1
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Pirro F, La Gatta S, Arrigoni F, Famulari A, Maglio O, Del Vecchio P, Chiesa M, De Gioia L, Bertini L, Chino M, Nastri F, Lombardi A. A De Novo-Designed Type 3 Copper Protein Tunes Catechol Substrate Recognition and Reactivity. Angew Chem Int Ed Engl 2023; 62:e202211552. [PMID: 36334012 DOI: 10.1002/anie.202211552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Indexed: 11/07/2022]
Abstract
De novo metalloprotein design is a remarkable approach to shape protein scaffolds toward specific functions. Here, we report the design and characterization of Due Rame 1 (DR1), a de novo designed protein housing a di-copper site and mimicking the Type 3 (T3) copper-containing polyphenol oxidases (PPOs). To achieve this goal, we hierarchically designed the first and the second di-metal coordination spheres to engineer the di-copper site into a simple four-helix bundle scaffold. Spectroscopic, thermodynamic, and functional characterization revealed that DR1 recapitulates the T3 copper site, supporting different copper redox states, and being active in the O2 -dependent oxidation of catechols to o-quinones. Careful design of the residues lining the substrate access site endows DR1 with substrate recognition, as revealed by Hammet analysis and computational studies on substituted catechols. This study represents a premier example in the construction of a functional T3 copper site into a designed four-helix bundle protein.
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Affiliation(s)
- Fabio Pirro
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia, 80126, Naples, Italy
| | - Salvatore La Gatta
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia, 80126, Naples, Italy
| | - Federica Arrigoni
- Department of Biotechnology and Biosciences, University of Milan-Bicocca, Piazza della Scienza 2, 20126, Milan, Italy
| | - Antonino Famulari
- Department of Chemistry, University of Torino, Via Giuria 9, 10125, Torino, Italy.,Department of Condensed Matter Physics, University of of Zaragoza, Calle Pedro Cerbuna 12, 50009, Zaragoza, Spain
| | - Ornella Maglio
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia, 80126, Naples, Italy.,Institute of Biostructures and Bioimaging (IBB), National Research Council (CNR), Via Pietro Castellino 111, 80131, Napoli, Italy
| | - Pompea Del Vecchio
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia, 80126, Naples, Italy
| | - Mario Chiesa
- Department of Chemistry, University of Torino, Via Giuria 9, 10125, Torino, Italy
| | - Luca De Gioia
- Department of Biotechnology and Biosciences, University of Milan-Bicocca, Piazza della Scienza 2, 20126, Milan, Italy
| | - Luca Bertini
- Department of Biotechnology and Biosciences, University of Milan-Bicocca, Piazza della Scienza 2, 20126, Milan, Italy
| | - Marco Chino
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia, 80126, Naples, Italy
| | - Flavia Nastri
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia, 80126, Naples, Italy
| | - Angela Lombardi
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia, 80126, Naples, Italy
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2
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Jung SM, Yang M, Song WJ. Symmetry-Adapted Synthesis of Dicopper Oxidases with Divergent Dioxygen Reactivity. Inorg Chem 2022; 61:12433-12441. [DOI: 10.1021/acs.inorgchem.2c01898] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Se-Min Jung
- Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Minwoo Yang
- 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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3
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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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4
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Tsurkan D, Simon P, Schimpf C, Motylenko M, Rafaja D, Roth F, Inosov DS, Makarova AA, Stepniak I, Petrenko I, Springer A, Langer E, Kulbakov AA, Avdeev M, Stefankiewicz AR, Heimler K, Kononchuk O, Hippmann S, Kaiser D, Viehweger C, Rogoll A, Voronkina A, Kovalchuk V, Bazhenov VV, Galli R, Rahimi-Nasrabadi M, Molodtsov SL, Rahimi P, Falahi S, Joseph Y, Vogt C, Vyalikh DV, Bertau M, Ehrlich H. Extreme Biomimetics: Designing of the First Nanostructured 3D Spongin-Atacamite Composite and its Application. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2021; 33:e2101682. [PMID: 34085323 DOI: 10.1002/adma.202101682] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 04/27/2021] [Indexed: 06/12/2023]
Abstract
The design of new composite materials using extreme biomimetics is of crucial importance for bioinspired materials science. Further progress in research and application of these new materials is impossible without understanding the mechanisms of formation, as well as structural features at the molecular and nano-level. It presents a challenge to obtain a holistic understanding of the mechanisms underlying the interaction of organic and inorganic phases under conditions of harsh chemical reactions for biopolymers. Yet, an understanding of these mechanisms can lead to the development of unusual-but functional-hybrid materials. In this work, a key way of designing centimeter-scale macroporous 3D composites, using renewable marine biopolymer spongin and a model industrial solution that simulates the highly toxic copper-containing waste generated in the production of printed circuit boards worldwide, is proposed. A new spongin-atacamite composite material is developed and its structure is confirmed using neutron diffraction, X-ray diffraction, high-resolution transmission electron microscopy/selected-area electron diffraction, X-ray photoelectron spectroscopy, near-edge X-ray absorption fine structure spectroscopy, and electron paramagnetic resonance spectroscopy. The formation mechanism for this material is also proposed. This study provides experimental evidence suggesting multifunctional applicability of the designed composite in the development of 3D constructed sensors, catalysts, and antibacterial filter systems.
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Affiliation(s)
- Dmitry Tsurkan
- Institut of Electronic- und Sensor Materials, TU Bergakademie Freiberg, Gustav-Zeuner-Str. 3, 09599, Freiberg, Germany
| | - Paul Simon
- Max-Planck Institute for Chemical Physics of Solids, Nöthnitzer Str. 40, 01187, Dresden, Germany
| | - Christian Schimpf
- Institute of Materials Science, TU Bergakademie Freiberg, 09599, Freiberg, Germany
| | - Mykhaylo Motylenko
- Institute of Materials Science, TU Bergakademie Freiberg, 09599, Freiberg, Germany
| | - David Rafaja
- Institute of Materials Science, TU Bergakademie Freiberg, 09599, Freiberg, Germany
| | - Friedrich Roth
- Institute of Experimental Physics, TU Bergakademie Freiberg, 09599, Freiberg, Germany
| | - Dmytro S Inosov
- Institute of Solid State and Materials Physics, TU Dresden, D-01069, Dresden, Germany
- Dresden-Würzburg Cluster of Excellence on Complexity and Topology in Quantum Matter (ct.qmat), TU Dresden, D-01062, Dresden, Germany
| | - Anna A Makarova
- Institute of Chemistry and Biochemistry, Free University of Berlin, D-14195, Berlin, Germany
| | - Izabela Stepniak
- Institute of Chemistry and Technical Electrochemistry, Poznan University of Technology, ul. Berdychowo 4, Poznan, 60-965, Poland
| | - Iaroslav Petrenko
- Institut of Electronic- und Sensor Materials, TU Bergakademie Freiberg, Gustav-Zeuner-Str. 3, 09599, Freiberg, Germany
| | - Armin Springer
- Medizinische Biologie und Elektronenmikroskopisches Zentrum (EMZ), Strempelstraße 14, 18057, Rostock, Germany
- Universitätsmedizin Rostock, Strempelstraße 14, 18057, Rostock, Germany
| | - Enrico Langer
- Institute of Semiconductors and Microsystems, TU Dresden, 01062, Dresden, Germany
| | - Anton A Kulbakov
- Institute of Solid State and Materials Physics, TU Dresden, D-01069, Dresden, Germany
- Dresden-Würzburg Cluster of Excellence on Complexity and Topology in Quantum Matter (ct.qmat), TU Dresden, D-01062, Dresden, Germany
| | - Maxim Avdeev
- Australian Nuclear Science and Technology Organisation, New Illawarra Road, Lucas Heights, NSW, 2234, Australia
| | - Artur R Stefankiewicz
- Center for Advanced Technologies, Adam Mickiewicz University, Poznań, Poland
- Faculty of Chemistry, Adam Mickiewicz University, Poznań, Poland
| | - Korbinian Heimler
- Institute of Analytical Chemistry, TU Bergakademie Freiberg, Leipziger Str. 29, 09599, Freiberg, Germany
| | - Olga Kononchuk
- Institute of Chemical Technology, TU Bergakademie Freiberg, Leipziger Straße 29, 09599, Freiberg, Germany
| | - Sebastian Hippmann
- Institute of Chemical Technology, TU Bergakademie Freiberg, Leipziger Straße 29, 09599, Freiberg, Germany
| | - Doreen Kaiser
- Institute of Chemical Technology, TU Bergakademie Freiberg, Leipziger Straße 29, 09599, Freiberg, Germany
| | - Christine Viehweger
- Institute of Analytical Chemistry, TU Bergakademie Freiberg, Leipziger Str. 29, 09599, Freiberg, Germany
| | - Anika Rogoll
- Institute of Analytical Chemistry, TU Bergakademie Freiberg, Leipziger Str. 29, 09599, Freiberg, Germany
| | - Alona Voronkina
- Department of Pharmacy, National Pirogov Memorial Medical University, Vinnytsia, 21018, Ukraine
| | - Valentine Kovalchuk
- Department of Pharmacy, National Pirogov Memorial Medical University, Vinnytsia, 21018, Ukraine
- Department of Microbiology, National Pirogov Memorial Medical University, Vinnytsia, 21018, Ukraine
| | | | - Roberta Galli
- Department of Medical Physics and Biomedical Engineering, Clinical Sensoring and Monitoring - Anesthesiology and Intensive Care Medicine, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Fetscherstraße 74, 01307, Dresden, Germany
| | - Mehdi Rahimi-Nasrabadi
- Chemical Injuries Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, 1951683759, Iran
- Faculty of Pharmacy, Baqiyatallah University of Medical Sciences, Tehran, 1951683759, Iran
- Saint-Petersburg National Research University of Information Technologies, Mechanics and Optics, ITMO University, St. Petersburg, 197101, Russia
| | - Serguei L Molodtsov
- Institute of Experimental Physics, TU Bergakademie Freiberg, 09599, Freiberg, Germany
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Parvaneh Rahimi
- Institut of Electronic- und Sensor Materials, TU Bergakademie Freiberg, Gustav-Zeuner-Str. 3, 09599, Freiberg, Germany
| | - Sedigheh Falahi
- Institut of Electronic- und Sensor Materials, TU Bergakademie Freiberg, Gustav-Zeuner-Str. 3, 09599, Freiberg, Germany
| | - Yvonne Joseph
- Institut of Electronic- und Sensor Materials, TU Bergakademie Freiberg, Gustav-Zeuner-Str. 3, 09599, Freiberg, Germany
| | - Carla Vogt
- Institute of Analytical Chemistry, TU Bergakademie Freiberg, Leipziger Str. 29, 09599, Freiberg, Germany
| | - Denis V Vyalikh
- Donostia International Physics Center (DIPC), Donostia-San Sebastián, 20018, Spain
- IKERBASQUE, Basque Foundation for Science, Bilbao, 48011, Spain
| | - Martin Bertau
- Institute of Chemical Technology, TU Bergakademie Freiberg, Leipziger Straße 29, 09599, Freiberg, Germany
| | - Hermann Ehrlich
- Institut of Electronic- und Sensor Materials, TU Bergakademie Freiberg, Gustav-Zeuner-Str. 3, 09599, Freiberg, Germany
- Center for Advanced Technologies, Adam Mickiewicz University, Poznań, Poland
- Centre for Climate Change Research, Toronto, ON, M4P 1J4, Canada
- A.R. Environmental Solutions, ICUBE-University of Toronto Mississauga, Mississauga, ON, L5L 1C6, Canada
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5
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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 K m and a 7-fold decrease in k cat These studies establish the feasibility of designing allosterically regulated catalytic proteins, entirely from scratch.
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6
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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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Lombardi A, Pirro F, Maglio O, Chino M, DeGrado WF. De Novo Design of Four-Helix Bundle Metalloproteins: One Scaffold, Diverse Reactivities. Acc Chem Res 2019; 52:1148-1159. [PMID: 30973707 DOI: 10.1021/acs.accounts.8b00674] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
De novo protein design represents an attractive approach for testing and extending our understanding of metalloprotein structure and function. Here, we describe our work on the design of DF (Due Ferri or two-iron in Italian), a minimalist model for the active sites of much larger and more complex natural diiron and dimanganese proteins. In nature, diiron and dimanganese proteins protypically bind their ions in 4-Glu, 2-His environments, and they catalyze diverse reactions, ranging from hydrolysis, to O2-dependent chemistry, to decarbonylation of aldehydes. In the design of DF, the position of each atom-including the backbone, the first-shell ligands, the second-shell hydrogen-bonded groups, and the well-packed hydrophobic core-was bespoke using precise mathematical equations and chemical principles. The first member of the DF family was designed to be of minimal size and complexity and yet to display the quintessential elements required for binding the dimetal cofactor. After thoroughly characterizing its structural, dynamic, spectroscopic, and functional properties, we added additional complexity in a rational stepwise manner to achieve increasingly sophisticated catalytic functions, ultimately demonstrating substrate-gated four-electron reduction of O2 to water. We also briefly describe the extension of these studies to the design of proteins that bind nonbiological metal cofactors (a synthetic porphyrin and a tetranuclear cluster), and a Zn2+/proton antiporting membrane protein. Together these studies demonstrate a successful and generally applicable strategy for de novo metalloprotein design, which might indeed mimic the process by which primordial metalloproteins evolved. We began the design process with a highly symmetrical backbone and binding site, by using point-group symmetry to assemble the secondary structures that position the amino acid side chains required for binding. The resulting models provided a rough starting point and initial parameters for the subsequent precise design of the final protein using modern methods of computational protein design. Unless the desired site is itself symmetrical, this process requires reduction of the symmetry or lifting it altogether. Nevertheless, the initial symmetrical structure can be helpful to restrain the search space during assembly of the backbone. Finally, the methods described here should be generally applicable to the design of highly stable and robust catalysts and sensors. There is considerable potential in combining the efficiency and knowledge base associated with homogeneous metal catalysis with the programmability, biocompatibility, and versatility of proteins. While the work reported here focuses on testing and learning the principles of natural metalloproteins by designing and studying proteins one at a time, there is also considerable potential for using designed proteins that incorporate both biological and nonbiological metal ion cofactors for the evolution of novel catalysts.
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Affiliation(s)
- Angela Lombardi
- Department of Chemical Sciences, University of Napoli Federico II, Via Cintia, 26, 80126 Napoli, Italy
| | - Fabio Pirro
- Department of Chemical Sciences, University of Napoli Federico II, Via Cintia, 26, 80126 Napoli, Italy
- Department of Pharmaceutical Chemistry and the Cardiovascular Research Institute, University of California at San Francisco, San Francisco, California 94158-9001, United States
| | - Ornella Maglio
- Department of Chemical Sciences, University of Napoli Federico II, Via Cintia, 26, 80126 Napoli, Italy
- IBB, National Research Council, Via Mezzocannone 16, 80134 Napoli, Italy
| | - Marco Chino
- Department of Chemical Sciences, University of Napoli Federico II, Via Cintia, 26, 80126 Napoli, Italy
| | - William F. DeGrado
- Department of Pharmaceutical Chemistry and the Cardiovascular Research Institute, University of California at San Francisco, San Francisco, California 94158-9001, United States
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Espiritu E, Olson TL, Williams JC, Allen JP. Binding and Energetics of Electron Transfer between an Artificial Four-Helix Mn-Protein and Reaction Centers from Rhodobacter sphaeroides. Biochemistry 2017; 56:6460-6469. [PMID: 29131579 DOI: 10.1021/acs.biochem.7b00978] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The ability of an artificial four-helix bundle Mn-protein, P1, to bind and transfer an electron to photosynthetic reaction centers from the purple bacterium Rhodobacter sphaeroides was characterized using optical spectroscopy. Upon illumination of reaction centers, an electron is transferred from P, the bacteriochlorophyll dimer, to QA, the primary electron acceptor. The P1 Mn-protein can bind to the reaction center and reduce the oxidized bacteriochlorophyll dimer, P+, with a dissociation constant of 1.2 μM at pH 9.4, comparable to the binding constant of c-type cytochromes. Amino acid substitutions of surface residues on the Mn-protein resulted in increases in the dissociation constant to 8.3 μM. The extent of reduction of P+ by the P1 Mn-protein was dependent on the P/P+ midpoint potential and the pH. Analysis of the free energy difference yielded a midpoint potential of approximately 635 mV at pH 9.4 for the Mn cofactor of the P1 Mn-protein, a value similar to those found for other Mn cofactors in proteins. The linear dependence of -56 mV/pH is consistent with one proton being released upon Mn oxidation, allowing the complex to maintain overall charge neutrality. These outcomes demonstrate the feasibility of designing four-helix bundles and other artificial metalloproteins to bind and transfer electrons to bacterial reaction centers and establish the usefulness of this system as a platform for designing sites to bind novel metal cofactors capable of performing complex oxidation-reduction reactions.
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Affiliation(s)
- Eduardo Espiritu
- School of Molecular Sciences, Arizona State University , Tempe, Arizona 85287-1604, United States
| | - Tien L Olson
- School of Molecular Sciences, Arizona State University , Tempe, Arizona 85287-1604, United States
| | - JoAnn C Williams
- School of Molecular Sciences, Arizona State University , Tempe, Arizona 85287-1604, United States
| | - James P Allen
- School of Molecular Sciences, Arizona State University , Tempe, Arizona 85287-1604, United States
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9
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Olson TL, Espiritu E, Edwardraja S, Canarie E, Flores M, Williams JC, Ghirlanda G, Allen JP. Biochemical and spectroscopic characterization of dinuclear Mn-sites in artificial four-helix bundle proteins. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2017; 1858:945-954. [PMID: 28882760 DOI: 10.1016/j.bbabio.2017.08.013] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Revised: 08/28/2017] [Accepted: 08/31/2017] [Indexed: 01/18/2023]
Abstract
To better understand metalloproteins with Mn-clusters, we have designed artificial four-helix bundles to have one, two, or three dinuclear metal centers able to bind Mn(II). Circular dichroism measurements showed that the Mn-proteins have substantial α-helix content, and analysis of electron paramagnetic resonance spectra is consistent with the designed number of bound Mn-clusters. The Mn-proteins were shown to catalyze the conversion of hydrogen peroxide into molecular oxygen. The loss of hydrogen peroxide was dependent upon the concentration of protein with bound Mn, with the proteins containing multiple Mn-clusters showing greater activity. Using an oxygen sensor, the oxygen concentration was found to increase with a rate up to 0.4μM/min, which was dependent upon the concentrations of hydrogen peroxide and the Mn-protein. In addition, the Mn-proteins were shown to serve as electron donors to bacterial reaction centers using optical spectroscopy. Similar binding of the Mn-proteins to reaction centers was observed with an average dissociation constant of 2.3μM. The Mn-proteins with three metal centers were more effective at this electron transfer reaction than the Mn-proteins with one or two metal centers. Thus, multiple Mn-clusters can be incorporated into four-helix bundles with the capability of performing catalysis and electron transfer to a natural protein.
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Affiliation(s)
- Tien L Olson
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA
| | - Eduardo Espiritu
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA
| | | | - Elizabeth Canarie
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA
| | - Marco Flores
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA
| | - JoAnn C Williams
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA
| | - Giovanna Ghirlanda
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA
| | - James P Allen
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA.
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10
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11
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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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12
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Olson TL, Espiritu E, Edwardraja S, Simmons CR, Williams JC, Ghirlanda G, Allen JP. Design of dinuclear manganese cofactors for bacterial reaction centers. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2015; 1857:539-547. [PMID: 26392146 DOI: 10.1016/j.bbabio.2015.09.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Accepted: 09/14/2015] [Indexed: 12/28/2022]
Abstract
A compelling target for the design of electron transfer proteins with novel cofactors is to create a model for the oxygen-evolving complex, a Mn4Ca cluster, of photosystem II. A mononuclear Mn cofactor can be added to the bacterial reaction center, but the addition of multiple metal centers is constrained by the native protein architecture. Alternatively, metal centers can be incorporated into artificial proteins. Designs for the addition of dinuclear metal centers to four-helix bundles resulted in three artificial proteins with ligands for one, two, or three dinuclear metal centers able to bind Mn. The three-dimensional structure determined by X-ray crystallography of one of the Mn-proteins confirmed the design features and revealed details concerning coordination of the Mn center. Electron transfer between these artificial Mn-proteins and bacterial reaction centers was investigated using optical spectroscopy. After formation of a light-induced, charge-separated state, the experiments showed that the Mn-proteins can donate an electron to the oxidized bacteriochlorophyll dimer of modified reaction centers, with the Mn-proteins having additional metal centers being more effective at this electron transfer reaction. Modeling of the structure of the Mn-protein docked to the reaction center showed that the artificial protein likely binds on the periplasmic surface similarly to cytochrome c2, the natural secondary donor. Combining reaction centers with exogenous artificial proteins provides the opportunity to create ligands and investigate the influence of inhomogeneous protein environments on multinuclear redox-active metal centers. 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)
- Tien L Olson
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA
| | - Eduardo Espiritu
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA
| | | | - Chad R Simmons
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA
| | - JoAnn C Williams
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA
| | - Giovanna Ghirlanda
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA
| | - James P Allen
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA.
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