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Günzel A, Engelbrecht V, Happe T. Changing the tracks: screening for electron transfer proteins to support hydrogen production. J Biol Inorg Chem 2022; 27:631-640. [PMID: 36038787 PMCID: PMC9569306 DOI: 10.1007/s00775-022-01956-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 07/28/2022] [Indexed: 11/26/2022]
Abstract
Ferredoxins are essential electron transferring proteins in organisms. Twelve plant-type ferredoxins in the green alga Chlamydomonas reinhardtii determine the fate of electrons, generated in multiple metabolic processes. The two hydrogenases HydA1 and HydA2 of. C. reinhardtii compete for electrons from the photosynthetic ferredoxin PetF, which is the first stromal mediator of the high-energy electrons derived from the absorption of light energy at the photosystems. While being involved in many chloroplast-located metabolic pathways, PetF shows the highest affinity for ferredoxin-NADP+ oxidoreductase (FNR), not for the hydrogenases. Aiming to identify other potential electron donors for the hydrogenases, we screened as yet uncharacterized ferredoxins Fdx7, 8, 10 and 11 for their capability to reduce the hydrogenases. Comparing the performance of the Fdx in presence and absence of competitor FNR, we show that Fdx7 has a higher affinity for HydA1 than for FNR. Additionally, we show that synthetic FeS-cluster-binding maquettes, which can be reduced by NADPH alone, can also be used to reduce the hydrogenases. Our findings pave the way for the creation of tailored electron donors to redirect electrons to enzymes of interest.
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Affiliation(s)
- Alexander Günzel
- Faculty of Biology and Biotechnology, Photobiotechnology, Ruhr-University Bochum, Universitätsstraße 150, 44801, Bochum, Germany
| | - Vera Engelbrecht
- Faculty of Biology and Biotechnology, Photobiotechnology, Ruhr-University Bochum, Universitätsstraße 150, 44801, Bochum, Germany
| | - Thomas Happe
- Faculty of Biology and Biotechnology, Photobiotechnology, Ruhr-University Bochum, Universitätsstraße 150, 44801, Bochum, Germany.
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2
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Boncella AE, Sabo ET, Santore RM, Carter J, Whalen J, Hudspeth JD, Morrison CN. The expanding utility of iron-sulfur clusters: Their functional roles in biology, synthetic small molecules, maquettes and artificial proteins, biomimetic materials, and therapeutic strategies. Coord Chem Rev 2022. [DOI: 10.1016/j.ccr.2021.214229] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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Abstract
Natural metalloproteins perform many functions - ranging from sensing to electron transfer and catalysis - in which the position and property of each ligand and metal, is dictated by protein structure. De novo protein design aims to define an amino acid sequence that encodes a specific structure and function, providing a critical test of the hypothetical inner workings of (metallo)proteins. To date, de novo metalloproteins have used simple, symmetric tertiary structures - uncomplicated by the large size and evolutionary marks of natural proteins - to interrogate structure-function hypotheses. In this Review, we discuss de novo design applications, such as proteins that induce complex, increasingly asymmetric ligand geometries to achieve function, as well as the use of more canonical ligand geometries to achieve stability. De novo design has been used to explore how proteins fine-tune redox potentials and catalyse both oxidative and hydrolytic reactions. With an increased understanding of structure-function relationships, functional proteins including O2-dependent oxidases, fast hydrolases, and multi-proton/multi-electron reductases, have been created. In addition, proteins can now be designed using xeno-biological metals or cofactors and principles from inorganic chemistry to derive new-to-nature functions. These results and the advances in computational protein design suggest a bright future for the de novo design of diverse, functional metalloproteins.
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Affiliation(s)
- Matthew J. Chalkley
- Department of Pharmaceutical Chemistry and the Cardiovascular Research Institute, University of California at San Francisco, San Francisco, (CA), USA
| | - Samuel I. Mann
- Department of Pharmaceutical Chemistry and the Cardiovascular Research Institute, University of California at San Francisco, San Francisco, (CA), USA
| | - William F. DeGrado
- Department of Pharmaceutical Chemistry and the Cardiovascular Research Institute, University of California at San Francisco, San Francisco, (CA), USA
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Grayson KJ, Anderson JLR. Designed for life: biocompatible de novo designed proteins and components. J R Soc Interface 2019; 15:rsif.2018.0472. [PMID: 30158186 PMCID: PMC6127164 DOI: 10.1098/rsif.2018.0472] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 08/01/2018] [Indexed: 12/30/2022] Open
Abstract
A principal goal of synthetic biology is the de novo design or redesign of biomolecular components. In addition to revealing fundamentally important information regarding natural biomolecular engineering and biochemistry, functional building blocks will ultimately be provided for applications including the manufacture of valuable products and therapeutics. To fully realize this ambitious goal, the designed components must be biocompatible, working in concert with natural biochemical processes and pathways, while not adversely affecting cellular function. For example, de novo protein design has provided us with a wide repertoire of structures and functions, including those that can be assembled and function in vivo. Here we discuss such biocompatible designs, as well as others that have the potential to become biocompatible, including non-protein molecules, and routes to achieving full biological integration.
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Affiliation(s)
- Katie J Grayson
- School of Biochemistry, University of Bristol, Biomedical Sciences Building, Bristol BS8 1TD, UK
| | - J L Ross Anderson
- School of Biochemistry, University of Bristol, Biomedical Sciences Building, Bristol BS8 1TD, UK .,BrisSynBio Synthetic Biology Research Centre, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK
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Lin YW. Rational Design of Artificial Metalloproteins and Metalloenzymes with Metal Clusters. Molecules 2019; 24:E2743. [PMID: 31362341 PMCID: PMC6696605 DOI: 10.3390/molecules24152743] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 07/24/2019] [Accepted: 07/26/2019] [Indexed: 01/22/2023] Open
Abstract
Metalloproteins and metalloenzymes play important roles in biological systems by using the limited metal ions, complexes, and clusters that are associated with the protein matrix. The design of artificial metalloproteins and metalloenzymes not only reveals the structure and function relationship of natural proteins, but also enables the synthesis of artificial proteins and enzymes with improved properties and functions. Acknowledging the progress in rational design from single to multiple active sites, this review focuses on recent achievements in the design of artificial metalloproteins and metalloenzymes with metal clusters, including zinc clusters, cadmium clusters, iron-sulfur clusters, and copper-sulfur clusters, as well as noble metal clusters and others. These metal clusters were designed in both native and de novo protein scaffolds for structural roles, electron transfer, or catalysis. Some synthetic metal clusters as functional models of native enzymes are also discussed. These achievements provide valuable insights for deep understanding of the natural proteins and enzymes, and practical clues for the further design of artificial enzymes with functions comparable or even beyond those of natural counterparts.
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Affiliation(s)
- Ying-Wu Lin
- School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China.
- Laboratory of Protein Structure and Function, University of South China, Hengyang 421001, China.
- Hunan Key Laboratory for the Design and Application of Actinide Complexes, University of South China, Hengyang 421001, China.
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6
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Alcala-Torano R, Walther M, Sommer DJ, Park CK, Ghirlanda G. Rational design of a hexameric protein assembly stabilized by metal chelation. Biopolymers 2018; 109:e23233. [PMID: 30191549 DOI: 10.1002/bip.23233] [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] [Received: 12/21/2017] [Revised: 06/15/2018] [Accepted: 07/05/2018] [Indexed: 12/27/2022]
Abstract
Protein-based self-assembled nanostructures hold tremendous promise as smart materials. One strategy to control the assembly of individual protein modules takes advantage of the directionality and high affinity bonding afforded by metal chelation. Here, we describe the use of 2,2'-bipyridine units (Bpy) as side chains to template the assembly of large structures (MW approx. 35 000 Da) in a metal-dependent manner. The structures are trimers of independently folded 3-helix bundles, and are held together by 2 Me(Bpy)3 complexes. The assemblies are stable to thermal denaturation, and are more than 90% helical at 90°C. Circular dichroism spectroscopy shows that one of the 2 possible (Bpy)3 enantiomers is favored over the other. Because of the sequence pliability of the starting peptides, these constructs could find use to organize functional groups at controlled positions within a supramolecular assembly.
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Affiliation(s)
| | - Mathieu Walther
- School of Molecular Sciences, Arizona State University, Tempe, Arizona
| | - Dayn J Sommer
- School of Molecular Sciences, Arizona State University, Tempe, Arizona
| | - Chad K Park
- Department of Biochemistry, University of Arizona, Tucson, Arizona
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Chino M, Zhang SQ, Pirro F, Leone L, Maglio O, Lombardi A, DeGrado WF. Spectroscopic and metal binding properties of a de novo metalloprotein binding a tetrazinc cluster. Biopolymers 2018; 109:e23339. [PMID: 30203532 PMCID: PMC6218314 DOI: 10.1002/bip.23229] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Revised: 05/18/2018] [Accepted: 05/22/2018] [Indexed: 12/27/2022]
Abstract
De novo design provides an attractive approach, which allows one to test and refine the principles guiding metalloproteins in defining the geometry and reactivity of their metal ion cofactors. Although impressive progress has been made in designing proteins that bind transition metal ions including iron-sulfur clusters, the design of tetranuclear clusters with oxygen-rich environments remains in its infancy. In previous work, we described the design of homotetrameric four-helix bundles that bind tetra-Zn2+ clusters. The crystal structures of the helical proteins were in good agreement with the overall design, and the metal-binding and conformational properties of the helical bundles in solution were consistent with the crystal structures. However, the corresponding apo-proteins were not fully folded in solution. In this work, we design three peptides, based on the crystal structure of the original bundles. One of the peptides forms tetramers in aqueous solution in the absence of metal ions as assessed by CD and NMR. It also binds Zn2+ in the intended stoichiometry. These studies strongly suggest that the desired structure has been achieved in the apo state, providing evidence that the peptide is able to actively impart the designed geometry to the metal cluster.
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Affiliation(s)
- Marco Chino
- Department of Chemical Sciences, University of Napoli “Federico II”, Via Cintia, 46, 80126 Napoli, Italy
| | - Shao-Qing Zhang
- Department of Pharmaceutical Chemistry and the Cardiovascular Research Institute, University of California at San Francisco, San Francisco, CA 94158-9001, United States
- Department of Chemistry, University of Pennsylvania, 209 South 33rd Street, Philadelphia, PA 19104-6396, United States
| | - Fabio Pirro
- Department of Chemical Sciences, University of Napoli “Federico II”, Via Cintia, 46, 80126 Napoli, Italy
| | - Linda Leone
- Department of Chemical Sciences, University of Napoli “Federico II”, Via Cintia, 46, 80126 Napoli, Italy
| | - Ornella Maglio
- Department of Chemical Sciences, University of Napoli “Federico II”, Via Cintia, 46, 80126 Napoli, Italy
- Institute of Biostructure and Bioimaging, National Research Council, via Mezzocannone, 16, 80134, Napoli, Italy
| | - Angela Lombardi
- Department of Chemical Sciences, University of Napoli “Federico II”, Via Cintia, 46, 80126 Napoli, Italy
| | - William F. DeGrado
- Department of Pharmaceutical Chemistry and the Cardiovascular Research Institute, University of California at San Francisco, San Francisco, CA 94158-9001, United States
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9
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Dizicheh ZB, Halloran N, Asma W, Ghirlanda G. De Novo Design of Iron–Sulfur Proteins. Methods Enzymol 2017; 595:33-53. [DOI: 10.1016/bs.mie.2017.07.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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10
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Design of Redox-Active Peptides: Towards Functional Materials. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016. [PMID: 27677515 DOI: 10.1007/978-3-319-39196-0_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register]
Abstract
In nature, the majority of processes that occur in the cell involve the cycling of electrons and protons, changing the reduction and oxidation state of substrates to alter their chemical reactivity and usefulness in vivo. One of the most relevant examples of these processes is the electron transport chain, a series of oxidoreductase proteins that shuttle electrons through well-defined pathways, concurrently moving protons across the cell membrane. Inspired by these processes, researchers have sought to develop materials to mimic natural systems for a number of applications, including fuel production. The most common cofactors found in proteins to carry out electron transfer are iron sulfur clusters and porphyrin-like molecules. Both types have been studied within natural proteins, such as in photosynthetic machinery or soluble electron carriers; in parallel, an extensive literature has developed over recent years attempting to model and study these cofactors within peptide-based materials. This chapter will focus on major designs that have significantly advanced the field.
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Maeda Y, Makhlynets OV, Matsui H, Korendovych IV. Design of Catalytic Peptides and Proteins Through Rational and Combinatorial Approaches. Annu Rev Biomed Eng 2016; 18:311-28. [PMID: 27022702 PMCID: PMC6345664 DOI: 10.1146/annurev-bioeng-111215-024421] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
This review focuses on recent progress in noncomputational methods to introduce catalytic function into proteins, peptides, and peptide assemblies. We discuss various approaches to creating catalytic activity and classification of noncomputational methods into rational and combinatorial classes. The section on rational design covers recent progress in the development of short peptides and oligomeric peptide assemblies for various natural and unnatural reactions. The section on combinatorial design describes recent advances in the discovery of catalytic peptides. We present the future prospects of these and other new approaches in a broader context, including implications for functional material design.
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Affiliation(s)
- Yoshiaki Maeda
- Department of Chemistry, City University of New York-Hunter College, New York, New York 10065;
- Division of Biotechnology and Life Science, Institute of Engineering, Tokyo University of Agriculture and Technology, Tokyo 184-8588, Japan
| | - Olga V Makhlynets
- Department of Chemistry, Syracuse University, Syracuse, New York 13244;
| | - Hiroshi Matsui
- Department of Chemistry, City University of New York-Hunter College, New York, New York 10065;
- Department of Biochemistry, Weill Medical College of Cornell University, New York, New York 10021
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12
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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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13
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Recent advances in designed coiled coils and helical bundles with inorganic prosthetic groups — from structural to functional applications. Curr Opin Chem Biol 2016; 31:160-5. [DOI: 10.1016/j.cbpa.2016.03.009] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Revised: 03/08/2016] [Accepted: 03/08/2016] [Indexed: 11/17/2022]
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Nanda V, Senn S, Pike DH, Rodriguez-Granillo A, Hansen WA, Khare SD, Noy D. Structural principles for computational and de novo design of 4Fe-4S metalloproteins. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2015; 1857:531-538. [PMID: 26449207 DOI: 10.1016/j.bbabio.2015.10.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Accepted: 10/01/2015] [Indexed: 11/30/2022]
Abstract
Iron-sulfur centers in metalloproteins can access multiple oxidation states over a broad range of potentials, allowing them to participate in a variety of electron transfer reactions and serving as catalysts for high-energy redox processes. The nitrogenase FeMoCO cluster converts di-nitrogen to ammonia in an eight-electron transfer step. The 2(Fe4S4) containing bacterial ferredoxin is an evolutionarily ancient metalloprotein fold and is thought to be a primordial progenitor of extant oxidoreductases. Controlling chemical transformations mediated by iron-sulfur centers such as nitrogen fixation, hydrogen production as well as electron transfer reactions involved in photosynthesis are of tremendous importance for sustainable chemistry and energy production initiatives. As such, there is significant interest in the design of iron-sulfur proteins as minimal models to gain fundamental understanding of complex natural systems and as lead-molecules for industrial and energy applications. Herein, we discuss salient structural characteristics of natural iron-sulfur proteins and how they guide principles for design. Model structures of past designs are analyzed in the context of these principles and potential directions for enhanced designs are presented, and new areas of iron-sulfur protein design are proposed. This article is part of a Special issue entitled Biodesign for Bioenergetics--the design and engineering of electronic transfer cofactors, protein networks, edited by Ronald L. Koder and J.L Ross Anderson.
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Affiliation(s)
- Vikas Nanda
- Department of Biochemistry and Molecular Biology and the Center for Advanced Biotechnology and Medicine, Robert Wood Johnson Medical School, Rutgers University, 679 Hoes Lane West, Piscataway, NJ, 08854, USA.
| | - Stefan Senn
- Department of Biochemistry and Molecular Biology and the Center for Advanced Biotechnology and Medicine, Robert Wood Johnson Medical School, Rutgers University, 679 Hoes Lane West, Piscataway, NJ, 08854, USA
| | - Douglas H Pike
- Department of Biochemistry and Molecular Biology and the Center for Advanced Biotechnology and Medicine, Robert Wood Johnson Medical School, Rutgers University, 679 Hoes Lane West, Piscataway, NJ, 08854, USA
| | - Agustina Rodriguez-Granillo
- Department of Biochemistry and Molecular Biology and the Center for Advanced Biotechnology and Medicine, Robert Wood Johnson Medical School, Rutgers University, 679 Hoes Lane West, Piscataway, NJ, 08854, USA
| | - Will A Hansen
- Department of Chemistry and the Center for Integrated Proteomics Research, Rutgers University, 174 Frelinghuysen Rd, Piscataway, NJ 08854, USA
| | - Sagar D Khare
- Department of Chemistry and the Center for Integrated Proteomics Research, Rutgers University, 174 Frelinghuysen Rd, Piscataway, NJ 08854, USA
| | - Dror Noy
- Bioenergetics and Protein Design Laboratory, Migal - Galilee Research Institute, South Industrial Zone, Kiryat Shmona 11016, Israel
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