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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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2
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Szuster J, Zitare UA, Castro MA, Leguto AJ, Morgada MN, Vila AJ, Murgida DH. Cu A-based chimeric T1 copper sites allow for independent modulation of reorganization energy and reduction potential. Chem Sci 2020; 11:6193-6201. [PMID: 32953013 PMCID: PMC7480511 DOI: 10.1039/d0sc01620a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 06/01/2020] [Indexed: 01/19/2023] Open
Abstract
Attaining rational modulation of thermodynamic and kinetic redox parameters of metalloproteins is a key milestone towards the (re)design of proteins with new or improved redox functions. Here we report that implantation of ligand loops from natural T1 proteins into the scaffold of a CuA protein leads to a series of distorted T1-like sites that allow for independent modulation of reduction potentials (E°') and electron transfer reorganization energies (λ). On the one hand E°' values could be fine-tuned over 120 mV without affecting λ. On the other, λ values could be modulated by more than a factor of two while affecting E°' only by a few millivolts. These results are in sharp contrast to previous studies that used T1 cupredoxin folds, thus highlighting the importance of the protein scaffold in determining such parameters.
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Affiliation(s)
- Jonathan Szuster
- Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE, CONICET-UBA) , Argentina .
- Departamento de Química Inorgánica, Analítica y Química-Física , Facultad de Ciencias Exactas y Naturales , Universidad de Buenos Aires , Buenos Aires , Argentina
| | - Ulises A Zitare
- Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE, CONICET-UBA) , Argentina .
- Departamento de Química Inorgánica, Analítica y Química-Física , Facultad de Ciencias Exactas y Naturales , Universidad de Buenos Aires , Buenos Aires , Argentina
| | - María A Castro
- Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE, CONICET-UBA) , Argentina .
- Departamento de Química Inorgánica, Analítica y Química-Física , Facultad de Ciencias Exactas y Naturales , Universidad de Buenos Aires , Buenos Aires , Argentina
| | - Alcides J Leguto
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET-UNR) , Argentina
- Departamento de Química Biológica , Facultad de Ciencias Bioquímicas y Farmacéuticas , Universidad Nacional de Rosario , Rosario , Argentina
| | - Marcos N Morgada
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET-UNR) , Argentina
- Departamento de Química Biológica , Facultad de Ciencias Bioquímicas y Farmacéuticas , Universidad Nacional de Rosario , Rosario , Argentina
| | - Alejandro J Vila
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET-UNR) , Argentina
- Departamento de Química Biológica , Facultad de Ciencias Bioquímicas y Farmacéuticas , Universidad Nacional de Rosario , Rosario , Argentina
| | - Daniel H Murgida
- Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE, CONICET-UBA) , Argentina .
- Departamento de Química Inorgánica, Analítica y Química-Física , Facultad de Ciencias Exactas y Naturales , Universidad de Buenos Aires , Buenos Aires , Argentina
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3
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Bhagi-Damodaran A, Lu Y. The Periodic Table's Impact on Bioinorganic Chemistry and Biology's Selective Use of Metal Ions. STRUCTURE AND BONDING 2019; 182:153-173. [PMID: 36567794 PMCID: PMC9788643 DOI: 10.1007/430_2019_45] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Despite the availability of a vast variety of metal ions in the periodic table, biology uses only a selective few metal ions. Most of the redox active metals used belong to the first row of transition metals in the periodic table and include Fe, Co, Ni, Mn and Cu. On the other hand, Ca, Zn and Mg are the most commonly used redox inactive metals in biology. In this chapter, we discuss the periodic table's impact on bio-inorganic chemistry, by exploring reasons behind this selective choice of metals biology. A special focus is placed on the chemical and functional reasons why one metal ion is preferred over another one. We discuss the implications of metal choice in various biological processes including catalysis, electron transfer, redox sensing and signaling. We find that bioavailability of metal ions along with their redox potentials, coordination flexibility, valency and ligand affinity determine the specificity of metals for biological processes. Understanding the implications underlying the selective choice of metals of the periodic table in these biological processes can help design more efficient catalysts, more precise biosensors and more effective drugs.
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Affiliation(s)
| | - Yi Lu
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801
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4
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Fowler NJ, Blanford CF, Warwicker J, de Visser SP. Prediction of Reduction Potentials of Copper Proteins with Continuum Electrostatics and Density Functional Theory. Chemistry 2017; 23:15436-15445. [PMID: 28815759 PMCID: PMC5698706 DOI: 10.1002/chem.201702901] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Indexed: 12/20/2022]
Abstract
Blue copper proteins, such as azurin, show dramatic changes in Cu2+/Cu+ reduction potential upon mutation over the full physiological range. Hence, they have important functions in electron transfer and oxidation chemistry and have applications in industrial biotechnology. The details of what determines these reduction potential changes upon mutation are still unclear. Moreover, it has been difficult to model and predict the reduction potential of azurin mutants and currently no unique procedure or workflow pattern exists. Furthermore, high‐level computational methods can be accurate but are too time consuming for practical use. In this work, a novel approach for calculating reduction potentials of azurin mutants is shown, based on a combination of continuum electrostatics, density functional theory and empirical hydrophobicity factors. Our method accurately reproduces experimental reduction potential changes of 30 mutants with respect to wildtype within experimental error and highlights the factors contributing to the reduction potential change. Finally, reduction potentials are predicted for a series of 124 new mutants that have not yet been investigated experimentally. Several mutants are identified that are located well over 10 Å from the copper center that change the reduction potential by more than 85 mV. The work shows that secondary coordination sphere mutations mostly lead to long‐range electrostatic changes and hence can be modeled accurately with continuum electrostatics.
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Affiliation(s)
- Nicholas J Fowler
- Manchester Institute of Biotechnology and School of Chemistry, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
| | - Christopher F Blanford
- Manchester Institute of Biotechnology and School of Materials, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
| | - Jim Warwicker
- Manchester Institute of Biotechnology and School of Chemistry, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
| | - Sam P de Visser
- Manchester Institute of Biotechnology, and School of Chemical Engineering and Analytical Science, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
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5
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Yamaguchi T, Nihei Y, Sutherland DEK, Stillman MJ, Kohzuma T. Stabilization of protein structure through π-π interaction in the second coordination sphere of pseudoazurin. Protein Sci 2017; 26:1921-1931. [PMID: 28691165 DOI: 10.1002/pro.3226] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Revised: 07/01/2017] [Accepted: 07/04/2017] [Indexed: 11/11/2022]
Abstract
Noncovalent, weak interactions in the second coordination sphere of the copper active site of Pseudoazurin (PAz) from Achromobacter cycloclastes were examined using a series of Met16X variants. In this study, the differences in protein stability due to the changes in the nature of the 16th amino acid (Met, Phe, Val, Ile) were investigated by electrospray ionization mass spectrometry (ESI-MS) and far-UV circular dichroism (CD) as a result of acid denaturation. The percentage of native states (folded holo forms) of Met16Phe variants was estimated to be 75% at pH 2.9 although the wild-type (WT), Met16Val and Met16Ile PAz, became completely unfolded. The high stability under acidic conditions is correlated with the result of the active site being stabilized by the aromatic substitution of the Met16 residue. The π-π interaction in the second coordination sphere makes a significant contribution to the stability of active site and the protein matrix.
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Affiliation(s)
- Takahide Yamaguchi
- Graduate School of Science and Engineering, Institute of Quantum Beam Science, Ibaraki University, Mito, Ibaraki, 310-8512, Japan
| | - Yuko Nihei
- Graduate School of Science and Engineering, Institute of Quantum Beam Science, Ibaraki University, Mito, Ibaraki, 310-8512, Japan
| | - Duncan E K Sutherland
- Department of Biology, The University of Western Ontario, London, Ontario, Canada.,Department of Chemistry, The University of Western Ontario, London, Ontario, Canada
| | - Martin J Stillman
- Department of Biology, The University of Western Ontario, London, Ontario, Canada.,Department of Chemistry, The University of Western Ontario, London, Ontario, Canada
| | - Takamitsu Kohzuma
- Graduate School of Science and Engineering, Institute of Quantum Beam Science, Ibaraki University, Mito, Ibaraki, 310-8512, Japan
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7
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Bhagi-Damodaran A, Hosseinzadeh P, Mirts E, Reed J, Petrik ID, Lu Y. Design of Heteronuclear Metalloenzymes. Methods Enzymol 2016; 580:501-37. [PMID: 27586347 PMCID: PMC5156654 DOI: 10.1016/bs.mie.2016.05.050] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Heteronuclear metalloenzymes catalyze some of the most fundamentally interesting and practically useful reactions in nature. However, the presence of two or more metal ions in close proximity in these enzymes makes them more difficult to prepare and study than homonuclear metalloenzymes. To meet these challenges, heteronuclear metal centers have been designed into small and stable proteins with rigid scaffolds to understand how these heteronuclear centers are constructed and the mechanism of their function. This chapter describes methods for designing heterobinuclear metal centers in a protein scaffold by giving specific examples of a few heme-nonheme bimetallic centers engineered in myoglobin and cytochrome c peroxidase. We provide step-by-step procedures on how to choose the protein scaffold, design a heterobinuclear metal center in the protein scaffold computationally, incorporate metal ions into the protein, and characterize the resulting metalloproteins, both structurally and functionally. Finally, we discuss how an initial design can be further improved by rationally tuning its secondary coordination sphere, electron/proton transfer rates, and the substrate affinity.
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Affiliation(s)
- A Bhagi-Damodaran
- University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - P Hosseinzadeh
- University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - E Mirts
- University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - J Reed
- University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - I D Petrik
- University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Y Lu
- University of Illinois at Urbana-Champaign, Urbana, IL, United States.
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8
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Hosseinzadeh P, Lu Y. Design and fine-tuning redox potentials of metalloproteins involved in electron transfer in bioenergetics. BIOCHIMICA ET BIOPHYSICA ACTA 2016; 1857:557-581. [PMID: 26301482 PMCID: PMC4761536 DOI: 10.1016/j.bbabio.2015.08.006] [Citation(s) in RCA: 114] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2015] [Accepted: 08/20/2015] [Indexed: 12/25/2022]
Abstract
Redox potentials are a major contributor in controlling the electron transfer (ET) rates and thus regulating the ET processes in the bioenergetics. To maximize the efficiency of the ET process, one needs to master the art of tuning the redox potential, especially in metalloproteins, as they represent major classes of ET proteins. In this review, we first describe the importance of tuning the redox potential of ET centers and its role in regulating the ET in bioenergetic processes including photosynthesis and respiration. The main focus of this review is to summarize recent work in designing the ET centers, namely cupredoxins, cytochromes, and iron-sulfur proteins, and examples in design of protein networks involved these ET centers. We then discuss the factors that affect redox potentials of these ET centers including metal ion, the ligands to metal center and interactions beyond the primary ligand, especially non-covalent secondary coordination sphere interactions. We provide examples of strategies to fine-tune the redox potential using both natural and unnatural amino acids and native and nonnative cofactors. Several case studies are used to illustrate recent successes in this area. Outlooks for future endeavors are also provided. This article is part of a Special Issue entitled Biodesign for Bioenergetics--the design and engineering of electronic transfer cofactors, proteins and protein networks, edited by Ronald L. Koder and J.L. Ross Anderson.
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Affiliation(s)
- Parisa Hosseinzadeh
- Department of Chemistry and Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews St., Urbana, IL, 61801, USA
| | - Yi Lu
- Department of Chemistry and Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews St., Urbana, IL, 61801, USA.
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9
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Dahl EW, Szymczak NK. Hydrogen Bonds Dictate the Coordination Geometry of Copper: Characterization of a Square-Planar Copper(I) Complex. Angew Chem Int Ed Engl 2016; 55:3101-5. [PMID: 26822857 PMCID: PMC4804195 DOI: 10.1002/anie.201511527] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Indexed: 12/31/2022]
Abstract
6,6''-Bis(2,4,6-trimethylanilido)terpyridine (H2Tpy(NMes)) was prepared as a rigid, tridentate pincer ligand containing pendent anilines as hydrogen bond donor groups in the secondary coordination sphere. The coordination geometry of (H2 Tpy(NMes))copper(I)-halide (Cl, Br and I) complexes is dictated by the strength of the NH-halide hydrogen bond. The Cu(I)Cl and Cu(II)Cl complexes are nearly isostructural, the former presenting a highly unusual square-planar geometry about Cu(I) . The geometric constraints provided by secondary interactions are reminiscent of blue copper proteins where a constrained geometry, or entatic state, allows for extremely rapid Cu(I)/Cu(II) electron-transfer self-exchange rates. Cu(H2 Tpy(NMes))Cl shows similar fast electron transfer (≈10(5) m(-1) s(-1)) which is the same order of magnitude as biological systems.
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Affiliation(s)
- Eric W Dahl
- Department of Chemistry, University of Michigan, 930 N. University, Ann Arbor, MI, 48109, USA
| | - Nathaniel K Szymczak
- Department of Chemistry, University of Michigan, 930 N. University, Ann Arbor, MI, 48109, USA.
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10
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Dahl EW, Szymczak NK. Hydrogen Bonds Dictate the Coordination Geometry of Copper: Characterization of a Square‐Planar Copper(I) Complex. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201511527] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Eric W. Dahl
- Department of Chemistry University of Michigan 930 N. University Ann Arbor MI 48109 USA
| | - Nathaniel K. Szymczak
- Department of Chemistry University of Michigan 930 N. University Ann Arbor MI 48109 USA
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11
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Design of a single protein that spans the entire 2-V range of physiological redox potentials. Proc Natl Acad Sci U S A 2015; 113:262-7. [PMID: 26631748 DOI: 10.1073/pnas.1515897112] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The reduction potential (E°') is a critical parameter in determining the efficiency of most biological and chemical reactions. Biology employs three classes of metalloproteins to cover the majority of the 2-V range of physiological E°'s. An ultimate test of our understanding of E°' is to find out the minimal number of proteins and their variants that can cover this entire range and the structural features responsible for the extreme E°'. We report herein the design of the protein azurin to cover a range from +970 mV to -954 mV vs. standard hydrogen electrode (SHE) by mutating only five residues and using two metal ions. Spectroscopic methods have revealed geometric parameters important for the high E°'. The knowledge gained and the resulting water-soluble redox agents with predictable E°'s, in the same scaffold with the same surface properties, will find wide applications in chemical, biochemical, biophysical, and biotechnological fields.
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12
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Garcia L, Cisnetti F, Gillet N, Guillot R, Aumont-Nicaise M, Piquemal JP, Desmadril M, Lambert F, Policar C. Entasis through Hook-and-Loop Fastening in a Glycoligand with Cumulative Weak Forces Stabilizing CuI. J Am Chem Soc 2015; 137:1141-6. [DOI: 10.1021/ja510259p] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Ludivine Garcia
- Institut
de chimie moléculaire et des matériaux d’Orsay, UMR CNRS 8182, Bât. 420, Université Paris-Sud 11, F-91405 Orsay Cedex, France
| | - Federico Cisnetti
- Institut
de chimie moléculaire et des matériaux d’Orsay, UMR CNRS 8182, Bât. 420, Université Paris-Sud 11, F-91405 Orsay Cedex, France
| | - Natacha Gillet
- Laboratoire
de Chimie Théorique (UMR CNRS 7616), Sorbonne Universités, UPMC Univ Paris 06, Tour 12-13, 4 place Jussieu, F-75252 Paris Cedex 05, France
| | - Régis Guillot
- Institut
de chimie moléculaire et des matériaux d’Orsay, UMR CNRS 8182, Bât. 420, Université Paris-Sud 11, F-91405 Orsay Cedex, France
| | - Magali Aumont-Nicaise
- Institut
de Biochimie et Biophysique Moléculaire et Cellulaire, CNRS-UMR8619, Bât. 430, Université Paris-Sud 11, F-91405 Orsay Cedex, France
| | - Jean-Philip Piquemal
- Laboratoire
de Chimie Théorique (UMR CNRS 7616), Sorbonne Universités, UPMC Univ Paris 06, Tour 12-13, 4 place Jussieu, F-75252 Paris Cedex 05, France
| | - Michel Desmadril
- Institut
de Biochimie et Biophysique Moléculaire et Cellulaire, CNRS-UMR8619, Bât. 430, Université Paris-Sud 11, F-91405 Orsay Cedex, France
| | - François Lambert
- Ecole Normale Supérieure-PSL Research University, Département de Chimie, 24 rue Lhomond, F-75005 Paris, France
- Sorbonne Universités, UPMC Univ Paris 06, LBM, 4 place Jussieu, F-75005 Paris, France
- CNRS, UMR 7203 LBM, F-75005 Paris, France
| | - Clotilde Policar
- Ecole Normale Supérieure-PSL Research University, Département de Chimie, 24 rue Lhomond, F-75005 Paris, France
- Sorbonne Universités, UPMC Univ Paris 06, LBM, 4 place Jussieu, F-75005 Paris, France
- CNRS, UMR 7203 LBM, F-75005 Paris, France
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13
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Liu J, Chakraborty S, Hosseinzadeh P, Yu Y, Tian S, Petrik I, Bhagi A, Lu Y. Metalloproteins containing cytochrome, iron-sulfur, or copper redox centers. Chem Rev 2014; 114:4366-469. [PMID: 24758379 PMCID: PMC4002152 DOI: 10.1021/cr400479b] [Citation(s) in RCA: 549] [Impact Index Per Article: 54.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Indexed: 02/07/2023]
Affiliation(s)
- Jing Liu
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Saumen Chakraborty
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Parisa Hosseinzadeh
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Yang Yu
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Shiliang Tian
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Igor Petrik
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Ambika Bhagi
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Yi Lu
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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14
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Yu F, Cangelosi VM, Zastrow ML, Tegoni M, Plegaria JS, Tebo AG, Mocny CS, Ruckthong L, Qayyum H, Pecoraro VL. Protein design: toward functional metalloenzymes. Chem Rev 2014; 114:3495-578. [PMID: 24661096 PMCID: PMC4300145 DOI: 10.1021/cr400458x] [Citation(s) in RCA: 340] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Fangting Yu
- University of Michigan, Ann Arbor, Michigan 48109, United States
| | | | | | | | | | - Alison G. Tebo
- University of Michigan, Ann Arbor, Michigan 48109, United States
| | | | - Leela Ruckthong
- University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Hira Qayyum
- University of Michigan, Ann Arbor, Michigan 48109, United States
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15
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Yu F, Penner-Hahn JE, Pecoraro VL. De novo-designed metallopeptides with type 2 copper centers: modulation of reduction potentials and nitrite reductase activities. J Am Chem Soc 2013; 135:18096-107. [PMID: 24182361 DOI: 10.1021/ja406648n] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Enzymatic reactions involving redox processes are highly sensitive to the local electrostatic environment. Despite considerable effort, the complex interactions among different influential factors in native proteins impede progress toward complete understanding of the structure-function relationship. Of particular interest is the type 2 copper center Cu(His)3, which may act as an electron transfer center in peptidylglycine α-hydroxylating monooxygenase (PHM) or a catalytic center in copper nitrite reductase (CuNiR). A de novo design strategy is used to probe the effect of modifying charged amino acid residues around, but not directly bound to, a Cu(His)3 center embedded in three-stranded coiled coils (TRI-H)3 [TRI-H = Ac-G WKALEEK LKALEEK LKALEEK HKALEEK G-NH2]. Specifically, the peptide TRI-EH (=TRI-HK22E) alters an important lysine to glutamate just above the copper binding center. With a series of TRI-EH peptides mutated below the metal center, we use a variety of spectroscopies (EPR, UV-vis, XAS) to show a direct impact on the protonation equilibria, copper binding affinities, reduction potentials, and nitrite reductase activities of these copper-peptide complexes. The potentials at a specific pH vary by 100 mV, and the nitrite reductase activities range over a factor of 4 in rates. We also observe that the affinities, potentials, and catalytic activities are strongly influenced by the pH conditions (pH 5.8-7.4). In general, Cu(II) affinities for the peptides are diminished at low pH values. The interplay among these factors can lead to a 200 mV shift in reduction potential across these peptides, which is determined by the pH-dependent affinities of copper in both oxidation states. This study illustrates the strength of de novo protein design in elucidating the influence of ionizable residues on a particular redox system, an important step toward understanding the factors that govern the properties of this metalloenzyme with a goal of eventually improving the catalytic activity.
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Affiliation(s)
- Fangting Yu
- Department of Chemistry, University of Michigan , 930 North University Avenue, Ann Arbor, Michigan 48109-1055, United States
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Designed azurins show lower reorganization free energies for intraprotein electron transfer. Proc Natl Acad Sci U S A 2013; 110:10536-40. [PMID: 23759745 DOI: 10.1073/pnas.1215081110] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Low reorganization free energies are necessary for fast electron transfer (ET) reactions. Hence, rational design of redox proteins with lower reorganization free energies has been a long-standing challenge, promising to yield a deeper understanding of the underlying principles of ET reactivity and to enable potential applications in different energy conversion systems. Herein we report studies of the intramolecular ET from pulse radiolytically produced disulfide radicals to Cu(II) in rationally designed azurin mutants. In these mutants, the copper coordination sphere has been fine-tuned to span a wide range of reduction potentials while leaving the metal binding site effectively undisrupted. We find that the reorganization free energies of ET within the mutants are indeed lower than that of WT azurin, increasing the intramolecular ET rate constants almost 10-fold: changes that are correlated with increased flexibility of their copper sites. Moreover, the lower reorganization free energy results in the ET rate constants reaching a maximum value at higher driving forces, as predicted by the Marcus theory.
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