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Liu F, He L, Dong S, Xuan J, Cui Q, Feng Y. Artificial Small Molecules as Cofactors and Biomacromolecular Building Blocks in Synthetic Biology: Design, Synthesis, Applications, and Challenges. Molecules 2023; 28:5850. [PMID: 37570818 PMCID: PMC10421094 DOI: 10.3390/molecules28155850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 07/25/2023] [Accepted: 07/28/2023] [Indexed: 08/13/2023] Open
Abstract
Enzymes are essential catalysts for various chemical reactions in biological systems and often rely on metal ions or cofactors to stabilize their structure or perform functions. Improving enzyme performance has always been an important direction of protein engineering. In recent years, various artificial small molecules have been successfully used in enzyme engineering. The types of enzymatic reactions and metabolic pathways in cells can be expanded by the incorporation of these artificial small molecules either as cofactors or as building blocks of proteins and nucleic acids, which greatly promotes the development and application of biotechnology. In this review, we summarized research on artificial small molecules including biological metal cluster mimics, coenzyme analogs (mNADs), designer cofactors, non-natural nucleotides (XNAs), and non-natural amino acids (nnAAs), focusing on their design, synthesis, and applications as well as the current challenges in synthetic biology.
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Affiliation(s)
- Fenghua Liu
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, 189 Songling Road, Qingdao 266101, China
- Shandong Energy Institute, 189 Songling Road, Qingdao 266101, China
- Qingdao New Energy Shandong Laboratory, 189 Songling Road, Qingdao 266101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lingling He
- Department of Bioscience and Bioengineering, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Beijing 100083, China
| | - Sheng Dong
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, 189 Songling Road, Qingdao 266101, China
- Shandong Energy Institute, 189 Songling Road, Qingdao 266101, China
- Qingdao New Energy Shandong Laboratory, 189 Songling Road, Qingdao 266101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jinsong Xuan
- Department of Bioscience and Bioengineering, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Beijing 100083, China
| | - Qiu Cui
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, 189 Songling Road, Qingdao 266101, China
- Shandong Energy Institute, 189 Songling Road, Qingdao 266101, China
- Qingdao New Energy Shandong Laboratory, 189 Songling Road, Qingdao 266101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yingang Feng
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, 189 Songling Road, Qingdao 266101, China
- Shandong Energy Institute, 189 Songling Road, Qingdao 266101, China
- Qingdao New Energy Shandong Laboratory, 189 Songling Road, Qingdao 266101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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2
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Reyes Cruz EA, Nishiori D, Wadsworth BL, Nguyen NP, Hensleigh LK, Khusnutdinova D, Beiler AM, Moore GF. Molecular-Modified Photocathodes for Applications in Artificial Photosynthesis and Solar-to-Fuel Technologies. Chem Rev 2022; 122:16051-16109. [PMID: 36173689 DOI: 10.1021/acs.chemrev.2c00200] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Nature offers inspiration for developing technologies that integrate the capture, conversion, and storage of solar energy. In this review article, we highlight principles of natural photosynthesis and artificial photosynthesis, drawing comparisons between solar energy transduction in biology and emerging solar-to-fuel technologies. Key features of the biological approach include use of earth-abundant elements and molecular interfaces for driving photoinduced charge separation reactions that power chemical transformations at global scales. For the artificial systems described in this review, emphasis is placed on advancements involving hybrid photocathodes that power fuel-forming reactions using molecular catalysts interfaced with visible-light-absorbing semiconductors.
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Affiliation(s)
- Edgar A Reyes Cruz
- School of Molecular Sciences and the Biodesign Institute Center for Applied Structural Discovery (CASD), Arizona State University, Tempe, Arizona 85287-1604, United States
| | - Daiki Nishiori
- School of Molecular Sciences and the Biodesign Institute Center for Applied Structural Discovery (CASD), Arizona State University, Tempe, Arizona 85287-1604, United States
| | - Brian L Wadsworth
- School of Molecular Sciences and the Biodesign Institute Center for Applied Structural Discovery (CASD), Arizona State University, Tempe, Arizona 85287-1604, United States
| | - Nghi P Nguyen
- School of Molecular Sciences and the Biodesign Institute Center for Applied Structural Discovery (CASD), Arizona State University, Tempe, Arizona 85287-1604, United States
| | - Lillian K Hensleigh
- School of Molecular Sciences and the Biodesign Institute Center for Applied Structural Discovery (CASD), Arizona State University, Tempe, Arizona 85287-1604, United States
| | - Diana Khusnutdinova
- School of Molecular Sciences and the Biodesign Institute Center for Applied Structural Discovery (CASD), Arizona State University, Tempe, Arizona 85287-1604, United States
| | - Anna M Beiler
- School of Molecular Sciences and the Biodesign Institute Center for Applied Structural Discovery (CASD), Arizona State University, Tempe, Arizona 85287-1604, United States
| | - G F Moore
- School of Molecular Sciences and the Biodesign Institute Center for Applied Structural Discovery (CASD), Arizona State University, Tempe, Arizona 85287-1604, United States
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Jagilinki BP, Ilic S, Trncik C, Tyryshkin AM, Pike DH, Lubitz W, Bill E, Einsle O, Birrell JA, Akabayov B, Noy D, Nanda V. In Vivo Biogenesis of a De Novo Designed Iron-Sulfur Protein. ACS Synth Biol 2020; 9:3400-3407. [PMID: 33186033 DOI: 10.1021/acssynbio.0c00514] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In vivo expression of metalloproteins requires specific metal trafficking and incorporation machinery inside the cell. Synthetic designed metalloproteins are typically purified without the target metal, which is subsequently introduced through in vitro reconstitution. The extra step complicates protein optimization by high-throughput library screening or laboratory evolution. We demonstrate that a designed coiled-coil iron-sulfur protein (CCIS) assembles robustly with [4Fe-4S] clusters in vivo. While in vitro reconstitution produces a mixture of oligomers that depends on solution conditions, in vivo production generates a stable homotrimer coordinating a single, diamagnetic [4Fe-4S]2+ cluster. The multinuclear cluster of in vivo assembled CCIS is more resistant to degradation by molecular oxygen. Only one of the two metal coordinating half-sites is required in vivo, indicating specificity of molecular recognition in recruitment of the metal cluster. CCIS, unbiased by evolution, is a unique platform to examine iron-sulfur protein biogenesis and develop synthetic multinuclear oxidoreductases.
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Affiliation(s)
- Bhanu P. Jagilinki
- Center for Advanced Biotechnology and Medicine and the Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, New Jersey 08854 United States
- Migal-Galilee Research Institute, Kiryat Shmona, 11016, Israel
| | - Stefan Ilic
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva, 84105, Israel
| | - Cristian Trncik
- Institute for Biochemistry, Albert-Ludwigs-University, Freiburg, Albertstrasse 21, Freiburg, 79085, Germany
| | - Alexei M. Tyryshkin
- Center for Advanced Biotechnology and Medicine and the Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, New Jersey 08854 United States
| | - Douglas H. Pike
- Center for Advanced Biotechnology and Medicine and the Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, New Jersey 08854 United States
| | - Wolfgang Lubitz
- Max Planck Institute for Chemical Energy Conversion, Stiftstraße 34-36, Mülheim an der Ruhr, 45470, Germany
| | - Eckhard Bill
- Max Planck Institute for Chemical Energy Conversion, Stiftstraße 34-36, Mülheim an der Ruhr, 45470, Germany
| | - Oliver Einsle
- Institute for Biochemistry, Albert-Ludwigs-University, Freiburg, Albertstrasse 21, Freiburg, 79085, Germany
| | - James A. Birrell
- Max Planck Institute for Chemical Energy Conversion, Stiftstraße 34-36, Mülheim an der Ruhr, 45470, Germany
| | - Barak Akabayov
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva, 84105, Israel
| | - Dror Noy
- Migal-Galilee Research Institute, Kiryat Shmona, 11016, Israel
| | - Vikas Nanda
- Center for Advanced Biotechnology and Medicine and the Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, New Jersey 08854 United States
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Call A, Casadevall C, Romero-Rivera A, Martin-Diaconescu V, Sommer DJ, Osuna S, Ghirlanda G, Lloret-Fillol J. Improved Electro- and Photocatalytic Water Reduction by Confined Cobalt Catalysts in Streptavidin. ACS Catal 2019. [DOI: 10.1021/acscatal.8b04981] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Arnau Call
- Institute of Chemical Research of Catalonia (ICIQ), The Barcelona Institute of Science and Technology, Avinguda Països Catalans 16, 43007 Tarragona, Spain
| | - Carla Casadevall
- Institute of Chemical Research of Catalonia (ICIQ), The Barcelona Institute of Science and Technology, Avinguda Països Catalans 16, 43007 Tarragona, Spain
| | - Adrian Romero-Rivera
- Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona, Carrer Maria Aurèlia Capmany 69, 17003 Girona, Spain
| | - Vlad Martin-Diaconescu
- Institute of Chemical Research of Catalonia (ICIQ), The Barcelona Institute of Science and Technology, Avinguda Països Catalans 16, 43007 Tarragona, Spain
| | - Dayn J. Sommer
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287-1604, United States
| | - Sílvia Osuna
- Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona, Carrer Maria Aurèlia Capmany 69, 17003 Girona, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), Passeig Lluïs Companys, 23, 08010, Barcelona, Spain
| | - Giovanna Ghirlanda
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287-1604, United States
| | - Julio Lloret-Fillol
- Institute of Chemical Research of Catalonia (ICIQ), The Barcelona Institute of Science and Technology, Avinguda Països Catalans 16, 43007 Tarragona, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), Passeig Lluïs Companys, 23, 08010, Barcelona, Spain
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5
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Keller SG, Probst B, Heinisch T, Alberto R, Ward TR. Photo-Driven Hydrogen Evolution by an Artificial Hydrogenase Utilizing the Biotin-Streptavidin Technology. Helv Chim Acta 2018. [DOI: 10.1002/hlca.201800036] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Sascha G. Keller
- Department of Chemistry; University of Basel; Mattenstrasse 24a 4002 Basel Switzerland
| | - Benjamin Probst
- Department of Chemistry; University of Zürich; Winterthurerstrasse 190 8057 Zürich Switzerland
| | - Tillmann Heinisch
- Department of Chemistry; University of Basel; Mattenstrasse 24a 4002 Basel Switzerland
| | - Roger Alberto
- Department of Chemistry; University of Zürich; Winterthurerstrasse 190 8057 Zürich Switzerland
| | - Thomas R. Ward
- Department of Chemistry; University of Basel; Mattenstrasse 24a 4002 Basel Switzerland
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6
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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: 475] [Impact Index Per Article: 67.9] [Reference Citation Analysis] [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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7
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Bacchi M, Veinberg E, Field MJ, Niklas J, Matsui T, Tiede DM, Poluektov OG, Ikeda‐Saito M, Fontecave M, Artero V. Artificial Hydrogenases Based on Cobaloximes and Heme Oxygenase. Chempluschem 2016; 81:1083-1089. [DOI: 10.1002/cplu.201600218] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Revised: 06/06/2016] [Indexed: 11/07/2022]
Affiliation(s)
- Marine Bacchi
- Laboratory of Chemistry and Biology of Metals, UMR 5249 Université Grenoble Alpes, CNRS, CEA 17 rue des Martyrs 38054 Grenoble Cedex 9 France
| | - Elias Veinberg
- DYNAMO/DYNAMOP Institut de Biologie Structurale “Jean-Pierre Ebel”, UMR 5075 Université Grenoble Alpes, CNRS, CEA 41 rue Jules Horowitz 38027 Grenoble Cedex 1 France
| | - Martin J. Field
- DYNAMO/DYNAMOP Institut de Biologie Structurale “Jean-Pierre Ebel”, UMR 5075 Université Grenoble Alpes, CNRS, CEA 41 rue Jules Horowitz 38027 Grenoble Cedex 1 France
| | - Jens Niklas
- Chemical Sciences and Engineering Division Argonne National Laboratory 9700 South Cass Avenue, Lemont, IL 60439 USA
| | - Toshitaka Matsui
- Institute of Multidisciplinary Research for Advanced Materials Tohoku University Katahira, Aoba Sendai 980-8577 Japan
| | - D. M. Tiede
- Chemical Sciences and Engineering Division Argonne National Laboratory 9700 South Cass Avenue, Lemont, IL 60439 USA
| | - Oleg G. Poluektov
- Chemical Sciences and Engineering Division Argonne National Laboratory 9700 South Cass Avenue, Lemont, IL 60439 USA
| | - Masao Ikeda‐Saito
- Institute of Multidisciplinary Research for Advanced Materials Tohoku University Katahira, Aoba Sendai 980-8577 Japan
| | - Marc Fontecave
- Laboratory of Chemistry and Biology of Metals, UMR 5249 Université Grenoble Alpes, CNRS, CEA 17 rue des Martyrs 38054 Grenoble Cedex 9 France
- Laboratoire de Chimie des Processus Biologiques, UMR 8229 Collège de France, CNRS Université Pierre et Marie Curie 11 place Marcellin Berthelot 75005 Paris France
| | - Vincent Artero
- Laboratory of Chemistry and Biology of Metals, UMR 5249 Université Grenoble Alpes, CNRS, CEA 17 rue des Martyrs 38054 Grenoble Cedex 9 France
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Sommer DJ, Roy A, Astashkin A, Ghirlanda G. Modulation of cluster incorporation specificity in a de novo iron-sulfur cluster binding peptide. Biopolymers 2016; 104:412-8. [PMID: 25808361 DOI: 10.1002/bip.22635] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2015] [Revised: 02/10/2015] [Accepted: 02/11/2015] [Indexed: 12/20/2022]
Abstract
iron-sulfur cluster binding proteins perform an astounding variety of functions, and represent one of the most abundant classes of metalloproteins. Most often, they constitute pairs or chains and act as electron transfer modules either within complex redox enzymes or within small diffusible proteins. We have previously described the design of a three-helix bundle that can bind two clusters within its hydrophobic core. Here, we use single-point mutations to exchange one of the Cys ligands coordinating the cluster to either Leu or Ser. We show that the mutants modulate the redox potential of the clusters and stabilize the [3Fe-4S] form over the [4Fe-4S] form, supporting the use of model iron-sulfur cluster proteins as modules in the design of complex redox enzymes.
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Affiliation(s)
| | - Anindya Roy
- Chemistry and Biochemistry, Arizona State University, Tempe, AZ
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9
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Alcala-Torano R, Sommer DJ, Bahrami Dizicheh Z, Ghirlanda G. Design Strategies for Redox Active Metalloenzymes: Applications in Hydrogen Production. Methods Enzymol 2016; 580:389-416. [PMID: 27586342 DOI: 10.1016/bs.mie.2016.06.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/25/2023]
Abstract
The last decades have seen an increased interest in finding alternative means to produce renewable fuels in order to satisfy the growing energy demands and to minimize environmental impact. Nature can serve as an inspiration for development of these methodologies, as enzymes are able to carry out a wide variety of redox processes at high efficiency, employing a wide array of earth-abundant transition metals to do so. While it is well recognized that the protein environment plays an important role in tuning the properties of the different metal centers, the structure/function relationships between amino acids and catalytic centers are not well resolved. One specific approach to study the role of proteins in both electron and proton transfer is the biomimetic design of redox active peptides, binding organometallic clusters in well-understood protein environments. Here we discuss different strategies for the design of peptides incorporating redox active FeS clusters, [FeFe]-hydrogenase organometallic mimics, and porphyrin centers into different peptide and protein environments in order to understand natural redox enzymes.
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Affiliation(s)
- R Alcala-Torano
- School of Molecular Sciences, Arizona State University, Tempe, AZ, United States
| | - D J Sommer
- School of Molecular Sciences, Arizona State University, Tempe, AZ, United States
| | - Z Bahrami Dizicheh
- School of Molecular Sciences, Arizona State University, Tempe, AZ, United States
| | - G Ghirlanda
- School of Molecular Sciences, Arizona State University, Tempe, AZ, United States.
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10
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Ulas G, Lemmin T, Wu Y, Gassner GT, DeGrado WF. Designed metalloprotein stabilizes a semiquinone radical. Nat Chem 2016; 8:354-9. [PMID: 27001731 PMCID: PMC4857601 DOI: 10.1038/nchem.2453] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Accepted: 01/07/2016] [Indexed: 12/25/2022]
Abstract
Enzymes use binding energy to stabilize their substrates in high-energy states that are otherwise inaccessible at ambient temperature. Here we show that a de novo designed Zn(II) metalloprotein stabilizes a chemically reactive organic radical that is otherwise unstable in aqueous media. The protein binds tightly to and stabilizes the radical semiquinone form of 3,5-di-tert-butylcatechol. Solution NMR spectroscopy in conjunction with molecular dynamics simulations show that the substrate binds in the active site pocket where it is stabilized by metal-ligand interactions as well as by burial of its hydrophobic groups. Spectrochemical redox titrations show that the protein stabilized the semiquinone by reducing the electrochemical midpoint potential for its formation via the one-electron oxidation of the catechol by approximately 400 mV (9 kcal mol(-1)). Therefore, the inherent chemical properties of the radical were changed drastically by harnessing its binding energy to the metalloprotein. This model sets the basis for designed enzymes with radical cofactors to tackle challenging chemistry.
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Affiliation(s)
- Gözde Ulas
- Department of Pharmaceutical Chemistry, University of California – San Francisco, San Francisco, California 94158, USA
| | - Thomas Lemmin
- Department of Pharmaceutical Chemistry, University of California – San Francisco, San Francisco, California 94158, USA
| | - Yibing Wu
- Department of Pharmaceutical Chemistry, University of California – San Francisco, San Francisco, California 94158, USA
| | - George T. Gassner
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, California 94132, USA
| | - William F. DeGrado
- Department of Pharmaceutical Chemistry, University of California – San Francisco, San Francisco, California 94158, USA
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11
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Sandhya S, Mudgal R, Kumar G, Sowdhamini R, Srinivasan N. Protein sequence design and its applications. Curr Opin Struct Biol 2016; 37:71-80. [PMID: 26773478 DOI: 10.1016/j.sbi.2015.12.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Revised: 12/07/2015] [Accepted: 12/15/2015] [Indexed: 01/14/2023]
Abstract
Design of proteins has far-reaching potentials in diverse areas that span repurposing of the protein scaffold for reactions and substrates that they were not naturally meant for, to catching a glimpse of the ephemeral proteins that nature might have sampled during evolution. These non-natural proteins, either in synthesized or virtual form have opened the scope for the design of entities that not only rival their natural counterparts but also offer a chance to visualize the protein space continuum that might help to relate proteins and understand their associations. Here, we review the recent advances in protein engineering and design, in multiple areas, with a view to drawing attention to their future potential.
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Affiliation(s)
- Sankaran Sandhya
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
| | - Richa Mudgal
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India; IISc Mathematics Initiative, Indian Institute of Science, Bangalore 560 012, India
| | - Gayatri Kumar
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
| | - Ramanathan Sowdhamini
- National Centre for Biological Sciences-TIFR, UAS-GKVK Campus, Bangalore 560065, India
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12
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Morra S, Maurelli S, Chiesa M, Mulder DW, Ratzloff MW, Giamello E, King PW, Gilardi G, Valetti F. The effect of a C298D mutation in CaHydA [FeFe]-hydrogenase: Insights into the protein-metal cluster interaction by EPR and FTIR spectroscopic investigation. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2015; 1857:98-106. [PMID: 26482707 DOI: 10.1016/j.bbabio.2015.10.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Revised: 10/01/2015] [Accepted: 10/15/2015] [Indexed: 01/17/2023]
Abstract
A conserved cysteine located in the signature motif of the catalytic center (H-cluster) of [FeFe]-hydrogenases functions in proton transfer. This residue corresponds to C298 in Clostridium acetobutylicum CaHydA. Despite the chemical and structural difference, the mutant C298D retains fast catalytic activity, while replacement with any other amino acid causes significant activity loss. Given the proximity of C298 to the H-cluster, the effect of the C298D mutation on the catalytic center was studied by continuous wave (CW) and pulse electron paramagnetic resonance (EPR) and by Fourier transform infrared (FTIR) spectroscopies. Comparison of the C298D mutant with the wild type CaHydA by CW and pulse EPR showed that the electronic structure of the center is not altered. FTIR spectroscopy confirmed that absorption peak values observed in the mutant are virtually identical to those observed in the wild type, indicating that the H-cluster is not generally affected by the mutation. Significant differences were observed only in the inhibited state Hox-CO: the vibrational modes assigned to the COexo and Fed-CO in this state are shifted to lower values in C298D, suggesting different interaction of these ligands with the protein moiety when C298 is changed to D298. More relevant to the catalytic cycle, the redox equilibrium between the Hox and Hred states is modified by the mutation, causing a prevalence of the oxidized state. This work highlights how the interactions between the protein environment and the H-cluster, a dynamic closely interconnected system, can be engineered and studied in the perspective of designing bio-inspired catalysts and mimics.
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Affiliation(s)
- Simone Morra
- Department of Life Sciences and Systems Biology, University of Torino, Torino 10133, Italy
| | - Sara Maurelli
- Department of Chemistry, University of Torino, Torino 10133, Italy
| | - Mario Chiesa
- Department of Chemistry, University of Torino, Torino 10133, Italy
| | - David W Mulder
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401, USA
| | - Michael W Ratzloff
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401, USA
| | - Elio Giamello
- Department of Chemistry, University of Torino, Torino 10133, Italy
| | - Paul W King
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401, USA
| | - Gianfranco Gilardi
- Department of Life Sciences and Systems Biology, University of Torino, Torino 10133, Italy
| | - Francesca Valetti
- Department of Life Sciences and Systems Biology, University of Torino, Torino 10133, Italy.
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Reengineering cyt b562 for hydrogen production: A facile route to artificial hydrogenases. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2015; 1857:598-603. [PMID: 26375327 DOI: 10.1016/j.bbabio.2015.09.001] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Accepted: 09/09/2015] [Indexed: 11/20/2022]
Abstract
Bioinspired, protein-based molecular catalysts utilizing base metals at the active are emerging as a promising avenue to sustainable hydrogen production. The protein matrix modulates the intrinsic reactivity of organometallic active sites by tuning second-sphere and long-range interactions. Here, we show that swapping Co-Protoporphyrin IX for Fe-Protoporphyrin IX in cytochrome b562 results in an efficient catalyst for photoinduced proton reduction to molecular hydrogen. Further, the activity of wild type Co-cyt b562 can be modulated by a factor of 2.5 by exchanging the coordinating methionine with alanine or aspartic acid. The observed turnover numbers (TON) range between 125 and 305, and correlate well with the redox potential of the Co-cyt b562 mutants. The photosensitized system catalyzes proton reduction with high efficiency even under an aerobic atmosphere, implicating its use for biotechnological applications. 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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14
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Artero V, Berggren G, Atta M, Caserta G, Roy S, Pecqueur L, Fontecave M. From enzyme maturation to synthetic chemistry: the case of hydrogenases. Acc Chem Res 2015; 48:2380-7. [PMID: 26165393 DOI: 10.1021/acs.accounts.5b00157] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Water splitting into oxygen and hydrogen is one of the most attractive strategies for storing solar energy and electricity. Because the processes at work are multielectronic, there is a crucial need for efficient and stable catalysts, which in addition have to be cheap for future industrial developments (electrolyzers, photoelectrochemicals, and fuel cells). Specifically for the water/hydrogen interconversion, Nature is an exquisite source of inspiration since this chemistry contributes to the bioenergetic metabolism of a number of living organisms via the activity of fascinating metalloenzymes, the hydrogenases. In this Account, we first briefly describe the structure of the unique dinuclear organometallic active sites of the two classes of hydrogenases as well as the complex protein machineries involved in their biosynthesis, their so-called maturation processes. This knowledge allows for the development of a fruitful bioinspired chemistry approach, which has already led to a number of interesting and original catalysts mimicking the natural active sites. More specifically, we describe our own attempts to prepare artificial hydrogenases. This can be achieved via the standard bioinspired approach using the combination of a synthetic bioinspired catalyst and a polypeptide scaffold. Such hybrid complexes provide the opportunity to optimize the system by manipulating both the catalyst through chemical synthesis and the protein component through mutagenesis. We also raise the possibility to reach such artificial systems via an original strategy based on mimicking the enzyme maturation pathways. This is illustrated in this Account by two examples developed in our laboratory. First, we show how the preparation of a lysozyme-{Mn(I)(CO)3} hybrid and its clean reaction with a nickel complex led us to generate a new class of binuclear Ni-Mn H2-evolving catalysts mimicking the active site of [NiFe]-hydrogenases. Then we describe how we were able to rationally design and prepare a hybrid system, displaying remarkable structural similarities to an [FeFe]-hydrogenase, and we show here for the first time that it is catalytically active for proton reduction. This system is based on the combination of HydF, a protein involved in the maturation of [FeFe]-hydrogenase (HydA), and a close mimic of the active site of this class of enzymes. Moreover, the synthetic [Fe2(adt)(CO)4(CN)2](2-) (adt(2-)= aza-propanedithiol) mimic, alone or within a HydF hybrid system, was shown to be able to maturate and activate a form of HydA itself lacking its diiron active site. We discuss the exciting perspectives this "synthetic maturation" opens regarding the "invention" of novel hydrogenases by the chemists.
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Affiliation(s)
- Vincent Artero
- Laboratory of Chemistry and Biology of Metals, Univ. Grenoble Alpes, CNRS, CEA, 17 rue des Martyrs, 38000 Grenoble, France
| | - Gustav Berggren
- Department of Chemistry−the
Ångström Laboratory, Uppsala University, Lägerhyddsvägen
1, 751 20 Uppsala, Sweden
| | - Mohamed Atta
- Laboratory of Chemistry and Biology of Metals, Univ. Grenoble Alpes, CNRS, CEA, 17 rue des Martyrs, 38000 Grenoble, France
| | - Giorgio Caserta
- Laboratoire de Chimie des Processus Biologiques,
Collège de France, CNRS, Université Pierre et Marie Curie, 11 Place Marcelin Berthelot, 75005 Paris, France
| | - Souvik Roy
- Laboratory of Chemistry and Biology of Metals, Univ. Grenoble Alpes, CNRS, CEA, 17 rue des Martyrs, 38000 Grenoble, France
| | - Ludovic Pecqueur
- Laboratoire de Chimie des Processus Biologiques,
Collège de France, CNRS, Université Pierre et Marie Curie, 11 Place Marcelin Berthelot, 75005 Paris, France
| | - Marc Fontecave
- Laboratory of Chemistry and Biology of Metals, Univ. Grenoble Alpes, CNRS, CEA, 17 rue des Martyrs, 38000 Grenoble, France
- Laboratoire de Chimie des Processus Biologiques,
Collège de France, CNRS, Université Pierre et Marie Curie, 11 Place Marcelin Berthelot, 75005 Paris, France
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15
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Bacchi M, Berggren G, Niklas J, Veinberg E, Mara MW, Shelby ML, Poluektov OG, Chen LX, Tiede DM, Cavazza C, Field MJ, Fontecave M, Artero V. Cobaloxime-Based Artificial Hydrogenases. Inorg Chem 2014; 53:8071-82. [DOI: 10.1021/ic501014c] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Marine Bacchi
- Laboratory of Chemistry and Biology of
Metals, Université Grenoble Alpes, CNRS, CEA, 17 rue des
Martyrs, F-38000 Grenoble, France
| | - Gustav Berggren
- Laboratory of Chemistry and Biology of
Metals, Université Grenoble Alpes, CNRS, CEA, 17 rue des
Martyrs, F-38000 Grenoble, France
| | - Jens Niklas
- Chemical Sciences and Engineering
Division, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439, United States
| | - Elias Veinberg
- DYNAMO/DYNAMOP, Institut de Biologie Structurale, UMR
CNRS/Université Grenoble Alpes/CEA 5075, EPN Campus, 6 rue Jules Horowitz F-38000 Grenoble, France
| | - Michael W. Mara
- Department of Chemistry, Northwestern University, 2145 Sheridan
Road, Evanston, Illinois 60208, United States
| | - Megan L. Shelby
- Department of Chemistry, Northwestern University, 2145 Sheridan
Road, Evanston, Illinois 60208, United States
| | - Oleg G. Poluektov
- Chemical Sciences and Engineering
Division, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439, United States
| | - Lin X. Chen
- Chemical Sciences and Engineering
Division, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439, United States
- Department of Chemistry, Northwestern University, 2145 Sheridan
Road, Evanston, Illinois 60208, United States
| | - David M. Tiede
- Chemical Sciences and Engineering
Division, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439, United States
| | - Christine Cavazza
- Laboratory of Chemistry and Biology of
Metals, Université Grenoble Alpes, CNRS, CEA, 17 rue des
Martyrs, F-38000 Grenoble, France
| | - Martin J. Field
- DYNAMO/DYNAMOP, Institut de Biologie Structurale, UMR
CNRS/Université Grenoble Alpes/CEA 5075, EPN Campus, 6 rue Jules Horowitz F-38000 Grenoble, France
| | - Marc Fontecave
- Laboratory of Chemistry and Biology of
Metals, Université Grenoble Alpes, CNRS, CEA, 17 rue des
Martyrs, F-38000 Grenoble, France
- Laboratoire de Chimie des Processus Biologiques, UMR 8229 (Collège
de France, CNRS, Université Pierre et Marie Curie), 11 place Marcellin Berthelot 75005 Paris, France
| | - Vincent Artero
- Laboratory of Chemistry and Biology of
Metals, Université Grenoble Alpes, CNRS, CEA, 17 rue des
Martyrs, F-38000 Grenoble, France
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16
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Onoda A, Kihara Y, Fukumoto K, Sano Y, Hayashi T. Photoinduced Hydrogen Evolution Catalyzed by a Synthetic Diiron Dithiolate Complex Embedded within a Protein Matrix. ACS Catal 2014. [DOI: 10.1021/cs500392e] [Citation(s) in RCA: 85] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Akira Onoda
- Department of Applied Chemistry,
Graduate School of Engineering, Osaka University, Suita, Osaka 565-0871, Japan
| | - Yoshihiko Kihara
- Department of Applied Chemistry,
Graduate School of Engineering, Osaka University, Suita, Osaka 565-0871, Japan
| | - Kazuki Fukumoto
- Department of Applied Chemistry,
Graduate School of Engineering, Osaka University, Suita, Osaka 565-0871, Japan
| | - Yohei Sano
- Department of Applied Chemistry,
Graduate School of Engineering, Osaka University, Suita, Osaka 565-0871, Japan
| | - Takashi Hayashi
- Department of Applied Chemistry,
Graduate School of Engineering, Osaka University, Suita, Osaka 565-0871, Japan
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17
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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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18
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Happe T, Hemschemeier A. Metalloprotein mimics – old tools in a new light. Trends Biotechnol 2014; 32:170-6. [DOI: 10.1016/j.tibtech.2014.02.004] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Revised: 02/07/2014] [Accepted: 02/07/2014] [Indexed: 01/03/2023]
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19
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Sommer DJ, Vaughn MD, Ghirlanda G. Protein secondary-shell interactions enhance the photoinduced hydrogen production of cobalt protoporphyrin IX. Chem Commun (Camb) 2014; 50:15852-5. [DOI: 10.1039/c4cc06700b] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
An efficient molecular catalyst for hydrogen production is generated by incorporating Co-protoporphyrin IX into myoglobin. The activity is modulated by engineered mutations.
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