1
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Lin GM, Warden-Rothman R, Voigt CA. Retrosynthetic design of metabolic pathways to chemicals not found in nature. ACTA ACUST UNITED AC 2019. [DOI: 10.1016/j.coisb.2019.04.004] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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2
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White A, Koelper A, Russell A, Larsen EM, Kim C, Lavis LD, Hoops GC, Johnson RJ. Fluorogenic structure activity library pinpoints molecular variations in substrate specificity of structurally homologous esterases. J Biol Chem 2018; 293:13851-13862. [PMID: 30006352 DOI: 10.1074/jbc.ra118.003972] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 07/11/2018] [Indexed: 01/08/2023] Open
Abstract
Cellular esterases catalyze many essential biological functions by performing hydrolysis reactions on diverse substrates. The promiscuity of esterases complicates assignment of their substrate preferences and biological functions. To identify universal factors controlling esterase substrate recognition, we designed a 32-member structure-activity relationship (SAR) library of fluorogenic ester substrates and used this library to systematically interrogate esterase preference for chain length, branching patterns, and polarity to differentiate common classes of esterase substrates. Two structurally homologous bacterial esterases were screened against this library, refining their previously broad overlapping substrate specificity. Vibrio cholerae esterase ybfF displayed a preference for γ-position thioethers and ethers, whereas Rv0045c from Mycobacterium tuberculosis displayed a preference for branched substrates with and without thioethers. We determined that this substrate differentiation was partially controlled by individual substrate selectivity residues Tyr-119 in ybfF and His-187 in Rv0045c; reciprocal substitution of these residues shifted each esterase's substrate preference. This work demonstrates that the selectivity of esterases is tuned based on transition state stabilization, identifies thioethers as an underutilized functional group for esterase substrates, and provides a rapid method for differentiating structural isozymes. This SAR library could have multifaceted future applications, including in vivo imaging, biocatalyst screening, molecular fingerprinting, and inhibitor design.
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Affiliation(s)
- Alex White
- From the Department of Chemistry and Biochemistry, Butler University, Indianapolis, Indiana 46208-3443 and
| | - Andrew Koelper
- From the Department of Chemistry and Biochemistry, Butler University, Indianapolis, Indiana 46208-3443 and
| | - Arielle Russell
- From the Department of Chemistry and Biochemistry, Butler University, Indianapolis, Indiana 46208-3443 and
| | - Erik M Larsen
- From the Department of Chemistry and Biochemistry, Butler University, Indianapolis, Indiana 46208-3443 and
| | - Charles Kim
- the Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, Virginia 20147-2439
| | - Luke D Lavis
- the Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, Virginia 20147-2439
| | - Geoffrey C Hoops
- From the Department of Chemistry and Biochemistry, Butler University, Indianapolis, Indiana 46208-3443 and
| | - R Jeremy Johnson
- From the Department of Chemistry and Biochemistry, Butler University, Indianapolis, Indiana 46208-3443 and
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3
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Bayer CD, van Loo B, Hollfelder F. Specificity Effects of Amino Acid Substitutions in Promiscuous Hydrolases: Context-Dependence of Catalytic Residue Contributions to Local Fitness Landscapes in Nearby Sequence Space. Chembiochem 2017; 18:1001-1015. [PMID: 28464395 PMCID: PMC5488252 DOI: 10.1002/cbic.201600657] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Indexed: 12/18/2022]
Abstract
Catalytic promiscuity can facilitate evolution of enzyme functions-a multifunctional catalyst may act as a springboard for efficient functional adaptation. We test the effect of single mutations on multiple activities in two groups of promiscuous AP superfamily members to probe this hypothesis. We quantify the effect of site-saturating mutagenesis of an analogous, nucleophile-flanking residue in two superfamily members: an arylsulfatase (AS) and a phosphonate monoester hydrolase (PMH). Statistical analysis suggests that no one physicochemical characteristic alone explains the mutational effects. Instead, these effects appear to be dominated by their structural context. Likewise, the effect of changing the catalytic nucleophile itself is not reaction-type-specific. Mapping of "fitness landscapes" of four activities onto the possible variation of a chosen sequence position revealed tremendous potential for respecialization of AP superfamily members through single-point mutations, highlighting catalytic promiscuity as a powerful predictor of adaptive potential.
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Affiliation(s)
- Christopher D. Bayer
- Department of BiochemistryUniversity of Cambridge80 Tennis Court RoadCB2 1GACambridgeUK
- Present address: c-LEcta GmbHPerlickstrasse 504103LeipzigGermany
| | - Bert van Loo
- Department of BiochemistryUniversity of Cambridge80 Tennis Court RoadCB2 1GACambridgeUK
- Present address: Institute for Evolution and BiodiversityUniversity of MünsterHüfferstrasse 148149MünsterGermany
| | - Florian Hollfelder
- Department of BiochemistryUniversity of Cambridge80 Tennis Court RoadCB2 1GACambridgeUK
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4
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Syal P, Gupta R. Heterologous expression of lipases YLIP4, YLIP5, YLIP7, YLIP13, and YLIP15 fromYarrowia lipolyticaMSR80 inEscherichia coli: Substrate specificity, kinetic comparison, and enantioselectivity. Biotechnol Appl Biochem 2017; 64:851-861. [DOI: 10.1002/bab.1542] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Accepted: 10/16/2016] [Indexed: 01/14/2023]
Affiliation(s)
- Poonam Syal
- Department of Microbiology; University of Delhi South Campus; New Delhi India
| | - Rani Gupta
- Department of Microbiology; University of Delhi South Campus; New Delhi India
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5
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Tallman KR, Beatty KE. Far-red fluorogenic probes for esterase and lipase detection. Chembiochem 2014; 16:70-5. [PMID: 25469918 DOI: 10.1002/cbic.201402548] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Indexed: 11/05/2022]
Abstract
Fluorogenic enzyme probes go from a dark to a bright state following hydrolysis and can provide a sensitive, real-time readout of enzyme activity. They are useful for examining enzymatic activity in bacteria, including the human pathogen Mycobacterium tuberculosis. Herein, we describe two fluorogenic esterase probes derived from the far-red fluorophore 7-hydroxy-9H-(1,3-dichloro-9,9-dimethylacridin-2-one) (DDAO). These probes offer enhanced optical properties compared to existing esterase probes because the hydrolysis product, DDAO, excites above 600 nm while retaining a good quantum yield (ϕ=0.40). We validated both probes with a panel of commercially available enzymes alongside known resorufin- and fluorescein-derived esterase substrates. Furthermore, we used these probes to reveal esterase activity in protein gel-resolved mycobacterial lysates. These probes represent new tools for esterase detection and characterization and should find use in a variety of applications.
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Affiliation(s)
- Katie R Tallman
- Department of Physiology and Pharmacology, Department of Biomedical Engineering, Oregon Health & Science University, 2730 SW Moody Avenue, CL3B, Portland, OR 97201 (USA)
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6
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Jang H, Lee J, Min DH. Graphene oxide for fluorescence-mediated enzymatic activity assays. J Mater Chem B 2014; 2:2452-2460. [DOI: 10.1039/c4tb00199k] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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7
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Proteomics of model and crop plant species: Status, current limitations and strategic advances for crop improvement. J Proteomics 2013; 93:5-19. [DOI: 10.1016/j.jprot.2013.05.036] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2013] [Revised: 05/20/2013] [Accepted: 05/29/2013] [Indexed: 12/22/2022]
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8
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Liu JY, Zheng GW, Li CX, Yu HL, Pan J, Xu JH. Multi-substrate fingerprinting of esterolytic enzymes with a group of acetylated alcohols and statistic analysis of substrate spectrum. ACTA ACUST UNITED AC 2013. [DOI: 10.1016/j.molcatb.2012.12.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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9
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Fink MJ, Rial DV, Kapitanova P, Lengar A, Rehdorf J, Cheng Q, Rudroff F, Mihovilovic MD. Quantitative Comparison of Chiral Catalysts Selectivity and Performance: A Generic Concept Illustrated with Cyclododecanone Monooxygenase as Baeyer-Villiger Biocatalyst. Adv Synth Catal 2012. [DOI: 10.1002/adsc.201200453] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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10
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New tools for exploring "old friends-microbial lipases". Appl Biochem Biotechnol 2012; 168:1163-96. [PMID: 22956276 DOI: 10.1007/s12010-012-9849-7] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2012] [Accepted: 08/20/2012] [Indexed: 10/27/2022]
Abstract
Fat-splitting enzymes (lipases), due to their natural, industrial, and medical relevance, attract enough attention as fats do in our lives. Starting from the paper that we write, cheese and oil that we consume, detergent that we use to remove oil stains, biodiesel that we use as transportation fuel, to the enantiopure drugs that we use in therapeutics, all these applications are facilitated directly or indirectly by lipases. Due to their uniqueness, versatility, and dexterity, decades of research work have been carried out on microbial lipases. The hunt for novel lipases and strategies to improve them continues unabated as evidenced by new families of microbial lipases that are still being discovered mostly by metagenomic approaches. A separate database for true lipases termed LIPABASE has been created recently which provides taxonomic, structural, biochemical information about true lipases from various species. The present review attempts to summarize new approaches that are employed in various aspects of microbial lipase research, viz., screening, isolation, production, purification, improvement by protein engineering, and surface display. Finally, novel applications facilitated by microbial lipases are also presented.
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11
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An approach for differentiating isozymes. Construction of libraries containing short aromatic peptides as part of a method to design selective inhibitors against lipases. Bioorg Med Chem Lett 2012; 22:3147-51. [DOI: 10.1016/j.bmcl.2012.03.048] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2012] [Revised: 03/12/2012] [Accepted: 03/13/2012] [Indexed: 11/21/2022]
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12
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Alkhalil A, Babu Nanubolu J, Burley JC. Analysis of phase transitions in molecular solids: quantitative assessment of phonon-mode vs intra-molecular spectral data. RSC Adv 2012. [DOI: 10.1039/c1ra00422k] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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13
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Kobayashi K, Matsui N, Usui K. Use of a designed Peptide library to screen for binders to a particular DNA g-quadruplex sequence. J Nucleic Acids 2011; 2011:572873. [PMID: 21912736 PMCID: PMC3168274 DOI: 10.4061/2011/572873] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2011] [Revised: 07/06/2011] [Accepted: 07/06/2011] [Indexed: 01/31/2023] Open
Abstract
We demonstrated a method to screen for binders to a particular G-quadruplex sequence using easily designed short peptides consisting of naturally occurring amino acids and mining of binding data using statistical methods such as hierarchical clustering analysis (HCA). Despite the small size of the library used in this study, candidates of specific binders were identified. In addition, a selected peptide stabilized the G-quadruplex structure of a DNA oligonucleotide derived from the promoter region of the protooncogene c-MYC. This study illustrates how a peptide library can be designed and presents a screening guideline for construction of G-quadruplex binders. Such G-quadruplex peptide binders could be functionally modified to enable switching, cellular penetration, and organelle-targeting for cell and tissue engineering.
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Affiliation(s)
- Keita Kobayashi
- Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20 Minatojima-Minamimachi, Chuo-ku, Kobe 650-0047, Japan
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14
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Maillard N, Babiak P, Syed S, Biswas R, Mandrich L, Manco G, Reymond JL. Five-Substrate Cocktail as a Sensor Array for Measuring Enzyme Activity Fingerprints of Lipases and Esterases. Anal Chem 2011; 83:1437-42. [DOI: 10.1021/ac102994n] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Noélie Maillard
- Department of Chemistry and Biochemistry, University of Berne, Freiestrasse 3, 3012 Berne, Switzerland
| | - Peter Babiak
- Department of Chemistry and Biochemistry, University of Berne, Freiestrasse 3, 3012 Berne, Switzerland
| | - Salahuddin Syed
- Department of Chemistry and Biochemistry, University of Berne, Freiestrasse 3, 3012 Berne, Switzerland
| | - Rasomoy Biswas
- Department of Chemistry and Biochemistry, University of Berne, Freiestrasse 3, 3012 Berne, Switzerland
| | - Luigi Mandrich
- Institute of Protein Biochemistry, National Research Council, Via Pietro Castellino 111, 80131 Naples, Italy
| | - Giuseppe Manco
- Institute of Protein Biochemistry, National Research Council, Via Pietro Castellino 111, 80131 Naples, Italy
| | - Jean-Louis Reymond
- Department of Chemistry and Biochemistry, University of Berne, Freiestrasse 3, 3012 Berne, Switzerland
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15
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Schmidt M, Böttcher D, Bornscheuer UT. Directed Evolution of Industrial Biocatalysts. Ind Biotechnol (New Rochelle N Y) 2010. [DOI: 10.1002/9783527630233.ch4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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16
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Wang B, Tang X, Ren G, Liu J, Yu H. A new high-throughput screening method for determining active and enantioselective hydrolases. Biochem Eng J 2009. [DOI: 10.1016/j.bej.2009.06.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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17
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Abstract
Enzyme assays are analytical tools to visualize enzyme activities. In recent years a large variety of enzyme assays have been developed to assist the discovery and optimization of industrial enzymes, in particular for "white biotechnology" where selective enzymes are used with great success for economically viable, mild and environmentally benign production processes. The present article highlights the aspects of fluorogenic and chromogenic substrates, sensors, and enzyme fingerprinting, which are our particular areas of interest.
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Affiliation(s)
- Jean-Louis Reymond
- Department of Chemistry and Biochemistry, University of Berne, Freiestrasse 3, Berne, 3012, Switzerland.
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18
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Reymond JL. Substrate Arrays for Fluorescence-Based Enzyme Fingerprinting and High-Throughput Screening. Ann N Y Acad Sci 2008; 1130:12-20. [DOI: 10.1196/annals.1430.000] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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19
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Kurtovic S, Shokeer A, Mannervik B. Diverging catalytic capacities and selectivity profiles with haloalkane substrates of chimeric alpha class glutathione transferases. Protein Eng Des Sel 2008; 21:329-41. [DOI: 10.1093/protein/gzn010] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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20
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Reymond JL, Babiak P. Screening systems. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2007; 105:31-58. [PMID: 17408081 DOI: 10.1007/10_2006_032] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Enzyme screening technology has undergone massive developments in recent years, particularly in the area of high-throughput screening and microarray methods. Screening consists of testing each sample of a sample library individually for the targeted reaction. This requires enzyme assays that accurately test relevant parameters of the reaction, such as catalytic turnover with a given substrate and selectivity parameters such as enantio- and regioselectivity. Enzyme assays also play an important role outside of enzyme screening, in particular for drug screening, medical diagnostics, and in the area of cellular and tissue imaging. In the 1990s, methods for high-throughput screening of enzyme activities were perceived as a critical bottleneck. As illustrated partly in this chapter, a large repertoire of efficient screening strategies are available today that allow testing of almost any reaction with high-throughput.
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Affiliation(s)
- Jean-Louis Reymond
- Department of Chemistry & Biochemistry, University of Berne, Freiestrasse 3, 3012 Berne, Switzerland.
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21
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Grognux J, Reymond JL. A red-fluorescent substrate microarray for lipase fingerprinting. MOLECULAR BIOSYSTEMS 2006; 2:492-8. [PMID: 17216030 DOI: 10.1039/b609275f] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A lipase substrate microarray was obtained by printing aliphatic C2-C12 monoesters of (5R)- and (5S)-3-(5,6-dihydroxyhexyloxy)benzaldehyde by reductive alkylation on amine-functionalized glass slides coated with bovine serum albumin and a short PEG linker. The microarray features 12 substrates and their 66 possible binary mixtures spotted in a 9 x 36 spot array. Lipase reactions are detected by chemoselective NaIO(4)-oxidation of the 1,2-diol hydrolysis product to form an aldehyde, which is then tagged with the red-fluorescent dye rhodamine B sulfohydrazide . Specific fingerprints are produced by active enzymes. These experiments provide the first example of lipase fingerprinting using microarrays.
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Affiliation(s)
- Johann Grognux
- Department of Chemistry & Biochemistry, University of Berne, Freiestrasse 3, 3012 Berne, Switzerland
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22
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Yang Y, Babiak P, Reymond JL. New Monofunctionalized Fluorescein Derivatives for the Efficient High-Throughput Screening of Lipases and Esterases in Aqueous Media. Helv Chim Acta 2006. [DOI: 10.1002/hlca.200690041] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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23
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Zhou H, Baldini L, Hong J, Wilson AJ, Hamilton AD. Pattern Recognition of Proteins Based on an Array of Functionalized Porphyrins. J Am Chem Soc 2006; 128:2421-5. [PMID: 16478197 DOI: 10.1021/ja056833c] [Citation(s) in RCA: 194] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A practical protein-detecting array is desirable for its potential application in proteomics, medical diagnostics, and pathogen detection. Here, we report a novel protein-detecting array based on porphyrins containing peripheral amino acids as protein surface receptors. The array of porphyrin receptors showed a unique pattern of fluorescence change upon interaction with certain protein samples. Both metal and nonmetal-containing proteins and mixtures of proteins gave distinct patterns, allowing their unambiguous identification. The composite pattern for each sample was subjected to principal component analysis (PCA) to generate a clustering map for more practical visualization. Increasing the number of porphyrin receptors from eight to sixteen gave improved resolution, suggesting that this array is expandable to give satisfactory resolution for any given sample system by carefully maximizing the chemical diversity of the receptors.
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Affiliation(s)
- Huchen Zhou
- Department of Chemistry, Yale University, P.O. Box 208107, 225 Prospect Street, New Haven, CT 06520-8107, USA
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24
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Usui K, Tomizaki KY, Mihara H. Protein-fingerprint data mining of a designed α-helical peptide array. ACTA ACUST UNITED AC 2006; 2:417-20. [PMID: 17153138 DOI: 10.1039/b608875a] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The data generated from protein fingerprints with an alpha-helical peptide array were analyzed using several statistical methods such as hierarchical clustering analysis and principal component analysis to discriminate target proteins.
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Affiliation(s)
- Kenji Usui
- Department of Bioengineering, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Nagatsuta-cho 4259 B-40, Midori-ku, Yokohama, 226-8501, Japan
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25
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Usui K, Tomizaki KY, Ohyama T, Nokihara K, Mihara H. A novel peptide microarray for protein detection and analysis utilizing a dry peptide array system. ACTA ACUST UNITED AC 2006; 2:113-21. [PMID: 16880928 DOI: 10.1039/b514263f] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A novel dry peptide microarray system has been constructed that affords a practical solution for protein detection and analysis. This system is an array preparation and assay procedure under dry conditions that uses designed peptides as non-immobilized capture agents for the detection of proteins. The system has several advantages that include its portability and ease-of-use, as well as the fact that vaporization of sample solutions need not be considered. In this study, various proteins have been characterized with an alpha-helical peptide mini-library. When proteins were added to the peptide library array, the fluorescent peptides showed different fluorescent intensities depending on their sequences. The patterns of these responses could be regarded as 'protein fingerprints' (PFPs), which are sufficient to establish the identities of the target proteins. Furthermore, statistical analysis of the resulting PFPs was performed using cluster analysis. The PFPs of the proteins were clustered successfully depending on their families and binding properties. Additionally, the target protein was characterized using a nanolitre system and could be detected down to 1.2 fmol. These studies imply that the dry peptide array system is a promising tool for detecting and analyzing target proteins. The dry peptide array will play a role in development of high-throughput protein-detecting nano/micro arrays for proteomics and ligand screening studies.
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Affiliation(s)
- Kenji Usui
- Department of Bioengineering and the COE21 program, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Nagatsuta-cho 4259 B-40, Midori-ku, Yokohama 226-8501, Japan
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26
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Yang Y, Babiak P, Reymond JL. Low background FRET-substrates for lipases and esterases suitable for high-throughput screening under basic (pH 11) conditions. Org Biomol Chem 2006; 4:1746-54. [PMID: 16633567 DOI: 10.1039/b601151a] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
FRET-based fluorogenic substrates for lipases and esterases were prepared in four steps from commercially available building blocks. The substrates are pyrenebutyric acid monoesters of aliphatic 1,2-diols bearing a dinitrophenylamino group as a quencher. The most enzyme-reactive substrate is ester 2a. The substrates do not show any measurable background reaction in the absence of enzyme even at pH 11, but react fast and specifically with lipases and esterases. These substrates offer an unprecedented and practical solution to the long-standing problem of a simple yet efficient high-throughput screening tool for lipase activities under basic conditions.
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Affiliation(s)
- Yongzheng Yang
- Department of Chemistry & Biochemistry, University of Berne, Switzerland
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27
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Affiliation(s)
- Rajavel Srinivasan
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543 (Republic of Singapore)
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28
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Schmidt M, Bornscheuer UT. High-throughput assays for lipases and esterases. ACTA ACUST UNITED AC 2005; 22:51-6. [PMID: 15857783 DOI: 10.1016/j.bioeng.2004.09.004] [Citation(s) in RCA: 85] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2004] [Revised: 09/23/2004] [Accepted: 09/24/2004] [Indexed: 11/21/2022]
Abstract
In the past few years a considerable number of high-throughput screening (HTS) systems have been developed, especially for lipases and esterases. In this review, a range of HTS methods for the directed evolution of these hydrolases are covered. This includes spectrophotometric and fluorimetric formats as well as other approaches to allow for fast, efficient and reliable identification of desired enzyme variants within large mutant libraries. In addition, methods for library creation and application of lipases and esterases are briefly covered.
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Affiliation(s)
- Marlen Schmidt
- Institute of Chemistry and Biochemistry, Department of Technical Chemistry and Biotechnology, Greifswald University, Soldmannstr. 16, D-17487 Greifswald, Germany
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29
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Sicard R, Goddard JP, Mazel M, Audiffrin C, Fourage L, Ravot G, Wahler D, Lefèvre F, Reymond JL. Multienzyme Profiling of Thermophilic Microorganisms with a Substrate Cocktail Assay. Adv Synth Catal 2005. [DOI: 10.1002/adsc.200505056] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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30
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Sicard R, Chen L, Marsaioli A, Reymond JL. A Fluorescence-Based Assay for Baeyer-Villiger Monooxygenases, Hydroxylases and Lactonases. Adv Synth Catal 2005. [DOI: 10.1002/adsc.200505040] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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31
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Abstract
In the postgenomic era, emphasis is shifting from protein identification to protein functional analysis. Enzyme function can be characterized by measuring activity across series of substrates, which generates an activity profile or fingerprint. Activity fingerprinting is particularly useful to differentiate closely related enzymes. Previously reported fingerprinting methods use series of parallel measurements, which are complex and difficult to reproduce. Here we report a new method for fingerprinting enzyme activities based on using mixtures of substrates, or substrate cocktails, in a single reaction that is then analyzed by HPLC. The fingerprints produced are highly reproducible and allow functional differentiation and classification of closely related enzymes, as demonstrated for a series of lipases and esterases. The method is practical, general, and flexible in terms of reaction conditions and can be adapted to any reaction type.
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Affiliation(s)
- Jean-Philippe Goddard
- Department of Chemistry and Biochemistry, University of Berne, Freiestrasse 3, 3012 Berne, Switzerland
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Yongzheng Y, Reymond JL. Protease profiling using a fluorescent domino peptide cocktail. MOLECULAR BIOSYSTEMS 2005; 1:57-63. [PMID: 16880964 DOI: 10.1039/b419446b] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Five hexapeptides were prepared containing, in a domino-type arrangement, all 25 possible dipeptides between (1) aromatic, (2) hydrophobic, (3) positively charged, (4) negatively charged, and (5) small and polar amino acids. The peptides were fluorescence labeled at the N-terminus with a (7-coumaryl)oxyacetyl group, allowing the selective detection of N-terminal cleavage products. The five peptides were used as a cocktail reagent in an HPLC analysis. The cocktail produced specific cleavage patterns, or fingerprints, for a variety of proteases. This domino peptide cocktail can be used as a general reagent for protease identification and functional profiling.
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Affiliation(s)
- Yang Yongzheng
- Department of Chemistry & Biochemistry, University of Berne, Freiestrasse 3, 3012 Berne, Switzerland
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Abstract
Enzyme assays for high-throughput screening and enzyme engineering, which are often based on derivatives of coumarin, nitrophenol, fluorescein, nitrobenzofurazane or rhodamine dyes, can be divided into two categories: those that depend on labelled substrates, and those that depend on sensing the reactions of unmodified substrates. Labelled substrates include, for example, fluorogenic and chromogenic substrates that generate a reporter molecule by beta-elimination, fluorescence resonance energy transfer (FRET) substrates and isotopic labels for enantioselectivity screening. By contrast, endpoint sensing can be done using amine reagents, fluorescent affinity labels for phosphorylated proteins, or synthetic multifunctional pores. Sensing assays can also be done in real time by using, for example, aldehyde trapping to follow vinyl ester acylation in organic solvent or calcein-copper fluorescence for sensing amino acids. The current trend is to assemble many such assays in parallel for enzyme profiling and enzyme fingerprinting.
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Affiliation(s)
- Jean-Philippe Goddard
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
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