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Gay R, Masson Y, Ghattas W, Udry GAO, Herrero C, Urvoas A, Mahy JP, Ricoux R. Binding and Stabilization of a Semiquinone Radical by an Artificial Metalloenzyme Containing a Binuclear Copper (II) Cofactor. Chembiochem 2024:e202400139. [PMID: 38682718 DOI: 10.1002/cbic.202400139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Revised: 04/27/2024] [Accepted: 04/29/2024] [Indexed: 05/01/2024]
Abstract
A binuclear Cu(II) cofactor was covalently bound to a lauric acid anchor. The resulting conjugate was characterized then combined with beta-lactoglobulin (βLG) to generate a new biohybrid following the so-called "Trojan horse" strategy. This biohybrid was examined for its effectiveness in the oxidation of a catechol derivative to the corresponding quinone. The resulting biohybrid did not exhibit the sought after catecholase activity, likely due to its ability to bind and stabilize the semiquinone radical intermediate DTB-SQ. This semi-quinone radical was stabilized only in the presence of the protein and was characterized using optical and magnetic spectroscopic techniques, demonstrating stability for over 16 hours. Molecular docking studies revealed that this stabilization could occur owing to interactions of the semi-quinone with hydrophobic amino acid residues of βLG.
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Affiliation(s)
- Rémy Gay
- Équipe de Chimie Bioorganique et Bioinorganique, Institut de Chimie Moléculaire et des Matériaux d'Orsay, UMR 8182, Université Paris-Saclay, CNRS, Bât. 670, 17 avenue des Sciences, 91400, Orsay Cedex, France
| | - Yannick Masson
- Équipe de Chimie Bioorganique et Bioinorganique, Institut de Chimie Moléculaire et des Matériaux d'Orsay, UMR 8182, Université Paris-Saclay, CNRS, Bât. 670, 17 avenue des Sciences, 91400, Orsay Cedex, France
| | - Wadih Ghattas
- Équipe de Chimie Bioorganique et Bioinorganique, Institut de Chimie Moléculaire et des Matériaux d'Orsay, UMR 8182, Université Paris-Saclay, CNRS, Bât. 670, 17 avenue des Sciences, 91400, Orsay Cedex, France
| | - Guillermo A Oliveira Udry
- Équipe de Chimie Bioorganique et Bioinorganique, Institut de Chimie Moléculaire et des Matériaux d'Orsay, UMR 8182, Université Paris-Saclay, CNRS, Bât. 670, 17 avenue des Sciences, 91400, Orsay Cedex, France
| | - Christian Herrero
- Institut de Chimie Moléculaire et des Matériaux d'Orsay, UMR 8182, Université Paris-Saclay, CNRS, Bât. 670, 17 avenue des Sciences, 91400, Orsay Cedex, France
| | - Agathe Urvoas
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Bât. 21, 1 Avenue de la Terrasse, 91198, Gif-sur-Yvette, France
| | - Jean-Pierre Mahy
- Équipe de Chimie Bioorganique et Bioinorganique, Institut de Chimie Moléculaire et des Matériaux d'Orsay, UMR 8182, Université Paris-Saclay, CNRS, Bât. 670, 17 avenue des Sciences, 91400, Orsay Cedex, France
| | - Rémy Ricoux
- Équipe de Chimie Bioorganique et Bioinorganique, Institut de Chimie Moléculaire et des Matériaux d'Orsay, UMR 8182, Université Paris-Saclay, CNRS, Bât. 670, 17 avenue des Sciences, 91400, Orsay Cedex, France
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Wang Z, Liu P, Ye P, Dai S, Liu L, Yang P. Effects of semiquinone-rich surface on the behaviors of vascular cells. J Biomater Appl 2023; 37:1195-1204. [PMID: 36633217 DOI: 10.1177/08853282231151230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Dopamine has been widely used for surface modification of cardiovascular medical devices as it forms films on most substrates that provide functional groups for surface chemical modification. However, under oxidative stress, the phenolic hydroxyl group on dopamine can undergo reversible transformation into phenol-semiquinone-quinone, which can cause cytotoxicity and immunotoxicity. In this study, we measured the effects of semiquinone on the behavior of vascular wall cells and inflammatory cells under oxidative stress via ultraviolet irradiation with a hydrogen peroxide diluent. Na2S2O3 was used as a stabilizer to obtain a semiquinone-rich poly-dopamine film, then phenol-semiquinone-quinone ratio on its surface was evaluated at three irradiation-oxidation time points. We found that the poly-dopamine film with ultraviolet irradiation in hydrogen peroxide solution for 15 min had the highest semiquinone occupancy of 19.18%. In the experimental group irradiated for 15 min, endothelial cells were cultured statically for 3 days and the number of surface adherent endothelial cells in the group with added semiquinone stabilizer was reduced to 73% of that in the group without stabilizer, indicating that semiquinone rich surface inhibits adhesion and proliferation of endothelial cells; Smooth muscle cells were cultured statically for 3 days, and the number of adherent smooth muscle on surfaces without stabilizer was reduced to 75% of that on surfaces with stabilizer added, indicating that semiquinone rich surfaces promote smooth muscle proliferation. These results demonstrate that semiquinone can adversely affect the repair effect after implantation of cardiovascular materials. Therefore, our study provides a reference for the application and optimization of dopamine in cardiovascular implant materials.
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Affiliation(s)
- Zhixing Wang
- Institute of Biomaterials and Surface Engineering Key Lab. for Advanced Technologies of Materials, Ministry of Education, 56711Southwest Jiaotong University, Chengdu, China
| | - Peng Liu
- Institute of Biomaterials and Surface Engineering Key Lab. for Advanced Technologies of Materials, Ministry of Education, 56711Southwest Jiaotong University, Chengdu, China
| | - Peng Ye
- Institute of Biomaterials and Surface Engineering Key Lab. for Advanced Technologies of Materials, Ministry of Education, 56711Southwest Jiaotong University, Chengdu, China
| | - Sheng Dai
- Institute of Biomaterials and Surface Engineering Key Lab. for Advanced Technologies of Materials, Ministry of Education, 56711Southwest Jiaotong University, Chengdu, China
| | - LuYing Liu
- Institute of Biomaterials and Surface Engineering Key Lab. for Advanced Technologies of Materials, Ministry of Education, 56711Southwest Jiaotong University, Chengdu, China
| | - Ping Yang
- Institute of Biomaterials and Surface Engineering Key Lab. for Advanced Technologies of Materials, Ministry of Education, 56711Southwest Jiaotong University, Chengdu, China
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Klein AS, Zeymer C. Design and engineering of artificial metalloproteins: from de novo metal coordination to catalysis. Protein Eng Des Sel 2021; 34:6150309. [PMID: 33635315 DOI: 10.1093/protein/gzab003] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 01/15/2021] [Accepted: 01/19/2021] [Indexed: 11/13/2022] Open
Abstract
Metalloproteins are essential to sustain life. Natural evolution optimized them for intricate structural, regulatory and catalytic functions that cannot be fulfilled by either a protein or a metal ion alone. In order to understand this synergy and the complex design principles behind the natural systems, simpler mimics were engineered from the bottom up by installing de novo metal sites in either natural or fully designed, artificial protein scaffolds. This review focuses on key challenges associated with this approach. We discuss how proteins can be equipped with binding sites that provide an optimal coordination environment for a metal cofactor of choice, which can be a single metal ion or a complex multinuclear cluster. Furthermore, we highlight recent studies in which artificial metalloproteins were engineered towards new functions, including electron transfer and catalysis. In this context, the powerful combination of de novo protein design and directed evolution is emphasized for metalloenzyme development.
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Affiliation(s)
- Andreas S Klein
- Department of Chemistry, Technische Universität München, 85747 Garching, Germany
| | - Cathleen Zeymer
- Department of Chemistry, Technische Universität München, 85747 Garching, Germany
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Pirro F, Schmidt N, Lincoff J, Widel ZX, Polizzi NF, Liu L, Therien MJ, Grabe M, Chino M, Lombardi A, DeGrado WF. Allosteric cooperation in a de novo-designed two-domain protein. Proc Natl Acad Sci U S A 2020; 117:33246-33253. [PMID: 33318174 PMCID: PMC7776816 DOI: 10.1073/pnas.2017062117] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We describe the de novo design of an allosterically regulated protein, which comprises two tightly coupled domains. One domain is based on the DF (Due Ferri in Italian or two-iron in English) family of de novo proteins, which have a diiron cofactor that catalyzes a phenol oxidase reaction, while the second domain is based on PS1 (Porphyrin-binding Sequence), which binds a synthetic Zn-porphyrin (ZnP). The binding of ZnP to the original PS1 protein induces changes in structure and dynamics, which we expected to influence the catalytic rate of a fused DF domain when appropriately coupled. Both DF and PS1 are four-helix bundles, but they have distinct bundle architectures. To achieve tight coupling between the domains, they were connected by four helical linkers using a computational method to discover the most designable connections capable of spanning the two architectures. The resulting protein, DFP1 (Due Ferri Porphyrin), bound the two cofactors in the expected manner. The crystal structure of fully reconstituted DFP1 was also in excellent agreement with the design, and it showed the ZnP cofactor bound over 12 Å from the dimetal center. Next, a substrate-binding cleft leading to the diiron center was introduced into DFP1. The resulting protein acts as an allosterically modulated phenol oxidase. Its Michaelis-Menten parameters were strongly affected by the binding of ZnP, resulting in a fourfold tighter Km and a 7-fold decrease in kcat These studies establish the feasibility of designing allosterically regulated catalytic proteins, entirely from scratch.
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Affiliation(s)
- Fabio Pirro
- Department of Chemical Sciences, University of Napoli Federico II, 80126 Napoli, Italy
| | - Nathan Schmidt
- Department of Pharmaceutical Chemistry and the Cardiovascular Research Institute, University of California, San Francisco, CA 94158-9001
| | - James Lincoff
- Department of Pharmaceutical Chemistry and the Cardiovascular Research Institute, University of California, San Francisco, CA 94158-9001
| | - Zachary X Widel
- Department of Chemistry, Duke University, Durham, NC 27708-0346
| | - Nicholas F Polizzi
- Department of Pharmaceutical Chemistry and the Cardiovascular Research Institute, University of California, San Francisco, CA 94158-9001
| | - Lijun Liu
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, 518055 Shenzhen, China
- DLX Scientific, Lawrence, KS 66049
| | | | - Michael Grabe
- Department of Pharmaceutical Chemistry and the Cardiovascular Research Institute, University of California, San Francisco, CA 94158-9001
| | - Marco Chino
- Department of Chemical Sciences, University of Napoli Federico II, 80126 Napoli, Italy
| | - Angela Lombardi
- Department of Chemical Sciences, University of Napoli Federico II, 80126 Napoli, Italy;
| | - William F DeGrado
- Department of Pharmaceutical Chemistry and the Cardiovascular Research Institute, University of California, San Francisco, CA 94158-9001;
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Kulesha A, Yoon JH, Chester C, D'Souza A, Costeas C, Makhlynets OV. Contributions of primary coordination ligands and importance of outer sphere interactions in UFsc, a de novo designed protein with high affinity for metal ions. J Inorg Biochem 2020; 212:111224. [PMID: 32871348 DOI: 10.1016/j.jinorgbio.2020.111224] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 08/04/2020] [Accepted: 08/05/2020] [Indexed: 12/15/2022]
Abstract
Metalloproteins constitute nearly half of all proteins and catalyze some of the most complex chemical reactions. Recently, we reported a design of 4G-UFsc (Uno Ferro single chain), a single chain four-helical bundle with extraordinarily high (30 pM) affinity for zinc. We evaluated the contribution of different side chains to binding of Co(II), Ni(II), Zn(II) and Mn(II) using systematic mutagenesis of the amino acids that constitute the primary metal coordination and outer spheres. The binding affinity of proteins for metals was then measured using isothermal titration calorimetry. Our results show that both primary metal coordination environment and side chains in the outer sphere of UFsc are highly sensitive to even slight changes and can be adapted to binding different 3d metals, including hard-to-tightly bind metal ions such as Mn(II). The studies on the origins of tight metal binding will guide future metalloprotein design efforts.
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Affiliation(s)
- Alona Kulesha
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY 13244, United States
| | - Jennifer H Yoon
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY 13244, United States
| | - Cara Chester
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY 13244, United States
| | - Areetha D'Souza
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY 13244, United States
| | - Christos Costeas
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY 13244, United States
| | - Olga V Makhlynets
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY 13244, United States.
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Paredes A, Loh BM, Peduzzi OM, Reig AJ, Buettner KM. DNA Cleavage by a De Novo Designed Protein-Titanium Complex. Inorg Chem 2020; 59:11248-11252. [PMID: 32799485 DOI: 10.1021/acs.inorgchem.0c01707] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Titanium is one of the most abundant elements on Earth but is commonly thought to have no role in biology because of its propensity to hydrolyze. Nature stabilizes hard Lewis acidic metals from hydrolysis using a variety of mechanisms, providing inspiration for how titanium can be stabilized using biological ligands. The well-characterized Due Ferri single-chain (DFsc) de novo designed protein was developed to bind and stabilize iron and provides a binding site with hard Lewis basic residues able to bind two metal ions. We demonstrate that the DFsc scaffold stably binds 2 equiv of titanium and protects them from unwanted hydrolysis. The Ti4+-DFsc protein complex was tested for its ability to hydrolytically cleave DNA, where it was seen to linearize plasmid DNA in an overnight reaction. Ti4+-DFsc is thus the first example of a functional, soluble titanium-protein complex.
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Affiliation(s)
- Alexander Paredes
- Department of Chemistry, Gettysburg College, Gettysburg, Pennsylvania 17325, United States
| | - Brittany M Loh
- Department of Chemistry, Gettysburg College, Gettysburg, Pennsylvania 17325, United States
| | - Olivia M Peduzzi
- Department of Chemistry, Gettysburg College, Gettysburg, Pennsylvania 17325, United States
| | - Amanda J Reig
- Department of Chemistry, Ursinus College, Collegeville, Pennsylvania 19426, United States
| | - Katherine M Buettner
- Department of Chemistry, Gettysburg College, Gettysburg, Pennsylvania 17325, United States
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