUST UNITED AC 2016. [DOI: 10.1016/j.molcatb.2017.02.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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4
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Tsai SW. Enantiopreference of Candida antarctica lipase B toward carboxylic acids: Substrate models and enantioselectivity thereof. ACTA ACUST UNITED AC 2016. [DOI: 10.1016/j.molcatb.2014.07.010] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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5
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Sun H, Wang H, Gao W, Chen L, Wu K, Wei D. Directed evolution of nitrilase PpL19 from Pseudomonas psychrotolerans L19 and identification of enantiocomplementary mutants toward mandelonitrile. Biochem Biophys Res Commun 2015; 468:820-5. [PMID: 26577409 DOI: 10.1016/j.bbrc.2015.11.038] [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: 10/23/2015] [Accepted: 11/07/2015] [Indexed: 10/22/2022]
Abstract
Nitrilase PpL19 from Pseudomonas psychrotolerans L19 can hydrolyze racemic mandelonitrile to (S)-mandelic acid with an enantiomeric excess (ee) value of 52.7%. In this study, random mutagenesis combined with site-directed mutagenesis was performed to identify the key residues responsible for nitrilase enantioselectivity. Five enzyme mutants exhibiting distinct selectivity were generated and four "hot spots" (M113, R128, A136, and I168) responsible for enantioselectivity toward mandelonitrile were identified and characterized. Furthermore, through saturation mutagenesis, positions 113 and 128 were confirmed to substantially influence the enantioselectivity of PpL19, and certain replacements of the methionine at position 113, in particular, were found to reverse the enantioselectivity of PpL19 from S- to R-selectivity. Two other single mutants of the enzyme, PpL19-A136Y and -I168Y, also showed reversed selectivity and preferentially produced (R)-mandelic acid (ee values: 66.7% and 74.3%, respectively). By combining the beneficial mutations, two enantiocomplementary nitrilase mutants, PpL19-LH and PpL19-GYY, were created, which exhibited high S- and R-selectivity toward mandelonitrile, respectively: PpL19-LH showed the highest S-selectivity toward mandelonitrile ever reported (91.1% ee), and, notably, the PpL19-GYY mutant was identified to be highly R-selective (90.1% ee) and thus an unexpected enantiocomplementary mutant for mandelonitrile.
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Affiliation(s)
- Huihui Sun
- State Key Laboratory of Bioreactor Engineering, New World Institute of Biotechnology, East China University of Science and Technology, Shanghai 200237, PR China
| | - Hualei Wang
- State Key Laboratory of Bioreactor Engineering, New World Institute of Biotechnology, East China University of Science and Technology, Shanghai 200237, PR China.
| | - Wenyuan Gao
- State Key Laboratory of Bioreactor Engineering, New World Institute of Biotechnology, East China University of Science and Technology, Shanghai 200237, PR China
| | - Lifeng Chen
- State Key Laboratory of Bioreactor Engineering, New World Institute of Biotechnology, East China University of Science and Technology, Shanghai 200237, PR China
| | - Kai Wu
- State Key Laboratory of Bioreactor Engineering, New World Institute of Biotechnology, East China University of Science and Technology, Shanghai 200237, PR China
| | - Dongzhi Wei
- State Key Laboratory of Bioreactor Engineering, New World Institute of Biotechnology, East China University of Science and Technology, Shanghai 200237, PR China.
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6
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Gu J, Ye L, Guo F, Lv X, Lu W, Yu H. Improved apparent enantioselectivity of a hydrolase by sequential hydrolysis and racemization. Tetrahedron Lett 2015. [DOI: 10.1016/j.tetlet.2014.12.139] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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7
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Analytical characterization and purification of a commercial extract of enzymes: a case study. Colloids Surf B Biointerfaces 2014; 121:11-20. [PMID: 24929523 DOI: 10.1016/j.colsurfb.2014.05.029] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Revised: 03/31/2014] [Accepted: 05/17/2014] [Indexed: 11/22/2022]
Abstract
This paper presents a rational strategy to identify and quantify the components of a commercial extract of the lipase B of Candida antarctica that can be extended to the analytical investigation of other crude extracts of enzymes. These information provided the fundamental knowledge for the development of a methodology to obtain highly pure and catalytically active CALB enzyme. The commercial extract Lipozyme(®) was subjected to a series of analytical techniques that allowed determining the presence of a non-soluble fraction; nucleic acids; benzoate and sorbate species and a mixture of three proteins. Particularly, it is worth noticing that the Bradford assay using CALB as standard instead of BSA proved to be a more reliable and accurate methodology to quantify the protein content of the assayed enzymatic samples. Size exclusion chromatography coupled with anionic exchange chromatography using a non-conventional, easy to remove buffer system such as ammonia-ammonium acetate afforded a sample that retains 47% of the proteins (being CALB the only enzymatic component of the purified sample) with a hydrolytic activity higher than the crude extract.
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8
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Lichtor PA, Miller SJ. Experimental lineage and functional analysis of a remotely directed peptide epoxidation catalyst. J Am Chem Soc 2014; 136:5301-8. [PMID: 24690108 PMCID: PMC4333582 DOI: 10.1021/ja410567a] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
![]()
We
describe mechanistic investigations of a catalyst (1)
that leads to selective epoxidation of farnesol at the 6,7-position,
remote from the hydroxyl directing group. The experimental lineage
of peptide 1 and a number of resin-bound peptide analogues
were examined to reveal the importance of four N-terminal residues.
We examined the selectivity of truncated analogues to find that a
trimer is sufficient to furnish the remote selectivity. Both 1D and
2D 1H NMR studies were used to determine possible catalyst
conformations, culminating in proposed models showing possible interactions
of farnesol with a protected Thr side chain and backbone NH. The models
were used to rationalize the selectivity of a modified catalyst (17) for the 6,7-position relative to an ether moiety in two
related substrates.
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Affiliation(s)
- Phillip A Lichtor
- Department of Chemistry, Yale University , P.O. Box 208107, New Haven, Connecticut 06520, United States
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9
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Huang YK, Tsai SW. Kinetic and thermodynamic analysis of Candida antarctica lipase B-catalyzed alcoholytic resolution of (R,S)-β-butyrolactone in organic solvents. Appl Microbiol Biotechnol 2013; 98:621-8. [DOI: 10.1007/s00253-013-5331-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2013] [Revised: 09/29/2013] [Accepted: 10/10/2013] [Indexed: 11/29/2022]
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10
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Qin B, Liang P, Jia X, Zhang X, Mu M, Wang XY, Ma GZ, Jin DN, You S. Directed evolution of Candida antarctica lipase B for kinetic resolution of profen esters. CATAL COMMUN 2013. [DOI: 10.1016/j.catcom.2013.03.040] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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11
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Campillo-Alvarado G, Tovar-Miranda R. Recent advances and applications of the lipolytic activity of Carica papaya latex. ACTA ACUST UNITED AC 2013. [DOI: 10.1016/j.molcatb.2013.01.015] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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12
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Hamberg A, Magnusson AO, Hu FJ, Hult K. Selective Monoacylation of Diols by Substrate Assisted Catalysis in T40ACandida antarcticaLipase B. ChemCatChem 2013. [DOI: 10.1002/cctc.201200560] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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13
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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]
Affiliation(s)
- Qi Wu
- Department of Chemistry, Zhejiang University, Hangzhou, 310027, People’s
Republic of China
- Max-Planck-Institut
für
Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der
Ruhr, Germany
| | - Pankaj Soni
- Max-Planck-Institut
für
Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der
Ruhr, Germany
- CSIR-Institute
of Microbial Technology,
Chandigarh, 160036, India
| | - 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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14
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Köhler J, Wünsch B. Conversion of a pentane-1,3,5-triol derivative using lipases as chiral catalysts and possible function of the lid for the regulation of substrate selectivity and enantioselectivity. BIOCATAL BIOTRANSFOR 2012. [DOI: 10.3109/10242422.2012.661726] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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15
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Carrasco N, Hiller DA, Strobel SA. Minimal Transition State Charge Stabilization of the Oxyanion during Peptide Bond Formation by the Ribosome. Biochemistry 2011; 50:10491-8. [DOI: 10.1021/bi201290s] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Nicolas Carrasco
- Departments of Molecular Biophysics & Biochemistry and Chemistry, Yale University, 260 Whitney Ave., New Haven, Connecticut 06520-81114, United States
| | - David A. Hiller
- Departments of Molecular Biophysics & Biochemistry and Chemistry, Yale University, 260 Whitney Ave., New Haven, Connecticut 06520-81114, United States
| | - Scott A. Strobel
- Departments of Molecular Biophysics & Biochemistry and Chemistry, Yale University, 260 Whitney Ave., New Haven, Connecticut 06520-81114, United States
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16
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Juhl PB, Doderer K, Hollmann F, Thum O, Pleiss J. Engineering of Candida antarctica lipase B for hydrolysis of bulky carboxylic acid esters. J Biotechnol 2010; 150:474-80. [PMID: 20887757 DOI: 10.1016/j.jbiotec.2010.09.951] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2010] [Revised: 09/17/2010] [Accepted: 09/21/2010] [Indexed: 10/19/2022]
Abstract
Candida antarctica lipase B (CALB) is a widely used biocatalyst with high activity and specificity for a wide range of primary and secondary alcohols. However, the range of converted carboxylic acids is more narrow and mainly limited to unbranched fatty acids. To further broaden the biotechnological applications of CALB it is of interest to expand the range of converted carboxylic acid and extend it to carboxylic acids that are branched or substituted in close proximity of the carboxyl group. An in silico library of 2400 CALB variants was built and screened in silico by substrate-imprinted docking, a four step docking procedure. First, reaction intermediates of putative substrates are covalently docked into enzyme active sites. Second, the geometry of the resulting enzyme-substrate complex is optimized. Third, the substrate is removed from the complex and then docked again into the optimized structure. Fourth, the resulting substrate poses are rated by geometric filter criteria as productive or non-productive poses. Eleven enzyme variants resulting from the in silico screening were expressed in Escherichia coli BL21 and measured in the hydrolysis of two branched fatty acid esters, isononanoic acid ethyl ester and 2-ethyl hexanoic acid ethyl esters. Five variants showed an initial increase in activity. The variant with the highest wet mass activity (T138S) was purified and further characterized. It showed a 5-fold increase in hydrolysis of isononanoic acid ethyl ester, but not toward sterically more demanding 2-ethyl hexanoic acid ethyl ester.
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Affiliation(s)
- P B Juhl
- Institute of Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany.
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17
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Marton Z, Léonard-Nevers V, Syrén PO, Bauer C, Lamare S, Hult K, Tranc V, Graber M. Mutations in the stereospecificity pocket and at the entrance of the active site of Candida antarctica lipase B enhancing enzyme enantioselectivity. ACTA ACUST UNITED AC 2010. [DOI: 10.1016/j.molcatb.2010.01.007] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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18
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Rodríguez-Mata M, García-Urdiales E, Gotor-Fernández V, Gotor V. Stereoselective Chemoenzymatic Preparation of β-Amino Esters: Molecular Modelling Considerations in Lipase-Mediated Processes and Application to the Synthesis of (S)-Dapoxetine. Adv Synth Catal 2010. [DOI: 10.1002/adsc.200900676] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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19
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Busto E, Gotor-Fernández V, Gotor V. Hydrolases: catalytically promiscuous enzymes for non-conventional reactions in organic synthesis. Chem Soc Rev 2010; 39:4504-23. [DOI: 10.1039/c003811c] [Citation(s) in RCA: 246] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Meriläinen G, Poikela V, Kursula P, Wierenga RK. The thiolase reaction mechanism: the importance of Asn316 and His348 for stabilizing the enolate intermediate of the Claisen condensation. Biochemistry 2009; 48:11011-25. [PMID: 19842716 DOI: 10.1021/bi901069h] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The biosynthetic thiolase catalyzes a Claisen condensation reaction between acetyl-CoA and the enzyme acetylated at Cys89. Two oxyanion holes facilitate this catalysis: oxyanion hole I stabilizes the enolate intermediate generated from acetyl-CoA, whereas oxyanion hole II stabilizes the tetrahedral intermediate of the acetylated enzyme. The latter intermediate is formed when the alpha-carbanion of acetyl-CoA enolate reacts with the carbonyl carbon of acetyl-Cys89, after which C-C bond formation is completed. Oxyanion hole II is made of two main chain peptide NH groups, whereas oxyanion hole I is formed by a water molecule (Wat82) and NE2(His348). Wat82 is anchored in the active site by an optimal set of hydrogen bonding interactions, including a hydrogen bond to ND2(Asn316). Here, the importance of Asn316 and His348 for catalysis has been studied; in particular, the properties of the N316D, N316A, N316H, H348A, and H348N variants have been determined. For the N316D variant, no activity could be detected. For each of the remaining variants, the k(cat)/K(m) value for the Claisen condensation catalysis is reduced by a factor of several hundred, whereas the thiolytic degradation catalysis is much less affected. The crystal structures of the variants show that the structural changes in the active site are minimal. Our studies confirm that oxyanion hole I is critically important for the condensation catalysis. Removing either one of the hydrogen bond donors causes the loss of at least 3.4 kcal/mol of transition state stabilization. It appears that in the thiolytic degradation direction, oxyanion hole I is not involved in stabilizing the transition state of its rate limiting step. However, His348 has a dual role in the catalytic cycle, contributing to oxyanion hole I and activating Cys89. The analysis of the hydrogen bonding interactions in the very polar catalytic cavity shows the importance of two conserved water molecules, Wat82 and Wat49, for the formation of oxyanion hole I and for influencing the reactivity of the catalytic base, Cys378, respectively. Cys89, Asn316, and His348 form the CNH-catalytic triad of the thiolase superfamily. Our findings are also discussed in the context of the importance of this triad for the catalytic mechanism of other enzymes of the thiolase superfamily.
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Affiliation(s)
- Gitte Meriläinen
- Department of Biochemistry, University of Oulu, P.O. Box 3000, 90014 Oulu, Finland
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21
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Molecular Basis for the Stereoselective Ammoniolysis ofN-Alkyl Aziridine-2-Carboxylates Catalyzed byCandida antarcticaLipase B. Chembiochem 2009; 10:2213-22. [DOI: 10.1002/cbic.200900343] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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22
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García-Urdiales E, Ríos-Lombardía N, Mangas-Sánchez J, Gotor-Fernández V, Gotor V. Influence of the Nucleophile on the Candida antarctica Lipase B-Catalysed Resolution of a Chiral Acyl Donor. Chembiochem 2009; 10:1830-8. [DOI: 10.1002/cbic.200900204] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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23
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Wang PY, Tsai SW. Modification of enzyme surface negative charges via covalent immobilization for tailoring the activity and enantioselectivity. J Taiwan Inst Chem Eng 2009. [DOI: 10.1016/j.jtice.2008.12.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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24
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Skjøt M, De Maria L, Chatterjee R, Svendsen A, Patkar SA, Østergaard PR, Brask J. Understanding the Plasticity of the α/β Hydrolase Fold: Lid Swapping on theCandida antarcticaLipase B Results in Chimeras with Interesting Biocatalytic Properties. Chembiochem 2009; 10:520-7. [DOI: 10.1002/cbic.200800668] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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25
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Nyhlén J, Martín-Matute B, Sandström AG, Bocola M, Bäckvall JE. Influence of delta-functional groups on the enantiorecognition of secondary alcohols by Candida antarctica lipase B. Chembiochem 2008; 9:1968-74. [PMID: 18655082 DOI: 10.1002/cbic.200800036] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The selectivity of acetylation of delta-functionalized secondary alcohols catalyzed by Candida antarctica lipase B has been examined by molecular dynamics. The results from the simulation show that a delta-alcohol functionality forms a hydrogen bond with the carbonyl group of Thr 40. This interaction stabilizes the tetrahedral intermediate and thus leads to selective acetylation of the R enantiomer. A stabilizing interaction of the delta-(R)-acetoxy group with the peptide NH of alanine 282 was also observed. No stabilizing interaction could be found for the delta-keto functionality, and it is proposed that this is the reason for the experimentally observed decrease in enantioselectivity. From these results, it was hypothesized that the enantioselectivity could be restored by mutating the alanine in position 281 for serine. The mutation was made experimentally, and the results show that the E value increased from 9 to 120.
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Affiliation(s)
- Jonas Nyhlén
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, 106 91 Stockholm, Sweden
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26
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Wang PY, Tsai SW, Chen TL. Improvements of enzyme activity and enantioselectivity via combined substrate engineering and covalent immobilization. Biotechnol Bioeng 2008; 101:460-9. [PMID: 18435484 DOI: 10.1002/bit.21916] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Esterases, lipases, and serine proteases have been applied as versatile biocatalysts for preparing a variety of chiral compounds in industry via the kinetic resolution of their racemates. In order to meet this requirement, three approaches of enzyme engineering, medium engineering, and substrate engineering are exploited to improve the enzyme activity and enantioselectivity. With the hydrolysis of (R,S)-mandelates in biphasic media consisting of isooctane and pH 6 buffer at 55 degrees C as the model system, the strategy of combined substrate engineering and covalent immobilization leads to an increase of enzyme activity and enantioselectivity from V(S)/(E(t)) = 1.62 mmol/h g and V(S)/V(R) = 43.6 of (R,S)-ethyl mandelate (1) for a Klebsiella oxytoca esterase (named as SNSM-87 from the producer) to 16.7 mmol/h g and 867 of (R,S)-2-methoxyethyl mandelate (4) for the enzyme immobilized on Eupergit C 250L. The analysis is then extended to other (R,S)-2-hydroxycarboxylic acid esters, giving improvements of the enzyme performance from V(S)/(E(t)) = 1.56 mmol/h g and V(S)/V(R) = 41.9 of (R,S)-ethyl 3-chloromandelate (9) for the free esterase to 39.4 mmol/h g and 401 of (R,S)-2-methoxyethyl 3-chloromandelate (16) for the immobilized enzyme, V(S)/(E(t)) = 5.46 mmol/h g and V(S)/V(R) = 8.27 of (R,S)-ethyl 4-chloromandelate (10) for free SNSM-87 to 33.5 mmol/h g and 123 of (R,S)-methyl 4-chloromandelate (14) for the immobilized enzyme, as well as V(S)/(E(t)) = 3.0 mmol/h g and V(S)/V(R) = 7.94 of (R,S)-ethyl 3-phenyllactate (11) for the free esterase to 40.7 mmol/h g and 158 of (R,S)-2-methoxyethyl 3-phenyllactate (18) for the immobilized enzyme. The great enantioselectivty enhancement is rationalized from the alteration of ionization constants of imidazolium moiety of catalytic histidine for both enantiomers and conformation distortion of active site after the covalent immobilization, as well as the selection of leaving alcohol moiety via substrate engineering approach.
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Affiliation(s)
- Pei-Yun Wang
- Institute of Biochemical and Biomedical Engineering, Chang Gung University, Kwei-Shan, Tao-Yuan 33302, Taiwan
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27
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Svedendahl M, Carlqvist P, Branneby C, Allnér O, Frise A, Hult K, Berglund P, Brinck T. Direct Epoxidation inCandida antarcticaLipase B Studied by Experiment and Theory. Chembiochem 2008; 9:2443-51. [DOI: 10.1002/cbic.200800318] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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28
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Kanca ÜM, Van Buijtenen J, Van As BAC, Korevaar PA, Vekemans JAJM, Palmans ARA, Meijer EW. Iterative tandem catalysis of racemic AB monomers. ACTA ACUST UNITED AC 2008. [DOI: 10.1002/pola.22605] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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29
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Wang PY, Chen TL, Tsai SW, Kroutil W. Hydrolytic resolution of (R,S)-2-hydroxycarboxylic acid esters in biphasic media: Implication for rate-limiting formation or breakdown of tetrahedral intermediates in acylation step. Biotechnol Bioeng 2007; 98:30-8. [PMID: 17323376 DOI: 10.1002/bit.21394] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
A thermally stable esterase (SNSM-87) from Klebsiella oxytoca is explored as an enantioselective biocatalyst for the hydrolytic resolution of (R,S)-2-hydroxycarboxylic acid esters in biphasic media, where the best methyl esters possessing the highest enantioselectivity and reactivity are selected and elucidated in terms of the structure-enantioselectivity correlations and substrate partitioning in the aqueous phase. With (R,S)-2-chloromandelates as the model substrates, an expanded Michaelis-Menten mechanism for the rate-limiting acylation step is adopted for the kinetic analysis. The Brønsted slope of 25.7 for the fast-reacting (S)-2-chloromandelates containing a difficult leaving alcohol moiety, as well as that of 4.13 for the slow-reacting (R)-2-chloromandelates in the whole range of leaving alcohol moieties, indicates that the breakdown of tetrahedral intermediates to acyl-enzyme intermediates is rate-limiting. However, the rate-limiting step shifts to the formation of tetrahedral intermediates for the (S)-2-chloromandelates containing an easy leaving alcohol moiety, and leads to an optimal enantioselectivity for the methyl ester substrate.
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Affiliation(s)
- Pei-Yun Wang
- Department of Chemical Engineering, National Cheng Kung University, Tainan, Taiwan
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30
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31
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Ivancic M, Valinger G, Gruber K, Schwab H. Inverting enantioselectivity of Burkholderia gladioli esterase EstB by directed and designed evolution. J Biotechnol 2007; 129:109-22. [PMID: 17147964 DOI: 10.1016/j.jbiotec.2006.10.007] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2006] [Revised: 09/29/2006] [Accepted: 10/09/2006] [Indexed: 11/22/2022]
Abstract
Esterase EstB from Burkholderia gladioli, showing moderate S-enantioselectivity (E(S)=6.1) in the hydrolytic kinetic resolution of methyl-beta-hydroxyisobutyrate, was subjected to directed evolution in order to reverse its enantioselectivity. After one round of ep-PCR, saturation mutagenesis and high-throughput screening, it was found that different mutations at position 152 (in the vicinity of the active site) increase, decrease and even reverse the natural enantioselectivity of this enzyme. The newly created R-enantioselectivity of the esterase mutein (E(Rapp)=1.5) has been further enhanced by a designed evolution strategy involving random mutations close to the active site. Based on the three-dimensional structure nineteen amino acid residues have been selected as mutation sites for saturation mutagenesis. Mutations at three sites (135, 253 and 351) were found to increase R-enantioselectivity. Successive rounds of saturation mutagenesis at these "hot spots" resulted in an increase in R-enantioselectivity from E(Rapp)=1.5 for the parent mutant to E(Rapp)=28.9 for the best variant which carried four amino acid substitutions. Our results prove designed evolution followed by high-throughput screening to be an efficient strategy for engineering enzyme enantioselectivity.
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Affiliation(s)
- Mirela Ivancic
- Institut für Molekulare Biotechnologie, Technische Universität Graz, Petersgasse 14, 8010 Graz, Austria
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32
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Cipolla L, Lotti M, De Gioia L, Nicotra F. Application of Site‐Directed Lipase Mutants on Regioselective Acylation of Monosaccharides. J Carbohydr Chem 2007. [DOI: 10.1081/car-120026464] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Laura Cipolla
- a Department of Biotechnology and Biosciences , University of Milano‐Bicocca , Piazza della Scienza 2, 20126 , Milano , Italy
| | - Marina Lotti
- a Department of Biotechnology and Biosciences , University of Milano‐Bicocca , Piazza della Scienza 2, 20126 , Milano , Italy
| | - Luca De Gioia
- a Department of Biotechnology and Biosciences , University of Milano‐Bicocca , Piazza della Scienza 2, 20126 , Milano , Italy
| | - Francesco Nicotra
- a Department of Biotechnology and Biosciences , University of Milano‐Bicocca , Piazza della Scienza 2, 20126 , Milano , Italy
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Tsai SW, Chen CC, Yang HS, Ng IS, Chen TL. Implication of substrate-assisted catalysis on improving lipase activity or enantioselectivity in organic solvents. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2006; 1764:1424-8. [PMID: 16919508 DOI: 10.1016/j.bbapap.2006.07.001] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2006] [Revised: 07/10/2006] [Accepted: 07/11/2006] [Indexed: 11/21/2022]
Abstract
In comparison with the biocatalyst engineering and medium engineering approaches, very few examples have been reported on using the substrate engineering approach such as substrate-assisted catalysis (SAC) for naturally occurring or engineered lipases and serine proteases to improve the enzyme activity and enantioselectivity. By employing lipase-catalyzed hydrolysis of (R,S)-naproxen esters in water-saturated isooctane as the model system, we demonstrate the proton shuttle device to the leaving alcohol of the substrate as a new means of SAC to effectively improve the lipase activity or enantioselectivity. The result cannot only provide a strong evidence for the rate-limiting proton transfer for the bond-breaking of tetrahedron intermediate of the acylation step, but also sheds light for performing the hydrolysis, transesterification or aminolysis in organic solvents for the ester substrate that originally lipases cannot catalyze, but now can after introducing the device.
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Affiliation(s)
- Shau-Wei Tsai
- Institute of Biochemical and Biomedical Engineering, Chang Gung University, Kwei-Shan Tao-Yuan, 33302, Taiwan.
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34
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Biocatalytic preparation of enantioenriched 3,4-dihydroxypiperidines and theoretical study of Candida antarctica lipase B enantioselectivity. Tetrahedron 2006. [DOI: 10.1016/j.tet.2006.01.061] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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35
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Park S, Morley KL, Horsman GP, Holmquist M, Hult K, Kazlauskas RJ. Focusing mutations into the P. fluorescens esterase binding site increases enantioselectivity more effectively than distant mutations. ACTA ACUST UNITED AC 2005; 12:45-54. [PMID: 15664514 DOI: 10.1016/j.chembiol.2004.10.012] [Citation(s) in RCA: 107] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2004] [Revised: 09/24/2004] [Accepted: 10/13/2004] [Indexed: 11/16/2022]
Abstract
Rational design of enzymes with improved properties, such as enantioselectivity, usually focuses mutations within the substrate binding site. On the other hand, directed evolution of enzymes usually targets the entire protein and discovers beneficial mutations far from the substrate binding site. In this paper, we propose an explanation for this discrepancy and show that a combined approach--random mutagenesis within the substrate binding site--is better. To increase the enantioselectivity (E) of a Pseudomonas fluorescens esterase (PFE) toward methyl 3-bromo-2-methylpropionate, we focused mutagenesis into the substrate binding site at Trp28, Val121, Phe198, and Val225. Five of the catalytically active mutants (13%) showed better enantioselectivity than wild-type PFE. The increases in enantioselectivity were higher (up to 5-fold, reaching E = 61) than with mutants identified by random mutagenesis of the entire enzyme.
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Affiliation(s)
- Seongsoon Park
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montréal, Québec H3A 2K6, Canada
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36
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Lavandera I, Fernández S, Magdalena J, Ferrero M, Kazlauskas RJ, Gotor V. An Inverse Substrate Orientation for the Regioselective Acylation of 3′,5′-Diaminonucleosides Catalyzed by Candida antarctica lipase B? Chembiochem 2005; 6:1381-90. [PMID: 15977272 DOI: 10.1002/cbic.200400422] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Candida antarctica lipase B (CAL-B) catalyzes the regioselective acylation of natural thymidine with oxime esters and also the regioselective acylation of an analogue, 3',5'-diamino-3',5'-dideoxythymidine with nonactivated esters. In both cases, acylation favors the less hindered 5'-position over the 3'-position by upto 80-fold. Computer modeling of phosphonate transition-state analogues for the acylation of thymidine suggests that CAL-B favors acylation of the 5'-position because this orientation allows the thymine ring to bind in a hydrophobic pocket and forms stronger key hydrogen bonds than acylation of the 3'-position. On the other hand, computer modeling of phosphonamidate analogues of the transition states for acylation of either the 3'- or 5'-amino groups in 3',5'-diamino-3',5'-dideoxythymidine shows similar orientations and hydrogen bonds and, thus, does not explain the high regioselectivity. However, computer modeling of inverse structures, in which the acyl chain binds in the nucleophile pocket and vice versa, does rationalize the observed regioselectivity. The inverse structures fit the 5'-, but not the 3'-intermediate thymine ring, into the hydrophobic pocket, and form a weak new hydrogen bond between the O-2 carbonyl atom of the thymine and the nucleophile amine only for the 5'-intermediate. A water molecule might transfer a proton from the ammonium group to the active-site histidine. As a test of this inverse orientation, we compared the acylation of thymidine and 3',5'-diamino-3',5'-dideoxythymidine with butyryl acyl donors and with isosteric methoxyacetyl acyl donors. Both acyl donors reacted at equal rates with thymidine, but the methoxyacetyl acyl donor reacted four times faster than the butyryl acyl donor with 3',5'-diamino-3',5'-dideoxythymidine. This faster rate is consistent with an inverse orientation for 3',5'-diamino-3',5'-dideoxythymidine, in which the ether oxygen atom of the methoxyacetyl group can form a similar hydrogen bond to the nucleophilic amine. This combination of modeling and experiments suggests that such lipase-catalyzed reactions of apparently close substrate analogues like alcohols and amines might follow different pathways.
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Affiliation(s)
- Iván Lavandera
- Departamento de Química Orgánica e Inorgánica, Facultad de Química, Universidad de Oviedo, 33071 Oviedo, Spain
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37
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38
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Bornscheuer UT, Kazlauskas RJ. Untreue Enzyme in der Biokatalyse: mit alten Enzymen zu neuen Bindungen und Synthesewegen. Angew Chem Int Ed Engl 2004. [DOI: 10.1002/ange.200460416] [Citation(s) in RCA: 110] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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39
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Bornscheuer UT, Kazlauskas RJ. Catalytic Promiscuity in Biocatalysis: Using Old Enzymes to Form New Bonds and Follow New Pathways. Angew Chem Int Ed Engl 2004; 43:6032-40. [PMID: 15523680 DOI: 10.1002/anie.200460416] [Citation(s) in RCA: 428] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Biocatalysis has expanded rapidly in the last decades with the discoveries of highly stereoselective enzymes with broad substrate specificity. A new frontier for biocatalysis is broad reaction specificity, where enzymes catalyze alternate reactions. Although often under-appreciated, catalytic promiscuity has a natural role in evolution and occasionally in the biosynthesis of secondary metabolites. Examples of catalytic promiscuity with current or potential applications in synthesis are reviewed here. Combined with protein engineering, the catalytic promiscuity of enzymes may broadly extend their usefulness in organic synthesis.
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Affiliation(s)
- Uwe T Bornscheuer
- Institute of Chemistry and Biochemistry, Department of Technical Chemistry and Biotechnology, Greifswald University, Soldmannstrasse 16, 17487 Greifswald, Germany.
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40
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Koga Y, Kato K, Nakano H, Yamane T. Inverting enantioselectivity of Burkholderia cepacia KWI-56 lipase by combinatorial mutation and high-throughput screening using single-molecule PCR and in vitro expression. J Mol Biol 2003; 331:585-92. [PMID: 12899830 DOI: 10.1016/s0022-2836(03)00782-4] [Citation(s) in RCA: 88] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
The enantioselectivity of lipase from Burkhorderia cepacia KWI-56 has been inverted using a novel in vitro technique for construction and screening of a protein library by single-molecule DNA amplification by PCR followed by in vitro coupled transcription/translation system termed single-molecule-PCR-linked in vitro expression (SIMPLEX). Four amino acid residues (L17, F119, L167, and L266) in the hydrophobic substrate-binding pocket of the lipase were selected for mutation based on a structural model of a substrate-enzyme complex, and a combinatorial mutation library was constructed by SIMPLEX and screened for (R) and (S)-configurations of p-nitrophenyl 3-phenylbutyrate. Some combinations of amino acid substitutions in the four positions of the lipase were found as effective for changing the enantiopreference from the (S)-form substrate to the (R)-form. Two variants were expressed in the original host cells and purified to homogeneity, showing completely reversed enantioselectivity for the (R)-form of ethyl 3-phenylbutyrate (selectivity factor E(R)=38 or 33), whereas the wild-type lipase was (S)-selective (selectivity factor E(S)=33). Thus the semi-rational and semi-random combinatorial design of a mutant library followed by a high-throughput screening based on their enzymatic activity should be a powerful tool to engineer the enantioselectivity of enzymes.
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Affiliation(s)
- Yuichi Koga
- New Energy and Industrial Technology Development Organization, Sunshine 60 Bldg, 3-1-1 Higashi Ikebukuro, Toshima-ku, Tokyo 170-6028, Japan
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41
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Abstract
New strategies are continually being developed for using enzymes to efficiently catalyse the enantioselective synthesis of chiral non-racemic compounds. Alternatives to asymmetric synthesis or kinetic resolution include dynamic kinetic resolution, deracemisation and enantioconvergent transformations. Moreover, a much greater understanding is being developed of the parameters that can affect the stereochemical outcome of the reaction (e.g. solvent, substrate design, immobilization and directed evolution).
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Affiliation(s)
- Nicholas J Turner
- School of Chemistry, University of Edinburgh, King's Buildings, West Mains Road, Edinburgh, EH9 3JJ, UK.
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42
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Abstract
Recent developments to modify enzymes for use in organic synthesis have targeted several areas. These include altering the reaction mechanism of the enzyme to catalyse new reactions, switching substrate specificity, expanding substrate specificity, and improving substrate specificity, such as enantioselectivity in kinetic resolutions. Such modifications can be achieved either by rational redesign, which requires knowledge of the enzyme structure, or by random mutagenesis methods followed by screening. Both strategies of enzyme engineering can be successful and are very useful for improving the utility of enzymes for applied catalysis. Several examples illustrating these concepts in a variety of enzyme classes have appeared recently.
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Affiliation(s)
- Karl Hult
- Department of Biotechnology, Royal Institute of Technology (KTH), AlbaNova University Center, SE-106 91 Stockholm, Sweden.
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43
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Vallikivi I, Lille Ü, Lookene A, Metsala A, Sikk P, Tõugu V, Vija H, Villo L, Parve O. Lipase action on some non-triglyceride substrates. ACTA ACUST UNITED AC 2003. [DOI: 10.1016/s1381-1177(03)00043-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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44
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Edin M, Bäckvall JE. On the mechanism of the unexpected facile formation of meso-diacetate products in enzymatic acetylation of alkanediols. J Org Chem 2003; 68:2216-22. [PMID: 12636384 DOI: 10.1021/jo026652i] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The mechanism of the unexpected facile formation of meso-diacetate previously observed in the enzymatic resolution of dl/meso mixtures of 2,4-pentanediol and 2,5-hexanediol with Candida antarctica lipase B has been elucidated. It was found that the formation of meso-diacetate proceeds via different mechanisms for the two diols. Enzyme-catalyzed acylation of AcO-d(3) labeled (R)-monoacetates of meso-2,4-pentanediol and meso-2,5-hexanediol and analysis of the meso-diacetates obtained show that the former reaction proceeds via intramolecular acyl migration while the latter occurs via direct S-acylation of the alcohol. For the (R)-monoacetate of (R,S)-2,4-pentanediol the intramolecular acyl migration was fast and therefore direct S-acylation by the external acyl donor is suppressed. For the hexanediol monoacetate the rate ratio (pseudo E value) between (5R,2R)- and (5R,2S)-5-acetoxy-2-hexanol was experimentally determined to be k(R,R)/k(R,S) = 25, which is about 10-20 times lower than the E value for 2-pentanol and 2-octanol. In a preliminary experiment it was demonstrated that facile acyl migration in the 1,3-diol derivative can be utilized to prepare syn-1,3-diacetoxynonane (>90% syn) in high enantioselectivity (>99% ee) via a chemoenzymatic dynamic kinetic asymmetric transformation of a meso/dl mixture of 1,3-nonanediol.
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Affiliation(s)
- Michaela Edin
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, SE-106 91 Stockholm, Sweden
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45
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Abstract
Lipases and esterases are frequently used in the synthesis of optically pure compounds; however, natural enzymes do not always show sufficiently high enantioselectivity. Variation of the structure of the substrates, modification of the reaction system or protein engineering (e.g. the expression of pure enzymes, rational design or directed evolution) are strategies that can be employed to improve the distinction between two enantiomers or enantiotopic groups.
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Affiliation(s)
- Uwe T Bornscheuer
- Institute of Chemistry & Biochemistry, Department of Technical Chemistry & Biotechnology, Greifswald University, Soldmannstrasse 16, D-17487, Greifswald, Germany.
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46
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Tomić S, Kojić-Prodić B. A quantitative model for predicting enzyme enantioselectivity: application to Burkholderia cepacia lipase and 3-(aryloxy)-1,2-propanediol derivatives. J Mol Graph Model 2002; 21:241-52. [PMID: 12463642 DOI: 10.1016/s1093-3263(02)00148-1] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We describe a new approach for predicting the enantioselectivity of enzymes towards racemic compounds. It is based on comparative binding energy (COMBINE) analysis. The approach is used to rationalise the enantioselectivity of Burkholderia cepacia lipase (BCL) towards thirteen racemic 3-(aryloxy)-1,2-propanediols in the process of acylation. According to our molecular modelling study the two 3-(aryloxy)-1,2-propanediols enantiomers bind in the BCL active site in different orientations. To derive a quantitative structure-activity relationship (QSAR), the difference in the interaction energy between two enantiomers with each amino acid residue was computed. These residue-based energy differences were then subjected to chemometric analysis and 3D QSAR models were derived. The models were able to unambiguously predict the fast-reacting enantiomer and the approximate magnitude of the enantioselectivity. The study enabled identification of interactions between the substrate and the lipase amino acid residues that play key roles in secondary alcohol enantiodifferentiation. From the results, it was possible to propose modifications of both, substrate and protein, which would directionally modify enantioselectivity of BCL towards secondary aryl-alcohols.
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Affiliation(s)
- Sanja Tomić
- Ruder Bosković Institute, PO Box 180, HR-10002 Zagreb, Croatia.
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47
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Abstract
The conventional notion that enzymes are only active in aqueous media has long been discarded, thanks to the numerous studies documenting enzyme activities in nonaqueous media, including pure organic solvents and supercritical fluids. Enzymatic reactions in nonaqueous solvents offer new possibilities for producing useful chemicals (emulsifiers, surfactants, wax esters, chiral drug molecules, biopolymers, peptides and proteins, modified fats and oils, structured lipids and flavor esters). The use of enzymes in both macro- and microaqueous systems has been investigated especially intensively in the last two decades. Although enzymes exhibit considerable activity in nonaqueous media, the activity is low compared to that in water. This observation has led to numerous studies to modify enzymes for specific purposes by various means including protein engineering. This review covers the historical developments, major technological advances and recent trends of enzyme catalysis in nonconventional media. A brief description of different classes of enzymes and their use in industry is provided with representative examples. Recent trends including use of novel solvent systems, role of water activity, stability issues, medium and biocatalyst engineering aspects have been discussed with examples. Special attention is given to protein engineering and directed evolution.
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Affiliation(s)
- Sajja Hari Krishna
- AK-Technische Chemie und Biotechnologie, Institut für Chemie und Biochemie, Universität Greifswald, Soldmannstrasse 16, D-17487 Greifswald, Germany.
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48
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Bornscheuer UT, Bessler C, Srinivas R, Krishna SH. Optimizing lipases and related enzymes for efficient application. Trends Biotechnol 2002; 20:433-7. [PMID: 12220906 DOI: 10.1016/s0167-7799(02)02046-2] [Citation(s) in RCA: 161] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Although numerous reactions have been performed using lipases and related enzymes (e.g. esterases and phospholipases), it is still a challenge to identify the most suitable biocatalyst and best reaction conditions for an efficient application. Frequently used methods such as immobilization and optimization of the reaction medium cannot be transferred from one reaction system or substrate to another. However, in the past few years, rational protein design and directed evolution have emerged as efficient alternative methods to optimize biocatalytic reactions.
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Affiliation(s)
- Uwe T Bornscheuer
- Institute of Chemistry & Biochemistry, Department of Technical Chemistry & Biotechnology, Greifswald University, Soldmannstr. 16, D-17487 Greifswald, Germany.
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49
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Summa CM, Rosenblatt MM, Hong JK, Lear JD, DeGrado WF. Computational de novo design, and characterization of an A(2)B(2) diiron protein. J Mol Biol 2002; 321:923-38. [PMID: 12206771 DOI: 10.1016/s0022-2836(02)00589-2] [Citation(s) in RCA: 117] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Diiron proteins are found throughout nature and have a diverse range of functions; proteins in this class include methane monooxygenase, ribonucleotide reductase, Delta(9)-acyl carrier protein desaturase, rubrerythrin, hemerythrin, and the ferritins. Although each of these proteins has a very different overall fold, in every case the diiron active site is situated within a four-helix bundle. Additionally, nearly all of these proteins have a conserved Glu-Xxx-Xxx-His motif on two of the four helices with the Glu and His residues ligating the iron atoms. Intriguingly, subtle differences in the active site can result in a wide variety of functions. To probe the structural basis for this diversity, we designed an A(2)B(2) heterotetrameric four-helix bundle with an active site similar to those found in the naturally occurring diiron proteins. A novel computational approach was developed for the design, which considers the energy of not only the desired fold but also alternatively folded structures. Circular dichroism spectroscopy, analytical ultracentrifugation, and thermal unfolding studies indicate that the A and B peptides specifically associate to form an A(2)B(2) heterotetramer. Further, the protein binds Zn(II) and Co(II) in the expected manner and shows ferroxidase activity under single turnover conditions.
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Affiliation(s)
- Christopher M Summa
- Department of Biochemistry and Biophysics, School of Medicine, The University of Pennsylvania, 1010 Stellar-Chance Bldg, 421 Curie Blvd, Philadelphia 19104-6059, USA
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50
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Abstract
Lipases are the most used enzymes in synthetic organic chemistry, catalyzing the hydrolysis of carboxylic acid esters in aqueous medium or the reverse reaction in organic solvents. Recent methodological advancements regarding practical factors affecting lipase activity and enantioselectivity are reviewed. Select practical examples concerning the use of lipases in the production of chiral intermediates are also highlighted.
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Affiliation(s)
- Manfred T Reetz
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470, Mülheim/Ruhr, Germany.
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