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Van Stappen C, Deng Y, Liu Y, Heidari H, Wang JX, Zhou Y, Ledray AP, Lu Y. Designing Artificial Metalloenzymes by Tuning of the Environment beyond the Primary Coordination Sphere. Chem Rev 2022; 122:11974-12045. [PMID: 35816578 DOI: 10.1021/acs.chemrev.2c00106] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Metalloenzymes catalyze a variety of reactions using a limited number of natural amino acids and metallocofactors. Therefore, the environment beyond the primary coordination sphere must play an important role in both conferring and tuning their phenomenal catalytic properties, enabling active sites with otherwise similar primary coordination environments to perform a diverse array of biological functions. However, since the interactions beyond the primary coordination sphere are numerous and weak, it has been difficult to pinpoint structural features responsible for the tuning of activities of native enzymes. Designing artificial metalloenzymes (ArMs) offers an excellent basis to elucidate the roles of these interactions and to further develop practical biological catalysts. In this review, we highlight how the secondary coordination spheres of ArMs influence metal binding and catalysis, with particular focus on the use of native protein scaffolds as templates for the design of ArMs by either rational design aided by computational modeling, directed evolution, or a combination of both approaches. In describing successes in designing heme, nonheme Fe, and Cu metalloenzymes, heteronuclear metalloenzymes containing heme, and those ArMs containing other metal centers (including those with non-native metal ions and metallocofactors), we have summarized insights gained on how careful controls of the interactions in the secondary coordination sphere, including hydrophobic and hydrogen bonding interactions, allow the generation and tuning of these respective systems to approach, rival, and, in a few cases, exceed those of native enzymes. We have also provided an outlook on the remaining challenges in the field and future directions that will allow for a deeper understanding of the secondary coordination sphere a deeper understanding of the secondary coordintion sphere to be gained, and in turn to guide the design of a broader and more efficient variety of ArMs.
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Affiliation(s)
- Casey Van Stappen
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States
| | - Yunling Deng
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States
| | - Yiwei Liu
- Department of Chemistry, University of Illinois, Urbana-Champaign, 505 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Hirbod Heidari
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States
| | - Jing-Xiang Wang
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States
| | - Yu Zhou
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States
| | - Aaron P Ledray
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States
| | - Yi Lu
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States.,Department of Chemistry, University of Illinois, Urbana-Champaign, 505 South Mathews Avenue, Urbana, Illinois 61801, United States
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Hou C, Zhao G, Xu D, Zhao B. Enantioselective biomimetic transamination of α-keto acids catalyzed by H4-naphthalene-derived axially chiral biaryl pyridoxamines. Tetrahedron Lett 2018. [DOI: 10.1016/j.tetlet.2018.01.089] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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Schwizer F, Okamoto Y, Heinisch T, Gu Y, Pellizzoni MM, Lebrun V, Reuter R, Köhler V, Lewis JC, Ward TR. Artificial Metalloenzymes: Reaction Scope and Optimization Strategies. Chem Rev 2017; 118:142-231. [PMID: 28714313 DOI: 10.1021/acs.chemrev.7b00014] [Citation(s) in RCA: 465] [Impact Index Per Article: 66.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The incorporation of a synthetic, catalytically competent metallocofactor into a protein scaffold to generate an artificial metalloenzyme (ArM) has been explored since the late 1970's. Progress in the ensuing years was limited by the tools available for both organometallic synthesis and protein engineering. Advances in both of these areas, combined with increased appreciation of the potential benefits of combining attractive features of both homogeneous catalysis and enzymatic catalysis, led to a resurgence of interest in ArMs starting in the early 2000's. Perhaps the most intriguing of potential ArM properties is their ability to endow homogeneous catalysts with a genetic memory. Indeed, incorporating a homogeneous catalyst into a genetically encoded scaffold offers the opportunity to improve ArM performance by directed evolution. This capability could, in turn, lead to improvements in ArM efficiency similar to those obtained for natural enzymes, providing systems suitable for practical applications and greater insight into the role of second coordination sphere interactions in organometallic catalysis. Since its renaissance in the early 2000's, different aspects of artificial metalloenzymes have been extensively reviewed and highlighted. Our intent is to provide a comprehensive overview of all work in the field up to December 2016, organized according to reaction class. Because of the wide range of non-natural reactions catalyzed by ArMs, this was done using a functional-group transformation classification. The review begins with a summary of the proteins and the anchoring strategies used to date for the creation of ArMs, followed by a historical perspective. Then follows a summary of the reactions catalyzed by ArMs and a concluding critical outlook. This analysis allows for comparison of similar reactions catalyzed by ArMs constructed using different metallocofactor anchoring strategies, cofactors, protein scaffolds, and mutagenesis strategies. These data will be used to construct a searchable Web site on ArMs that will be updated regularly by the authors.
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Affiliation(s)
- Fabian Schwizer
- Department of Chemistry, Spitalstrasse 51, University of Basel , CH-4056 Basel, Switzerland
| | - Yasunori Okamoto
- Department of Chemistry, Spitalstrasse 51, University of Basel , CH-4056 Basel, Switzerland
| | - Tillmann Heinisch
- Department of Chemistry, Spitalstrasse 51, University of Basel , CH-4056 Basel, Switzerland
| | - Yifan Gu
- Searle Chemistry Laboratory, University of Chicago , 5735 S. Ellis Ave., Chicago, Illinois 60637, United States
| | - Michela M Pellizzoni
- Department of Chemistry, Spitalstrasse 51, University of Basel , CH-4056 Basel, Switzerland
| | - Vincent Lebrun
- Department of Chemistry, Spitalstrasse 51, University of Basel , CH-4056 Basel, Switzerland
| | - Raphael Reuter
- Department of Chemistry, Spitalstrasse 51, University of Basel , CH-4056 Basel, Switzerland
| | - Valentin Köhler
- Department of Chemistry, Spitalstrasse 51, University of Basel , CH-4056 Basel, Switzerland
| | - Jared C Lewis
- Searle Chemistry Laboratory, University of Chicago , 5735 S. Ellis Ave., Chicago, Illinois 60637, United States
| | - Thomas R Ward
- Department of Chemistry, Spitalstrasse 51, University of Basel , CH-4056 Basel, Switzerland
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Affiliation(s)
- Xiaoyu Lan
- The Education Ministry Key
Lab of Resource Chemistry and Shanghai Key Laboratory of Rare Earth
Functional Materials, Shanghai Normal University, Shanghai 200234, P. R. China
| | - Chuangan Tao
- The Education Ministry Key
Lab of Resource Chemistry and Shanghai Key Laboratory of Rare Earth
Functional Materials, Shanghai Normal University, Shanghai 200234, P. R. China
| | - Xuliang Liu
- The Education Ministry Key
Lab of Resource Chemistry and Shanghai Key Laboratory of Rare Earth
Functional Materials, Shanghai Normal University, Shanghai 200234, P. R. China
| | - Aina Zhang
- The Education Ministry Key
Lab of Resource Chemistry and Shanghai Key Laboratory of Rare Earth
Functional Materials, Shanghai Normal University, Shanghai 200234, P. R. China
| | - Baoguo Zhao
- The Education Ministry Key
Lab of Resource Chemistry and Shanghai Key Laboratory of Rare Earth
Functional Materials, Shanghai Normal University, Shanghai 200234, P. R. China
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Shi L, Tao C, Yang Q, Liu YE, Chen J, Chen J, Tian J, Liu F, Li B, Du Y, Zhao B. Chiral Pyridoxal-Catalyzed Asymmetric Biomimetic Transamination of α-Keto Acids. Org Lett 2015; 17:5784-7. [DOI: 10.1021/acs.orglett.5b02895] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Limin Shi
- The Education Ministry Key
Lab of Resource Chemistry and Shanghai Key Laboratory of Rare Earth
Functional Materials, Shanghai Normal University, Shanghai 200234, P. R. China
| | - Chuangan Tao
- The Education Ministry Key
Lab of Resource Chemistry and Shanghai Key Laboratory of Rare Earth
Functional Materials, Shanghai Normal University, Shanghai 200234, P. R. China
| | - Qin Yang
- The Education Ministry Key
Lab of Resource Chemistry and Shanghai Key Laboratory of Rare Earth
Functional Materials, Shanghai Normal University, Shanghai 200234, P. R. China
| | - Yong Ethan Liu
- The Education Ministry Key
Lab of Resource Chemistry and Shanghai Key Laboratory of Rare Earth
Functional Materials, Shanghai Normal University, Shanghai 200234, P. R. China
| | - Jing Chen
- The Education Ministry Key
Lab of Resource Chemistry and Shanghai Key Laboratory of Rare Earth
Functional Materials, Shanghai Normal University, Shanghai 200234, P. R. China
| | - Jianfeng Chen
- The Education Ministry Key
Lab of Resource Chemistry and Shanghai Key Laboratory of Rare Earth
Functional Materials, Shanghai Normal University, Shanghai 200234, P. R. China
| | - Jiaxin Tian
- The Education Ministry Key
Lab of Resource Chemistry and Shanghai Key Laboratory of Rare Earth
Functional Materials, Shanghai Normal University, Shanghai 200234, P. R. China
| | - Feng Liu
- The Education Ministry Key
Lab of Resource Chemistry and Shanghai Key Laboratory of Rare Earth
Functional Materials, Shanghai Normal University, Shanghai 200234, P. R. China
| | - Bo Li
- The Education Ministry Key
Lab of Resource Chemistry and Shanghai Key Laboratory of Rare Earth
Functional Materials, Shanghai Normal University, Shanghai 200234, P. R. China
| | - Yongling Du
- The Education Ministry Key
Lab of Resource Chemistry and Shanghai Key Laboratory of Rare Earth
Functional Materials, Shanghai Normal University, Shanghai 200234, P. R. China
| | - Baoguo Zhao
- The Education Ministry Key
Lab of Resource Chemistry and Shanghai Key Laboratory of Rare Earth
Functional Materials, Shanghai Normal University, Shanghai 200234, P. R. China
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Chruma JJ, Liu L, Zhou W, Breslow R. Hydrophobic and electronic factors in the design of dialkylglycine decarboxylase mimics. Bioorg Med Chem 2005; 13:5873-83. [PMID: 15953728 DOI: 10.1016/j.bmc.2005.05.019] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2005] [Accepted: 05/10/2005] [Indexed: 10/25/2022]
Abstract
The first functional catalytic mimic of the enzyme dialkylglycine decarboxylase is described. This system utilizes a hydrophobically modified polyethylenimine polymer, a pyridoxamine cofactor, and a 2-aryl-2-alkylglycine sacrificial amine source to convert alpha-keto acids to alpha-amino acids at biologically relevant temperatures with multiple turnovers of the pyridoxamine catalyst. The effects of hydrophobic and electronic factors in the 2,2-disubstituted sacrificial amine source and the pyridoxamine catalyst on turnover frequency and turnover number are explored.
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Affiliation(s)
- Jason J Chruma
- Columbia University, Department of Chemistry, 3000 Broadway, New York, NY 10027, USA
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Affiliation(s)
- D Qi
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, USA
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Häring D, Kuang H, Qi D, Distefano MD. Converting a fatty acid binding protein to an artificial transaminase: novel catalysts by chemical and genetic modification of a protein cavity. ACTA ACUST UNITED AC 2001; 11:967-70. [DOI: 10.1016/s1381-1177(00)00051-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Imperiali B, Mcdonnell KA, Shogren-knaak M. Design and Construction of Novel Peptides and Proteins by Tailored Incorporation of Coenzyme Functionality. In: Schmidtchen FP, Baltzer L, Chamberlin AR, Mcdonnell KA, Famulok M, Gilmore MA, Imperiali B, Jenne A, Shogren-knaak M, Steward LE, editors. Implementation and Redesign of Catalytic Function in Biopolymers. Berlin: Springer Berlin Heidelberg; 1999. pp. 1-38. [DOI: 10.1007/3-540-48990-8_1] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
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Davies RR, Kuang H, Qi D, Mazhary A, Mayaan E, Distefano MD. Artificial metalloenzymes based on protein cavities: exploring the effect of altering the metal ligand attachment position by site directed mutagenesis. Bioorg Med Chem Lett 1999; 9:79-84. [PMID: 9990461 DOI: 10.1016/s0960-894x(98)00684-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
In an effort to construct catalysts with enzyme-like properties, we are employing a small, cavity-containing protein as a scaffold for the attachment of catalytic groups. In earlier work we demonstrated that a phenanthroline ligand could be introduced into the cavity of the protein ALBP and used to catalyze ester hydrolysis. To examine the effect of positioning the phenanthroline catalyst at different locations within the protein cavity, three new constructs--Phen60, Phen72 and Phen104--were prepared. Each new conjugate was characterized by UV/vis spectroscopy, fluorescence spectroscopy, guanidine hydrochloride denaturation, gel filtration chromatography, and CD spectroscopy to confirm the preparation of the desired construct. Analysis of reactions containing Ala-OiPr showed that Phen60 catalyzed ester hydrolysis with less selectivity than ALBP-Phen while Phen72 promoted this same reaction with higher selectivity. Reactions with Tyr-OMe were catalyzed with higher selectivity by Phen60 and more rapidly by Phen104. These results demonstrate that both the rates and selectivities of hydrolysis reactions catalyzed by these constructs are dependent on the precise site of attachment of the metal ligand within the protein cavity.
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Affiliation(s)
- R R Davies
- Department of Chemistry, University of Minnesota, Minneapolis 55455, USA
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Abstract
The combination of site-directed mutagenesis and chemical modification has resulted in the preparation of protein conjugates with new and useful properties. Proteins modified with metal-chelating groups are proving useful for mapping tertiary and quaternary interactions using the technique of affinity cleavage. The attachment of cofactors, including pyridoxal and pyridoxamine, has resulted in the preparation of semisynthetic transaminases that display enzyme-like properties, including enantioselectivity, substrate specificity and reaction-rate acceleration.
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Affiliation(s)
- M D Distefano
- Department of Chemistry, University of Minnesota, Minneapolis 55455, USA.
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