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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] [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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Espinoza-Cara A, Zitare U, Alvarez-Paggi D, Klinke S, Otero LH, Murgida DH, Vila AJ. Engineering a bifunctional copper site in the cupredoxin fold by loop-directed mutagenesis. Chem Sci 2018; 9:6692-6702. [PMID: 30310603 PMCID: PMC6115626 DOI: 10.1039/c8sc01444b] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 06/27/2018] [Indexed: 12/30/2022] Open
Abstract
Copper sites in proteins are designed to perform either electron transfer or redox catalysis. Type 1 and CuA sites are electron transfer hubs bound to a rigid protein fold that prevents binding of exogenous ligands and side reactions. Here we report the engineering of two Type 1 sites by loop-directed mutagenesis within a CuA scaffold with unique electronic structures and functional features. A copper-thioether axial bond shorter than the copper-thiolate bond is responsible for the electronic structure features, in contrast to all other natural or chimeric sites where the copper thiolate bond is short. These sites display highly unusual features, such as: (1) a high reduction potential despite a strong interaction with the axial ligand, which we attribute to changes in the hydrogen bond network and (2) the ability to bind exogenous ligands such as imidazole and azide. This strategy widens the possibility of using natural protein scaffolds with functional features not present in nature.
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Affiliation(s)
- Andrés Espinoza-Cara
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET-UNR) , Rosario , Argentina .
- Área Biofísica , Departamento de Química Biológica , Facultad de Ciencias Bioquímicas y Farmacéuticas , Universidad Nacional de Rosario , Rosario , Argentina
| | - Ulises Zitare
- Departamento de Química Inorgánica , Analítica y Química Física-INQUIMAE , Facultad de Ciencias Exactas y Naturales , Universidad de Buenos Aires-CONICET , Buenos Aires , Argentina
| | - Damián Alvarez-Paggi
- Departamento de Química Inorgánica , Analítica y Química Física-INQUIMAE , Facultad de Ciencias Exactas y Naturales , Universidad de Buenos Aires-CONICET , Buenos Aires , Argentina
- Fundación Instituto Leloir , IIBBA-CONICET , Buenos Aires , Argentina
| | - Sebastián Klinke
- Fundación Instituto Leloir , IIBBA-CONICET , Buenos Aires , Argentina
- Plataforma Argentina de Biología Estructural y Metabolómica PLABEM. , Buenos Aires , Argentina
| | - Lisandro H Otero
- Fundación Instituto Leloir , IIBBA-CONICET , Buenos Aires , Argentina
- Plataforma Argentina de Biología Estructural y Metabolómica PLABEM. , Buenos Aires , Argentina
| | - Daniel H Murgida
- Departamento de Química Inorgánica , Analítica y Química Física-INQUIMAE , Facultad de Ciencias Exactas y Naturales , Universidad de Buenos Aires-CONICET , Buenos Aires , Argentina
| | - Alejandro J Vila
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET-UNR) , Rosario , Argentina .
- Área Biofísica , Departamento de Química Biológica , Facultad de Ciencias Bioquímicas y Farmacéuticas , Universidad Nacional de Rosario , Rosario , Argentina
- Plataforma Argentina de Biología Estructural y Metabolómica PLABEM. , Buenos Aires , Argentina
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Chen H, Su B, Zhang T, Huang A, Liu H, Yu Y, Wang J. Engineering the metal-binding loop at a type 1 copper center by circular permutation. RSC Adv 2017. [DOI: 10.1039/c7ra11512a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Circular permutation of the cupredoxin azurin creates a break on the metal binding loop, highlighting the loop's flexibility.
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Affiliation(s)
- Honghui Chen
- College of Biotechnology
- Tianjin University of Science and Technology
- Tianjin
- China
- Tianjin Institute of Industrial Biotechnology
| | - Binbin Su
- College of Biotechnology
- Tianjin University of Science and Technology
- Tianjin
- China
- Tianjin Institute of Industrial Biotechnology
| | - Tongtong Zhang
- Tianjin Institute of Industrial Biotechnology
- Chinese Academy of Sciences
- Tianjin
- China
| | - Aiping Huang
- Tianjin Institute of Industrial Biotechnology
- Chinese Academy of Sciences
- Tianjin
- China
| | - Haiping Liu
- Tianjin Institute of Industrial Biotechnology
- Chinese Academy of Sciences
- Tianjin
- China
| | - Yang Yu
- Tianjin Institute of Industrial Biotechnology
- Chinese Academy of Sciences
- Tianjin
- China
| | - Jiangyun Wang
- Laboratory of RNA Biology
- Institute of Biophysics
- Chinese Academy of Sciences
- Beijing
- China
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Synthesis, structure and properties of tris(1-ethyl-4-isopropyl-imidazolyl-κN)phosphine copper(II). Inorganica Chim Acta 2015. [DOI: 10.1016/j.ica.2015.05.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Leferink NGH, Han C, Antonyuk SV, Heyes DJ, Rigby SEJ, Hough MA, Eady RR, Scrutton NS, Hasnain SS. Proton-Coupled Electron Transfer in the Catalytic Cycle of Alcaligenes xylosoxidans Copper-Dependent Nitrite Reductase. Biochemistry 2011; 50:4121-31. [DOI: 10.1021/bi200246f] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Nicole G. H. Leferink
- Manchester Interdisciplinary Biocentre and Faculty of Life Sciences, University of Manchester, Manchester M1 7DN, United Kingdom
| | - Cong Han
- Molecular Biophysics Group, Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZB, United Kingdom
| | - Svetlana V. Antonyuk
- Molecular Biophysics Group, Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZB, United Kingdom
| | - Derren J. Heyes
- Manchester Interdisciplinary Biocentre and Faculty of Life Sciences, University of Manchester, Manchester M1 7DN, United Kingdom
| | - Stephen E. J. Rigby
- Manchester Interdisciplinary Biocentre and Faculty of Life Sciences, University of Manchester, Manchester M1 7DN, United Kingdom
| | - Michael A. Hough
- Molecular Biophysics Group, Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZB, United Kingdom
| | - Robert R. Eady
- Molecular Biophysics Group, Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZB, United Kingdom
| | - Nigel S. Scrutton
- Manchester Interdisciplinary Biocentre and Faculty of Life Sciences, University of Manchester, Manchester M1 7DN, United Kingdom
| | - S. Samar Hasnain
- Molecular Biophysics Group, Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZB, United Kingdom
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Active site loop dictates the thermodynamics of reduction and ligand protonation in cupredoxins. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2009; 1794:995-1000. [PMID: 19230853 DOI: 10.1016/j.bbapap.2009.02.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2008] [Revised: 01/28/2009] [Accepted: 02/03/2009] [Indexed: 11/21/2022]
Abstract
The thermodynamics of reduction and His ligand protonation have been determined for a range of loop-contraction variants of the electron transferring type 1 copper protein azurin (AZ). For AZPC, in which the native C-terminal loop containing the Cys, His and Met ligands has been replaced with the shorter sequence from plastocyanin (PC) and AZAMI, in which the even shorter amicyanin (AMI) loop has been inserted, the thermodynamics of reduction match those of the protein whose loop has been introduced which are different to the values for AZ. The enthalpic contribution to His ligand protonation, which is not observed in AZ, is similar in AZAMI and AMI. The thermodynamics of this process in AZPC are more dissimilar to those for PC. In the case of AZAMI-F, a variant possessing the (non natural) minimal loop that can bind a type 1 copper site, the reduction thermodynamics are intermediate between those of AZPC and AZAMI, whilst the thermodynamic data for His ligand protonation are very similar to those for AMI. The results for AZAMI and AZPC are primarily due to protein based enthalpic effects related to the interaction of the metal with permanent protein dipoles from the loop, and to the decreased loop length which favors His ligand protonation in the cuprous proteins. Entropic factors related to loop flexibility have little influence because of constraints imposed by metal coordination and the fact that the introduced loops pack well against the AZ scaffold. Thus, the host scaffold in general plays a minor thermodynamic role in both processes, although for AZAMI-F differences in the first and second coordination spheres influence the thermodynamics of reduction.
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