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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Heck J, Kucenko A, Hoffmann A, Herres-Pawlis S. Position of substituents directs the electron transfer properties of entatic state complexes: new insights from guanidine-quinoline copper complexes. Dalton Trans 2024; 53:12527-12542. [PMID: 39016043 DOI: 10.1039/d4dt01539h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2024]
Abstract
In a previous study, we showed that the properties and the ability as an entatic state model of copper guanidine quinoline complexes are significantly influenced by a methyl or methyl ester substituent in the 2-position. To prove the importance of the 2-position of the substituent, two novel guanidine quinoline ligands with a methyl or methyl ester substituent in the 4-position and the corresponding copper complexes were synthesized and characterized in this study. The influence of the substituent position on the copper complexes was investigated with various experimental and theoretical methods. The molecular structures of the copper complexes were examined in the solid state by single-crystal X-ray diffraction (SCXRD) and by density functional theory (DFT) calculations indicating a strong dependency on the substituent position compared to the systems substituted in the 2-position from the previous study. Further, the significantly different influence on the donor properties in dependency on the substituent position was analyzed with natural bond orbital (NBO) calculations. By the determination of the redox potentials, the impact on the electrochemical stabilization was examined. With regard to further previously analyzed guanidine quinoline copper complexes, the electrochemical stabilization was correlated with the charge-transfer energies calculated by NBO analysis and ground state energies, revealing the substituent influence and enabling a comparatively easy and accurate possibility for the theoretical calculation of the relative redox potential. Finally, the electron transfer properties were quantified by determining the electron self-exchange rates via the Marcus theory and by theoretical calculation of the reorganization energies via Nelsen's four-point method. The results gave important insights into the dependency between the ability of the copper complexes as entatic state model and the type and position of the substituent.
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Affiliation(s)
- Joshua Heck
- Institute of Inorganic Chemistry, RWTH Aachen University, Landoltweg 1a, 52074 Aachen, Germany.
| | - Anastasia Kucenko
- Institute of Inorganic Chemistry, RWTH Aachen University, Landoltweg 1a, 52074 Aachen, Germany.
| | - Alexander Hoffmann
- Institute of Inorganic Chemistry, RWTH Aachen University, Landoltweg 1a, 52074 Aachen, Germany.
| | - Sonja Herres-Pawlis
- Institute of Inorganic Chemistry, RWTH Aachen University, Landoltweg 1a, 52074 Aachen, Germany.
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3
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Rossotti M, Arceri D, Mansuelle P, Bornet O, Durand A, Ouchane S, Launay H, Dorlet P. The green cupredoxin CopI is a multicopper protein able to oxidize Cu(I). J Inorg Biochem 2024; 254:112503. [PMID: 38364337 DOI: 10.1016/j.jinorgbio.2024.112503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 02/02/2024] [Accepted: 02/06/2024] [Indexed: 02/18/2024]
Abstract
Anthropogenic activities in agriculture and health use the antimicrobial properties of copper. This has led to copper accumulation in the environment and contributed to the emergence of copper resistant microorganisms. Understanding bacterial copper homeostasis diversity is therefore highly relevant since it could provide valuable targets for novel antimicrobial treatments. The periplasmic CopI protein is a monodomain cupredoxin comprising several copper binding sites and is directly involved in copper resistance in bacteria. However, its structure and mechanism of action are yet to be determined. To study the different binding sites for cupric and cuprous ions and to understand their possible interactions, we have used mutants of the putative copper binding modules of CopI and spectroscopic methods to characterize their properties. We show that CopI is able to bind a cuprous ion in its central histidine/methionine-rich region and oxidize it thanks to its cupredoxin center. The resulting cupric ion can bind to a third site at the N-terminus of the protein. Nuclear magnetic resonance spectroscopy revealed that the central histidine/methionine-rich region exhibits a dynamic behavior and interacts with the cupredoxin binding region. CopI is therefore likely to participate in copper resistance by detoxifying the cuprous ions from the periplasm.
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Affiliation(s)
- Melanie Rossotti
- CNRS, Aix Marseille Univ, BIP, Institut de Microbiologie de la Méditerranée (IMM), Marseille, France
| | - Diletta Arceri
- CNRS, Aix Marseille Univ, BIP, Institut de Microbiologie de la Méditerranée (IMM), Marseille, France
| | - Pascal Mansuelle
- CNRS, FR3479, Institut de Microbiologie de la Méditerranée (IMM), Plateforme Protéomique, Marseille Protéomique (MaP), IbiSA Labelled, Aix Marseille Univ, Marseille, France
| | - Olivier Bornet
- CNRS, Aix Marseille Univ, Institut de Microbiologie de la Méditerranée (IMM), Marseille, France
| | - Anne Durand
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Soufian Ouchane
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Hélène Launay
- CNRS, Aix Marseille Univ, BIP, Institut de Microbiologie de la Méditerranée (IMM), Marseille, France
| | - Pierre Dorlet
- CNRS, Aix Marseille Univ, BIP, Institut de Microbiologie de la Méditerranée (IMM), Marseille, France.
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4
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Roger M, Leone P, Blackburn NJ, Horrell S, Chicano TM, Biaso F, Giudici-Orticoni MT, Abriata LA, Hura GL, Hough MA, Sciara G, Ilbert M. Beyond the coupled distortion model: structural analysis of the single domain cupredoxin AcoP, a green mononuclear copper centre with original features. Dalton Trans 2024; 53:1794-1808. [PMID: 38170898 PMCID: PMC10804444 DOI: 10.1039/d3dt03372d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 11/30/2023] [Indexed: 01/05/2024]
Abstract
Cupredoxins are widely occurring copper-binding proteins with a typical Greek-key beta barrel fold. They are generally described as electron carriers that rely on a T1 copper centre coordinated by four ligands provided by the folded polypeptide. The discovery of novel cupredoxins demonstrates the high diversity of this family, with variations in terms of copper-binding ligands, copper centre geometry, redox potential, as well as biological function. AcoP is a periplasmic cupredoxin belonging to the iron respiratory chain of the acidophilic bacterium Acidithiobacillus ferrooxidans. AcoP presents original features, including high resistance to acidic pH and a constrained green-type copper centre of high redox potential. To understand the unique properties of AcoP, we undertook structural and biophysical characterization of wild-type AcoP and of two Cu-ligand mutants (H166A and M171A). The crystallographic structures, including native reduced AcoP at 1.65 Å resolution, unveil a typical cupredoxin fold. The presence of extended loops, never observed in previously characterized cupredoxins, might account for the interaction of AcoP with physiological partners. The Cu-ligand distances, determined by both X-ray diffraction and EXAFS, show that the AcoP metal centre seems to present both T1 and T1.5 features, in turn suggesting that AcoP might not fit well to the coupled distortion model. The crystal structures of two AcoP mutants confirm that the active centre of AcoP is highly constrained. Comparative analysis with other cupredoxins of known structures, suggests that in AcoP the second coordination sphere might be an important determinant of active centre rigidity due to the presence of an extensive hydrogen bond network. Finally, we show that other cupredoxins do not perfectly follow the coupled distortion model as well, raising the suspicion that further alternative models to describe copper centre geometries need to be developed, while the importance of rack-induced contributions should not be underestimated.
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Affiliation(s)
- Magali Roger
- CNRS, Aix-Marseille University, Bioenergetic and Protein Engineering Laboratory, BIP UMR 7281, Mediterranean Institute of Microbiology, 13009 Marseille, France.
| | - Philippe Leone
- CNRS, Aix-Marseille University, Laboratoire d'Ingénierie des Systèmes Macromoléculaires, LISM UMR7255, 13009 Marseille, France
| | - Ninian J Blackburn
- Department of Chemical Physiology and Biochemistry, School of Medicine, Oregon Health and Science University, Portland, Oregon 97239, USA
| | - Sam Horrell
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, Essex CO4 3SQ, UK
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK
| | - Tadeo Moreno Chicano
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, Essex CO4 3SQ, UK
| | - Frédéric Biaso
- CNRS, Aix-Marseille University, Bioenergetic and Protein Engineering Laboratory, BIP UMR 7281, Mediterranean Institute of Microbiology, 13009 Marseille, France.
| | - Marie-Thérèse Giudici-Orticoni
- CNRS, Aix-Marseille University, Bioenergetic and Protein Engineering Laboratory, BIP UMR 7281, Mediterranean Institute of Microbiology, 13009 Marseille, France.
| | - Luciano A Abriata
- Laboratory for Biomolecular Modeling and Protein Purification and Structure Core Facility, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Greg L Hura
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Lab, Berkeley, CA, USA
| | - Michael A Hough
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, Essex CO4 3SQ, UK
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK
| | - Giuliano Sciara
- CNRS, Aix-Marseille University, Bioenergetic and Protein Engineering Laboratory, BIP UMR 7281, Mediterranean Institute of Microbiology, 13009 Marseille, France.
- Aix Marseille Univ, INRAE, BBF UMR1163, Biodiversité et Biotechnologie Fongiques, 13288 Marseille, France
| | - Marianne Ilbert
- CNRS, Aix-Marseille University, Bioenergetic and Protein Engineering Laboratory, BIP UMR 7281, Mediterranean Institute of Microbiology, 13009 Marseille, France.
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5
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Wang JX, Vilbert AC, Cui C, Mirts EN, Williams LH, Kim W, Jessie Zhang Y, Lu Y. Increasing Reduction Potentials of Type 1 Copper Center and Catalytic Efficiency of Small Laccase from Streptomyces coelicolor through Secondary Coordination Sphere Mutations. Angew Chem Int Ed Engl 2023; 62:e202314019. [PMID: 37926680 PMCID: PMC10842694 DOI: 10.1002/anie.202314019] [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: 09/19/2023] [Revised: 10/30/2023] [Accepted: 10/30/2023] [Indexed: 11/07/2023]
Abstract
The key to type 1 copper (T1Cu) function lies in the fine tuning of the CuII/I reduction potential (E°'T1Cu ) to match those of its redox partners, enabling efficient electron transfer in a wide range of biological systems. While the secondary coordination sphere (SCS) effects have been used to tune E°'T1Cu in azurin over a wide range, these principles are yet to be generalized to other T1Cu-containing proteins to tune catalytic properties. To this end, we have examined the effects of Y229F, V290N and S292F mutations around the T1Cu of small laccase (SLAC) from Streptomyces coelicolor to match the high E°'T1Cu of fungal laccases. Using ultraviolet-visible absorption and electron paramagnetic resonance spectroscopies, together with X-ray crystallography and redox titrations, we have probed the influence of SCS mutations on the T1Cu and corresponding E°'T1Cu . While minimal and small E°'T1Cu increases are observed in Y229F- and S292F-SLAC, the V290N mutant exhibits a major E°'T1Cu increase. Moreover, the influence of these mutations on E°'T1Cu is additive, culminating in a triple mutant Y229F/V290N/S292F-SLAC with the highest E°'T1Cu of 556 mV vs. SHE reported to date. Further activity assays indicate that all mutants retain oxygen reduction reaction activity, and display improved catalytic efficiencies (kcat /KM ) relative to WT-SLAC.
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Affiliation(s)
- Jing-Xiang Wang
- Department of Chemistry, The University of Texas at Austin, 105 East 24th Street, Austin, TX 78712, USA
| | - Avery C Vilbert
- Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA 99354, USA
| | - Chang Cui
- Department of Chemistry, The University of Illinois at Urbana-Champaign, 600 South Matthews Avenue, Urbana, IL 61801, USA
| | - Evan N Mirts
- Department of Chemistry, The University of Illinois at Urbana-Champaign, 600 South Matthews Avenue, Urbana, IL 61801, USA
| | - Lucas H Williams
- Department of Molecular Biosciences, The University of Texas at Austin, 100 East 24th St., Austin, TX 78712, USA
| | - Wantae Kim
- McKetta Department of Chemical Engineering, The University of Texas at Austin, 200 East Dean Keeton Street, Austin, TX 78712, USA
| | - Y Jessie Zhang
- Department of Molecular Biosciences, The University of Texas at Austin, 100 East 24th St., Austin, TX 78712, USA
- Interdisciplinary Life Sciences Graduate Programs, The University of Texas at Austin, 100 East 24th St., Austin, TX 78712, USA
| | - Yi Lu
- Department of Chemistry, The University of Texas at Austin, 105 East 24th Street, Austin, TX 78712, USA
- Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA 99354, USA
- Department of Chemistry, The University of Illinois at Urbana-Champaign, 600 South Matthews Avenue, Urbana, IL 61801, USA
- McKetta Department of Chemical Engineering, The University of Texas at Austin, 200 East Dean Keeton Street, Austin, TX 78712, USA
- Interdisciplinary Life Sciences Graduate Programs, The University of Texas at Austin, 100 East 24th St., Austin, TX 78712, USA
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6
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Singha A, Sekretareva A, Tao L, Lim H, Ha Y, Braun A, Jones SM, Hedman B, Hodgson KO, Britt RD, Kosman DJ, Solomon EI. Tuning the Type 1 Reduction Potential of Multicopper Oxidases: Uncoupling the Effects of Electrostatics and H-Bonding to Histidine Ligands. J Am Chem Soc 2023. [PMID: 37294874 PMCID: PMC10392966 DOI: 10.1021/jacs.3c03241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
In multicopper oxidases (MCOs), the type 1 (T1) Cu accepts electrons from the substrate and transfers these to the trinuclear Cu cluster (TNC) where O2 is reduced to H2O. The T1 potential in MCOs varies from 340 to 780 mV, a range not explained by the existing literature. This study focused on the ∼350 mV difference in potential of the T1 center in Fet3p and Trametes versicolor laccase (TvL) that have the same 2His1Cys ligand set. A range of spectroscopies performed on the oxidized and reduced T1 sites in these MCOs shows that they have equivalent geometric and electronic structures. However, the two His ligands of the T1 Cu in Fet3p are H-bonded to carboxylate residues, while in TvL they are H-bonded to noncharged groups. Electron spin echo envelope modulation spectroscopy shows that there are significant differences in the second-sphere H-bonding interactions in the two T1 centers. Redox titrations on type 2-depleted derivatives of Fet3p and its D409A and E185A variants reveal that the two carboxylates (D409 and E185) lower the T1 potential by 110 and 255-285 mV, respectively. Density functional theory calculations uncouple the effects of the charge of the carboxylates and their difference in H-bonding interactions with the His ligands on the T1 potential, indicating 90-150 mV for anionic charge and ∼100 mV for a strong H-bond. Finally, this study provides an explanation for the generally low potentials of metallooxidases relative to the wide range of potentials of the organic oxidases in terms of different oxidized states of their TNCs involved in catalytic turnover.
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Affiliation(s)
- Asmita Singha
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Alina Sekretareva
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Lizhi Tao
- Department of Chemistry, University of California at Davis, Davis, California 95616, United States
| | - Hyeongtaek Lim
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Yang Ha
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Augustin Braun
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Stephen M Jones
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Britt Hedman
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, California 94025, United States
| | - Keith O Hodgson
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, California 94025, United States
| | - R David Britt
- Department of Chemistry, University of California at Davis, Davis, California 95616, United States
| | - Daniel J Kosman
- Department of Biochemistry, The University at Buffalo, Buffalo, New York 14214, United States
| | - Edward I Solomon
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, California 94025, United States
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7
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Lee J, Dalton RA, Baslé A, Vita N, Dennison C. Important Structural Features of Thiolate-Rich Four-Helix Bundles for Cu(I) Uptake and Removal. Inorg Chem 2023; 62:6617-6628. [PMID: 37057906 PMCID: PMC10155185 DOI: 10.1021/acs.inorgchem.2c04490] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Indexed: 04/15/2023]
Abstract
A family of bacterial copper storage proteins (the Csps) possess thiolate-lined four-helix bundles whose cores can be filled with Cu(I) ions. The majority of Csps are cytosolic (Csp3s), and in vitro studies carried out to date indicate that the Csp3s from Methylosinus trichosporium OB3b (MtCsp3), Bacillus subtilis (BsCsp3), and Streptomyces lividans (SlCsp3) are alike. Bioinformatics have highlighted homologues with potentially different Cu(I)-binding properties from these characterized "classical" Csp3s. Determination herein of the crystal structure of the protein (RkCsp3) from the methanotroph Methylocystis sp. strain Rockwell with Cu(I) bound identifies this as the first studied example of a new subgroup of Csp3s. The most significant structural difference from classical Csp3s is the presence of only two Cu(I) sites at the mouth of the bundle via which Cu(I) ions enter and leave. This is due to the absence of three Cys residues and a His-containing motif, which allow classical Csp3s to bind five to six Cu(I) ions in this region. Regardless, RkCsp3 exhibits rapid Cu(I) binding and the fastest measured Cu(I) removal rate for a Csp3 when using high-affinity ligands as surrogate partners. New experiments on classical Csp3s demonstrate that their His-containing motif is not essential for fast Cu(I) uptake and removal. Other structural features that could be important for these functionally relevant in vitro properties are discussed.
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Affiliation(s)
- Jaeick Lee
- Biosciences Institute, Newcastle University, Newcastle
upon Tyne NE2 4HH, U.K.
| | - Rosemary A. Dalton
- Biosciences Institute, Newcastle University, Newcastle
upon Tyne NE2 4HH, U.K.
| | - Arnaud Baslé
- Biosciences Institute, Newcastle University, Newcastle
upon Tyne NE2 4HH, U.K.
| | - Nicolas Vita
- Biosciences Institute, Newcastle University, Newcastle
upon Tyne NE2 4HH, U.K.
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8
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Guo J, Fisher OS. Orchestrating copper binding: structure and variations on the cupredoxin fold. J Biol Inorg Chem 2022; 27:529-540. [PMID: 35994119 DOI: 10.1007/s00775-022-01955-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 08/07/2022] [Indexed: 11/26/2022]
Abstract
A large number of copper binding proteins coordinate metal ions using a shared three-dimensional fold called the cupredoxin domain. This domain was originally identified in Type 1 "blue copper" centers but has since proven to be a common domain architecture within an increasingly large and diverse group of copper binding domains. The cupredoxin fold has a number of qualities that make it ideal for coordinating Cu ions for purposes including electron transfer, enzyme catalysis, assembly of other copper sites, and copper sequestration. The structural core does not undergo major conformational changes upon metal binding, but variations within the coordination environment of the metal site confer a range of Cu-binding affinities, reduction potentials, and spectroscopic properties. Here, we discuss these proteins from a structural perspective, examining how variations within the overall cupredoxin fold and metal binding sites are linked to distinct spectroscopic properties and biological functions. Expanding far beyond the blue copper proteins, cupredoxin domains are used by a growing number of proteins and enzymes as a means of binding copper ions, with many more likely remaining to be identified.
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Affiliation(s)
- Jing Guo
- Department of Chemistry, Lehigh University, Bethlehem, PA, USA
| | - Oriana S Fisher
- Department of Chemistry, Lehigh University, Bethlehem, PA, USA.
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9
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Van Stappen C, Deng Y, Liu Y, Heidari H, Wang JX, Zhou Y, Ledray AP, Lu Y. Designing Artificial Metalloenzymes by Tuning of the Environment beyond the Primary Coordination Sphere. Chem Rev 2022; 122:11974-12045. [PMID: 35816578 DOI: 10.1021/acs.chemrev.2c00106] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Metalloenzymes catalyze a variety of reactions using a limited number of natural amino acids and metallocofactors. Therefore, the environment beyond the primary coordination sphere must play an important role in both conferring and tuning their phenomenal catalytic properties, enabling active sites with otherwise similar primary coordination environments to perform a diverse array of biological functions. However, since the interactions beyond the primary coordination sphere are numerous and weak, it has been difficult to pinpoint structural features responsible for the tuning of activities of native enzymes. Designing artificial metalloenzymes (ArMs) offers an excellent basis to elucidate the roles of these interactions and to further develop practical biological catalysts. In this review, we highlight how the secondary coordination spheres of ArMs influence metal binding and catalysis, with particular focus on the use of native protein scaffolds as templates for the design of ArMs by either rational design aided by computational modeling, directed evolution, or a combination of both approaches. In describing successes in designing heme, nonheme Fe, and Cu metalloenzymes, heteronuclear metalloenzymes containing heme, and those ArMs containing other metal centers (including those with non-native metal ions and metallocofactors), we have summarized insights gained on how careful controls of the interactions in the secondary coordination sphere, including hydrophobic and hydrogen bonding interactions, allow the generation and tuning of these respective systems to approach, rival, and, in a few cases, exceed those of native enzymes. We have also provided an outlook on the remaining challenges in the field and future directions that will allow for a deeper understanding of the secondary coordination sphere a deeper understanding of the secondary coordintion sphere to be gained, and in turn to guide the design of a broader and more efficient variety of ArMs.
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Affiliation(s)
- Casey Van Stappen
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States
| | - Yunling Deng
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States
| | - Yiwei Liu
- Department of Chemistry, University of Illinois, Urbana-Champaign, 505 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Hirbod Heidari
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States
| | - Jing-Xiang Wang
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States
| | - Yu Zhou
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States
| | - Aaron P Ledray
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States
| | - Yi Lu
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States.,Department of Chemistry, University of Illinois, Urbana-Champaign, 505 South Mathews Avenue, Urbana, Illinois 61801, United States
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10
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Identification of Toxoplasma gondii adhesins through a machine learning approach. Exp Parasitol 2022; 238:108261. [PMID: 35460696 DOI: 10.1016/j.exppara.2022.108261] [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: 07/10/2021] [Revised: 04/10/2022] [Accepted: 04/14/2022] [Indexed: 11/23/2022]
Abstract
Toxoplasma gondii, as other apicomplexa, employs adhesins transmembrane proteins for binding and invasion to host cells. Search and characterization of adhesins is pivotal in understanding Apicomplexa invasion mechanisms and targeting new druggable candidates. This work developed a machine learning software called ApiPredictor UniQE V2.0, based on two approaches: support vector machines and multilayer perceptron, to predict adhesins proteins from amino acid sequences. By using ApiPredictor UniQE V2.0, five SAG-Related Sequences (SRSs) were identified within the Toxoplasma gondii proteome. One of those candidates, TgSRS12B, was cloned in plasmid pEXP5-CT/TOPO and expressed in E. coli BL21 DE3. The resulting recombinant protein was purified via affinity chromatography. Co-precipitation assays in CaCo and Muller cells showed interactions between TgSRS12B-His-tagged and the membrane fractions from both human cell lines. In conclusion, we demonstrated that ApiPredictor UniQE V2.0, a bioinformatic free software, was able to identify TgSRS12B as a new adhesin protein.
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11
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Electrochemical Characterization of an Engineered Red Copper Protein Featuring an Unprecedented Entropic Control of the Reduction Potential. Bioelectrochemistry 2022; 146:108095. [DOI: 10.1016/j.bioelechem.2022.108095] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 03/04/2022] [Accepted: 03/10/2022] [Indexed: 12/12/2022]
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12
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Nakatsuji S, Okumura K, Takase R, Watanabe D, Mikami B, Hashimoto W. Crystal structures of EfeB and EfeO in a bacterial siderophore-independent iron transport system. Biochem Biophys Res Commun 2022; 594:124-130. [PMID: 35081501 DOI: 10.1016/j.bbrc.2022.01.055] [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: 01/10/2022] [Revised: 01/13/2022] [Accepted: 01/13/2022] [Indexed: 11/17/2022]
Abstract
EfeUOB is a siderophore-independent iron uptake mechanism in bacteria. EfeU, EfeO, and EfeB are a permease, an iron-binding or electron-transfer protein, and a peroxidase, respectively. A Gram-negative bacterium, Sphingomonas sp. strain A1, encodes EfeU, EfeO, EfeB together with alginate-binding protein Algp7, a truncated EfeO-like protein (EfeOII), in the genome. The typical EfeO (EfeOI) consists of N-terminal cupredoxin and C-terminal M75 peptidase domains. Here, we detail the structure and function of bacterial EfeB and EfeO. Crystal structures of strain A1 EfeB and Escherichia coli EfeOI were determined at 2.30 Å and 1.85 Å resolutions, respectively. A molecule of heme involved in oxidase activity was bound to the C-terminal Dyp peroxidase domain of EfeB. Two domains of EfeOI were connected by a short loop, and a zinc ion was bound to four residues, Glu156, Glu159, Asp173, and Glu255, in the C-terminal M75 peptidase domain. These residues formed tetrahedron geometry suitable for metal binding and are well conserved among various EfeO proteins including Algp7 (EfeOII), although the metal-binding site (HxxE) is proposed in the C-terminal M75 peptidase domain. This is the first report on structure of a typical EfeO with two domains, postulating a novel metal-binding motif "ExxE-//-D-//-E" in the EfeO C-terminal M75 peptidase domain.
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Affiliation(s)
- Sakiko Nakatsuji
- Laboratory of Basic and Applied Molecular Biotechnology, Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Uji, Kyoto, 611-0011, Japan
| | - Kenji Okumura
- Laboratory of Basic and Applied Molecular Biotechnology, Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Uji, Kyoto, 611-0011, Japan
| | - Ryuichi Takase
- Laboratory of Basic and Applied Molecular Biotechnology, Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Uji, Kyoto, 611-0011, Japan
| | - Daisuke Watanabe
- Laboratory of Basic and Applied Molecular Biotechnology, Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Uji, Kyoto, 611-0011, Japan
| | - Bunzo Mikami
- Laboratory of Metabolic Sciences of Forest Plants and Microorganisms, Research Institute for Sustainable Humanosphere, Kyoto University, Uji, Kyoto, 611-0011, Japan
| | - Wataru Hashimoto
- Laboratory of Basic and Applied Molecular Biotechnology, Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Uji, Kyoto, 611-0011, Japan.
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13
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Chen X, Chen M, Wolynes PG, Wittung-Stafshede P, Gray HB. Frustration Dynamics and Electron-Transfer Reorganization Energies in Wild-Type and Mutant Azurins. J Am Chem Soc 2022; 144:4178-4185. [PMID: 35171591 PMCID: PMC8915257 DOI: 10.1021/jacs.1c13454] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
![]()
Long-range electron
tunneling through metalloproteins is facilitated
by evolutionary tuning of donor–acceptor electronic couplings,
formal electrochemical potentials, and active-site reorganization
energies. Although the minimal frustration of the folding landscape
enables this tuning, residual frustration in the vicinity of the metallocofactor
can allow conformational fluctuations required for protein function.
We show here that the constrained copper site in wild-type azurin
is governed by an intricate pattern of minimally frustrated local
and distant interactions that together enable rapid electron flow
to and from the protein. In contrast, sluggish electron transfer reactions
(unfavorable reorganization energies) of active-site azurin variants
are attributable to increased frustration near to as well as distant
from the copper site, along with an exaggerated oxidation-state dependence
of both minimally and highly frustrated interaction patterns.
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Affiliation(s)
- Xun Chen
- Center for Theoretical Biological Physics, Houston, Texas 77005, United States.,Department of Chemistry, Rice University, Houston, Texas 77005, United States
| | - Mingchen Chen
- Center for Theoretical Biological Physics, Houston, Texas 77005, United States
| | - Peter G Wolynes
- Center for Theoretical Biological Physics, Houston, Texas 77005, United States.,Department of Chemistry, Rice University, Houston, Texas 77005, United States.,Department of Biosciences, Rice University, Houston, Texas 77005, United States
| | - Pernilla Wittung-Stafshede
- Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96 Gothenburg, Sweden
| | - Harry B Gray
- Beckman Institute and Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
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14
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Advanced Optical Sensing of Phenolic Compounds for Environmental Applications. SENSORS 2021; 21:s21227563. [PMID: 34833640 PMCID: PMC8619556 DOI: 10.3390/s21227563] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 11/09/2021] [Accepted: 11/09/2021] [Indexed: 01/28/2023]
Abstract
Phenolic compounds are particularly dangerous due to their ability to remain in the environment for a long period of time and their toxic effects. They enter in the environment in different ways, such as waste from paper manufacturing, agriculture (pesticides, insecticides, herbicides), pharmaceuticals, the petrochemical industry, and coal processing. Conventional methods for phenolic compounds detection present some disadvantages, such as cumbersome sample preparation, complex and time-consuming procedures, and need of expensive equipment. Therefore, there is a very large interest in developing sensors and new sensing schemes for fast and easy-to-use methods for detecting and monitoring the phenolic compound concentration in the environment, with special attention to water. Good analytical properties, reliability, and adaptability are required for the developed sensors. The present paper aims at revising the most generally used optical methods for designing and fabricating biosensors and sensors for phenolic compounds. Some selected examples of the most interesting applications of these techniques are also proposed.
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15
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Jiang Y, Su B, Chen H, Zhang T, Liu H, Yu Y. An engineered azurin with a lanthanide binding site capable of copper sensing. Biochem Biophys Res Commun 2021; 561:40-44. [PMID: 34004515 DOI: 10.1016/j.bbrc.2021.05.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 05/06/2021] [Indexed: 10/21/2022]
Abstract
Proteins with hetero-bimetallic metal centers can catalyze important reactions and are challenging to design. Azurin is a mononuclear copper center that has been extensively studied for electron transfer. Here we inserted the lanthanide binding tag (LBT), which binds lanthanide with sub μM affinity, into the copper binding loop of azurin, while keeping the type 1 copper center unperturbed. The resulting protein, Az-LBT, which has two metal bonding centers, shows strong luminescence upon coordination with Tb3+ and luminescence quenching upon Cu2+ binding. The in vitro luminescence quenching has high metal specificity and a limit-of-detection of 0.65 μM for Cu2+. With the low background from lanthanide's long luminescence lifetime, bacterial cells expressing Az-LBT in the periplasm also shows sensitivity for metal sensing.
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Affiliation(s)
- Yujia Jiang
- Institute of Biochemical Engineering, School of Chemistry and Chemical Engineering, China; Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering of Ministry of Industry and Information Technology, Beijing Institute of Technology, Beijing 102488, China
| | - Binbin Su
- Institute of Biochemical Engineering, School of Chemistry and Chemical Engineering, China; Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering of Ministry of Industry and Information Technology, Beijing Institute of Technology, Beijing 102488, China
| | - Honghui Chen
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Tongtong Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Haiping Liu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Yang Yu
- Institute of Biochemical Engineering, School of Chemistry and Chemical Engineering, China; Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering of Ministry of Industry and Information Technology, Beijing Institute of Technology, Beijing 102488, China.
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16
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Singh Y, Patel RN, Patel SK, Jadeja R, Patel AK, Patel N, Roy H, Kumar P, Butcher R, Jasinski JP, Cortijo M, Herrero S. Non-covalent interactions governing the supramolecular assembly of copper(II) complexes with hydrazone-type ligand: Experimental and quantum chemical study. Polyhedron 2021. [DOI: 10.1016/j.poly.2021.115142] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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17
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Kolbeck S, Abele M, Hilgarth M, Vogel RF. Comparative Proteomics Reveals the Anaerobic Lifestyle of Meat-Spoiling Pseudomonas Species. Front Microbiol 2021; 12:664061. [PMID: 33889149 PMCID: PMC8055858 DOI: 10.3389/fmicb.2021.664061] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 03/08/2021] [Indexed: 11/13/2022] Open
Abstract
The ability of certain Pseudomonas (P.) species to grow or persist in anoxic habitats by either denitrification, acetate fermentation, or arginine fermentation has been described in several studies as a special property. Previously, we had isolated strains belonging to the species P. lundensis, P. weihenstephanensis, and P. fragi from anoxic modified atmosphere packaged (MAP) minced beef and further proved their anaerobic growth in vitro on agar plates. This follow-up study investigated the anaerobic growth of two strains per respective species in situ on inoculated chicken breast filet under 100% N2 modified atmosphere. We were able to prove anaerobic growth of all six strains on chicken breast filet with cell division rates of 0.2–0.8/day. Furthermore, we characterized the anaerobic metabolic lifestyle of these Pseudomonas strains by comparative proteomics, upon their cultivation in meat simulation media, which were constantly gassed with either air or 100% N2 atmospheres. From these proteomic predictions, and respective complementation by physiological experiments, we conclude that the Pseudomonas strains P. fragi, P. weihenstephanensis, P. lundensis exhibit a similar anaerobic lifestyle and employ arginine fermentation via the arginine deiminase (ADI) pathway to grow anaerobically also on MAP meats. Furthermore, glucose fermentation to ethanol via the ED-pathway is predicted to enable long term survival but no true growth, while respiratory growth with nitrate as alternative electron acceptor or glucose fermentation to acetate could be excluded due to absence of essential genes. The citric acid cycle is partially bypassed by the glyoxylate shunt, functioning as the gluconeogenetic route without production of NADH2 under carbon limiting conditions as e.g., in packaged meats. Triggered by an altered redox balance, we also detected upregulation of enzymes involved in protein folding as well as disulfide bonds isomerization under anoxic conditions as a counteracting mechanism to reduce protein misfolding. Hence, this study reveals the mechanisms enabling anaerobic grow and persistence of common meat-spoiling Pseudomonas species, and further complements the hitherto limited knowledge of the anaerobic lifestyle of Pseudomonas species in general.
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Affiliation(s)
- Sandra Kolbeck
- Lehrstuhl für Technische Mikrobiologie, Technische Universität München, Freising, Germany
| | - Miriam Abele
- Bayerisches Zentrum für Biomolekulare Massenspektrometrie (BayBioMS), Freising, Germany
| | - Maik Hilgarth
- Lehrstuhl für Technische Mikrobiologie, Technische Universität München, Freising, Germany
| | - Rudi F Vogel
- Lehrstuhl für Technische Mikrobiologie, Technische Universität München, Freising, Germany
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18
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Llanos L, Vera C, Vega A, Aravena D, Lemus L. Reactivity of Cu IN 4 Flattened Complexes: Interplay between Coordination Geometry and Ligand Flexibility. Inorg Chem 2020; 59:15061-15073. [PMID: 33021785 DOI: 10.1021/acs.inorgchem.0c02037] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The relation between redox activity and coordination geometry in CuIN4 complexes indicates that more flattened structures tend to be more reactive. Such a preorganization of the ligand confers to the complex geometries closer to a transition state, which has been termed the "entatic" state in metalloproteins, more recently extending this concept for copper complexes. However, many aspects of the redox chemistry of CuI complexes cannot be explained only by flattening. For instance, the role of ligand flexibility in this context is an open debate nowadays. To analyze this point, we studied oxidation properties of a series of five monometallic CuI Schiff-base complexes, [CuI(Ln)]+, which span a range of geometries from a distorted square planar (n = 3) to a distorted tetrahedron (n = 6, 7). This stepped control of the structure around the CuI atom allows us to explore the effect of the flattening distortion on both the electronic and redox properties through the series. Experimental studies were complemented by a theoretical analysis based on density functional theory calculations. As expected, oxidation was favored in the flattened structures, spanning a broad potential window of 370 mV for the complete series. This orderly behavior was tested in the reductive dehalogenation reaction of tetrachloroethane (TCE). Kinetic studies show that CuI oxidation by TCE is faster as the flattening distortion is higher and the oxidation potentials of the metal are lower. However, the most reactive complex was not the more planar, contradicting the trend expected from oxidation potentials. The origin of this irregularity is related to ligand flexibility and its connection with the atom/electron transfer reaction path, highlighting the need to consider effects beyond flattening distortion to better understand the reactivity of this important class of complexes.
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Affiliation(s)
- Leonel Llanos
- Departamento de Química de los Materiales, Facultad de Química y Biología, Universidad de Santiago de Chile, Av. Libertador Bernardo O'Higgins 3363, Estacio'n Central, Santiago, Chile
| | - Cristian Vera
- Departamento de Química de los Materiales, Facultad de Química y Biología, Universidad de Santiago de Chile, Av. Libertador Bernardo O'Higgins 3363, Estacio'n Central, Santiago, Chile
| | - Andrés Vega
- Facultad de Ciencias Exactas, Departamento de Ciencias Químicas, Universidad Andrés Bello, Quillota 980, Viña del Mar, Chile.,Centro para el Desarrollo de Nanociencias y Nanotecnología, CEDENNA, Santiago, Chile
| | - Daniel Aravena
- Departamento de Química de los Materiales, Facultad de Química y Biología, Universidad de Santiago de Chile, Av. Libertador Bernardo O'Higgins 3363, Estacio'n Central, Santiago, Chile
| | - Luis Lemus
- Departamento de Química de los Materiales, Facultad de Química y Biología, Universidad de Santiago de Chile, Av. Libertador Bernardo O'Higgins 3363, Estacio'n Central, Santiago, Chile
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19
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Barahona S, Castro-Severyn J, Dorador C, Saavedra C, Remonsellez F. Determinants of Copper Resistance in Acidithiobacillus Ferrivorans ACH Isolated from the Chilean Altiplano. Genes (Basel) 2020; 11:genes11080844. [PMID: 32722087 PMCID: PMC7463520 DOI: 10.3390/genes11080844] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 07/22/2020] [Accepted: 07/22/2020] [Indexed: 11/16/2022] Open
Abstract
The use of microorganisms in mining processes is a technology widely employed around the world. Leaching bacteria are characterized by having resistance mechanisms for several metals found in their acidic environments, some of which have been partially described in the Acidithiobacillus genus (mainly on ferrooxidans species). However, the response to copper has not been studied in the psychrotolerant Acidithiobacillus ferrivorans strains. Therefore, we propose to elucidate the response mechanisms of A. ferrivorans ACH to high copper concentrations (0-800 mM), describing its genetic repertoire and transcriptional regulation. Our results show that A. ferrivorans ACH can grow in up to 400 mM of copper. Moreover, we found the presence of several copper-related makers, belonging to cop and cus systems, as well as rusticyanins and periplasmatic acop protein in the genome. Interestingly, the ACH strain is the only one in which we find three copies of copB and copZ genes. Moreover, transcriptional expression showed an up-regulation response (acop, copZ, cusA, rusA, and rusB) to high copper concentrations. Finally, our results support the important role of these genes in A. ferrivorans copper stress resistance, promoting the use of the ACH strain in industrial leaching under low temperatures, which could decrease the activation times of oxidation processes and the energy costs.
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Affiliation(s)
- Sergio Barahona
- Laboratorio de Microbiología Aplicada y Extremófilos, Departamento de Ingeniería Química, Universidad Católica del Norte, Antofagasta 1240000, Chile;
- Laboratorio de Complejidad Microbiana y Ecología Funcional, Departamento de Biotecnología, Facultad de Ciencias del Mar y Recurso Biológicos, Universidad de Antofagasta, Antofagasta 1240000, Chile;
- Programa de Doctorado en Ingeniería de Procesos de Minerales, Facultad de Ingeniería, Universidad de Antofagasta, Antofagasta 1240000, Chile
- Correspondence: (S.B.); (F.R.)
| | - Juan Castro-Severyn
- Laboratorio de Microbiología Aplicada y Extremófilos, Departamento de Ingeniería Química, Universidad Católica del Norte, Antofagasta 1240000, Chile;
| | - Cristina Dorador
- Laboratorio de Complejidad Microbiana y Ecología Funcional, Departamento de Biotecnología, Facultad de Ciencias del Mar y Recurso Biológicos, Universidad de Antofagasta, Antofagasta 1240000, Chile;
- Centro de Biotecnología y Bioingeniería (CeBiB), Universidad de Antofagasta, Antofagasta 1240000, Chile
| | - Claudia Saavedra
- Laboratorio de Microbiología Molecular, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago 8320000, Chile;
| | - Francisco Remonsellez
- Laboratorio de Microbiología Aplicada y Extremófilos, Departamento de Ingeniería Química, Universidad Católica del Norte, Antofagasta 1240000, Chile;
- Centro de Investigación Tecnológica del Agua en el Desierto (CEITSAZA), Universidad Católica del Norte, Antofagasta 1240000, Chile
- Correspondence: (S.B.); (F.R.)
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20
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Yu SS, Li JJ, Cui C, Tian S, Chen JJ, Yu HQ, Hou C, Nilges MJ, Lu Y. Structural Basis for a Quadratic Relationship between Electronic Absorption and Electronic Paramagnetic Resonance Parameters of Type 1 Copper Proteins. Inorg Chem 2020; 59:10620-10627. [PMID: 32689800 DOI: 10.1021/acs.inorgchem.0c01065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Type 1 copper (T1Cu) proteins play important roles in electron transfer in biology, largely due to the unique structure of the T1Cu center, which is reflected by its spectroscopic properties. Previous reports have suggested a correlation between a high ratio of electronic absorbance at ∼450 nm to that at ∼600 nm (R = A450/A600) and a large copper(II) hyperfine coupling in the z direction (Az) in electron paramagnetic resonance (EPR). However, this correlation does not have a clear physical meaning, nor does it hold for many proteins with a perturbed T1Cu center. To address this issue, a new parameter of R' [A450/(A450 + A600)] with a better physical meaning of a fractional SCys pseudo-σ to Cu(II) charge transfer transition intensity is defined and a quadratic relationship between R' and Az is found on the basis of a comprehensive analysis of ultraviolet-visible absorption, EPR, and structural parameters of T1Cu proteins. We are able to find good correlations between R' and the displacement of copper from the trigonal plane defined by the His2Cys ligands and the angle between the NHis1-Cu-NHis2 plane and the SCys-Cu-axial ligand plane, providing a structural basis for the observed correlation. These findings and analyses provide a new framework for a deeper understanding of the spectroscopic and electronic properties of T1Cu proteins, which may allow better design and applications of this important class of proteins for redox and electron transfer functions.
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Affiliation(s)
- Sheng-Song Yu
- Department of Applied Chemistry, University of Science & Technology of China, Hefei, Anhui 230026, P. R. China.,Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Jun-Jie Li
- Key Laboratory of Biorheology Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400044, P. R. China.,Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Chang Cui
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Shiliang Tian
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Jie-Jie Chen
- Department of Applied Chemistry, University of Science & Technology of China, Hefei, Anhui 230026, P. R. China
| | - Han-Qing Yu
- Department of Applied Chemistry, University of Science & Technology of China, Hefei, Anhui 230026, P. R. China
| | - Changjun Hou
- Key Laboratory of Biorheology Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400044, P. R. China
| | - Mark J Nilges
- School of Chemical Sciences Electron Paramagnetic Resonance Lab, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Yi Lu
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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21
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Szuster J, Zitare UA, Castro MA, Leguto AJ, Morgada MN, Vila AJ, Murgida DH. Cu A-based chimeric T1 copper sites allow for independent modulation of reorganization energy and reduction potential. Chem Sci 2020; 11:6193-6201. [PMID: 32953013 PMCID: PMC7480511 DOI: 10.1039/d0sc01620a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 06/01/2020] [Indexed: 01/19/2023] Open
Abstract
Attaining rational modulation of thermodynamic and kinetic redox parameters of metalloproteins is a key milestone towards the (re)design of proteins with new or improved redox functions. Here we report that implantation of ligand loops from natural T1 proteins into the scaffold of a CuA protein leads to a series of distorted T1-like sites that allow for independent modulation of reduction potentials (E°') and electron transfer reorganization energies (λ). On the one hand E°' values could be fine-tuned over 120 mV without affecting λ. On the other, λ values could be modulated by more than a factor of two while affecting E°' only by a few millivolts. These results are in sharp contrast to previous studies that used T1 cupredoxin folds, thus highlighting the importance of the protein scaffold in determining such parameters.
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Affiliation(s)
- Jonathan Szuster
- Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE, CONICET-UBA) , Argentina .
- Departamento de Química Inorgánica, Analítica y Química-Física , Facultad de Ciencias Exactas y Naturales , Universidad de Buenos Aires , Buenos Aires , Argentina
| | - Ulises A Zitare
- Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE, CONICET-UBA) , Argentina .
- Departamento de Química Inorgánica, Analítica y Química-Física , Facultad de Ciencias Exactas y Naturales , Universidad de Buenos Aires , Buenos Aires , Argentina
| | - María A Castro
- Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE, CONICET-UBA) , Argentina .
- Departamento de Química Inorgánica, Analítica y Química-Física , Facultad de Ciencias Exactas y Naturales , Universidad de Buenos Aires , Buenos Aires , Argentina
| | - Alcides J Leguto
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET-UNR) , Argentina
- Departamento de Química Biológica , Facultad de Ciencias Bioquímicas y Farmacéuticas , Universidad Nacional de Rosario , Rosario , Argentina
| | - Marcos N Morgada
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET-UNR) , Argentina
- Departamento de Química Biológica , Facultad de Ciencias Bioquímicas y Farmacéuticas , Universidad Nacional de Rosario , Rosario , Argentina
| | - Alejandro J Vila
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET-UNR) , Argentina
- Departamento de Química Biológica , Facultad de Ciencias Bioquímicas y Farmacéuticas , Universidad Nacional de Rosario , Rosario , Argentina
| | - Daniel H Murgida
- Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE, CONICET-UBA) , Argentina .
- Departamento de Química Inorgánica, Analítica y Química-Física , Facultad de Ciencias Exactas y Naturales , Universidad de Buenos Aires , Buenos Aires , Argentina
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22
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Cahyono RN, Yamanaka M, Nagao S, Shibata N, Higuchi Y, Hirota S. 3D domain swapping of azurin from Alcaligenes xylosoxidans. Metallomics 2020; 12:337-345. [PMID: 31956880 DOI: 10.1039/c9mt00255c] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Protein oligomers have gained interest, owing to their increased knowledge in cells and promising utilization for future materials. Various proteins have been shown to 3D domain swap, but there has been no domain swapping report on a blue copper protein. Here, we found that azurin from Alcaligenes xylosoxidans oligomerizes by the procedure of 2,2,2-trifluoroethanol addition to Cu(i)-azurin at pH 5.0, lyophilization, and dissolution at pH 7.0, whereas it slightly oligomerizes when using Cu(ii)-azurin. The amount of high order oligomers increased with the addition of Cu(ii) ions to the dissolution process of a similar procedure for apoazurin, indicating that Cu(ii) ions enhance azurin oligomerization. The ratio of the absorbance at 460 nm to that at ∼620 nm of the azurin dimer (Abs460/Abs618 = 0.113) was higher than that of the monomer (Abs460/Abs622 = 0.067) and the EPR A‖ value of the dimer (5.85 mT) was slightly smaller than that of the monomer (5.95 mT), indicating a slightly more rhombic copper coordination for the dimer. The redox potential of the azurin dimer was 342 ± 5 mV vs. NHE, which was 50 mV higher than that of the monomer. According to X-ray crystal analysis, the azurin dimer exhibited a domain-swapped structure, where the N-terminal region containing three β-strands was exchanged between protomers. The copper coordination structure was tetrahedrally distorted in the azurin dimer, similar to that in the monomer; however, the Cu-O(Gly45) bond length was longer for the dimer (monomer, 2.46-2.59 Å; dimer, 2.98-3.25 Å). These results open the door for designing oligomers of blue copper proteins by domain swapping.
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Affiliation(s)
- Robby Noor Cahyono
- Division of Materials Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan. and Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Gadjah Mada, Sekip Utara, Yogyakarta, 55281, Indonesia
| | - Masaru Yamanaka
- Division of Materials Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan.
| | - Satoshi Nagao
- Division of Materials Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan.
| | - Naoki Shibata
- Department of Life Science, Graduate School of Life Science, University of Hyogo, 3-2-1 Koto, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan
| | - Yoshiki Higuchi
- Department of Life Science, Graduate School of Life Science, University of Hyogo, 3-2-1 Koto, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan
| | - Shun Hirota
- Division of Materials Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan.
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23
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Pradhan B, Engelhard C, Van Mulken S, Miao X, Canters GW, Orrit M. Single electron transfer events and dynamical heterogeneity in the small protein azurin from Pseudomonas aeruginosa. Chem Sci 2019; 11:763-771. [PMID: 34123050 PMCID: PMC8146731 DOI: 10.1039/c9sc05405g] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 11/25/2019] [Indexed: 01/07/2023] Open
Abstract
Monitoring the fluorescence of single-dye-labeled azurin molecules, we observed the reaction of azurin with hexacyanoferrate under controlled redox potential yielding data on the timing of individual (forward and backward) electron transfer (ET) events. Change-point analysis of the time traces demonstrates significant fluctuations of ET rates and of mid-point potential E 0. These fluctuations are a signature of dynamical heterogeneity, here observed on a 14 kDa protein, the smallest to date. By correlating changes in forward and backward reaction rates we found that 6% of the observed change events could be explained by a change in midpoint potential, while for 25% a change of the donor-acceptor coupling could explain the data. The remaining 69% are driven by variations in complex association constants or structural changes that cause forward and back ET rates to vary independently. Thus, the observed spread in individual ET rates could be related in a unique way to variations in molecular parameters. The relevance for the understanding of metabolic processes is briefly discussed.
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Affiliation(s)
- Biswajit Pradhan
- Huygens-Kamerlingh Onnes Laboratory, Leiden University 2300 RA Leiden Netherlands
| | | | | | - Xueyan Miao
- School of Public Health, Guilin Medical University 541004 Guilin China
| | - Gerard W Canters
- Huygens-Kamerlingh Onnes Laboratory, Leiden University 2300 RA Leiden Netherlands
| | - Michel Orrit
- Huygens-Kamerlingh Onnes Laboratory, Leiden University 2300 RA Leiden Netherlands
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24
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Zerk TJ, Saouma CT, Mayer JM, Tolman WB. Low Reorganization Energy for Electron Self-Exchange by a Formally Copper(III,II) Redox Couple. Inorg Chem 2019; 58:14151-14158. [PMID: 31577145 DOI: 10.1021/acs.inorgchem.9b02185] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The rate constant for electron self-exchange (k11) between LCuOH and [LCuOH]- (L = bis-2,6-(2,6-diisopropylphenyl)carboximidopyridine) was determined using the Marcus cross relation. This work involved measurement of the rate of the cross-reaction between [Bu4N][LCuOH] and [Fc][BAr4F] (Fc+ = ferrocenium; BAr4F = tetrakis[3,5-bis(trifluoromethyl)phenyl]borate)) by stopped-flow methods at -88 °C in CH2Cl2 and measurement of the equilibrium constant for the redox process by UV-vis titrations under the same conditions. A value of k11 = 3 × 104 M-1 s-1 (-88 °C) led to estimation of a value 9 × 106 M-1 s-1 at 25 °C, which is among the highest values known for copper redox couples. Further Marcus analysis enabled determination of a low reorganization energy, λ = 0.95 ± 0.17 eV, attributed to minimal structural variation between the redox partners. In addition, the reaction entropy (ΔS°) associated with the LCuOH/[LCuOH]- self-exchange was determined from the temperature dependence of the redox potentials, and found to be dependent upon ionic strength. Comparisons to other Cu redox systems and potential new applications for the formally CuIII,II system are discussed.
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Affiliation(s)
- Timothy J Zerk
- Department of Chemistry , Washington University in St. Louis , One Brookings Hall, Campus Box 1134 , St. Louis , Missouri 63130-4899 , United States
| | - Caroline T Saouma
- Department of Chemistry , University of Utah , 315 S 1400 E , Salt Lake City , Utah 84112 , United States
| | - James M Mayer
- Department of Chemistry , Yale University , 225 Prospect Street , New Haven , Connecticut 06520-8107 , United States
| | - William B Tolman
- Department of Chemistry , Washington University in St. Louis , One Brookings Hall, Campus Box 1134 , St. Louis , Missouri 63130-4899 , United States
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25
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Lee HB, Agapie T. Redox Tuning via Ligand-Induced Geometric Distortions at a YMn 3O 4 Cubane Model of the Biological Oxygen Evolving Complex. Inorg Chem 2019; 58:14998-15003. [PMID: 31095368 PMCID: PMC6876925 DOI: 10.1021/acs.inorgchem.9b00510] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
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The function of proteins
involved in electron transfer is dependent
on cofactors attaining the necessary reduction potentials. We establish
a mode of cluster redox tuning through steric pressure on a synthetic
model related to Photosystem II. Resembling the cuboidal [CaMn3O4] subsite of the biological oxygen evolving complex
(OEC), [Mn4O4] and [YMn3O4] complexes featuring ligands of different basicity and chelating
properties were characterized by cyclic voltammetry. In the absence
of ligand-induced distortions, increasing the basicity of the ligands
results in a decrease of cluster reduction potential. Contraction
of Y-oxo/Y–Mn distances by 0.1/0.15 Å enforced by a chelating
ligand results in an increase of cluster reduction potential even
in the presence of strongly basic donors. Related protein-induced
changes in Ca-oxo/Ca–Mn distances may have similar effects
in tuning the redox potential of the OEC through entatic states and
may explain the cation size dependence on the progression of the S-state
cycle. The redox properties of [YMn3O4] and
[Mn4O4] complexes featuring bridging ligands
of different basicity and chelating properties are reported. In the
absence of ligand-induced geometric distortions, increasing the basicity
of the ligands results in a decrease of cluster reduction potential.
A chelating ligand results in contractions of Y-oxo distances by ∼0.1
Å, which correlates with an increase of cluster reduction potential
even in the presence of strongly basic donors.
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Affiliation(s)
- Heui Beom Lee
- Department of Chemistry and Chemical Engineering , California Institute of Technology , 1200 E. California Blvd MC 127-72 , Pasadena , California 91125 , United States
| | - Theodor Agapie
- Department of Chemistry and Chemical Engineering , California Institute of Technology , 1200 E. California Blvd MC 127-72 , Pasadena , California 91125 , United States
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26
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Krishnan A, Degnan BM, Degnan SM. The first identification of complete Eph-ephrin signalling in ctenophores and sponges reveals a role for neofunctionalization in the emergence of signalling domains. BMC Evol Biol 2019; 19:96. [PMID: 31023220 PMCID: PMC6485061 DOI: 10.1186/s12862-019-1418-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 03/31/2019] [Indexed: 11/25/2022] Open
Abstract
Background Animals have a greater diversity of signalling pathways than their unicellular relatives, consistent with the evolution and expansion of these pathways occurring in parallel with the origin of animal multicellularity. However, the genomes of sponges and ctenophores – non-bilaterian basal animals – typically encode no, or far fewer, recognisable signalling ligands compared to bilaterians and cnidarians. For instance, the largest subclass of receptor tyrosine kinases (RTKs) in bilaterians, the Eph receptors (Ephs), are present in sponges and ctenophores, but their cognate ligands, the ephrins, have not yet been detected. Results Here, we use an iterative HMM analysis to identify for the first time membrane-bound ephrins in sponges and ctenophores. We also expand the number of Eph-receptor subtypes identified in these animals and in cnidarians. Both sequence and structural analyses are consistent with the Eph ligand binding domain (LBD) and the ephrin receptor binding domain (RBD) having evolved via the co-option of ancient galactose-binding (discoidin-domain)-like and monodomain cupredoxin domains, respectively. Although we did not detect a complete Eph-ephrin signalling pathway in closely-related unicellular holozoans or in other non-metazoan eukaryotes, truncated proteins with Eph receptor LBDs and ephrin RBDs are present in some choanoflagellates. Together, these results indicate that Eph-ephrin signalling was present in the last common ancestor of extant metazoans, and perhaps even in the last common ancestor of animals and choanoflagellates. Either scenario pushes the origin of Eph-ephrin signalling back much earlier than previously reported. Conclusions We propose that the Eph-LBD and ephrin-RBD, which were ancestrally localised in the cytosol, became linked to the extracellular parts of two cell surface proteins before the divergence of sponges and ctenophores from the rest of the animal kingdom. The ephrin-RBD lost the ancestral capacity to bind copper, and the Eph-LBD became linked to an ancient RTK. The identification of divergent ephrin ligands in sponges and ctenophores suggests that these ligands evolve faster than their cognate receptors. As this may be a general phenomena, we propose that the sequence-structure approach used in this study may be usefully applied to other signalling systems where no, or a small number of, ligands have been identified. Electronic supplementary material The online version of this article (10.1186/s12862-019-1418-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Arunkumar Krishnan
- School of Biological Sciences, The University of Queensland, Brisbane, Queensland, Australia.,Present Address: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA
| | - Bernard M Degnan
- School of Biological Sciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Sandie M Degnan
- School of Biological Sciences, The University of Queensland, Brisbane, Queensland, Australia.
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27
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Dennison C. The Coordination Chemistry of Copper Uptake and Storage for Methane Oxidation. Chemistry 2018; 25:74-86. [PMID: 30281847 DOI: 10.1002/chem.201803444] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Indexed: 11/09/2022]
Abstract
Methanotrophs are remarkable bacteria that utilise large quantities of copper (Cu) to oxidize the potent greenhouse gas methane. To assist in providing the Cu they require for this process some methanotrophs can secrete the Cu-sequestering modified peptide methanobactin. These small molecules bind CuI with very high affinity and crystal structures have given insight into why this is the case, and also how the metal ion may be released within the cell. A much greater proportion of methanotrophs, genomes of which have been sequenced, possess a member of a newly discovered bacterial family of copper storage proteins (the Csps). These are tetramers of four-helix bundles whose cores are lined with Cys residues enabling the binding of large numbers of CuI ions. In methanotrophs, a Csp exported from the cytosol stores CuI for the active site of the ubiquitous enzyme that catalyses the oxidation of methane. The presence of cytosolic Csps, not only in methanotrophs but in a wide range of bacteria, challenges the dogma that these organisms have no requirement for Cu in this location. The properties of the Csps, with an emphasis on CuI binding and the structures of the sites formed, are the primary focus of this review.
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Affiliation(s)
- Christopher Dennison
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
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28
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Kurniawan I, Kawaguchi K, Sugimori K, Sakurai T, Nagao H. Quantum Chemical Study of Axial Ligand Effect on the Electronic Properties of Type I Copper Protein. CHEM LETT 2018. [DOI: 10.1246/cl.180521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Isman Kurniawan
- Division of Mathematical and Physical Sciences, Graduate School of Natural Science and Technology, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
- School of Computing, Telkom University, Jl. Telekomunikasi, Terusan Buah Batu, Bandung, Indonesia 40257
| | - Kazutomo Kawaguchi
- Division of Mathematical and Physical Sciences, Graduate School of Natural Science and Technology, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
| | - Kimikazu Sugimori
- Division of Higher Education Research and Development, Institute of Liberal Arts and Science, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
| | - Takeshi Sakurai
- Division of Material Chemistry, Graduate School of Natural Science and Technology, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
| | - Hidemi Nagao
- Division of Mathematical and Physical Sciences, Graduate School of Natural Science and Technology, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
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29
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Espinoza-Cara A, Zitare U, Alvarez-Paggi D, Klinke S, Otero LH, Murgida DH, Vila AJ. Engineering a bifunctional copper site in the cupredoxin fold by loop-directed mutagenesis. Chem Sci 2018; 9:6692-6702. [PMID: 30310603 PMCID: PMC6115626 DOI: 10.1039/c8sc01444b] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 06/27/2018] [Indexed: 12/30/2022] Open
Abstract
Copper sites in proteins are designed to perform either electron transfer or redox catalysis. Type 1 and CuA sites are electron transfer hubs bound to a rigid protein fold that prevents binding of exogenous ligands and side reactions. Here we report the engineering of two Type 1 sites by loop-directed mutagenesis within a CuA scaffold with unique electronic structures and functional features. A copper-thioether axial bond shorter than the copper-thiolate bond is responsible for the electronic structure features, in contrast to all other natural or chimeric sites where the copper thiolate bond is short. These sites display highly unusual features, such as: (1) a high reduction potential despite a strong interaction with the axial ligand, which we attribute to changes in the hydrogen bond network and (2) the ability to bind exogenous ligands such as imidazole and azide. This strategy widens the possibility of using natural protein scaffolds with functional features not present in nature.
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Affiliation(s)
- Andrés Espinoza-Cara
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET-UNR) , Rosario , Argentina .
- Área Biofísica , Departamento de Química Biológica , Facultad de Ciencias Bioquímicas y Farmacéuticas , Universidad Nacional de Rosario , Rosario , Argentina
| | - Ulises Zitare
- Departamento de Química Inorgánica , Analítica y Química Física-INQUIMAE , Facultad de Ciencias Exactas y Naturales , Universidad de Buenos Aires-CONICET , Buenos Aires , Argentina
| | - Damián Alvarez-Paggi
- Departamento de Química Inorgánica , Analítica y Química Física-INQUIMAE , Facultad de Ciencias Exactas y Naturales , Universidad de Buenos Aires-CONICET , Buenos Aires , Argentina
- Fundación Instituto Leloir , IIBBA-CONICET , Buenos Aires , Argentina
| | - Sebastián Klinke
- Fundación Instituto Leloir , IIBBA-CONICET , Buenos Aires , Argentina
- Plataforma Argentina de Biología Estructural y Metabolómica PLABEM. , Buenos Aires , Argentina
| | - Lisandro H Otero
- Fundación Instituto Leloir , IIBBA-CONICET , Buenos Aires , Argentina
- Plataforma Argentina de Biología Estructural y Metabolómica PLABEM. , Buenos Aires , Argentina
| | - Daniel H Murgida
- Departamento de Química Inorgánica , Analítica y Química Física-INQUIMAE , Facultad de Ciencias Exactas y Naturales , Universidad de Buenos Aires-CONICET , Buenos Aires , Argentina
| | - Alejandro J Vila
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET-UNR) , Rosario , Argentina .
- Área Biofísica , Departamento de Química Biológica , Facultad de Ciencias Bioquímicas y Farmacéuticas , Universidad Nacional de Rosario , Rosario , Argentina
- Plataforma Argentina de Biología Estructural y Metabolómica PLABEM. , Buenos Aires , Argentina
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30
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Abstract
![]()
Work on the electronic
structures of metal–oxo complexes
began in Copenhagen over 50 years ago. This work led to the prediction
that tetragonal multiply bonded transition metal–oxos would
not be stable beyond the iron–ruthenium–osmium oxo wall
in the periodic table and that triply bonded metal–oxos could
not be protonated, even in the strongest Brønsted acids. In this
theory, only double bonded metal–oxos could attract protons,
with basicities being a function of the electron donating ability
of ancillary ligands. Such correlations of electronic structure with
reactivity have gained importance in recent years, most notably owing
to the widespread recognition that high-valent iron–oxos are
intermediates in biological reactions critical to life on Earth. In this Account, we focus attention on the oxygenations of inert
organic substrates by cytochromes P450, as these reactions involve
multiply bonded iron–oxos. We emphasize that P450 iron–oxos
are strong oxidants, so strong that they would destroy nearby amino
acids if substrates are not oxygenated rapidly; it is our view that
these high-valent iron–oxos are such dangerous reactive oxygen
species that Nature surely found ways to disable them. Looking more
deeply into this matter, mainly by examining many thousands of structures
in the Protein Data Bank, we have found that P450s and other enzymes
that require oxygen for function have chains of tyrosines and tryptophans
that extend from active-site regions to protein surfaces. Tyrosines
are near the heme active sites in bacterial P450s, whereas tryptophan
is closest in most human enzymes. High-valent iron–oxo survival
times taken from hole hopping maps range from a few nanoseconds to
milliseconds, depending on the distance of the closest Trp or Tyr
residue to the heme. In our proposed mechanism, multistep hole tunneling
(hopping) through Tyr/Trp chains guides the damaging oxidizing hole
to the protein surface, where it can be quenched by soluble protein
or small molecule reductants. As the Earth’s oxygenic atmosphere
is believed to have developed about 2.5 billion years ago, the increase
in occurrence frequency of tyrosine and tryptophan since the last
universal evolutionary ancestor may be in part a consequence of enzyme
protective functions that developed to cope with the environmental
toxin, O2.
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Affiliation(s)
- Harry B. Gray
- Beckman Institute, California Institute of Technology, Pasadena, California 91125, United States
| | - Jay R. Winkler
- Beckman Institute, California Institute of Technology, Pasadena, California 91125, United States
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31
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Schrempp DF, Kaifer E, Himmel HJ. Solvent Control of Ligand-Metal Electron Transfer in Mononuclear Copper Complexes with Redox-Active Bisguanidine Ligands. Eur J Inorg Chem 2018. [DOI: 10.1002/ejic.201800525] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- David F. Schrempp
- Anorganisch-Chemisches Institut; Ruprecht-Karls-Universität Heidelberg; Im Neuenheimer Feld 270 69120 Heidelberg Germany
| | - Elisabeth Kaifer
- Anorganisch-Chemisches Institut; Ruprecht-Karls-Universität Heidelberg; Im Neuenheimer Feld 270 69120 Heidelberg Germany
| | - Hans-Jörg Himmel
- Anorganisch-Chemisches Institut; Ruprecht-Karls-Universität Heidelberg; Im Neuenheimer Feld 270 69120 Heidelberg Germany
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32
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Planchestainer M, Segaud N, Shanmugam M, McMaster J, Paradisi F, Albrecht M. Carbene in Cupredoxin Protein Scaffolds: Replacement of a Histidine Ligand in the Active Site Substantially Alters Copper Redox Properties. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201807168] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
| | - Nathalie Segaud
- Department of Chemistry & BiochemistryUniversität Bern Freiestrasse 3 3012 Bern Switzerland
| | - Muralidharan Shanmugam
- Manchester Institute of BiotechnologyUniversity of Manchester 131 Princess St Manchester M1 7DN UK
| | - Jonathan McMaster
- School of ChemistryUniversity of Nottingham University Park Nottingham NG7 2RD UK
| | - Francesca Paradisi
- School of ChemistryUniversity of Nottingham University Park Nottingham NG7 2RD UK
| | - Martin Albrecht
- Department of Chemistry & BiochemistryUniversität Bern Freiestrasse 3 3012 Bern Switzerland
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33
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Planchestainer M, Segaud N, Shanmugam M, McMaster J, Paradisi F, Albrecht M. Carbene in Cupredoxin Protein Scaffolds: Replacement of a Histidine Ligand in the Active Site Substantially Alters Copper Redox Properties. Angew Chem Int Ed Engl 2018; 57:10677-10682. [DOI: 10.1002/anie.201807168] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Indexed: 01/17/2023]
Affiliation(s)
| | - Nathalie Segaud
- Department of Chemistry & BiochemistryUniversität Bern Freiestrasse 3 3012 Bern Switzerland
| | - Muralidharan Shanmugam
- Manchester Institute of BiotechnologyUniversity of Manchester 131 Princess St Manchester M1 7DN UK
| | - Jonathan McMaster
- School of ChemistryUniversity of Nottingham University Park Nottingham NG7 2RD UK
| | - Francesca Paradisi
- School of ChemistryUniversity of Nottingham University Park Nottingham NG7 2RD UK
| | - Martin Albrecht
- Department of Chemistry & BiochemistryUniversität Bern Freiestrasse 3 3012 Bern Switzerland
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34
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Abstract
Copper is essential for most organisms as a cofactor for key enzymes involved in fundamental processes such as respiration and photosynthesis. However, copper also has toxic effects in cells, which is why eukaryotes and prokaryotes have evolved mechanisms for safe copper handling. A new family of bacterial proteins uses a Cys-rich four-helix bundle to safely store large quantities of Cu(I). The work leading to the discovery of these proteins, their properties and physiological functions, and how their presence potentially impacts the current views of bacterial copper handling and use are discussed in this review.
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Affiliation(s)
- Christopher Dennison
- Institute for Cell and Molecular Biosciences, Medical School, Newcastle University, Newcastle upon Tyne, NE2 4HH, United Kingdom.
| | - Sholto David
- Institute for Cell and Molecular Biosciences, Medical School, Newcastle University, Newcastle upon Tyne, NE2 4HH, United Kingdom
| | - Jaeick Lee
- Institute for Cell and Molecular Biosciences, Medical School, Newcastle University, Newcastle upon Tyne, NE2 4HH, United Kingdom
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35
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Das AK, Meuwly M. Hydration Control Through Intramolecular Degrees of Freedom: Molecular Dynamics of [Cu(II)(Imidazole)4]. J Phys Chem B 2017; 121:9024-9031. [DOI: 10.1021/acs.jpcb.7b05949] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Akshaya K. Das
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, 4001 Basel, Switzerland
| | - Markus Meuwly
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, 4001 Basel, Switzerland
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36
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Schrempp DF, Leingang S, Schnurr M, Kaifer E, Wadepohl H, Himmel HJ. Inter- and Intramolecular Electron Transfer in Copper Complexes: Electronic Entatic State with Redox-Active Guanidine Ligands. Chemistry 2017; 23:13607-13611. [PMID: 28771843 DOI: 10.1002/chem.201703611] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Indexed: 02/01/2023]
Abstract
Fast and efficient electron transfer in blue copper proteins is realized by a structural harmonization between the CuI and CuII complex pair ("entatic state" model). Herein, we present now a CuI /CuII complex pair with redox-active guanidine ligands showing almost perfect match between both redox states. By modifying the ligand electron donor strength, the redox chemistry of the copper complex can be controlled to be either metal-centered or to cross the borderline to ligand-centered. This work is the first systematic study of complexes with redox-active ligands within the concept of the entatic state.
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Affiliation(s)
- David F Schrempp
- Anorganisch-Chemisches Institut, Ruprecht-Karls-Universität Heidelberg, Im Neuenheimer Feld 275, 69120, Heidelberg, Germany
| | - Simone Leingang
- Anorganisch-Chemisches Institut, Ruprecht-Karls-Universität Heidelberg, Im Neuenheimer Feld 275, 69120, Heidelberg, Germany
| | - Martin Schnurr
- Anorganisch-Chemisches Institut, Ruprecht-Karls-Universität Heidelberg, Im Neuenheimer Feld 275, 69120, Heidelberg, Germany
| | - Elisabeth Kaifer
- Anorganisch-Chemisches Institut, Ruprecht-Karls-Universität Heidelberg, Im Neuenheimer Feld 275, 69120, Heidelberg, Germany
| | - Hubert Wadepohl
- Anorganisch-Chemisches Institut, Ruprecht-Karls-Universität Heidelberg, Im Neuenheimer Feld 275, 69120, Heidelberg, Germany
| | - Hans-Jörg Himmel
- Anorganisch-Chemisches Institut, Ruprecht-Karls-Universität Heidelberg, Im Neuenheimer Feld 275, 69120, Heidelberg, Germany
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37
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Yamaguchi T, Nihei Y, Sutherland DEK, Stillman MJ, Kohzuma T. Stabilization of protein structure through π-π interaction in the second coordination sphere of pseudoazurin. Protein Sci 2017; 26:1921-1931. [PMID: 28691165 DOI: 10.1002/pro.3226] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Revised: 07/01/2017] [Accepted: 07/04/2017] [Indexed: 11/11/2022]
Abstract
Noncovalent, weak interactions in the second coordination sphere of the copper active site of Pseudoazurin (PAz) from Achromobacter cycloclastes were examined using a series of Met16X variants. In this study, the differences in protein stability due to the changes in the nature of the 16th amino acid (Met, Phe, Val, Ile) were investigated by electrospray ionization mass spectrometry (ESI-MS) and far-UV circular dichroism (CD) as a result of acid denaturation. The percentage of native states (folded holo forms) of Met16Phe variants was estimated to be 75% at pH 2.9 although the wild-type (WT), Met16Val and Met16Ile PAz, became completely unfolded. The high stability under acidic conditions is correlated with the result of the active site being stabilized by the aromatic substitution of the Met16 residue. The π-π interaction in the second coordination sphere makes a significant contribution to the stability of active site and the protein matrix.
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Affiliation(s)
- Takahide Yamaguchi
- Graduate School of Science and Engineering, Institute of Quantum Beam Science, Ibaraki University, Mito, Ibaraki, 310-8512, Japan
| | - Yuko Nihei
- Graduate School of Science and Engineering, Institute of Quantum Beam Science, Ibaraki University, Mito, Ibaraki, 310-8512, Japan
| | - Duncan E K Sutherland
- Department of Biology, The University of Western Ontario, London, Ontario, Canada.,Department of Chemistry, The University of Western Ontario, London, Ontario, Canada
| | - Martin J Stillman
- Department of Biology, The University of Western Ontario, London, Ontario, Canada.,Department of Chemistry, The University of Western Ontario, London, Ontario, Canada
| | - Takamitsu Kohzuma
- Graduate School of Science and Engineering, Institute of Quantum Beam Science, Ibaraki University, Mito, Ibaraki, 310-8512, Japan
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38
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Roger M, Sciara G, Biaso F, Lojou E, Wang X, Bauzan M, Giudici-Orticoni MT, Vila AJ, Ilbert M. Impact of copper ligand mutations on a cupredoxin with a green copper center. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2017; 1858:351-359. [DOI: 10.1016/j.bbabio.2017.02.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Revised: 02/10/2017] [Accepted: 02/14/2017] [Indexed: 11/26/2022]
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39
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Yu Y, Petrik ID, Chacón KN, Hosseinzadeh P, Chen H, Blackburn NJ, Lu Y. Effect of circular permutation on the structure and function of type 1 blue copper center in azurin. Protein Sci 2017; 26:218-226. [PMID: 27759897 PMCID: PMC5275729 DOI: 10.1002/pro.3071] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Revised: 10/13/2016] [Accepted: 10/14/2016] [Indexed: 11/10/2022]
Abstract
Type 1 copper (T1Cu) proteins are electron transfer (ET) proteins involved in many important biological processes. While the effects of changing primary and secondary coordination spheres in the T1Cu ET function have been extensively studied, few report has explored the effect of the overall protein structural perturbation on active site configuration or reduction potential of the protein, even though the protein scaffold has been proposed to play a critical role in enforcing the entatic or "rack-induced" state for ET functions. We herein report circular permutation of azurin by linking the N- and C-termini and creating new termini in the loops between 1st and 2nd β strands or between 3rd and 4th β strands. Characterization by electronic absorption, electron paramagnetic spectroscopies, as well as crystallography and cyclic voltammetry revealed that, while the overall structure and the primary coordination sphere of the circular permutated azurins remain the same as those of native azurin, their reduction potentials increased by 18 and 124 mV over that of WTAz. Such increases in reduction potentials can be attributed to subtle differences in the hydrogen-bonding network in secondary coordination sphere around the T1Cu center.
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Affiliation(s)
- Yang Yu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of SciencesTianjin300308China
| | - Igor D. Petrik
- Department of Chemistry, University of Illinois at Urbana‐ChampaignUrbanaIllinois61801
| | | | - Parisa Hosseinzadeh
- Department of BiochemistryUniversity of Illinois at Urbana‐ChampaignUrbanaIllinois61801
| | - Honghui Chen
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of SciencesTianjin300308China
- Tianjin University of Science and TechnologyTianjin300457China
| | - Ninian J. Blackburn
- Institute of Environmental Health, Oregon Health and Science UniversityPortlandOregon97239
| | - Yi Lu
- Department of Chemistry, University of Illinois at Urbana‐ChampaignUrbanaIllinois61801
- Department of BiochemistryUniversity of Illinois at Urbana‐ChampaignUrbanaIllinois61801
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40
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Zhao L, Wei J, Zhang F, He C, Zheng S, Duan C. Redox-active copper triangles as an enzymatic molecular flask for light-driven hydrogen production. RSC Adv 2017. [DOI: 10.1039/c7ra09285g] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
A redox-active Cu-based triangle was developed to encapsulate fluorescein for photocatalytic hydrogen production. Control experiments and inactive ATP as an inhibitor were performed to confirm this enzymatic photocatalytic behaviour.
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Affiliation(s)
- Liang Zhao
- State Key Laboratory of Fine Chemicals
- Dalian University of Technology
- Dalian 116024
- P. R. China
| | - Jianwei Wei
- State Key Laboratory of Fine Chemicals
- Dalian University of Technology
- Dalian 116024
- P. R. China
| | - Feili Zhang
- State Key Laboratory of Fine Chemicals
- Dalian University of Technology
- Dalian 116024
- P. R. China
| | - Cheng He
- State Key Laboratory of Fine Chemicals
- Dalian University of Technology
- Dalian 116024
- P. R. China
| | - Sijia Zheng
- State Key Laboratory of Fine Chemicals
- Dalian University of Technology
- Dalian 116024
- P. R. China
| | - Chunying Duan
- State Key Laboratory of Fine Chemicals
- Dalian University of Technology
- Dalian 116024
- P. R. China
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41
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Chen H, Su B, Zhang T, Huang A, Liu H, Yu Y, Wang J. Engineering the metal-binding loop at a type 1 copper center by circular permutation. RSC Adv 2017. [DOI: 10.1039/c7ra11512a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Circular permutation of the cupredoxin azurin creates a break on the metal binding loop, highlighting the loop's flexibility.
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Affiliation(s)
- Honghui Chen
- College of Biotechnology
- Tianjin University of Science and Technology
- Tianjin
- China
- Tianjin Institute of Industrial Biotechnology
| | - Binbin Su
- College of Biotechnology
- Tianjin University of Science and Technology
- Tianjin
- China
- Tianjin Institute of Industrial Biotechnology
| | - Tongtong Zhang
- Tianjin Institute of Industrial Biotechnology
- Chinese Academy of Sciences
- Tianjin
- China
| | - Aiping Huang
- Tianjin Institute of Industrial Biotechnology
- Chinese Academy of Sciences
- Tianjin
- China
| | - Haiping Liu
- Tianjin Institute of Industrial Biotechnology
- Chinese Academy of Sciences
- Tianjin
- China
| | - Yang Yu
- Tianjin Institute of Industrial Biotechnology
- Chinese Academy of Sciences
- Tianjin
- China
| | - Jiangyun Wang
- Laboratory of RNA Biology
- Institute of Biophysics
- Chinese Academy of Sciences
- Beijing
- China
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42
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Biosynthetic approach to modeling and understanding metalloproteins using unnatural amino acids. Sci China Chem 2016. [DOI: 10.1007/s11426-016-0343-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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43
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Hosseinzadeh P, Lu Y. Design and fine-tuning redox potentials of metalloproteins involved in electron transfer in bioenergetics. BIOCHIMICA ET BIOPHYSICA ACTA 2016; 1857:557-581. [PMID: 26301482 PMCID: PMC4761536 DOI: 10.1016/j.bbabio.2015.08.006] [Citation(s) in RCA: 114] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2015] [Accepted: 08/20/2015] [Indexed: 12/25/2022]
Abstract
Redox potentials are a major contributor in controlling the electron transfer (ET) rates and thus regulating the ET processes in the bioenergetics. To maximize the efficiency of the ET process, one needs to master the art of tuning the redox potential, especially in metalloproteins, as they represent major classes of ET proteins. In this review, we first describe the importance of tuning the redox potential of ET centers and its role in regulating the ET in bioenergetic processes including photosynthesis and respiration. The main focus of this review is to summarize recent work in designing the ET centers, namely cupredoxins, cytochromes, and iron-sulfur proteins, and examples in design of protein networks involved these ET centers. We then discuss the factors that affect redox potentials of these ET centers including metal ion, the ligands to metal center and interactions beyond the primary ligand, especially non-covalent secondary coordination sphere interactions. We provide examples of strategies to fine-tune the redox potential using both natural and unnatural amino acids and native and nonnative cofactors. Several case studies are used to illustrate recent successes in this area. Outlooks for future endeavors are also provided. 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)
- Parisa Hosseinzadeh
- Department of Chemistry and Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews St., Urbana, IL, 61801, USA
| | - Yi Lu
- Department of Chemistry and Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews St., Urbana, IL, 61801, USA.
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44
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45
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Marreiros BC, Calisto F, Castro PJ, Duarte AM, Sena FV, Silva AF, Sousa FM, Teixeira M, Refojo PN, Pereira MM. Exploring membrane respiratory chains. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2016; 1857:1039-1067. [PMID: 27044012 DOI: 10.1016/j.bbabio.2016.03.028] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Revised: 03/16/2016] [Accepted: 03/18/2016] [Indexed: 01/20/2023]
Abstract
Acquisition of energy is central to life. In addition to the synthesis of ATP, organisms need energy for the establishment and maintenance of a transmembrane difference in electrochemical potential, in order to import and export metabolites or to their motility. The membrane potential is established by a variety of membrane bound respiratory complexes. In this work we explored the diversity of membrane respiratory chains and the presence of the different enzyme complexes in the several phyla of life. We performed taxonomic profiles of the several membrane bound respiratory proteins and complexes evaluating the presence of their respective coding genes in all species deposited in KEGG database. We evaluated 26 quinone reductases, 5 quinol:electron carriers oxidoreductases and 18 terminal electron acceptor reductases. We further included in the analyses enzymes performing redox or decarboxylation driven ion translocation, ATP synthase and transhydrogenase and we also investigated the electron carriers that perform functional connection between the membrane complexes, quinones or soluble proteins. Our results bring a novel, broad and integrated perspective of membrane bound respiratory complexes and thus of the several energetic metabolisms of living systems. This article is part of a Special Issue entitled 'EBEC 2016: 19th European Bioenergetics Conference, Riva del Garda, Italy, July 2-6, 2016', edited by Prof. Paolo Bernardi.
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Affiliation(s)
- Bruno C Marreiros
- Instituto de Tecnologia Química e Biológica-António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157 Oeiras, Portugal
| | - Filipa Calisto
- Instituto de Tecnologia Química e Biológica-António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157 Oeiras, Portugal
| | - Paulo J Castro
- Instituto de Tecnologia Química e Biológica-António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157 Oeiras, Portugal
| | - Afonso M Duarte
- Instituto de Tecnologia Química e Biológica-António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157 Oeiras, Portugal
| | - Filipa V Sena
- Instituto de Tecnologia Química e Biológica-António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157 Oeiras, Portugal
| | - Andreia F Silva
- Instituto de Tecnologia Química e Biológica-António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157 Oeiras, Portugal
| | - Filipe M Sousa
- Instituto de Tecnologia Química e Biológica-António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157 Oeiras, Portugal
| | - Miguel Teixeira
- Instituto de Tecnologia Química e Biológica-António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157 Oeiras, Portugal
| | - Patrícia N Refojo
- Instituto de Tecnologia Química e Biológica-António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157 Oeiras, Portugal
| | - Manuela M Pereira
- Instituto de Tecnologia Química e Biológica-António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157 Oeiras, Portugal.
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46
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Dahl EW, Szymczak NK. Hydrogen Bonds Dictate the Coordination Geometry of Copper: Characterization of a Square-Planar Copper(I) Complex. Angew Chem Int Ed Engl 2016; 55:3101-5. [PMID: 26822857 PMCID: PMC4804195 DOI: 10.1002/anie.201511527] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Indexed: 12/31/2022]
Abstract
6,6''-Bis(2,4,6-trimethylanilido)terpyridine (H2Tpy(NMes)) was prepared as a rigid, tridentate pincer ligand containing pendent anilines as hydrogen bond donor groups in the secondary coordination sphere. The coordination geometry of (H2 Tpy(NMes))copper(I)-halide (Cl, Br and I) complexes is dictated by the strength of the NH-halide hydrogen bond. The Cu(I)Cl and Cu(II)Cl complexes are nearly isostructural, the former presenting a highly unusual square-planar geometry about Cu(I) . The geometric constraints provided by secondary interactions are reminiscent of blue copper proteins where a constrained geometry, or entatic state, allows for extremely rapid Cu(I)/Cu(II) electron-transfer self-exchange rates. Cu(H2 Tpy(NMes))Cl shows similar fast electron transfer (≈10(5) m(-1) s(-1)) which is the same order of magnitude as biological systems.
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Affiliation(s)
- Eric W Dahl
- Department of Chemistry, University of Michigan, 930 N. University, Ann Arbor, MI, 48109, USA
| | - Nathaniel K Szymczak
- Department of Chemistry, University of Michigan, 930 N. University, Ann Arbor, MI, 48109, USA.
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47
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Dahl EW, Szymczak NK. Hydrogen Bonds Dictate the Coordination Geometry of Copper: Characterization of a Square‐Planar Copper(I) Complex. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201511527] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Eric W. Dahl
- Department of Chemistry University of Michigan 930 N. University Ann Arbor MI 48109 USA
| | - Nathaniel K. Szymczak
- Department of Chemistry University of Michigan 930 N. University Ann Arbor MI 48109 USA
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48
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Yamaguchi T, Akao K, Takashina A, Asamura S, Unno M, Szilagyi RK, Kohzuma T. X-ray crystallographic evidence for the simultaneous presence of axial and rhombic sites in cupredoxins: atomic resolution X-ray crystal structure analysis of pseudoazurin and DFT modelling. RSC Adv 2016. [DOI: 10.1039/c6ra19282c] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The simultaneous presence of axial (blue) and rhombic (green) Cu sites in pseudoazurin is described from experiments and computational modelling.
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Affiliation(s)
- T. Yamaguchi
- Institute of Quantum Beam Science
- Ibaraki University
- Mito
- Japan
| | - K. Akao
- Institute of Quantum Beam Science
- Ibaraki University
- Mito
- Japan
| | - A. Takashina
- Institute of Quantum Beam Science
- Ibaraki University
- Mito
- Japan
| | - S. Asamura
- Institute of Quantum Beam Science
- Ibaraki University
- Mito
- Japan
| | - M. Unno
- Institute of Quantum Beam Science
- Ibaraki University
- Mito
- Japan
- Frontier Research Center for Applied Atomic Sciences
| | - R. K. Szilagyi
- Department of Chemistry and Biochemistry
- Montana State University
- Bozeman
- USA
- MTA-ELTE “Momentum” Chemical Structure/Function Laboratory
| | - T. Kohzuma
- Institute of Quantum Beam Science
- Ibaraki University
- Mito
- Japan
- Frontier Research Center for Applied Atomic Sciences
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49
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Dong XY, Zhang M, Pei RB, Wang Q, Wei DH, Zang SQ, Fan YT, Mak TCW. A Crystalline Copper(II) Coordination Polymer for the Efficient Visible-Light-Driven Generation of Hydrogen. Angew Chem Int Ed Engl 2015; 55:2073-7. [DOI: 10.1002/anie.201509744] [Citation(s) in RCA: 120] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2015] [Indexed: 12/26/2022]
Affiliation(s)
- Xi-Yan Dong
- College of Chemistry and Molecular Engineering; Zhengzhou University; Zhengzhou 450001 China
| | - Mei Zhang
- College of Chemistry and Molecular Engineering; Zhengzhou University; Zhengzhou 450001 China
| | - Ru-Bo Pei
- College of Chemistry and Molecular Engineering; Zhengzhou University; Zhengzhou 450001 China
| | - Qian Wang
- College of Chemistry and Molecular Engineering; Zhengzhou University; Zhengzhou 450001 China
| | - Dong-Hui Wei
- College of Chemistry and Molecular Engineering; Zhengzhou University; Zhengzhou 450001 China
| | - Shuang-Quan Zang
- College of Chemistry and Molecular Engineering; Zhengzhou University; Zhengzhou 450001 China
| | - Yao-Ting Fan
- College of Chemistry and Molecular Engineering; Zhengzhou University; Zhengzhou 450001 China
| | - Thomas C. W. Mak
- College of Chemistry and Molecular Engineering; Zhengzhou University; Zhengzhou 450001 China
- Department of Chemistry and Center of Novel Functional Molecules; The Chinese University of Hong Kong; Shatin, New Territories Hong Kong SAR China
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50
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Dong XY, Zhang M, Pei RB, Wang Q, Wei DH, Zang SQ, Fan YT, Mak TCW. A Crystalline Copper(II) Coordination Polymer for the Efficient Visible-Light-Driven Generation of Hydrogen. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201509744] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Xi-Yan Dong
- College of Chemistry and Molecular Engineering; Zhengzhou University; Zhengzhou 450001 China
| | - Mei Zhang
- College of Chemistry and Molecular Engineering; Zhengzhou University; Zhengzhou 450001 China
| | - Ru-Bo Pei
- College of Chemistry and Molecular Engineering; Zhengzhou University; Zhengzhou 450001 China
| | - Qian Wang
- College of Chemistry and Molecular Engineering; Zhengzhou University; Zhengzhou 450001 China
| | - Dong-Hui Wei
- College of Chemistry and Molecular Engineering; Zhengzhou University; Zhengzhou 450001 China
| | - Shuang-Quan Zang
- College of Chemistry and Molecular Engineering; Zhengzhou University; Zhengzhou 450001 China
| | - Yao-Ting Fan
- College of Chemistry and Molecular Engineering; Zhengzhou University; Zhengzhou 450001 China
| | - Thomas C. W. Mak
- College of Chemistry and Molecular Engineering; Zhengzhou University; Zhengzhou 450001 China
- Department of Chemistry and Center of Novel Functional Molecules; The Chinese University of Hong Kong; Shatin, New Territories Hong Kong SAR China
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