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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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2
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Mohammed TA, Meier CM, Kalvoda T, Kalt M, Rulíšek L, Shoshan MS. Potent Cyclic Tetrapeptide for Lead Detoxification. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202103217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Tagwa A. Mohammed
- Department of Chemistry University of Zurich Winterthurerstrasse 190 8057 Zurich Switzerland
| | - Christoph M. Meier
- Department of Chemistry University of Zurich Winterthurerstrasse 190 8057 Zurich Switzerland
| | - Tadeáš Kalvoda
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Flemingovo náměstí 2 16610 Praha 6 Czech Republic
| | - Martina Kalt
- Department of Chemistry University of Zurich Winterthurerstrasse 190 8057 Zurich Switzerland
| | - Lubomír Rulíšek
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Flemingovo náměstí 2 16610 Praha 6 Czech Republic
| | - Michal S. Shoshan
- Department of Chemistry University of Zurich Winterthurerstrasse 190 8057 Zurich Switzerland
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Mohammed TA, Meier CM, Kalvoda T, Kalt M, Rulíšek L, Shoshan MS. Potent Cyclic Tetrapeptide for Lead Detoxification. Angew Chem Int Ed Engl 2021; 60:12381-12385. [PMID: 33759306 DOI: 10.1002/anie.202103217] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Indexed: 11/05/2022]
Abstract
Lead (Pb) is a ubiquitous poisonous metal, affecting the health of vast populations worldwide. Medications to treat Pb poisoning suffer from various limitations and are often toxic owing to insufficient metal selectivity. Here, we report a cyclic tetrapeptide that selectively binds Pb and eradicates its toxic effect on the cellular level, with superior potency than state-of-the-art drugs. The Pb-peptide complex is remarkably strong and was characterized experimentally and computationally. Accompanied by the lack of toxicity and enhanced stability of this peptide, these qualities indicate its merit as a potential remedy for Pb poisoning.
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Affiliation(s)
- Tagwa A Mohammed
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Christoph M Meier
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Tadeáš Kalvoda
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo náměstí 2, 16610, Praha 6, Czech Republic
| | - Martina Kalt
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Lubomír Rulíšek
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo náměstí 2, 16610, Praha 6, Czech Republic
| | - Michal S Shoshan
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
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Pinter TBJ, Koebke KJ, Pecoraro VL. Catalysis and Electron Transfer in De Novo Designed Helical Scaffolds. Angew Chem Int Ed Engl 2020; 59:7678-7699. [PMID: 31441170 PMCID: PMC7035182 DOI: 10.1002/anie.201907502] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2019] [Indexed: 12/31/2022]
Abstract
The relationship between protein structure and function is one of the greatest puzzles within biochemistry. De novo metalloprotein design is a way to wipe the board clean and determine what is required to build in function from the ground up in an unrelated structure. This Review focuses on protein design efforts to create de novo metalloproteins within alpha-helical scaffolds. Examples of successful designs include those with carbonic anhydrase or nitrite reductase activity by incorporating a ZnHis3 or CuHis3 site, or that recapitulate the spectroscopic properties of unique electron-transfer sites in cupredoxins (CuHis2 Cys) or rubredoxins (FeCys4 ). This work showcases the versatility of alpha helices as scaffolds for metalloprotein design and the progress that is possible through careful rational design. Our studies cover the invariance of carbonic anhydrase activity with different site positions and scaffolds, refinement of our cupredoxin models, and enhancement of nitrite reductase activity up to 1000-fold.
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Affiliation(s)
- Tyler B. J. Pinter
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, United States, 48109-1055
| | - Karl J. Koebke
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, United States, 48109-1055
| | - Vincent L. Pecoraro
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, United States, 48109-1055
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Pinter TBJ, Koebke KJ, Pecoraro VL. Katalyse und Elektronentransfer in helikalen De‐novo‐Gerüststrukturen. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201907502] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Tyler B. J. Pinter
- Department of Chemistry University of Michigan Ann Arbor Michigan 48109-1055 USA
| | - Karl J. Koebke
- Department of Chemistry University of Michigan Ann Arbor Michigan 48109-1055 USA
| | - Vincent L. Pecoraro
- Department of Chemistry University of Michigan Ann Arbor Michigan 48109-1055 USA
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Taylor LLK, Riddell IA, Smulders MMJ. Selbstorganisation von funktionellen diskreten dreidimensionalen Architekturen in Wasser. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201806297] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Lauren L. K. Taylor
- School of Chemistry; University of Manchester; Oxford Road M13 9PL Großbritannien
| | - Imogen A. Riddell
- School of Chemistry; University of Manchester; Oxford Road M13 9PL Großbritannien
| | - Maarten M. J. Smulders
- Laboratory of Organic Chemistry; Wageningen University, P.O. Box 8026; 6700EG Wageningen Niederlande
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Taylor LLK, Riddell IA, Smulders MMJ. Self-Assembly of Functional Discrete Three-Dimensional Architectures in Water. Angew Chem Int Ed Engl 2018; 58:1280-1307. [DOI: 10.1002/anie.201806297] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Indexed: 01/01/2023]
Affiliation(s)
| | - Imogen A. Riddell
- School of Chemistry; University of Manchester; Oxford Road M13 9PL UK
| | - Maarten M. J. Smulders
- Laboratory of Organic Chemistry; Wageningen University, P.O. Box 8026; 6700EG Wageningen The Netherlands
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Tebo AG, Quaranta A, Herrero C, Pecoraro VL, Aukauloo A. Intramolecular Photogeneration of a Tyrosine Radical in a Designed Protein. CHEMPHOTOCHEM 2017; 1:89-92. [PMID: 29046892 DOI: 10.1002/cptc.201600044] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Long-distance biological electron transfer occurs through a hopping mechanism and often involves tyrosine as a high potential intermediate, for example in the early charge separation steps during photosynthesis. Protein design allows for the development of minimal systems to study the underlying principles of complex systems. Herein, we report the development of the first ruthenium-linked designed protein for the photogeneration of a tyrosine radical by intramolecular electron transfer.
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Affiliation(s)
- Alison G Tebo
- Dr. A. G. Tebo, Prof. V. L. Pecoraro, Department of Chemistry, University of Michigan, Ann Arbor, MI 48109 (USA)
| | - Annamaria Quaranta
- Dr. A. Quaranta, Prof. A. Aukauloo, CEA Saclay, iBiTecS, Service de Bioénergétique Biologie Structurale et Mécanismes (SB2SM), Gif-sur-Yvette, 91191 (France)
| | - Christian Herrero
- Dr. C. Herrero, Prof. A. Aukauloo, Institut de Chimie Moléculaire et des Matériaux D'Orsay, Université Paris Sud, Université Paris Saclay, CNRS UMR 8182, 91405 Orsay Cedex (France)
| | - Vincent L Pecoraro
- Dr. A. G. Tebo, Prof. V. L. Pecoraro, Department of Chemistry, University of Michigan, Ann Arbor, MI 48109 (USA)
| | - Ally Aukauloo
- Dr. C. Herrero, Prof. A. Aukauloo, Institut de Chimie Moléculaire et des Matériaux D'Orsay, Université Paris Sud, Université Paris Saclay, CNRS UMR 8182, 91405 Orsay Cedex (France).,Dr. A. Quaranta, Prof. A. Aukauloo, CEA Saclay, iBiTecS, Service de Bioénergétique Biologie Structurale et Mécanismes (SB2SM), Gif-sur-Yvette, 91191 (France)
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Cangelosi VM, Deb A, Penner-Hahn JE, Pecoraro VL. A De Novo Designed Metalloenzyme for the Hydration of CO2. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201404925] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Cangelosi VM, Deb A, Penner-Hahn JE, Pecoraro VL. A de novo designed metalloenzyme for the hydration of CO2. Angew Chem Int Ed Engl 2014; 53:7900-3. [PMID: 24943466 DOI: 10.1002/anie.201404925] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2014] [Indexed: 11/07/2022]
Abstract
Protein design will ultimately allow for the creation of artificial enzymes with novel functions and unprecedented stability. To test our current mastery of nature's approach to catalysis, a Zn(II) metalloenzyme was prepared using de novo design. α3DH3 folds into a stable single-stranded three-helix bundle and binds Zn(II) with high affinity using His3 O coordination. The resulting metalloenzyme catalyzes the hydration of CO2 better than any small molecule model of carbonic anhydrase and with an efficiency within 1400-fold of the fastest carbonic anhydrase isoform, CAII, and 11-fold of CAIII.
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Liu X, Li J, Hu C, Zhou Q, Zhang W, Hu M, Zhou J, Wang J. Significant Expansion of the Fluorescent Protein Chromophore through the Genetic Incorporation of a Metal-Chelating Unnatural Amino Acid. Angew Chem Int Ed Engl 2013; 52:4805-9. [DOI: 10.1002/anie.201301307] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2013] [Indexed: 02/04/2023]
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Liu X, Li J, Hu C, Zhou Q, Zhang W, Hu M, Zhou J, Wang J. Significant Expansion of the Fluorescent Protein Chromophore through the Genetic Incorporation of a Metal-Chelating Unnatural Amino Acid. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201301307] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Kiss G, Çelebi-Ölçüm N, Moretti R, Baker D, Houk KN. Computational enzyme design. Angew Chem Int Ed Engl 2013; 52:5700-25. [PMID: 23526810 DOI: 10.1002/anie.201204077] [Citation(s) in RCA: 355] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2012] [Indexed: 11/07/2022]
Abstract
Recent developments in computational chemistry and biology have come together in the "inside-out" approach to enzyme engineering. Proteins have been designed to catalyze reactions not previously accelerated in nature. Some of these proteins fold and act as catalysts, but the success rate is still low. The achievements and limitations of the current technology are highlighted and contrasted to other protein engineering techniques. On its own, computational "inside-out" design can lead to the production of catalytically active and selective proteins, but their kinetic performances fall short of natural enzymes. When combined with directed evolution, molecular dynamics simulations, and crowd-sourced structure-prediction approaches, however, computational designs can be significantly improved in terms of binding, turnover, and thermal stability.
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Affiliation(s)
- Gert Kiss
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 607 Charles E. Young Dr. East, Los Angeles, CA 90095, USA
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Kiss G, Çelebi-Ölçüm N, Moretti R, Baker D, Houk KN. Computerbasiertes Enzymdesign. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201204077] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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