1
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Patsch D, Schwander T, Voss M, Schaub D, Hüppi S, Eichenberger M, Stockinger P, Schelbert L, Giger S, Peccati F, Jiménez-Osés G, Mutný M, Krause A, Bornscheuer UT, Hilvert D, Buller RM. Enriching productive mutational paths accelerates enzyme evolution. Nat Chem Biol 2024:10.1038/s41589-024-01712-3. [PMID: 39261644 DOI: 10.1038/s41589-024-01712-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2024] [Accepted: 07/26/2024] [Indexed: 09/13/2024]
Abstract
Darwinian evolution has given rise to all the enzymes that enable life on Earth. Mimicking natural selection, scientists have learned to tailor these biocatalysts through recursive cycles of mutation, selection and amplification, often relying on screening large protein libraries to productively modulate the complex interplay between protein structure, dynamics and function. Here we show that by removing destabilizing mutations at the library design stage and taking advantage of recent advances in gene synthesis, we can accelerate the evolution of a computationally designed enzyme. In only five rounds of evolution, we generated a Kemp eliminase-an enzymatic model system for proton transfer from carbon-that accelerates the proton abstraction step >108-fold over the uncatalyzed reaction. Recombining the resulting variant with a previously evolved Kemp eliminase HG3.17, which exhibits similar activity but differs by 29 substitutions, allowed us to chart the topography of the designer enzyme's fitness landscape, highlighting that a given protein scaffold can accommodate several, equally viable solutions to a specific catalytic problem.
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Affiliation(s)
- David Patsch
- Competence Center for Biocatalysis, Zurich University of Applied Sciences, Waedenswil, Switzerland
- Department of Biotechnology and Enzyme Catalysis, University of Greifswald, Greifswald, Germany
| | - Thomas Schwander
- Competence Center for Biocatalysis, Zurich University of Applied Sciences, Waedenswil, Switzerland
| | - Moritz Voss
- Competence Center for Biocatalysis, Zurich University of Applied Sciences, Waedenswil, Switzerland
| | - Daniela Schaub
- Competence Center for Biocatalysis, Zurich University of Applied Sciences, Waedenswil, Switzerland
- Center for Functional Protein Assemblies & Department of Bioscience, TUM School of Natural Sciences, Technical University of Munich (TUM), Garching, Germany
| | - Sean Hüppi
- Competence Center for Biocatalysis, Zurich University of Applied Sciences, Waedenswil, Switzerland
- Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
| | - Michael Eichenberger
- Competence Center for Biocatalysis, Zurich University of Applied Sciences, Waedenswil, Switzerland
| | - Peter Stockinger
- Competence Center for Biocatalysis, Zurich University of Applied Sciences, Waedenswil, Switzerland
| | - Lisa Schelbert
- Competence Center for Biocatalysis, Zurich University of Applied Sciences, Waedenswil, Switzerland
| | - Sandro Giger
- Competence Center for Biocatalysis, Zurich University of Applied Sciences, Waedenswil, Switzerland
| | - Francesca Peccati
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Derio, Spain
- Ikerbasque, Basque Foundation for Science, Bilbao, Spain
| | - Gonzalo Jiménez-Osés
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Derio, Spain
- Ikerbasque, Basque Foundation for Science, Bilbao, Spain
| | - Mojmír Mutný
- Department of Computer Science, ETH Zurich, Zurich, Switzerland
| | - Andreas Krause
- Department of Computer Science, ETH Zurich, Zurich, Switzerland
| | - Uwe T Bornscheuer
- Department of Biotechnology and Enzyme Catalysis, University of Greifswald, Greifswald, Germany
| | - Donald Hilvert
- Laboratory of Organic Chemistry, ETH Zurich, Zurich, Switzerland
| | - Rebecca M Buller
- Competence Center for Biocatalysis, Zurich University of Applied Sciences, Waedenswil, Switzerland.
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2
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Shandilya E, Bains AS, Maiti S. Enzyme-Mediated Temporal Control over the Conformational Disposition of a Condensed Protein in Macromolecular Crowded Media. J Phys Chem B 2023; 127:10508-10517. [PMID: 38052045 DOI: 10.1021/acs.jpcb.3c07074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2023]
Abstract
Temporal regulation between input and output signals is one of the hallmarks of complex biological processes. Herein, we report that the conformational disposition of a protein in macromolecularly crowded media can be controlled with time using enzymes. First, we demonstrate the pH dependence of bovine serum albumin (BSA) condensation and conformational alteration in the presence of poly(ethylene glycol) as a crowder. However, by exploiting the strength of pH-modulatory enzymatic reactions (glucose oxidase and urease), the conversion time between the condensed and free forms can be tuned. Additionally, we demonstrate that the trapping of intermediate states with respect to the overall system at a particular α-helix or β-sheet composition and rotational mobility can be possible simply by altering the substrate concentration. Finally, we show that the intrinsic catalytic ability of BSA toward the Kemp elimination (KE) reaction is inhibited in the aggregated form but regained in the free form. In fact, the rate of KE reaction can also be actuated enzymatically in a temporal fashion, therefore demonstrating the programmability of a cascade of biochemical events in crowded media.
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Affiliation(s)
- Ekta Shandilya
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Manauli 140306, India
| | - Arshdeep Singh Bains
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Manauli 140306, India
| | - Subhabrata Maiti
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Manauli 140306, India
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3
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Liang Z, Sun Y, Zeng H, Qin H, Yang R, Qu L, Zhang K, Li Z. Broad-Specificity Screening of Pyrethroids Enabled by the Catalytic Function of Human Serum Albumin on Coumarin Hydrolysis. Anal Chem 2023; 95:5678-5686. [PMID: 36952638 DOI: 10.1021/acs.analchem.2c05556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/25/2023]
Abstract
Sensing systems based on cholinesterase and carboxylesterase coupled with different transduction technologies have emerged for pesticide screening owing to their simple operation, fast response, and suitability for on-site analysis. However, the broad spectrum and specificity screening of pyrethroids over organophosphates and carbamates remains an unmet challenge for current enzymatic sensors. Human serum albumin (HSA), a multifunctional protein, can promote various chemical transformations and show a high affinity for pyrethroids, which offer a route for specific and broad-spectrum pyrethroid screening. Herein, for the first time, we evaluated the catalytic hydrolysis function of human serum albumin (HSA) on the coumarin lactone bond and revealed that HSA can act as an enzyme to catalyze the hydrolysis of the coumarin lactone bond. Molecular docking and chemical modifications indicate that lysine 199 and tyrosine 411 serve as the catalytic general base and contribute to most of the catalytic activity. Utilizing this enzymatic activity, a broad specific ratiometric fluorescence pyrethroids sensing system was developed. The binding energetics and binding constants of pesticides and HSA show that pyrethroids bind to HSA more easily than organophosphates and carbamates, which is responsible for the specificity of the sensing system. This study provides a general sensor platform and strategy for screening pesticides and reveals the catalytic activity of HSA on the hydrolysis of the coumarin lactone bond, which may open innovative horizons for the chemical sensing and biomedical applications of HSA.
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Affiliation(s)
- Zengqiang Liang
- College of Chemistry, Green Catalysis Center, Henan Joint International Research Laboratory of Green Construction of Functional Molecules and Their Bioanalytical Applications, Zhengzhou Key Laboratory of Functional Nanomaterial and Medical Theranostic, Zhengzhou University, Zhengzhou 450001, China
| | - Yuanqiang Sun
- College of Chemistry, Green Catalysis Center, Henan Joint International Research Laboratory of Green Construction of Functional Molecules and Their Bioanalytical Applications, Zhengzhou Key Laboratory of Functional Nanomaterial and Medical Theranostic, Zhengzhou University, Zhengzhou 450001, China
| | - Huajin Zeng
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Haimei Qin
- Fujian Provincial Key Lab of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Ran Yang
- College of Chemistry, Green Catalysis Center, Henan Joint International Research Laboratory of Green Construction of Functional Molecules and Their Bioanalytical Applications, Zhengzhou Key Laboratory of Functional Nanomaterial and Medical Theranostic, Zhengzhou University, Zhengzhou 450001, China
| | - Lingbo Qu
- College of Chemistry, Green Catalysis Center, Henan Joint International Research Laboratory of Green Construction of Functional Molecules and Their Bioanalytical Applications, Zhengzhou Key Laboratory of Functional Nanomaterial and Medical Theranostic, Zhengzhou University, Zhengzhou 450001, China
- Key Laboratory of Food Safety Quick Testing and Smart Supervision Technology for State Market Regulation, Zhengzhou 450001, China
| | - Ke Zhang
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | - Zhaohui Li
- College of Chemistry, Green Catalysis Center, Henan Joint International Research Laboratory of Green Construction of Functional Molecules and Their Bioanalytical Applications, Zhengzhou Key Laboratory of Functional Nanomaterial and Medical Theranostic, Zhengzhou University, Zhengzhou 450001, China
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4
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Hanreich S, Bonandi E, Drienovská I. Design of Artificial Enzymes: Insights into Protein Scaffolds. Chembiochem 2023; 24:e202200566. [PMID: 36418221 DOI: 10.1002/cbic.202200566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 11/18/2022] [Accepted: 11/21/2022] [Indexed: 11/25/2022]
Abstract
The design of artificial enzymes has emerged as a promising tool for the generation of potent biocatalysts able to promote new-to-nature reactions with improved catalytic performances, providing a powerful platform for wide-ranging applications and a better understanding of protein functions and structures. The selection of an appropriate protein scaffold plays a key role in the design process. This review aims to give a general overview of the most common protein scaffolds that can be exploited for the generation of artificial enzymes. Several examples are discussed and categorized according to the strategy used for the design of the artificial biocatalyst, namely the functionalization of natural enzymes, the creation of a new catalytic site in a protein scaffold bearing a wide hydrophobic pocket and de novo protein design. The review is concluded by a comparison of these different methods and by our perspective on the topic.
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Affiliation(s)
- Stefanie Hanreich
- Department of Chemistry and Pharmaceutical Sciences Vrije Universiteit, Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam (The, Netherlands
| | - Elisa Bonandi
- Department of Chemistry and Pharmaceutical Sciences Vrije Universiteit, Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam (The, Netherlands
| | - Ivana Drienovská
- Department of Chemistry and Pharmaceutical Sciences Vrije Universiteit, Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam (The, Netherlands
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5
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Ludden MD, Taylor CGP, Tipping MB, Train JS, Williams NH, Dorrat JC, Tuck KL, Ward MD. Interaction of anions with the surface of a coordination cage in aqueous solution probed by their effect on a cage-catalysed Kemp elimination. Chem Sci 2021; 12:14781-14791. [PMID: 34820094 PMCID: PMC8597839 DOI: 10.1039/d1sc04887b] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 10/25/2021] [Indexed: 11/21/2022] Open
Abstract
An octanuclear M8L12 coordination cage catalyses the Kemp elimination reaction of 5-nitro-1,2-benzisoxazole (NBI) with hydroxide to give 2-cyano-4-nitrophenolate (CNP) as the product. In contrast to the previously-reported very efficient catalysis of the Kemp elimination reaction of unsubstituted benzisoxazole, which involves the substrate binding inside the cage cavity, the catalysed reaction of NBI with hydroxide is slower and occurs at the external surface of the cage, even though NBI can bind inside the cage cavity. The rate of the catalysed reaction is sensitive to the presence of added anions, which bind to the 16+ cage surface, displacing the hydroxide ions from around the cage which are essential reaction partners in the Kemp elimination. Thus we can observe different binding affinities of anions to the surface of the cationic cage in aqueous solution by the extent to which they displace hydroxide and thereby inhibit the catalysed Kemp elimination and slow down the appearance of CNP. For anions with a -1 charge the observed affinity order for binding to the cage surface is consistent with their ease of desolvation and their ordering in the Hofmeister series. With anions that are significantly basic (fluoride, hydrogen carbonate, carboxylates) the accumulation of the anion around the cage surface accelerates the Kemp elimination compared to the background reaction with hydroxide, which we ascribe to the ability of these anions to participate directly in the Kemp elimination. This work provides valuable mechanistic insights into the role of the cage in co-locating the substrate and the anionic reaction partners in a cage-catalysed reaction.
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Affiliation(s)
- Michael D Ludden
- Department of Chemistry, University of Warwick Coventry CV4 7AL UK
| | | | - Max B Tipping
- Department of Chemistry, University of Warwick Coventry CV4 7AL UK
| | - Jennifer S Train
- Department of Chemistry, University of Sheffield Sheffield S3 7HF UK
| | | | - Jack C Dorrat
- School of Chemistry, Monash University Melbourne VIC3800 Australia
| | - Kellie L Tuck
- School of Chemistry, Monash University Melbourne VIC3800 Australia
| | - Michael D Ward
- Department of Chemistry, University of Warwick Coventry CV4 7AL UK
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6
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Mahato RR, Shandilya E, Dasgupta B, Maiti S. Dictating Catalytic Preference and Activity of a Nanoparticle by Modulating Its Multivalent Engagement. ACS Catal 2021. [DOI: 10.1021/acscatal.1c01991] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Rishi Ram Mahato
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Manauli 140306, India
| | - Ekta Shandilya
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Manauli 140306, India
| | - Basundhara Dasgupta
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Manauli 140306, India
| | - Subhabrata Maiti
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Manauli 140306, India
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7
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Shandilya E, Dasgupta B, Maiti S. Interconnectivity between Surface Reactivity and Self-Assembly of Kemp Elimination Catalyzing Nanorods. Chemistry 2021; 27:7831-7836. [PMID: 33769607 DOI: 10.1002/chem.202100450] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Indexed: 11/08/2022]
Abstract
Understanding the fundamental facts behind dynamicity of catalytic processes has been a longstanding quest across disciplines. Herein, we report self-assembly of catalytically active gold nanorods that can be regulated by tuning its reactivity towards a proton transfer reaction at different pH. Unlike substrate-induced templating and co-operativity, the enhanced aggregation rate is due to alteration of catalytic surface charge only during reactivity as negatively charged transition state of reactant (5-nitrobenzisoxazole) is formed on positively charged nanorod while undergoing a concerted E2-pathway. Herein, enhanced diffusivity during catalytic processes might also act as an additional contributing factor. Furthermore, we have also shown that nanosized hydrophobic cavities of clustered nanorods can also efficiently accelerate the rate of an aromatic nucleophilic substitution reaction, which also demonstrates a catalytic phenomenon that can lead to cascading of other reactions where substrates and products of the starting reactions are not directly involved.
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Affiliation(s)
- Ekta Shandilya
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Manauli, 140306, India
| | - Basundhara Dasgupta
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Manauli, 140306, India
| | - Subhabrata Maiti
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Manauli, 140306, India
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8
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Liang Y, Li W, Liang H, Lou X, Liu R, Zhang Q, Bartlam M. Structural characterization and Kemp eliminase activity of the Mycobacterium smegmatis Ketosteroid Isomerase. Biochem Biophys Res Commun 2021; 560:159-164. [PMID: 33992958 DOI: 10.1016/j.bbrc.2021.05.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 05/04/2021] [Indexed: 11/26/2022]
Abstract
The Kemp elimination reaction, involving the ring-opening of benzoxazole and its derivatives under the action of natural enzymes or chemical catalysts, has been of interest to researchers since its discovery. Because this reaction does not exist in all currently known metabolic pathways, the computational design of Kemp eliminases has provided valuable insights into principles of enzymatic catalysis. However, it was discovered that the naturally occurring promiscuous enzymes ydbC, xapA and ketosteroid isomerase also can catalyze Kemp elimination. Here, we report the crystal structure of ketosteroid isomerase (KSI) from Mycobacterium smegmatis MC2 155. MsKSI crystallizes in the P212121 space group with two molecules in an asymmetric unit, and ultracentrifugation data confirms that it forms a stable dimer in solution, consistent with the 1.9 Å-resolution structure. Our assays confirm that MsKSI accelerates the Kemp elimination of 5-nitrobenzoxazole (5NBI) with an optimal pH of 5.5. A 2.35 Å resolution crystal structure of the MsKSI-5NBI complex reveals that the substrate 5NBI is bound in the active pocket of the enzyme composed of hydrophobic residues. In addition, the Glu127 residue is proposed to play an important role as a general base in proton transfer and breaking weak O-N bonds to open the five-membered ring. This work provides a starting point for exploring the artificial modification of MsKSI using the natural enzyme as the backbone.
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Affiliation(s)
- Yakun Liang
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Protein Science and College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Weiping Li
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Protein Science and College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Han Liang
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Protein Science and College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Xiaorui Lou
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Protein Science and College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Ruihua Liu
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Protein Science and College of Life Sciences, Nankai University, Tianjin, 300071, China.
| | - Qionglin Zhang
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Protein Science and College of Life Sciences, Nankai University, Tianjin, 300071, China.
| | - Mark Bartlam
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Protein Science and College of Life Sciences, Nankai University, Tianjin, 300071, China
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9
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Rani S, Dasgupta B, Bhati GK, Tomar K, Rakshit S, Maiti S. Superior Proton-Transfer Catalytic Promiscuity of Cytochrome c in Self-Organized Media. Chembiochem 2020; 22:1285-1291. [PMID: 33175409 DOI: 10.1002/cbic.202000768] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Indexed: 12/30/2022]
Abstract
Evolutionarily elderly proteins commonly feature greater catalytic promiscuity. Cytochrome c is among the first set of proteins in evolution to have known prospects in electron transport and peroxidative properties. Here, we report that cyt c is also a proficient proton-transfer catalyst and enhances the Kemp elimination (KE; model reaction to show proton transfer catalytic property) by ∼750-fold on self-organized systems like micelles and vesicles. The self-organized systems mimic the mitochondrial environment in vitro for cyt c. Using an array of biophysical and biochemical mutational assays, both acid-base and redox mechanistic pathways have been explored. The histidine moiety close to hemin group (His18) is mainly responsible for proton abstraction to promote the concerted E2 pathway for KE catalysis when cyt c is in its oxidized form; this has also been confirmed by a H18A mutant of cyt c. However, the redox pathway is predominant under reducing conditions in the presence of dithiothreitol over the pH range 6-7.4. Interestingly, we found almost 750-fold enhanced KE catalysis by cyt c compared to aqueous buffer. Overall, in addition to providing mechanistic insights, the data reveal an unprecedented catalytic property of cyt c that could be of high importance in an evolutionary perspective considering its role in delineating the phylogenic tree and also towards generating programmable designer biocatalysts.
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Affiliation(s)
- Sheetal Rani
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Manauli, 140306, India
| | - Basundhara Dasgupta
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Manauli, 140306, India
| | - Gaurav Kumar Bhati
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Manauli, 140306, India
| | - Kalpana Tomar
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Manauli, 140306, India
| | - Sabyasachi Rakshit
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Manauli, 140306, India
| | - Subhabrata Maiti
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Manauli, 140306, India
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10
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Nishihara R, Niwa K, Tomita T, Kurita R. Coelenterazine Analogue with Human Serum Albumin-Specific Bioluminescence. Bioconjug Chem 2020; 31:2679-2684. [PMID: 33236887 DOI: 10.1021/acs.bioconjchem.0c00536] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
A synthetic luciferin comprising an imidazopyrazinone core, named HuLumino1, was designed to generate specific bioluminescence with human serum albumin (HSA) in real serum samples. HuLumino1 was developed by attaching a methoxy-terminated alkyl chain to C-6 of coelenterazine and by eliminating a benzyl group at C-8. HSA levels were quantified within 5% error margins of an enzyme-linked immunosorbent assay without the need for any sample pretreatments because of the high specificity of HuLumino1.
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Affiliation(s)
- Ryo Nishihara
- National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan.,DAILAB, DBT-AIST International Centre for Translational and Environmental Research (DAICENTER), National Institute of Advanced Industrial Science and Technology (AIST), Central 5-41, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8565, Japan
| | - Kazuki Niwa
- National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan
| | - Tatsunosuke Tomita
- National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan.,DAILAB, DBT-AIST International Centre for Translational and Environmental Research (DAICENTER), National Institute of Advanced Industrial Science and Technology (AIST), Central 5-41, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8565, Japan
| | - Ryoji Kurita
- National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan.,DAILAB, DBT-AIST International Centre for Translational and Environmental Research (DAICENTER), National Institute of Advanced Industrial Science and Technology (AIST), Central 5-41, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8565, Japan.,Faculty of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8573, Japan
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11
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Liang Z, Sun Y, Zeng H, Sun K, Yang R, Li Z, Zhang K, Chen X, Qu L. Simultaneous Detection of Human Serum Albumin and Sulfur Dioxide in Living Cells Based on a Catalyzed Michael Addition Reaction. Anal Chem 2020; 92:16130-16137. [DOI: 10.1021/acs.analchem.0c03806] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Zengqiang Liang
- College of Chemistry, Green Catalysis Center, Henan Joint International Research Laboratory of Green Construction of Functional Molecules and Their Bioanalytical Applications, Zhengzhou Key Laboratory of Functional Nanomaterial and Medical Theranostic, Zhengzhou University, Zhengzhou 450001, China
| | - Yuanqiang Sun
- College of Chemistry, Green Catalysis Center, Henan Joint International Research Laboratory of Green Construction of Functional Molecules and Their Bioanalytical Applications, Zhengzhou Key Laboratory of Functional Nanomaterial and Medical Theranostic, Zhengzhou University, Zhengzhou 450001, China
| | - Huajin Zeng
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Kai Sun
- College of Chemistry, Green Catalysis Center, Henan Joint International Research Laboratory of Green Construction of Functional Molecules and Their Bioanalytical Applications, Zhengzhou Key Laboratory of Functional Nanomaterial and Medical Theranostic, Zhengzhou University, Zhengzhou 450001, China
| | - Ran Yang
- College of Chemistry, Green Catalysis Center, Henan Joint International Research Laboratory of Green Construction of Functional Molecules and Their Bioanalytical Applications, Zhengzhou Key Laboratory of Functional Nanomaterial and Medical Theranostic, Zhengzhou University, Zhengzhou 450001, China
| | - Zhaohui Li
- College of Chemistry, Green Catalysis Center, Henan Joint International Research Laboratory of Green Construction of Functional Molecules and Their Bioanalytical Applications, Zhengzhou Key Laboratory of Functional Nanomaterial and Medical Theranostic, Zhengzhou University, Zhengzhou 450001, China
| | - Ke Zhang
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | - Xiaolan Chen
- College of Chemistry, Green Catalysis Center, Henan Joint International Research Laboratory of Green Construction of Functional Molecules and Their Bioanalytical Applications, Zhengzhou Key Laboratory of Functional Nanomaterial and Medical Theranostic, Zhengzhou University, Zhengzhou 450001, China
| | - Lingbo Qu
- College of Chemistry, Green Catalysis Center, Henan Joint International Research Laboratory of Green Construction of Functional Molecules and Their Bioanalytical Applications, Zhengzhou Key Laboratory of Functional Nanomaterial and Medical Theranostic, Zhengzhou University, Zhengzhou 450001, China
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12
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Abstract
Bioorthogonal reactions that proceed readily under physiological conditions without interference from biomolecules have found widespread application in the life sciences. Complementary to the bioorthogonal reactions that ligate two molecules, reactions that release a molecule or cleave a linker are increasingly attracting interest. Such dissociative bioorthogonal reactions have a broad spectrum of uses, for example, in controlling bio-macromolecule activity, in drug delivery, and in diagnostic assays. This review article summarizes the developed bioorthogonal reactions linked to a release step, outlines representative areas of the applications of such reactions, and discusses aspects that require further improvement.
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Affiliation(s)
- Julian Tu
- Department of Medicinal Chemistry, University of Utah, 30 S 2000 E, Salt Lake City, Utah, 84112, USA
| | - Minghao Xu
- Department of Medicinal Chemistry, University of Utah, 30 S 2000 E, Salt Lake City, Utah, 84112, USA
| | - Raphael M Franzini
- Department of Medicinal Chemistry, University of Utah, 30 S 2000 E, Salt Lake City, Utah, 84112, USA
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13
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Serrano-Luginbühl S, Ruiz-Mirazo K, Ostaszewski R, Gallou F, Walde P. Soft and dispersed interface-rich aqueous systems that promote and guide chemical reactions. Nat Rev Chem 2018. [DOI: 10.1038/s41570-018-0042-6] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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14
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Hong NS, Petrović D, Lee R, Gryn'ova G, Purg M, Saunders J, Bauer P, Carr PD, Lin CY, Mabbitt PD, Zhang W, Altamore T, Easton C, Coote ML, Kamerlin SCL, Jackson CJ. The evolution of multiple active site configurations in a designed enzyme. Nat Commun 2018; 9:3900. [PMID: 30254369 PMCID: PMC6156567 DOI: 10.1038/s41467-018-06305-y] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 08/21/2018] [Indexed: 12/11/2022] Open
Abstract
Developments in computational chemistry, bioinformatics, and laboratory evolution have facilitated the de novo design and catalytic optimization of enzymes. Besides creating useful catalysts, the generation and iterative improvement of designed enzymes can provide valuable insight into the interplay between the many phenomena that have been suggested to contribute to catalysis. In this work, we follow changes in conformational sampling, electrostatic preorganization, and quantum tunneling along the evolutionary trajectory of a designed Kemp eliminase. We observe that in the Kemp Eliminase KE07, instability of the designed active site leads to the emergence of two additional active site configurations. Evolutionary conformational selection then gradually stabilizes the most efficient configuration, leading to an improved enzyme. This work exemplifies the link between conformational plasticity and evolvability and demonstrates that residues remote from the active sites of enzymes play crucial roles in controlling and shaping the active site for efficient catalysis.
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Affiliation(s)
- Nan-Sook Hong
- Research School of Chemistry, Australian National University, Canberra, ACT, 2601, Australia
| | - Dušan Petrović
- Department of Chemistry, BMC, Uppsala University, Box 576, 751 23, Uppsala, Sweden
| | - Richmond Lee
- Research School of Chemistry, Australian National University, Canberra, ACT, 2601, Australia
| | - Ganna Gryn'ova
- Research School of Chemistry, Australian National University, Canberra, ACT, 2601, Australia.,Institut des Sciences et Ingénierie Chimiques, École Polytechnique Fédérale de Lausanne, 1015, Lausanne, Switzerland
| | - Miha Purg
- Department of Chemistry, BMC, Uppsala University, Box 576, 751 23, Uppsala, Sweden
| | - Jake Saunders
- Research School of Chemistry, Australian National University, Canberra, ACT, 2601, Australia
| | - Paul Bauer
- Department of Chemistry, BMC, Uppsala University, Box 576, 751 23, Uppsala, Sweden
| | - Paul D Carr
- Research School of Chemistry, Australian National University, Canberra, ACT, 2601, Australia
| | - Ching-Yeh Lin
- Research School of Chemistry, Australian National University, Canberra, ACT, 2601, Australia
| | - Peter D Mabbitt
- Research School of Chemistry, Australian National University, Canberra, ACT, 2601, Australia
| | - William Zhang
- Research School of Chemistry, Australian National University, Canberra, ACT, 2601, Australia
| | - Timothy Altamore
- Research School of Chemistry, Australian National University, Canberra, ACT, 2601, Australia
| | - Chris Easton
- Research School of Chemistry, Australian National University, Canberra, ACT, 2601, Australia
| | - Michelle L Coote
- Research School of Chemistry, Australian National University, Canberra, ACT, 2601, Australia
| | - Shina C L Kamerlin
- Department of Chemistry, BMC, Uppsala University, Box 576, 751 23, Uppsala, Sweden.
| | - Colin J Jackson
- Research School of Chemistry, Australian National University, Canberra, ACT, 2601, Australia.
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15
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Incipient de novo genes can evolve from frozen accidents that escaped rapid transcript turnover. Nat Ecol Evol 2018; 2:1626-1632. [DOI: 10.1038/s41559-018-0639-7] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Accepted: 07/09/2018] [Indexed: 11/08/2022]
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16
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A Mild Procedure for Enone Preparation Catalysed by Bovine Serum Albumin in a Green and Easily Available Medium. Catal Letters 2018. [DOI: 10.1007/s10562-018-2386-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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17
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Vaissier V, Sharma SC, Schaettle K, Zhang T, Head-Gordon T. Computational Optimization of Electric Fields for Improving Catalysis of a Designed Kemp Eliminase. ACS Catal 2017. [DOI: 10.1021/acscatal.7b03151] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Valerie Vaissier
- Chemical
Sciences Division, Lawrence Berkeley National Laboratories, Berkeley, California 94720, United States
| | | | | | | | - Teresa Head-Gordon
- Chemical
Sciences Division, Lawrence Berkeley National Laboratories, Berkeley, California 94720, United States
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18
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Sakamoto S, Komatsu T, Ueno T, Hanaoka K, Urano Y. Fluorescence detection of serum albumin with a turnover-based sensor utilizing Kemp elimination reaction. Bioorg Med Chem Lett 2017; 27:3464-3467. [PMID: 28587820 DOI: 10.1016/j.bmcl.2017.05.076] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Revised: 05/23/2017] [Accepted: 05/25/2017] [Indexed: 11/28/2022]
Abstract
The Kemp elimination reaction is a well-known chemical reaction that is facilitated on a protein surface microenvironment, and in particular is highly accelerated in a unique binding pocket of serum albumin. We have designed and synthesized a fluorescently activatable coumarin derivative with a benzisoxazole scaffold to enable monitoring of the Kemp elimination reaction in terms of fluorescence change for the first time. We show that this fluorescent sensor can sensitively and selectively quantitate serum albumin in blood samples. It also works in a dry-chemistry format.
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Affiliation(s)
- Shingo Sakamoto
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Toru Komatsu
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
| | - Tasuku Ueno
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Kenjiro Hanaoka
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Yasuteru Urano
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan; Graduate School of Medicine, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan; Core Research for Evolutional Science and Technology (CREST) Investigator, Japan Agency for Medical Research and Development (AMED), 1-7-1 Otemachi, Chiyoda-ku, Tokyo 100-0004, Japan.
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19
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Risso VA, Martinez-Rodriguez S, Candel AM, Krüger DM, Pantoja-Uceda D, Ortega-Muñoz M, Santoyo-Gonzalez F, Gaucher EA, Kamerlin SCL, Bruix M, Gavira JA, Sanchez-Ruiz JM. De novo active sites for resurrected Precambrian enzymes. Nat Commun 2017; 8:16113. [PMID: 28719578 PMCID: PMC5520109 DOI: 10.1038/ncomms16113] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Accepted: 05/30/2017] [Indexed: 11/22/2022] Open
Abstract
Protein engineering studies often suggest the emergence of completely new enzyme functionalities to be highly improbable. However, enzymes likely catalysed many different reactions already in the last universal common ancestor. Mechanisms for the emergence of completely new active sites must therefore either plausibly exist or at least have existed at the primordial protein stage. Here, we use resurrected Precambrian proteins as scaffolds for protein engineering and demonstrate that a new active site can be generated through a single hydrophobic-to-ionizable amino acid replacement that generates a partially buried group with perturbed physico-chemical properties. We provide experimental and computational evidence that conformational flexibility can assist the emergence and subsequent evolution of new active sites by improving substrate and transition-state binding, through the sampling of many potentially productive conformations. Our results suggest a mechanism for the emergence of primordial enzymes and highlight the potential of ancestral reconstruction as a tool for protein engineering.
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Affiliation(s)
- Valeria A. Risso
- Departamento de Quimica Fisica, Facultad de Ciencias University of Granada, 18071 Granada, Spain
| | | | - Adela M. Candel
- Departamento de Quimica Fisica, Facultad de Ciencias University of Granada, 18071 Granada, Spain
| | - Dennis M. Krüger
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, BMC Box 596, S-751 24 Uppsala, Sweden
| | - David Pantoja-Uceda
- Departamento de Quimica Fisica Biologica, Instituto de Quimica Fisica Rocasolano, CSIC, c/Serrano 119, 28006-Madrid, Spain
| | - Mariano Ortega-Muñoz
- Departamento de Quimica Organica, Facultad de Ciencias University of Granada, 18071 Granada, Spain
| | | | - Eric A. Gaucher
- School of Biology, School of Chemistry and Biochemistry, Parker H. Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, Georgia 30322, USA
| | - Shina C. L. Kamerlin
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, BMC Box 596, S-751 24 Uppsala, Sweden
| | - Marta Bruix
- Departamento de Quimica Fisica Biologica, Instituto de Quimica Fisica Rocasolano, CSIC, c/Serrano 119, 28006-Madrid, Spain
| | - Jose A. Gavira
- Laboratorio de Estudios Cristalograficos, Instituto Andaluz de Ciencias de la Tierra, CSIC-University of Granada Avenida de la Palmeras 4, Granada, 18100 Armilla, Spain
| | - Jose M. Sanchez-Ruiz
- Departamento de Quimica Fisica, Facultad de Ciencias University of Granada, 18071 Granada, Spain
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20
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Miao Y, Metzner R, Asano Y. Kemp Elimination Catalyzed by Naturally Occurring Aldoxime Dehydratases. Chembiochem 2017; 18:451-454. [PMID: 28120515 DOI: 10.1002/cbic.201600596] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Indexed: 11/10/2022]
Abstract
Recently, the Kemp elimination reaction has been extensively studied in computational enzyme design of new catalysts, as no natural enzyme has evolved to catalyze this reaction. In contrast to in silico enzyme design, we were interested in searching for Kemp eliminase activity in natural enzymes with catalytic promiscuity. Based on similarities of substrate structures and reaction mechanisms, we assumed that the active sites of naturally abundant aldoxime dehydratases have the potential to catalyze the non-natural Kemp elimination reaction. We found several aldoxime dehydratases that are efficient catalysts of this reaction. Although a few natural enzymes have been identified with promiscuous Kemp eliminase activity, to the best of our knowledge, this is a rare example of Kemp elimination catalyzed by naturally occurring enzymes with high catalytic efficiency.
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Affiliation(s)
- Yufeng Miao
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan.,Asano Active Enzyme Molecule Project, ERATO, JST, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan
| | - Richard Metzner
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan.,Asano Active Enzyme Molecule Project, ERATO, JST, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan
| | - Yasuhisa Asano
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan.,Asano Active Enzyme Molecule Project, ERATO, JST, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan
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21
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Lamba V, Sanchez E, Fanning LR, Howe K, Alvarez MA, Herschlag D, Forconi M. Kemp Eliminase Activity of Ketosteroid Isomerase. Biochemistry 2017; 56:582-591. [PMID: 28045505 DOI: 10.1021/acs.biochem.6b00762] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Kemp eliminases represent the most successful class of computationally designed enzymes, with rate accelerations of up to 109-fold relative to the rate of the same reaction in aqueous solution. Nevertheless, several other systems such as micelles, catalytic antibodies, and cavitands are known to accelerate the Kemp elimination by several orders of magnitude. We found that the naturally occurring enzyme ketosteroid isomerase (KSI) also catalyzes the Kemp elimination. Surprisingly, mutations of D38, the residue that acts as a general base for its natural substrate, produced variants that catalyze the Kemp elimination up to 7000-fold better than wild-type KSI does, and some of these variants accelerate the Kemp elimination more than the computationally designed Kemp eliminases. Analysis of the D38N general base KSI variant suggests that a different active site carboxylate residue, D99, performs the proton abstraction. Docking simulations and analysis of inhibition by active site binders suggest that the Kemp elimination takes place in the active site of KSI and that KSI uses the same catalytic strategies of the computationally designed enzymes. In agreement with prior observations, our results strengthen the conclusion that significant rate accelerations of the Kemp elimination can be achieved with very few, nonspecific interactions with the substrate if a suitable catalytic base is present in a hydrophobic environment. Computational design can fulfill these requirements, and the design of more complex and precise environments represents the next level of challenges for protein design.
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Affiliation(s)
- Vandana Lamba
- Department of Biochemistry, Stanford University , Stanford, California 94305, United States
| | - Enis Sanchez
- Department of Chemistry and Biochemistry, College of Charleston , Charleston, South Carolina 29424, United States
| | - Lauren Rose Fanning
- Department of Chemistry and Biochemistry, College of Charleston , Charleston, South Carolina 29424, United States
| | - Kathryn Howe
- Palmetto Homeschool Association , Rock Hill, South Carolina 29730, United States
| | | | - Daniel Herschlag
- Department of Biochemistry, Stanford University , Stanford, California 94305, United States.,Department of Chemistry, Department of Chemical Engineering, and Stanford ChEM-H, Stanford University , Stanford, California 94305, United States
| | - Marcello Forconi
- Department of Chemistry and Biochemistry, College of Charleston , Charleston, South Carolina 29424, United States
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22
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Sanchez E, Lu S, Reed C, Schmidt J, Forconi M. Kemp Elimination in Cationic Micelles: Designed Enzyme-Like Rates Achieved through the Addition of Long-Chain Bases. J PHYS ORG CHEM 2016; 29:185-189. [PMID: 27162418 PMCID: PMC4859443 DOI: 10.1002/poc.3515] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The Kemp elimination is prototypical reaction used to study proton abstraction from carbon. Several hydrophobic systems are known to accelerate this reaction, including two classes of computationally-designed enzymes. However, it is unclear whether these computationally-designed enzymes establish specific interactions with their substrates, as natural enzymes do, or if most of the rate acceleration is due to the hydrophobicity of the substrate. We used a simple system composed of cationic micelles and a long chain base (such as lauryl phosphate or lauric acid) to measure the rate acceleration for the Kemp elimination. Remarkably, we found that this simple system can accelerate the reaction by 4 orders of magnitude, approaching the rates of more complex designed systems. Use of different substrates suggests that the reaction takes place at the interface between the micellar head and water (the Stern layer) with the long-chain base embedded in the micelle and the substrate in the aqueous solution. Thus, we suggest that significant rate accelerations can be achieved regardless of the precise positioning of substrates. Because natural enzymes use specific interactions to position their substrates, we propose that acceleration of the Kemp elimination is not a suitable benchmark for the success of the design process, and we suggest that more complex reactions should be used.
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Affiliation(s)
- Enis Sanchez
- Department of Chemistry and Biochemistry, College of Charleston, 202 Calhoun St, Charleston, SC 29424, U.S.A
| | - Steven Lu
- Academic Magnet High School, 5109 W Enterprise St, North Charleston, SC 29405. U.S.A
| | - Carson Reed
- Department of Chemistry and Biochemistry, College of Charleston, 202 Calhoun St, Charleston, SC 29424, U.S.A
| | - Joshua Schmidt
- Department of Chemistry and Biochemistry, College of Charleston, 202 Calhoun St, Charleston, SC 29424, U.S.A
| | - Marcello Forconi
- Department of Chemistry and Biochemistry, College of Charleston, 202 Calhoun St, Charleston, SC 29424, U.S.A
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23
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Bhowmick A, Sharma SC, Honma H, Head-Gordon T. The role of side chain entropy and mutual information for improving the de novo design of Kemp eliminases KE07 and KE70. Phys Chem Chem Phys 2016; 18:19386-96. [DOI: 10.1039/c6cp03622h] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Side chain entropy and mutual entropy information between residue pairs have been calculated for two de novo designed Kemp eliminase enzymes, KE07 and KE70, and for their most improved versions at the end of laboratory directed evolution (LDE).
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Affiliation(s)
- Asmit Bhowmick
- Department of Chemical and Biomolecular Engineering
- University of California Berkeley
- Berkeley
- USA
| | - Sudhir C. Sharma
- Department of Chemistry
- University of California Berkeley
- Berkeley
- USA
| | - Hallie Honma
- Department of Bioengineering, University of California Berkeley
- Berkeley
- USA
| | - Teresa Head-Gordon
- Department of Chemical and Biomolecular Engineering
- University of California Berkeley
- Berkeley
- USA
- Department of Chemistry
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24
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Świderek K, Tuñón I, Moliner V, Bertran J. Computational strategies for the design of new enzymatic functions. Arch Biochem Biophys 2015; 582:68-79. [PMID: 25797438 PMCID: PMC4554825 DOI: 10.1016/j.abb.2015.03.013] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Revised: 03/09/2015] [Accepted: 03/13/2015] [Indexed: 11/28/2022]
Abstract
In this contribution, recent developments in the design of biocatalysts are reviewed with particular emphasis in the de novo strategy. Studies based on three different reactions, Kemp elimination, Diels-Alder and Retro-Aldolase, are used to illustrate different success achieved during the last years. Finally, a section is devoted to the particular case of designed metalloenzymes. As a general conclusion, the interplay between new and more sophisticated engineering protocols and computational methods, based on molecular dynamics simulations with Quantum Mechanics/Molecular Mechanics potentials and fully flexible models, seems to constitute the bed rock for present and future successful design strategies.
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Affiliation(s)
- K Świderek
- Departament de Química Física, Universitat de València, 46100 Burjasot, Spain; Institute of Applied Radiation Chemistry, Lodz University of Technology, 90-924 Lodz, Poland
| | - I Tuñón
- Departament de Química Física, Universitat de València, 46100 Burjasot, Spain
| | - V Moliner
- Departament de Química Física i Analítica, Universitat Jaume I, 12071 Castellón, Spain
| | - J Bertran
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain.
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25
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Nimnual P, Tummatorn J, Thongsornkleeb C, Ruchirawat S. Utility of Nitrogen Extrusion of Azido Complexes for the Synthesis of Nitriles, Benzoxazoles, and Benzisoxazoles. J Org Chem 2015; 80:8657-67. [DOI: 10.1021/acs.joc.5b01305] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Phongprapan Nimnual
- Program
on Chemical Biology, Center of Excellence on Environmental Health
and Toxicology (EHT), Ministry of Education, Chulabhorn Graduate Institute, 54 Kamphaeng Phet 6, Laksi, Bangkok 10210, Thailand
| | - Jumreang Tummatorn
- Program
on Chemical Biology, Center of Excellence on Environmental Health
and Toxicology (EHT), Ministry of Education, Chulabhorn Graduate Institute, 54 Kamphaeng Phet 6, Laksi, Bangkok 10210, Thailand
- Laboratory
of Medicinal Chemistry, Chulabhorn Research Institute, 54 Kamphaeng
Phet 6, Laksi, Bangkok 10210, Thailand
| | - Charnsak Thongsornkleeb
- Program
on Chemical Biology, Center of Excellence on Environmental Health
and Toxicology (EHT), Ministry of Education, Chulabhorn Graduate Institute, 54 Kamphaeng Phet 6, Laksi, Bangkok 10210, Thailand
- Laboratory
of Medicinal Chemistry, Chulabhorn Research Institute, 54 Kamphaeng
Phet 6, Laksi, Bangkok 10210, Thailand
| | - Somsak Ruchirawat
- Program
on Chemical Biology, Center of Excellence on Environmental Health
and Toxicology (EHT), Ministry of Education, Chulabhorn Graduate Institute, 54 Kamphaeng Phet 6, Laksi, Bangkok 10210, Thailand
- Laboratory
of Medicinal Chemistry, Chulabhorn Research Institute, 54 Kamphaeng
Phet 6, Laksi, Bangkok 10210, Thailand
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26
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Abstract
Albumin emerged as a biocatalyst in 1980 and the continuing interest in this protein is proved by numerous papers.
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Affiliation(s)
| | - Nicoletta Gaggero
- Dipartimento di Scienze Farmaceutiche
- Sezione di Chimica Generale e Organica “A. Marchesini”
- Università degli Studi di Milano
- 20133-Milano
- Italia
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27
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Forconi M. Medium Effects in Biologically Related Catalysis. ADVANCES IN PHYSICAL ORGANIC CHEMISTRY 2015. [DOI: 10.1016/bs.apoc.2015.08.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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28
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Matsumoto K, Asakura S. Albumin-mediated asymmetric nitroaldol reaction of aromatic aldehydes with nitromethane in water. Tetrahedron Lett 2014. [DOI: 10.1016/j.tetlet.2014.10.109] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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29
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Richard JP, Amyes TL, Goryanova B, Zhai X. Enzyme architecture: on the importance of being in a protein cage. Curr Opin Chem Biol 2014; 21:1-10. [PMID: 24699188 DOI: 10.1016/j.cbpa.2014.03.001] [Citation(s) in RCA: 86] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Accepted: 03/01/2014] [Indexed: 11/30/2022]
Abstract
Substrate binding occludes water from the active sites of many enzymes. There is a correlation between the burden to enzymatic catalysis of deprotonation of carbon acids and the substrate immobilization at solvent-occluded active sites for ketosteroid isomerase (KSI--small burden, substrate pKa=13), triosephosphate isomerase (TIM, substrate pKa≈18) and diaminopimelate epimerase (DAP epimerase, large burden, substrate pKa≈29) catalyzed reaction. KSI binds substrates at a surface cleft, TIM binds substrate at an exposed 'cage' formed by closure of flexible loops; and, DAP epimerase binds substrate in a tight cage formed by an 'oyster-like' clamping motion of protein domains. Directed evolution of a solvent-occluded active site at a designed protein catalyst of the Kemp elimination reaction is discussed.
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Affiliation(s)
- John P Richard
- Department of Chemistry, University at Buffalo, SUNY, Buffalo, NY 14260-3000, USA.
| | - Tina L Amyes
- Department of Chemistry, University at Buffalo, SUNY, Buffalo, NY 14260-3000, USA
| | - Bogdana Goryanova
- Department of Chemistry, University at Buffalo, SUNY, Buffalo, NY 14260-3000, USA
| | - Xiang Zhai
- Department of Chemistry, University at Buffalo, SUNY, Buffalo, NY 14260-3000, USA
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30
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Herschlag D, Natarajan A. Fundamental challenges in mechanistic enzymology: progress toward understanding the rate enhancements of enzymes. Biochemistry 2013; 52:2050-67. [PMID: 23488725 DOI: 10.1021/bi4000113] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Enzymes are remarkable catalysts that lie at the heart of biology, accelerating chemical reactions to an astounding extent with extraordinary specificity. Enormous progress in understanding the chemical basis of enzymatic transformations and the basic mechanisms underlying rate enhancements over the past decades is apparent. Nevertheless, it has been difficult to achieve a quantitative understanding of how the underlying mechanisms account for the energetics of catalysis, because of the complexity of enzyme systems and the absence of underlying energetic additivity. We review case studies from our own work that illustrate the power of precisely defined and clearly articulated questions when dealing with such complex and multifaceted systems, and we also use this approach to evaluate our current ability to design enzymes. We close by highlighting a series of questions that help frame some of what remains to be understood, and we encourage the reader to define additional questions and directions that will deepen and broaden our understanding of enzymes and their catalysis.
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Affiliation(s)
- Daniel Herschlag
- Department of Biochemistry, Stanford University School of Medicine , Stanford, California 94305, United States
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31
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Luisi I, Pavan S, Fontanive G, Tossi A, Benedetti F, Savoini A, Maurizio E, Sgarra R, Sblattero D, Berti F. An albumin-derived peptide scaffold capable of binding and catalysis. PLoS One 2013; 8:e56469. [PMID: 23451052 PMCID: PMC3579865 DOI: 10.1371/journal.pone.0056469] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2012] [Accepted: 01/09/2013] [Indexed: 11/18/2022] Open
Abstract
We have identified a 101-amino-acid polypeptide derived from the sequence of the IIA binding site of human albumin. The polypeptide contains residues that make contact with IIA ligands in the parent protein, and eight cysteine residues to form disulfide bridges, that stabilize the polypeptide structure. Seventy-four amino acids are located in six α-helical regions, while the remaining thirty-seven amino acids form six connecting coil/loop regions. A soluble GST fusion protein was expressed in E. coli in yields as high as 4 mg/l. This protein retains the IIA fragment's capacity to bind typical ligands such as warfarin and efavirenz and other albumin's functional properties such as aldolase activity and the ability to direct the stereochemical outcome of a diketone reduction. This newly cloned polypeptide thus represents a valuable starting point for the construction of libraries of binders and catalysts with improved proficiency.
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Affiliation(s)
- Immacolata Luisi
- Dipartimento di Scienze Chimiche e Farmaceutiche, Università di Trieste, Trieste, Italy
- Dipartimento di Scienze della Vita, Università di Trieste, Trieste, Italy
| | - Silvia Pavan
- Dipartimento di Scienze Chimiche e Farmaceutiche, Università di Trieste, Trieste, Italy
| | - Giampaolo Fontanive
- Dipartimento di Scienze Chimiche e Farmaceutiche, Università di Trieste, Trieste, Italy
| | - Alessandro Tossi
- Dipartimento di Scienze della Vita, Università di Trieste, Trieste, Italy
| | - Fabio Benedetti
- Dipartimento di Scienze Chimiche e Farmaceutiche, Università di Trieste, Trieste, Italy
| | | | - Elisa Maurizio
- Dipartimento di Scienze della Vita, Università di Trieste, Trieste, Italy
| | - Riccardo Sgarra
- Dipartimento di Scienze della Vita, Università di Trieste, Trieste, Italy
| | - Daniele Sblattero
- Dipartimento di Scienze della Salute, Università del Piemonte Orientale “Amedeo Avogadro”, Novara, Italy
| | - Federico Berti
- Dipartimento di Scienze Chimiche e Farmaceutiche, Università di Trieste, Trieste, Italy
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Barrozo A, Borstnar R, Marloie G, Kamerlin SCL. Computational protein engineering: bridging the gap between rational design and laboratory evolution. Int J Mol Sci 2012. [PMID: 23202907 PMCID: PMC3497281 DOI: 10.3390/ijms131012428] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Enzymes are tremendously proficient catalysts, which can be used as extracellular catalysts for a whole host of processes, from chemical synthesis to the generation of novel biofuels. For them to be more amenable to the needs of biotechnology, however, it is often necessary to be able to manipulate their physico-chemical properties in an efficient and streamlined manner, and, ideally, to be able to train them to catalyze completely new reactions. Recent years have seen an explosion of interest in different approaches to achieve this, both in the laboratory, and in silico. There remains, however, a gap between current approaches to computational enzyme design, which have primarily focused on the early stages of the design process, and laboratory evolution, which is an extremely powerful tool for enzyme redesign, but will always be limited by the vastness of sequence space combined with the low frequency for desirable mutations. This review discusses different approaches towards computational enzyme design and demonstrates how combining newly developed screening approaches that can rapidly predict potential mutation “hotspots” with approaches that can quantitatively and reliably dissect the catalytic step can bridge the gap that currently exists between computational enzyme design and laboratory evolution studies.
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Affiliation(s)
- Alexandre Barrozo
- Department of Cell and Molecular Biology, Uppsala Biomedical Center (BMC), Uppsala University, Box 596, S-751 24 Uppsala, Sweden; E-Mails: (A.B.); (R.B.); (G.M.)
| | - Rok Borstnar
- Department of Cell and Molecular Biology, Uppsala Biomedical Center (BMC), Uppsala University, Box 596, S-751 24 Uppsala, Sweden; E-Mails: (A.B.); (R.B.); (G.M.)
- Laboratory for Biocomputing and Bioinformatics, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia
| | - Gaël Marloie
- Department of Cell and Molecular Biology, Uppsala Biomedical Center (BMC), Uppsala University, Box 596, S-751 24 Uppsala, Sweden; E-Mails: (A.B.); (R.B.); (G.M.)
| | - Shina Caroline Lynn Kamerlin
- Department of Cell and Molecular Biology, Uppsala Biomedical Center (BMC), Uppsala University, Box 596, S-751 24 Uppsala, Sweden; E-Mails: (A.B.); (R.B.); (G.M.)
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +46-18-471-4423; Fax: +46-18-530-396
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Bridging the gaps in design methodologies by evolutionary optimization of the stability and proficiency of designed Kemp eliminase KE59. Proc Natl Acad Sci U S A 2012; 109:10358-63. [PMID: 22685214 DOI: 10.1073/pnas.1121063109] [Citation(s) in RCA: 174] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Computational design is a test of our understanding of enzyme catalysis and a means of engineering novel, tailor-made enzymes. While the de novo computational design of catalytically efficient enzymes remains a challenge, designed enzymes may comprise unique starting points for further optimization by directed evolution. Directed evolution of two computationally designed Kemp eliminases, KE07 and KE70, led to low to moderately efficient enzymes (k(cat)/K(m) values of ≤ 5 10(4) M(-1)s(-1)). Here we describe the optimization of a third design, KE59. Although KE59 was the most catalytically efficient Kemp eliminase from this design series (by k(cat)/K(m), and by catalyzing the elimination of nonactivated benzisoxazoles), its impaired stability prevented its evolutionary optimization. To boost KE59's evolvability, stabilizing consensus mutations were included in the libraries throughout the directed evolution process. The libraries were also screened with less activated substrates. Sixteen rounds of mutation and selection led to > 2,000-fold increase in catalytic efficiency, mainly via higher k(cat) values. The best KE59 variants exhibited k(cat)/K(m) values up to 0.6 10(6) M(-1)s(-1), and k(cat)/k(uncat) values of ≤ 10(7) almost regardless of substrate reactivity. Biochemical, structural, and molecular dynamics (MD) simulation studies provided insights regarding the optimization of KE59. Overall, the directed evolution of three different designed Kemp eliminases, KE07, KE70, and KE59, demonstrates that computational designs are highly evolvable and can be optimized to high catalytic efficiencies.
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Servant A, Haupt K, Resmini M. Tuning Molecular Recognition in Water-Soluble Nanogels with Enzyme-Like Activity for the Kemp Elimination. Chemistry 2011; 17:11052-9. [DOI: 10.1002/chem.201002747] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2010] [Revised: 05/05/2011] [Indexed: 11/10/2022]
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Frushicheva MP, Cao J, Warshel A. Challenges and advances in validating enzyme design proposals: the case of kemp eliminase catalysis. Biochemistry 2011; 50:3849-58. [PMID: 21443179 DOI: 10.1021/bi200063a] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
One of the fundamental challenges in biotechnology and biochemistry is the ability to design effective enzymes. Despite recent progress, most of the advances on this front have been made by placing the reacting fragments in the proper places, rather than by optimizing the preorganization of the environment, which is the key factor in enzyme catalysis. Thus, rational improvement of the preorganization would require approaches capable of evaluating reliably the actual catalytic effect. This work considers the catalytic effects in different Kemp eliminases as a benchmark for a computer-aided enzyme design. It is shown that the empirical valence bond provides a powerful screening tool, with significant advantages over current alternative strategies. The insights provided by the empirical valence bond calculations are discussed with an emphasis on the ability to analyze the difference between the linear free energy relationships obtained in solution and those found in the enzymes. We also point out the trade-off between the reliability and speed of the calculations and try to determine what it takes to realize reliable computer-aided screening.
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Affiliation(s)
- Maria P Frushicheva
- Department of Chemistry, 418 SGM Building, University of Southern California, 3620 McClintock Avenue, Los Angeles, California 90089-1062, USA
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Abstract
The active sites of enzymes are lined with side chains whose dynamic, geometric, and chemical properties have been finely tuned relative to the corresponding residues in water. For example, the carboxylates of glutamate and aspartate are weakly basic in water but become strongly basic when dehydrated in enzymatic sites. The dehydration of the carboxylate, although intrinsically thermodynamically unfavorable, is achieved by harnessing the free energy of folding and substrate binding to reach the required basicity. Allosterically regulated enzymes additionally rely on the free energy of ligand binding to stabilize the protein in a catalytically competent state. We demonstrate the interplay of protein folding energetics and functional group tuning to convert calmodulin (CaM), a regulatory binding protein, into AlleyCat, an allosterically controlled eliminase. Upon binding Ca(II), native CaM opens a hydrophobic pocket on each of its domains. We computationally identified a mutant that (i) accommodates carboxylate as a general base within these pockets, (ii) interacts productively in the Michaelis complex with the substrate, and (iii) stabilizes the transition state for the reaction. Remarkably, a single mutation of an apolar residue at the bottom of an otherwise hydrophobic cavity confers catalytic activity on calmodulin. AlleyCat showed the expected pH-rate profile, and it was inactivated by mutation of its active site Glu to Gln. A variety of control mutants demonstrated the specificity of the design. The activity of this minimal 75-residue allosterically regulated catalyst is similar to that obtained using more elaborate computational approaches to redesign complex enzymes to catalyze the Kemp elimination reaction.
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Khersonsky O, Röthlisberger D, Wollacott AM, Murphy P, Dym O, Albeck S, Kiss G, Houk KN, Baker D, Tawfik DS. Optimization of the in-silico-designed kemp eliminase KE70 by computational design and directed evolution. J Mol Biol 2011; 407:391-412. [PMID: 21277311 DOI: 10.1016/j.jmb.2011.01.041] [Citation(s) in RCA: 125] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2010] [Accepted: 01/19/2011] [Indexed: 10/18/2022]
Abstract
Although de novo computational enzyme design has been shown to be feasible, the field is still in its infancy: the kinetic parameters of designed enzymes are still orders of magnitude lower than those of naturally occurring ones. Nonetheless, designed enzymes can be improved by directed evolution, as recently exemplified for the designed Kemp eliminase KE07. Random mutagenesis and screening resulted in variants with >200-fold higher catalytic efficiency and provided insights about features missing in the designed enzyme. Here we describe the optimization of KE70, another designed Kemp eliminase. Amino acid substitutions predicted to improve catalysis in design calculations involving extensive backbone sampling were individually tested. Those proven beneficial were combinatorially incorporated into the originally designed KE70 along with random mutations, and the resulting libraries were screened for improved eliminase activity. Nine rounds of mutation and selection resulted in >400-fold improvement in the catalytic efficiency of the original KE70 design, reflected in both higher k(cat) values and lower K(m) values, with the best variants exhibiting k(cat)/K(m) values of >5×10(4) s(-)(1) M(-1). The optimized KE70 variants were characterized structurally and biochemically, providing insights into the origins of the improvements in catalysis. Three primary contributions were identified: first, the reshaping of the active-site cavity to achieve tighter substrate binding; second, the fine-tuning of electrostatics around the catalytic His-Asp dyad; and, third, the stabilization of the active-site dyad in a conformation optimal for catalysis.
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Affiliation(s)
- Olga Khersonsky
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel
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Berti F, Bincoletto S, Donati I, Fontanive G, Fregonese M, Benedetti F. Albumin-directed stereoselective reduction of 1,3-diketones and β-hydroxyketones to anti diols. Org Biomol Chem 2011; 9:1987-99. [DOI: 10.1039/c0ob00648c] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Go MK, Malabanan MM, Amyes TL, Richard JP. Bovine serum albumin-catalyzed deprotonation of [1-(13)C]glycolaldehyde: protein reactivity toward deprotonation of the alpha-hydroxy alpha-carbonyl carbon. Biochemistry 2010; 49:7704-8. [PMID: 20687575 DOI: 10.1021/bi101118g] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Bovine serum albumin (BSA) in D(2)O at 25 degrees C and pD 7.0 was found to catalyze the deuterium exchange reactions of [1-(13)C]glycolaldehyde ([1-(13)C]GA) to form [1-(13)C,2-(2)H]GA and [1-(13)C,2,2-di-(2)H]GA. The formation of [1-(13)C,2-(2)H]GA and [1-(13)C,2,2-di-(2)H]GA in a total yield of 51 +/- 3% was observed at early reaction times, and at later times, [1-(13)C,2-(2)H]GA was found to undergo BSA-catalyzed conversion to [1-(13)C,2,2-di-(2)H]GA. The overall second-order rate constant for these deuterium exchange reactions [(k(E))(P)] equals 0.25 M(-1) s(-1). By comparison, (k(E))(P) values of 0.04 M(-1) s(-1) [Go, M. K., Amyes, T. L., and Richard, J. P. (2009) Biochemistry 48, 5769-5778] and 0.06 M(-1) s(-1) [Go, M. K., Koudelka, A., Amyes, T. L., and Richard, J. P. (2010) Biochemistry 49, 5377-5389] have been determined for the wild-type- and K12G mutant TIM-catalyzed deuterium exchange reactions of [1-(13)C]GA, respectively, to form [1-(13)C,2,2-di-(2)H]GA. These data show that TIM and BSA exhibit a modest catalytic activity toward deprotonation of the alpha-hydroxy alpha-carbonyl carbon. We suggest that this activity is intrinsic to many globular proteins, and that it must be enhanced to demonstrate meaningful de novo design of protein catalysts of proton transfer at alpha-carbonyl carbon.
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Affiliation(s)
- Maybelle K Go
- Department of Chemistry, University at Buffalo, State University of New York, Buffalo, New York 14260, USA
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Evolutionary Optimization of Computationally Designed Enzymes: Kemp Eliminases of the KE07 Series. J Mol Biol 2010; 396:1025-42. [DOI: 10.1016/j.jmb.2009.12.031] [Citation(s) in RCA: 133] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2009] [Revised: 12/15/2009] [Accepted: 12/17/2009] [Indexed: 11/17/2022]
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42
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D'Anna F, La Marca S, Lo Meo P, Noto R. A Study of the Influence of Ionic Liquids Properties on the Kemp Elimination Reaction. Chemistry 2009; 15:7896-7902. [DOI: 10.1002/chem.200900148] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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D’Anna F, Marca SL, Noto R. Kemp Elimination: A Probe Reaction To Study Ionic Liquids Properties. J Org Chem 2008; 73:3397-403. [DOI: 10.1021/jo702662z] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Francesca D’Anna
- Dipartimento di Chimica Organica “E. Paternò”, Università degli Studi di Palermo, Viale delle Scienze, Parco d’Orleans II, 90128 Palermo, Italy
| | - Sandra La Marca
- Dipartimento di Chimica Organica “E. Paternò”, Università degli Studi di Palermo, Viale delle Scienze, Parco d’Orleans II, 90128 Palermo, Italy
| | - Renato Noto
- Dipartimento di Chimica Organica “E. Paternò”, Università degli Studi di Palermo, Viale delle Scienze, Parco d’Orleans II, 90128 Palermo, Italy
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Kemp elimination catalysts by computational enzyme design. Nature 2008; 453:190-5. [PMID: 18354394 DOI: 10.1038/nature06879] [Citation(s) in RCA: 929] [Impact Index Per Article: 58.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2007] [Accepted: 03/03/2008] [Indexed: 11/08/2022]
Abstract
The design of new enzymes for reactions not catalysed by naturally occurring biocatalysts is a challenge for protein engineering and is a critical test of our understanding of enzyme catalysis. Here we describe the computational design of eight enzymes that use two different catalytic motifs to catalyse the Kemp elimination-a model reaction for proton transfer from carbon-with measured rate enhancements of up to 10(5) and multiple turnovers. Mutational analysis confirms that catalysis depends on the computationally designed active sites, and a high-resolution crystal structure suggests that the designs have close to atomic accuracy. Application of in vitro evolution to enhance the computational designs produced a >200-fold increase in k(cat)/K(m) (k(cat)/K(m) of 2,600 M(-1)s(-1) and k(cat)/k(uncat) of >10(6)). These results demonstrate the power of combining computational protein design with directed evolution for creating new enzymes, and we anticipate the creation of a wide range of useful new catalysts in the future.
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45
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Shi FQ, Li X, Xia Y, Zhang L, Yu ZX. DFT Study of the Mechanisms of In Water Au(I)-Catalyzed Tandem [3,3]-Rearrangement/Nazarov Reaction/[1,2]-Hydrogen Shift of Enynyl Acetates: A Proton-Transport Catalysis Strategy in the Water-Catalyzed [1,2]-Hydrogen Shift. J Am Chem Soc 2007; 129:15503-12. [DOI: 10.1021/ja071070+] [Citation(s) in RCA: 266] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Woycechowsky KJ, Vamvaca K, Hilvert D. Novel enzymes through design and evolution. ADVANCES IN ENZYMOLOGY AND RELATED AREAS OF MOLECULAR BIOLOGY 2007; 75:241-94, xiii. [PMID: 17124869 DOI: 10.1002/9780471224464.ch4] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The generation of enzymes with new catalytic activities remains a major challenge. So far, several different strategies have been developed to tackle this problem, including site-directed mutagenesis, random mutagenesis (directed evolution), antibody catalysis, computational redesign, and de novo methods. Using these techniques, a broad array of novel enzymes has been created (aldolases, decarboxylases, dehydratases, isomerases, oxidases, reductases, and others), although their low efficiencies (10 to 100 M(-1) s(-l)) compared to those of the best natural enzymes (10(6) to 10(8) M(-1) s(-1)) remains a significant concern. Whereas rational design might be the most promising and versatile approach to generating new activities, directed evolution seems to be the best way to optimize the catalytic properties of novel enzymes. Indeed, impressive successes in enzyme engineering have resulted from a combination of rational and random design.
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Gautier A, Pitrat D, Hasserodt J. An unusual functional group interaction and its potential to reproduce steric and electrostatic features of the transition states of peptidolysis. Bioorg Med Chem 2006; 14:3835-47. [PMID: 16464600 DOI: 10.1016/j.bmc.2006.01.031] [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] [Received: 10/28/2005] [Revised: 01/13/2006] [Accepted: 01/17/2006] [Indexed: 10/25/2022]
Abstract
The donor-acceptor interaction between a tertiary amine and an aldehyde, first observed among a select class of alkaloids, was deliberately established in a peptidomimetic (1a-c) to mimic features of the two principal transition states of peptide hydrolysis. Compounds 1a-c show preferential adoption in methanol and water of a 'folded' conformation displaying the interaction. Proportions of the folded form in MeOH range from 45% to 70% and can reach 84% in buffer. Significantly, three tendencies for the folded/unfolded equilibrium are observed: increasing solubility and polarity of the medium and decreasing temperature results in a higher extent of folding. In the absence of any parameter set available for this weak bond, no modeling studies were conducted to aid in the design of 1a-c. The successful straightforward synthesis of 1 and its folding and inhibition results with HIV-1 peptidase using FRET technology encourage studies to further pre-organize candidate molecules and to screen the structure space by modeling and parallel combinatorial chemistry.
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Affiliation(s)
- Arnaud Gautier
- Laboratoire de Chimie, UMR 5182 ENS/CNRS, Ecole Normale Supérieure de Lyon, 46 allée d'Italie, 69364 Lyon cedex 07, France
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Acevedo O, Jorgensen WL. Influence of inter- and intramolecular hydrogen bonding on kemp decarboxylations from QM/MM simulations. J Am Chem Soc 2005; 127:8829-34. [PMID: 15954791 DOI: 10.1021/ja051793y] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The Kemp decarboxylation reaction for benzisoxazole-3-carboxylic acid derivatives has been investigated using QM/MM calculations in protic and dipolar aprotic solvents. Aprotic solvents have been shown to accelerate the rates of reaction by 7-8 orders of magnitude over water; however, the inclusion of an internal hydrogen bond effectively inhibits the reaction with near solvent independence. The effects of solvation and intramolecular hydrogen bonding on the reactants, transition structures, and the rate of reaction are elucidated using two-dimensional potentials of mean force (PMF) derived from free energy perturbation calculations in Monte Carlo simulations (MC/FEP). Free energies of activation in six solvents have been computed to be in close agreement with experiment. Solute-solvent interaction energies show that poorer solvation of the reactant anion in the dipolar aprotic solvents is primarily responsible for the observed rate enhancements over protic media. In addition, a discrepancy for the experimental rate in chloroform has been studied in detail with the conclusion that ion-pairing between the reactant anion and tetramethylguanidinium counterion is responsible for the anomalously slow reaction rate. The overall quantitative success of the computations supports the present QM/MM/MC approach, which features PDDG/PM3 as the QM method.
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Affiliation(s)
- Orlando Acevedo
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520-8107, USA
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49
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Seebeck FP, Hilvert D. Positional ordering of reacting groups contributes significantly to the efficiency of proton transfer at an antibody active site. J Am Chem Soc 2005; 127:1307-12. [PMID: 15669871 DOI: 10.1021/ja044647l] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Catalytic antibody 34E4 accelerates the conversion of benzisoxazoles to salicylonitriles with surprising efficiency, exploiting a carboxylate base with an elevated pKa for proton abstraction. Mutagenesis of this antibody, produced as a chimeric Fab, confirms the prediction of a homology model that GluH50 is the essential catalytic residue. Replacement of this residue by glutamine, alanine, or glycine reduces catalytic activity by more than 2.6 x 10(4)-fold. By comparing the chemical proficiencies of the parent antibody with the chemical proficiencies of acetate and the mutants, the effective concentration of the catalytic side chain was estimated to be >51 000 M. The 2.1 kcal/mol destabilization of the transition state observed when GluH50 is replaced by aspartate suggests that positional ordering imposed by the antibody active site contributes significantly to the efficiency of proton transfer. The observation that the GluH50Ala and GluH50Gly variants could not be chemically rescued by exogenous addition of high concentrations of formate or acetate further underscores the advantage the antibody derives from covalently fixing its base at the active site. Although medium effects also play an important role in 34E4, for example in enhancing the reactivity of the carboxylate side chain through desolvation, comparison of 34E4 with less proficient antibodies shows that positioning a carboxylate in a hydrophobic binding pocket alone is insufficient for efficient general base catalysis. Our results demonstrate that structural complementarity between the antibody and its substrate in the transition state is an important and necessary component of 34E4's high activity. By harnessing an additional catalytic group that could serve as a general acid to stabilize developing negative charge in the leaving group, overall efficiencies rivaling those of highly evolved enzymes should be accessible.
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Affiliation(s)
- Florian P Seebeck
- Laboratorium für Organische Chemie, Swiss Federal Institute of Technology, ETH Hönggerberg, CH-8093, Zürich, Switzerland
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50
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Debler EW, Ito S, Seebeck FP, Heine A, Hilvert D, Wilson IA. Structural origins of efficient proton abstraction from carbon by a catalytic antibody. Proc Natl Acad Sci U S A 2005; 102:4984-9. [PMID: 15788533 PMCID: PMC555987 DOI: 10.1073/pnas.0409207102] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2004] [Indexed: 11/18/2022] Open
Abstract
Antibody 34E4 catalyzes the conversion of benzisoxazoles to salicylonitriles with high rates and multiple turnovers. The crystal structure of its complex with the benzimidazolium hapten at 2.5-angstroms resolution shows that a combination of hydrogen bonding, pi stacking, and van der Waals interactions is exploited to position both the base, Glu(H50), and the substrate for efficient proton transfer. Suboptimal placement of the catalytic carboxylate, as observed in the 2.8-angstroms structure of the Glu(H50)Asp variant, results in substantially reduced catalytic efficiency. In addition to imposing high positional order on the transition state, the antibody pocket provides a highly structured microenvironment for the reaction in which the carboxylate base is activated through partial desolvation, and the highly polarizable transition state is stabilized by dispersion interactions with the aromatic residue Trp(L91) and solvation of the leaving group oxygen by external water. The enzyme-like efficiency of general base catalysis in this system directly reflects the original hapten design, in which a charged guanidinium moiety was strategically used to elicit an accurately positioned functional group in an appropriate reaction environment and suggests that even larger catalytic effects may be achievable by extending this approach to the induction of acid-base pairs capable of bifunctional catalysis.
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Affiliation(s)
- Erik W Debler
- Department of Molecular Biology and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
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