1
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Leone L, De Fenza M, Esposito A, Maglio O, Nastri F, Lombardi A. Peptides and metal ions: A successful marriage for developing artificial metalloproteins. J Pept Sci 2024; 30:e3606. [PMID: 38719781 DOI: 10.1002/psc.3606] [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: 02/19/2024] [Revised: 03/27/2024] [Accepted: 03/28/2024] [Indexed: 10/12/2024]
Abstract
The mutual relationship between peptides and metal ions enables metalloproteins to have crucial roles in biological systems, including structural, sensing, electron transport, and catalytic functions. The effort to reproduce or/and enhance these roles, or even to create unprecedented functions, is the focus of protein design, the first step toward the comprehension of the complex machinery of nature. Nowadays, protein design allows the building of sophisticated scaffolds, with novel functions and exceptional stability. Recent progress in metalloprotein design has led to the building of peptides/proteins capable of orchestrating the desired functions of different metal cofactors. The structural diversity of peptides allows proper selection of first- and second-shell ligands, as well as long-range electrostatic and hydrophobic interactions, which represent precious tools for tuning metal properties. The scope of this review is to discuss the construction of metal sites in de novo designed and miniaturized scaffolds. Selected examples of mono-, di-, and multi-nuclear binding sites, from the last 20 years will be described in an effort to highlight key artificial models of catalytic or electron-transfer metalloproteins. The authors' goal is to make readers feel like guests at the marriage between peptides and metal ions while offering sources of inspiration for future architects of innovative, artificial metalloproteins.
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Affiliation(s)
- Linda Leone
- Department of Chemical Sciences, University of Naples Federico II, Naples, Italy
| | - Maria De Fenza
- Department of Chemical Sciences, University of Naples Federico II, Naples, Italy
| | - Alessandra Esposito
- Department of Chemical Sciences, University of Naples Federico II, Naples, Italy
| | - Ornella Maglio
- Department of Chemical Sciences, University of Naples Federico II, Naples, Italy
- Institute of Biostructures and Bioimaging, National Research Council, Naples, Italy
| | - Flavia Nastri
- Department of Chemical Sciences, University of Naples Federico II, Naples, Italy
| | - Angela Lombardi
- Department of Chemical Sciences, University of Naples Federico II, Naples, Italy
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2
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Fernandez-Lopez L, Cea-Rama I, Alvarez-Malmagro J, Ressmann AK, Gonzalez-Alfonso JL, Coscolín C, Shahgaldian P, Plou FJ, Modregger J, Pita M, Sanz-Aparicio J, Ferrer M. Transforming an esterase into an enantioselective catecholase through bioconjugation of a versatile metal-chelating inhibitor. Chem Commun (Camb) 2023. [PMID: 37376994 DOI: 10.1039/d3cc01946b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/29/2023]
Abstract
Metal complexes introduced into protein scaffolds can generate versatile biomimetic catalysts endowed with a variety of catalytic properties. Here, we synthesized and covalently bound a bipyridinyl derivative to the active centre of an esterase to generate a biomimetic catalyst that shows catecholase activity and enantioselective catalytic oxidation of (+)-catechin.
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Affiliation(s)
| | - Isabel Cea-Rama
- Instituto de Quimica Fisica Rocasolano (IQFR), CSIC, Madrid 28006, Spain
| | | | | | | | - Cristina Coscolín
- Instituto de Catalisis y Petroleoquimica (ICP), CSIC, Madrid 28049, Spain.
| | - Patrick Shahgaldian
- Institute for Ecopreneurship, School of Life Sciences, University of Applied Sciences and Arts Northwestern Switzerland, Muttenz 4132, Switzerland
| | - Francisco J Plou
- Instituto de Catalisis y Petroleoquimica (ICP), CSIC, Madrid 28049, Spain.
| | | | - Marcos Pita
- Instituto de Catalisis y Petroleoquimica (ICP), CSIC, Madrid 28049, Spain.
| | | | - Manuel Ferrer
- Instituto de Catalisis y Petroleoquimica (ICP), CSIC, Madrid 28049, Spain.
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3
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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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4
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Koebke KJ, Pinter TBJ, Pitts WC, Pecoraro VL. Catalysis and Electron Transfer in De Novo Designed Metalloproteins. Chem Rev 2022; 122:12046-12109. [PMID: 35763791 PMCID: PMC10735231 DOI: 10.1021/acs.chemrev.1c01025] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
One of the hallmark advances in our understanding of metalloprotein function is showcased in our ability to design new, non-native, catalytically active protein scaffolds. This review highlights progress and milestone achievements in the field of de novo metalloprotein design focused on reports from the past decade with special emphasis on de novo designs couched within common subfields of bioinorganic study: heme binding proteins, monometal- and dimetal-containing catalytic sites, and metal-containing electron transfer sites. Within each subfield, we highlight several of what we have identified as significant and important contributions to either our understanding of that subfield or de novo metalloprotein design as a discipline. These reports are placed in context both historically and scientifically. General suggestions for future directions that we feel will be important to advance our understanding or accelerate discovery are discussed.
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Affiliation(s)
- Karl J. Koebke
- Department of Chemistry, University of Michigan Ann Arbor, MI 48109 USA
| | | | - Winston C. Pitts
- Department of Chemistry, University of Michigan Ann Arbor, MI 48109 USA
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5
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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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6
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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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7
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Jung SM, Lee J, Song WJ. Design of artificial metalloenzymes with multiple inorganic elements: The more the merrier. J Inorg Biochem 2021; 223:111552. [PMID: 34332336 DOI: 10.1016/j.jinorgbio.2021.111552] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Revised: 06/21/2021] [Accepted: 07/15/2021] [Indexed: 11/27/2022]
Abstract
A large fraction of metalloenzymes harbors multiple metal-centers that are electronically and/or functionally arranged within their proteinaceous environments. To explore the orchestration of inorganic and biochemical components and to develop bioinorganic catalysts and materials, we have described selected examples of artificial metalloproteins having multiple metallocofactors that were grouped depending on their initial protein scaffolds, the nature of introduced inorganic moieties, and the method used to propagate the number of metal ions within a protein. They demonstrated that diverse inorganic moieties can be selectively grafted and modulated in protein environments, providing a retrosynthetic bottom-up approach in the design of versatile and proficient biocatalysts and biomimetic model systems to explore fundamental questions in bioinorganic chemistry.
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Affiliation(s)
- Se-Min Jung
- Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Jaehee Lee
- Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Woon Ju Song
- Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul 08826, Republic of Korea.
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8
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Roda S, Robles-Martín A, Xiang R, Kazemi M, Guallar V. Structural-Based Modeling in Protein Engineering. A Must Do. J Phys Chem B 2021; 125:6491-6500. [PMID: 34106727 DOI: 10.1021/acs.jpcb.1c02545] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Biotechnological solutions will be a key aspect in our immediate future society, where optimized enzymatic processes through enzyme engineering might be an important solution for waste transformation, clean energy production, biodegradable materials, and green chemistry, for example. Here we advocate the importance of structural-based bioinformatics and molecular modeling tools in such developments. We summarize our recent experiences indicating a great prediction/success ratio, and we suggest that an early in silico phase should be performed in enzyme engineering studies. Moreover, we demonstrate the potential of a new technique combining Rosetta and PELE, which could provide a faster and more automated procedure, an essential aspect for a broader use.
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Affiliation(s)
- Sergi Roda
- Barcelona Supercomputing Center (BSC), Barcelona 08034, Spain
| | | | - Ruite Xiang
- Barcelona Supercomputing Center (BSC), Barcelona 08034, Spain
| | - Masoud Kazemi
- Barcelona Supercomputing Center (BSC), Barcelona 08034, Spain
| | - Victor Guallar
- Barcelona Supercomputing Center (BSC), Barcelona 08034, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona 08010, Spain
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9
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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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10
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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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11
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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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12
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Mancini JA, Pike DH, Tyryshkin AM, Haramaty L, Wang MS, Poudel S, Hecht M, Nanda V. Design of a Fe 4 S 4 cluster into the core of a de novo four-helix bundle. Biotechnol Appl Biochem 2020; 67:574-585. [PMID: 32770861 DOI: 10.1002/bab.2003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 08/06/2020] [Indexed: 12/12/2022]
Abstract
We explore the capacity of the de novo protein, S824, to incorporate a multinuclear iron-sulfur cluster within the core of a single-chain four-helix bundle. This topology has a high intrinsic designability because sequences are constrained largely by the pattern of hydrophobic and hydrophilic amino acids, thereby allowing for the extensive substitution of individual side chains. Libraries of novel proteins based on these constraints have surprising functional potential and have been shown to complement the deletion of essential genes in E. coli. Our structure-based design of four first-shell cysteine ligands, one per helix, in S824 resulted in successful incorporation of a cubane Fe4 S4 cluster into the protein core. A number of challenges were encountered during the design and characterization process, including nonspecific metal-induced aggregation and the presence of competing metal-cluster stoichiometries. The introduction of buried iron-sulfur clusters into the helical bundle is an initial step toward converting libraries of designed structures into functional de novo proteins with catalytic or electron-transfer functionalities.
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Affiliation(s)
- Joshua A Mancini
- Environmental Biophysics and Molecular Ecology Program, Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, NJ, USA.,Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School and the Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, NJ, USA
| | - Douglas H Pike
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School and the Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, NJ, USA
| | - Alexei M Tyryshkin
- Environmental Biophysics and Molecular Ecology Program, Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, NJ, USA
| | - Liti Haramaty
- Environmental Biophysics and Molecular Ecology Program, Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, NJ, USA
| | - Michael S Wang
- Department of Chemistry, Princeton University, Princeton, NJ, USA
| | - Saroj Poudel
- Environmental Biophysics and Molecular Ecology Program, Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, NJ, USA.,Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School and the Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, NJ, USA
| | - Michael Hecht
- Department of Chemistry, Princeton University, Princeton, NJ, USA
| | - Vikas Nanda
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School and the Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, NJ, USA
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13
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Alonso S, Santiago G, Cea-Rama I, Fernandez-Lopez L, Coscolín C, Modregger J, Ressmann AK, Martínez-Martínez M, Marrero H, Bargiela R, Pita M, Gonzalez-Alfonso JL, Briand ML, Rojo D, Barbas C, Plou FJ, Golyshin PN, Shahgaldian P, Sanz-Aparicio J, Guallar V, Ferrer M. Genetically engineered proteins with two active sites for enhanced biocatalysis and synergistic chemo- and biocatalysis. Nat Catal 2019. [DOI: 10.1038/s41929-019-0394-4] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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14
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Engineering Metalloprotein Functions in Designed and Native Scaffolds. Trends Biochem Sci 2019; 44:1022-1040. [DOI: 10.1016/j.tibs.2019.06.006] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 06/05/2019] [Accepted: 06/11/2019] [Indexed: 12/15/2022]
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15
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Chen W, Cai X, Ji L, Li X, Wang X, Zhang X, Gao Y, Feng F. A photosynthesis-inspired supramolecular system: caging photosensitizer and photocatalyst in apoferritin. PHOTOSYNTHESIS RESEARCH 2019; 142:169-180. [PMID: 31522365 DOI: 10.1007/s11120-019-00671-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 08/19/2019] [Indexed: 06/10/2023]
Abstract
Inspired by the bioinorganic structure of natural [FeFe]-hydrogenase ([FeFe]-H2ase) that possesses iron sulfur clusters to catalyze proton reduction to hydrogen (H2), we design a supramolecular photosystem by sequentially integrating hydrophobic ruthenium complex (as a photosensitizer) and diiron dithiolate complex (as a photocatalyst) into the inner surface or cavity of apoferritin via noncovalent interactions. This platform allows photosensitizer and catalyst to localize in a close proximity and short-distance electron transfer process to occur within a confined space. The resulted uniform core-shell nanocomposites were stable and well dispersed in water, and showed enhanced H2 generation activity in acidic solution as compared to the homogenous system without apoferritin participation.
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Affiliation(s)
- Weijian Chen
- Key Laboratory of High Performance Polymer Material and Technology of Ministry of Education, Department of Polymer Science & Engineering, School of Chemistry & Chemical Engineering, Nanjing University, Nanjing, 210023, People's Republic of China
| | - Xuetong Cai
- Key Laboratory of High Performance Polymer Material and Technology of Ministry of Education, Department of Polymer Science & Engineering, School of Chemistry & Chemical Engineering, Nanjing University, Nanjing, 210023, People's Republic of China
| | - Luyang Ji
- Key Laboratory of High Performance Polymer Material and Technology of Ministry of Education, Department of Polymer Science & Engineering, School of Chemistry & Chemical Engineering, Nanjing University, Nanjing, 210023, People's Republic of China
| | - Xiao Li
- Key Laboratory of High Performance Polymer Material and Technology of Ministry of Education, Department of Polymer Science & Engineering, School of Chemistry & Chemical Engineering, Nanjing University, Nanjing, 210023, People's Republic of China
| | - Xuewei Wang
- Key Laboratory of High Performance Polymer Material and Technology of Ministry of Education, Department of Polymer Science & Engineering, School of Chemistry & Chemical Engineering, Nanjing University, Nanjing, 210023, People's Republic of China
| | - Xiaoran Zhang
- Key Laboratory of High Performance Polymer Material and Technology of Ministry of Education, Department of Polymer Science & Engineering, School of Chemistry & Chemical Engineering, Nanjing University, Nanjing, 210023, People's Republic of China
| | - Yajing Gao
- Key Laboratory of High Performance Polymer Material and Technology of Ministry of Education, Department of Polymer Science & Engineering, School of Chemistry & Chemical Engineering, Nanjing University, Nanjing, 210023, People's Republic of China
| | - Fude Feng
- Key Laboratory of High Performance Polymer Material and Technology of Ministry of Education, Department of Polymer Science & Engineering, School of Chemistry & Chemical Engineering, Nanjing University, Nanjing, 210023, People's Republic of China.
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16
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Boyle AL, Rabe M, Crone NSA, Rhys GG, Soler N, Voskamp P, Pannu NS, Kros A. Selective coordination of three transition metal ions within a coiled-coil peptide scaffold. Chem Sci 2019; 10:7456-7465. [PMID: 31489168 PMCID: PMC6713864 DOI: 10.1039/c9sc01165j] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 06/19/2019] [Indexed: 12/13/2022] Open
Abstract
Designing peptides that fold and assemble in response to metal ions tests our understanding of how peptide folding and metal binding influence one another. Here, histidine residues are introduced into the hydrophobic core of a coiled-coil trimer, generating a peptide that self-assembles upon the addition of metal ions. HisAD, the resulting peptide, is unstructured in the absence of metal and folds selectively to form an α-helical construct upon complexation with Cu(ii) and Ni(ii) but not Co(ii) or Zn(ii). The structure, and metal-binding ability, of HisAD is probed using a combination of circular dichroism (CD) spectroscopy, analytical ultracentrifugation (AUC), nuclear magnetic resonance (NMR) spectroscopy and X-ray crystallography. These show the peptide is trimeric and binds to both Cu(ii) and Ni(ii) in a 1 : 1 ratio with the histidine residues involved in the metal coordination, as designed. The X-ray crystal structure of the HisAD-Cu(ii) complex reveals the trimeric HisAD peptide coordinates three Cu(ii) ions; this is the first example of such a structure. Additionally, HisAD demonstrates an unprecedented discrimination between transition metal ions, the basis of which is likely to be related to the stability of the peptide-metal complexes formed.
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Affiliation(s)
- Aimee L Boyle
- Leiden Institute of Chemistry , Leiden University , Einsteinweg 55 , 2333 CC Leiden , The Netherlands .
| | - Martin Rabe
- Max-Planck-Institut für Eisenforschung GmbH , Max-Planck-Straße 1 , 40237 Düsseldorf , Germany
| | - Niek S A Crone
- Leiden Institute of Chemistry , Leiden University , Einsteinweg 55 , 2333 CC Leiden , The Netherlands .
| | - Guto G Rhys
- School of Chemistry , University of Bristol , Cantock's Close , Bristol , BS8 1TS , UK
| | - Nicolas Soler
- Structural Biology Unit , Institute of Molecular Biology of Barcelona (IBMB-CSIC) , Baldiri Reixac 15 , 08028 Barcelona , Spain
| | - Patrick Voskamp
- Leiden Institute of Chemistry , Leiden University , Einsteinweg 55 , 2333 CC Leiden , The Netherlands .
| | - Navraj S Pannu
- Leiden Institute of Chemistry , Leiden University , Einsteinweg 55 , 2333 CC Leiden , The Netherlands .
| | - Alexander Kros
- Leiden Institute of Chemistry , Leiden University , Einsteinweg 55 , 2333 CC Leiden , The Netherlands .
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17
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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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18
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De novo design of symmetric ferredoxins that shuttle electrons in vivo. Proc Natl Acad Sci U S A 2019; 116:14557-14562. [PMID: 31262814 DOI: 10.1073/pnas.1905643116] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A symmetric origin for bacterial ferredoxins was first proposed over 50 y ago, yet, to date, no functional symmetric molecule has been constructed. It is hypothesized that extant proteins have drifted from their symmetric roots via gene duplication followed by mutations. Phylogenetic analyses of extant ferredoxins support the independent evolution of N- and C-terminal sequences, thereby allowing consensus-based design of symmetric 4Fe-4S molecules. All designs bind two [4Fe-4S] clusters and exhibit strongly reducing midpoint potentials ranging from -405 to -515 mV. One of these constructs efficiently shuttles electrons through a designed metabolic pathway in Escherichia coli These finding establish that ferredoxins consisting of a symmetric core can be used as a platform to design novel electron transfer carriers for in vivo applications. Outer-shell asymmetry increases sequence space without compromising electron transfer functionality.
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19
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Mejias SH, Bahrami-Dizicheh Z, Liutkus M, Sommer DJ, Astashkin A, Kodis G, Ghirlanda G, Cortajarena AL. Repeat proteins as versatile scaffolds for arrays of redox-active FeS clusters. Chem Commun (Camb) 2019; 55:3319-3322. [PMID: 30829362 PMCID: PMC6484676 DOI: 10.1039/c8cc06827e] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Molecular string of beads: modular extension of a protein backbone builds a chain of electroactive clusters.
Arrays of one, two and four electron-transfer active [4Fe–4S] clusters were constructed on modular tetratricopeptide repeat protein scaffolds, with the number of clusters determined solely by the size of the scaffold. The constructs show reversible redox activity and transient charge stabilization necessary to facilitate charge transfer.
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Affiliation(s)
- Sara H Mejias
- CIC biomaGUNE Paseo de Miramón 182, E-20014 Donostia-San Sebastian, Spain
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20
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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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21
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Koebke KJ, Pecoraro VL. Development of de Novo Copper Nitrite Reductases: Where We Are and Where We Need To Go. ACS Catal 2018; 8:8046-8057. [PMID: 30294504 DOI: 10.1021/acscatal.8b02153] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The development of redox-active metalloprotein catalysts is a challenging objective of de novo protein design. Within this Perspective we detail our efforts to create a redox-active Cu nitrite reductase (NiR) by incorporating Cu into the hydrophobic interior of well-defined three-stranded coiled coils (3SCCs). The scaffold contains three histidine residues that provide a layer of three nitrogen donors that mimic the type 2 catalytic site of NiR. We have found that this strategy successfully produces an active and stable CuNiR model that functions for over 1000 turnovers. Spectroscopic evidence indicates that the Cu(I) site has a lower coordination number in comparison to the enzyme, whereas the Cu(II) geometry may more faithfully reproduce the NiR type 2 center. Mutations at the helical interface successfully produce a hydrogen bond between an interfacial Glu residue and the Culigating His residue, which allows for the tuning of the redox potential over a 100 mV range. We successfully created constructs with as much as a 120-fold improvement from the original design by modifying the steric bulk above or below the Cu binding site. These systems are now the most active water-soluble and stable artificial NiR catalysts yet produced. Several avenues for improving the catalytic efficiency of later designs are detailed within this Perspective, including adjustment of their resting oxidation state, the use of asymmetric scaffolds to allow for single amino acid mutation within the second coordination sphere, and the design of hydrogen-bonding networks to tune residue orientation and electronics. Through these studies the TRI-H system has given insight into the difficulties that arise in creating a de novo redox active enzyme. Work to improve upon this model will provide strategies by which redox-active de novo enzymes may be tuned and detail how native enzymes accomplish catalytic efficiencies through proton gated redox catalysis.
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Affiliation(s)
- Karl J. Koebke
- Department of Chemistry, University of Michigan Ann Arbor, Michigan 48109, United States
| | - Vincent L. Pecoraro
- Department of Chemistry, University of Michigan Ann Arbor, Michigan 48109, United States
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22
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Kim JD, Pike DH, Tyryshkin AM, Swapna GVT, Raanan H, Montelione GT, Nanda V, Falkowski PG. Minimal Heterochiral de Novo Designed 4Fe-4S Binding Peptide Capable of Robust Electron Transfer. J Am Chem Soc 2018; 140:11210-11213. [PMID: 30141918 DOI: 10.1021/jacs.8b07553] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Ambidoxin is a designed, minimal dodecapeptide consisting of alternating L and D amino acids that binds a 4Fe-4S cluster through ligand-metal interactions and an extensive network of second-shell hydrogen bonds. The peptide can withstand hundreds of oxidation-reduction cycles at room temperature. Ambidoxin suggests how simple, prebiotic peptides may have achieved robust redox catalysis on the early Earth.
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Affiliation(s)
- J Dongun Kim
- Environmental Biophysics and Molecular Ecology Program, Department of Marine and Coastal Sciences, Rutgers , the State University of New Jersey , New Brunswick , New Jersey 08901 , United States
| | - Douglas H Pike
- Center for Advanced Biotechnology and Medicine , Rutgers, the State University of New Jersey , Piscataway , New Jersey 08854 , United States
| | - Alexei M Tyryshkin
- Environmental Biophysics and Molecular Ecology Program, Department of Marine and Coastal Sciences, Rutgers , the State University of New Jersey , New Brunswick , New Jersey 08901 , United States
| | - G V T Swapna
- Center for Advanced Biotechnology and Medicine , Rutgers, the State University of New Jersey , Piscataway , New Jersey 08854 , United States.,Department of Molecular Biology and Biochemistry, Rutgers , the State University of New Jersey , Piscataway , New Jersey 08854 , United States
| | - Hagai Raanan
- Environmental Biophysics and Molecular Ecology Program, Department of Marine and Coastal Sciences, Rutgers , the State University of New Jersey , New Brunswick , New Jersey 08901 , United States
| | - Gaetano T Montelione
- Center for Advanced Biotechnology and Medicine , Rutgers, the State University of New Jersey , Piscataway , New Jersey 08854 , United States.,Department of Molecular Biology and Biochemistry, Rutgers , the State University of New Jersey , Piscataway , New Jersey 08854 , United States.,Department of Biochemistry and Molecular Biology , Robert Wood Johnson Medical School, Rutgers, the State University of New Jersey , Piscataway , New Jersey 08854 , United States
| | - Vikas Nanda
- Center for Advanced Biotechnology and Medicine , Rutgers, the State University of New Jersey , Piscataway , New Jersey 08854 , United States.,Department of Biochemistry and Molecular Biology , Robert Wood Johnson Medical School, Rutgers, the State University of New Jersey , Piscataway , New Jersey 08854 , United States
| | - Paul G Falkowski
- Environmental Biophysics and Molecular Ecology Program, Department of Marine and Coastal Sciences, Rutgers , the State University of New Jersey , New Brunswick , New Jersey 08901 , United States.,Department of Earth and Planetary Sciences, Rutgers , the State University of New Jersey , Piscataway , New Jersey 08854 , United States
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23
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Hemschemeier A, Happe T. The plasticity of redox cofactors: from metalloenzymes to redox-active DNA. Nat Rev Chem 2018. [DOI: 10.1038/s41570-018-0029-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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24
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Koebke KJ, Yu F, Salerno E, Van Stappen C, Tebo AG, Penner-Hahn JE, Pecoraro VL. Modifying the Steric Properties in the Second Coordination Sphere of Designed Peptides Leads to Enhancement of Nitrite Reductase Activity. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201712757] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Karl J. Koebke
- Department of Chemistry; University of Michigan; Ann Arbor MI 48109 USA
| | - Fangting Yu
- Department of Chemistry; University of Michigan; Ann Arbor MI 48109 USA
| | - Elvin Salerno
- Department of Chemistry; University of Michigan; Ann Arbor MI 48109 USA
| | - Casey Van Stappen
- Department of Chemistry; University of Michigan; Ann Arbor MI 48109 USA
| | - Alison G. Tebo
- Department of Chemistry; University of Michigan; Ann Arbor MI 48109 USA
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25
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Koebke KJ, Yu F, Salerno E, Van Stappen C, Tebo AG, Penner-Hahn JE, Pecoraro VL. Modifying the Steric Properties in the Second Coordination Sphere of Designed Peptides Leads to Enhancement of Nitrite Reductase Activity. Angew Chem Int Ed Engl 2018; 57:3954-3957. [PMID: 29316146 DOI: 10.1002/anie.201712757] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Indexed: 11/10/2022]
Abstract
Protein design is a useful strategy to interrogate the protein structure-function relationship. We demonstrate using a highly modular 3-stranded coiled coil (TRI-peptide system) that a functional type 2 copper center exhibiting copper nitrite reductase (NiR) activity exhibits the highest homogeneous catalytic efficiency under aqueous conditions for the reduction of nitrite to NO and H2 O. Modification of the amino acids in the second coordination sphere of the copper center increases the nitrite reductase activity up to 75-fold compared to previously reported systems. We find also that steric bulk can be used to enforce a three-coordinate CuI in a site, which tends toward two-coordination with decreased steric bulk. This study demonstrates the importance of the second coordination sphere environment both for controlling metal-center ligation and enhancing the catalytic efficiency of metalloenzymes and their analogues.
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Affiliation(s)
- Karl J Koebke
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| | - Fangting Yu
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| | - Elvin Salerno
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| | - Casey Van Stappen
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| | - Alison G Tebo
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| | | | - Vincent L Pecoraro
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
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26
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Hansen WA, Khare SD. Benchmarking a computational design method for the incorporation of metal ion-binding sites at symmetric protein interfaces. Protein Sci 2017; 26:1584-1594. [PMID: 28513090 PMCID: PMC5521545 DOI: 10.1002/pro.3194] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2017] [Revised: 04/07/2017] [Accepted: 05/06/2017] [Indexed: 11/12/2022]
Abstract
The design of novel metal-ion binding sites along symmetric axes in protein oligomers could provide new avenues for metalloenzyme design, construction of protein-based nanomaterials and novel ion transport systems. Here, we describe a computational design method, symmetric protein recursive ion-cofactor sampling (SyPRIS), for locating constellations of backbone positions within oligomeric protein structures that are capable of supporting desired symmetrically coordinated metal ion(s) chelated by sidechains (chelant model). Using SyPRIS on a curated benchmark set of protein structures with symmetric metal binding sites, we found high recovery of native metal coordinating rotamers: in 65 of the 67 (97.0%) cases, native rotamers featured in the best scoring model while in the remaining cases native rotamers were found within the top three scoring models. In a second test, chelant models were crossmatched against protein structures with identical cyclic symmetry. In addition to recovering all native placements, 10.4% (8939/86013) of the non-native placements, had acceptable geometric compatibility scores. Discrimination between native and non-native metal site placements was further enhanced upon constrained energy minimization using the Rosetta energy function. Upon sequence design of the surrounding first-shell residues, we found further stabilization of native placements and a small but significant (1.7%) number of non-native placement-based sites with favorable Rosetta energies, indicating their designability in existing protein interfaces. The generality of the SyPRIS approach allows design of novel symmetric metal sites including with non-natural amino acid sidechains, and should enable the predictive incorporation of a variety of metal-containing cofactors at symmetric protein interfaces.
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Affiliation(s)
- William A. Hansen
- Institute for Quantitative Biomedicine at Rutgers610 Taylor RoadPiscatawayNew Jersey08854
- Center for integrative Proteomics Research610 Taylor RoadPiscatawayNew Jersey08854
| | - Sagar D. Khare
- Institute for Quantitative Biomedicine at Rutgers610 Taylor RoadPiscatawayNew Jersey08854
- Center for integrative Proteomics Research610 Taylor RoadPiscatawayNew Jersey08854
- Chemistry and Chemical Biology at Rutgers610 Taylor RoadPiscatawayNew Jersey08854
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27
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28
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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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29
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Holm RH, Lo W. Structural Conversions of Synthetic and Protein-Bound Iron–Sulfur Clusters. Chem Rev 2016; 116:13685-13713. [DOI: 10.1021/acs.chemrev.6b00276] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- R. H. Holm
- Department
of Chemistry and
Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Wayne Lo
- Department
of Chemistry and
Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
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30
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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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31
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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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32
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Moser CC, Sheehan MM, Ennist NM, Kodali G, Bialas C, Englander MT, Discher BM, Dutton PL. De Novo Construction of Redox Active Proteins. Methods Enzymol 2016; 580:365-88. [PMID: 27586341 DOI: 10.1016/bs.mie.2016.05.048] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Relatively simple principles can be used to plan and construct de novo proteins that bind redox cofactors and participate in a range of electron-transfer reactions analogous to those seen in natural oxidoreductase proteins. These designed redox proteins are called maquettes. Hydrophobic/hydrophilic binary patterning of heptad repeats of amino acids linked together in a single-chain self-assemble into 4-alpha-helix bundles. These bundles form a robust and adaptable frame for uncovering the default properties of protein embedded cofactors independent of the complexities introduced by generations of natural selection and allow us to better understand what factors can be exploited by man or nature to manipulate the physical chemical properties of these cofactors. Anchoring of redox cofactors such as hemes, light active tetrapyrroles, FeS clusters, and flavins by His and Cys residues allow cofactors to be placed at positions in which electron-tunneling rates between cofactors within or between proteins can be predicted in advance. The modularity of heptad repeat designs facilitates the construction of electron-transfer chains and novel combinations of redox cofactors and new redox cofactor assisted functions. Developing de novo designs that can support cofactor incorporation upon expression in a cell is needed to support a synthetic biology advance that integrates with natural bioenergetic pathways.
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Affiliation(s)
- C C Moser
- University of Pennsylvania, Philadelphia, PA, United States
| | - M M Sheehan
- University of Pennsylvania, Philadelphia, PA, United States
| | - N M Ennist
- University of Pennsylvania, Philadelphia, PA, United States
| | - G Kodali
- University of Pennsylvania, Philadelphia, PA, United States
| | - C Bialas
- University of Pennsylvania, Philadelphia, PA, United States
| | - M T Englander
- University of Pennsylvania, Philadelphia, PA, United States
| | - B M Discher
- University of Pennsylvania, Philadelphia, PA, United States
| | - P L Dutton
- University of Pennsylvania, Philadelphia, PA, United States.
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33
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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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34
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Shu X, Su J, Du K, You Y, Gao S, Wen G, Tan X, Lin Y. Rational Design of Dual Active Sites in a Single Protein Scaffold: A Case Study of Heme Protein in Myoglobin. ChemistryOpen 2016; 5:192-196. [PMID: 27933225 PMCID: PMC5125789 DOI: 10.1002/open.201500224] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2015] [Indexed: 01/03/2023] Open
Abstract
Rational protein design has been proven to be a powerful tool for creating functional artificial proteins. Although many artificial metalloproteins with a single active site have been successfully created, those with dual active sites in a single protein scaffold are still relatively rare. In this study, we rationally designed dual active sites in a single heme protein scaffold, myoglobin (Mb), by retaining the native heme site and creating a copper-binding site remotely through a single mutation of Arg118 to His or Met. Isothermal titration calorimetry (ITC) and electron paramagnetic resonance (EPR) studies confirmed that a copper-binding site of [3-His] or [2-His-1-Met] motif was successfully created in the single mutant of R118H Mb and R118M Mb, respectively. UV/Vis kinetic spectroscopy and EPR studies further revealed that both the heme site and the designed copper site exhibited nitrite reductase activity. This study presents a new example for rational protein design with multiple active sites in a single protein scaffold, which also lays the groundwork for further investigation of the structure and function relationship of heme/non-heme proteins.
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Affiliation(s)
- Xiao‐Gang Shu
- School of Chemistry and Chemical EngineeringUniversity of South ChinaHengyang421001P. R. China
| | - Ji‐Hu Su
- Department of Modern PhysicsUniversity of Science and Technology of ChinaHefei230026P. R. China
| | - Ke‐Jie Du
- School of Chemistry and Chemical EngineeringUniversity of South ChinaHengyang421001P. R. China
| | - Yong You
- Laboratory of Protein Structure and FunctionUniversity of South ChinaHengyang421001P. R. China
| | - Shu‐Qin Gao
- Laboratory of Protein Structure and FunctionUniversity of South ChinaHengyang421001P. R. China
| | - Ge‐Bo Wen
- Laboratory of Protein Structure and FunctionUniversity of South ChinaHengyang421001P. R. China
| | - Xiangshi Tan
- Department of ChemistryShanghai Key Lab of Chemical Biology for Protein Research& Institute of Biomedical ScienceFudan UniversityShanghai200433P. R. China
| | - Ying‐Wu Lin
- School of Chemistry and Chemical EngineeringUniversity of South ChinaHengyang421001P. R. China
- Laboratory of Protein Structure and FunctionUniversity of South ChinaHengyang421001P. R. China
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Fehl C, Davis BG. Proteins as templates for complex synthetic metalloclusters: towards biologically programmed heterogeneous catalysis. Proc Math Phys Eng Sci 2016; 472:20160078. [PMID: 27279776 PMCID: PMC4893187 DOI: 10.1098/rspa.2016.0078] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Despite nature's prevalent use of metals as prosthetics to adapt or enhance the behaviour of proteins, our ability to programme such architectural organization remains underdeveloped. Multi-metal clusters buried in proteins underpin the most remarkable chemical transformations in nature, but we are not yet in a position to fully mimic or exploit such systems. With the advent of copious, relevant structural information, judicious mechanistic studies and the use of accessible computational methods in protein design coupled with new synthetic methods for building biomacromolecules, we can envisage a 'new dawn' that will allow us to build de novo metalloenzymes that move beyond mono-metal centres. In particular, we highlight the need for systems that approach the multi-centred clusters that have evolved to couple electron shuttling with catalysis. Such hybrids may be viewed as exciting mid-points between homogeneous and heterogeneous catalysts which also exploit the primary benefits of biocatalysis.
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Affiliation(s)
- Charlie Fehl
- Department of Chemistry , University of Oxford , Oxford OX1 3TA, UK
| | - Benjamin G Davis
- Department of Chemistry , University of Oxford , Oxford OX1 3TA, UK
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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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Fry BA, Solomon LA, Leslie Dutton P, Moser CC. Design and engineering of a man-made diffusive electron-transport protein. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2015; 1857:513-521. [PMID: 26423266 DOI: 10.1016/j.bbabio.2015.09.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Revised: 09/12/2015] [Accepted: 09/25/2015] [Indexed: 11/18/2022]
Abstract
Maquettes are man-made cofactor-binding oxidoreductases designed from first principles with minimal reference to natural protein sequences. Here we focus on water-soluble maquettes designed and engineered to perform diffusive electron transport of the kind typically carried out by cytochromes, ferredoxins and flavodoxins and other small proteins in photosynthetic and respiratory energy conversion and oxido-reductive metabolism. Our designs were tested by analysis of electron transfer between heme maquettes and the well-known natural electron transporter, cytochrome c. Electron-transfer kinetics were measured from seconds to milliseconds by stopped-flow, while sub-millisecond resolution was achieved through laser photolysis of the carbon monoxide maquette heme complex. These measurements demonstrate electron transfer from the maquette to cytochrome c, reproducing the timescales and charge complementarity modulation observed in natural systems. The ionic strength dependence of inter-protein electron transfer from 9.7×10(6) M(-1) s(-1) to 1.2×10(9) M(-1) s(-1) follows a simple Debye-Hückel model for attraction between +8 net charged oxidized cytochrome c and -19 net charged heme maquette, with no indication of significant protein dipole moment steering. Successfully recreating essential components of energy conversion and downstream metabolism in man-made proteins holds promise for in vivo clinical intervention and for the production of fuel or other industrial products. 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)
- Bryan A Fry
- Department of Biochemistry & Biophysics, Univ. of Pennsylvania, Philadelphia PA, USA
| | - Lee A Solomon
- Department of Biochemistry & Biophysics, Univ. of Pennsylvania, Philadelphia PA, USA
| | - P Leslie Dutton
- Department of Biochemistry & Biophysics, Univ. of Pennsylvania, Philadelphia PA, USA
| | - Christopher C Moser
- Department of Biochemistry & Biophysics, Univ. of Pennsylvania, Philadelphia PA, USA.
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Roy A, Sommer DJ, Schmitz RA, Brown CL, Gust D, Astashkin A, Ghirlanda G. A De Novo Designed 2[4Fe-4S] Ferredoxin Mimic Mediates Electron Transfer. J Am Chem Soc 2014; 136:17343-9. [DOI: 10.1021/ja510621e] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Anindya Roy
- Department
of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287-1604, United States
| | - Dayn Joseph Sommer
- Department
of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287-1604, United States
| | - Robert Arthur Schmitz
- Department
of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287-1604, United States
| | - Chelsea Lynn Brown
- Department
of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287-1604, United States
| | - Devens Gust
- Department
of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287-1604, United States
| | - Andrei Astashkin
- Department
of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona 85721, United States
| | - Giovanna Ghirlanda
- Department
of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287-1604, United States
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Lin YW, Nagao S, Zhang M, Shomura Y, Higuchi Y, Hirota S. Rational design of heterodimeric protein using domain swapping for myoglobin. Angew Chem Int Ed Engl 2014; 54:511-5. [PMID: 25370865 DOI: 10.1002/anie.201409267] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Indexed: 11/12/2022]
Abstract
Protein design is a useful method to create novel artificial proteins. A rational approach to design a heterodimeric protein using domain swapping for horse myoglobin (Mb) was developed. As confirmed by X-ray crystallographic analysis, a heterodimeric Mb with two different active sites was produced efficiently from two surface mutants of Mb, in which the charges of two amino acids involved in the dimer salt bridges were reversed in each mutant individually, with the active site of one mutant modified. This study shows that the method of constructing heterodimeric Mb with domain swapping is useful for designing artificial multiheme proteins.
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Affiliation(s)
- Ying-Wu Lin
- Graduate School of Materials Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara, 630-0192 (Japan); School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001 (China)
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Lin YW, Nagao S, Zhang M, Shomura Y, Higuchi Y, Hirota S. Rational Design of Heterodimeric Protein using Domain Swapping for Myoglobin. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201409267] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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Watkins DW, Armstrong CT, Anderson JLR. De novo protein components for oxidoreductase assembly and biological integration. Curr Opin Chem Biol 2014; 19:90-8. [DOI: 10.1016/j.cbpa.2014.01.016] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2013] [Revised: 01/23/2014] [Accepted: 01/29/2014] [Indexed: 01/03/2023]
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44
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Lin Y, Wang J, Lu Y. Functional tuning and expanding of myoglobin by rational protein design. Sci China Chem 2014. [DOI: 10.1007/s11426-014-5063-5] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Sontz PA, Song WJ, Tezcan FA. Interfacial metal coordination in engineered protein and peptide assemblies. Curr Opin Chem Biol 2014; 19:42-9. [PMID: 24780278 DOI: 10.1016/j.cbpa.2013.12.013] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Revised: 12/12/2013] [Accepted: 12/12/2013] [Indexed: 12/29/2022]
Abstract
Metal ions are frequently found in natural protein-protein interfaces, where they stabilize quaternary or supramolecular protein structures, mediate transient protein-protein interactions, and serve as catalytic centers. Paralleling these natural roles, coordination chemistry of metal ions is being increasingly utilized in creative ways toward engineering and controlling the assembly of functional supramolecular peptide and protein architectures. Here we provide a brief overview of this emerging branch of metalloprotein/peptide engineering and highlight a few select examples from the recent literature that best capture the diversity and future potential of approaches that are being developed.
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Affiliation(s)
- Pamela A Sontz
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, United States
| | - Woon Ju Song
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, United States
| | - F Akif Tezcan
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, United States.
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