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Smets B, Boschker HTS, Wetherington MT, Lelong G, Hidalgo-Martinez S, Polerecky L, Nuyts G, De Wael K, Meysman FJR. Multi-wavelength Raman microscopy of nickel-based electron transport in cable bacteria. Front Microbiol 2024; 15:1208033. [PMID: 38525072 PMCID: PMC10959288 DOI: 10.3389/fmicb.2024.1208033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 02/26/2024] [Indexed: 03/26/2024] Open
Abstract
Cable bacteria embed a network of conductive protein fibers in their cell envelope that efficiently guides electron transport over distances spanning up to several centimeters. This form of long-distance electron transport is unique in biology and is mediated by a metalloprotein with a sulfur-coordinated nickel (Ni) cofactor. However, the molecular structure of this cofactor remains presently unknown. Here, we applied multi-wavelength Raman microscopy to identify cell compounds linked to the unique cable bacterium physiology, combined with stable isotope labeling, and orientation-dependent and ultralow-frequency Raman microscopy to gain insight into the structure and organization of this novel Ni-cofactor. Raman spectra of native cable bacterium filaments reveal vibrational modes originating from cytochromes, polyphosphate granules, proteins, as well as the Ni-cofactor. After selective extraction of the conductive fiber network from the cell envelope, the Raman spectrum becomes simpler, and primarily retains vibrational modes associated with the Ni-cofactor. These Ni-cofactor modes exhibit intense Raman scattering as well as a strong orientation-dependent response. The signal intensity is particularly elevated when the polarization of incident laser light is parallel to the direction of the conductive fibers. This orientation dependence allows to selectively identify the modes that are associated with the Ni-cofactor. We identified 13 such modes, some of which display strong Raman signals across the entire range of applied wavelengths (405-1,064 nm). Assignment of vibrational modes, supported by stable isotope labeling, suggest that the structure of the Ni-cofactor shares a resemblance with that of nickel bis(1,2-dithiolene) complexes. Overall, our results indicate that cable bacteria have evolved a unique cofactor structure that does not resemble any of the known Ni-cofactors in biology.
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Affiliation(s)
- Bent Smets
- Department of Biology, University of Antwerp, Antwerp, Belgium
| | - Henricus T. S. Boschker
- Department of Biology, University of Antwerp, Antwerp, Belgium
- Department of Biotechnology, Delft University of Technology, Delft, Netherlands
| | - Maxwell T. Wetherington
- Materials Characterization Laboratory, Pennsylvania State University, State College, PA, United States
| | - Gérald Lelong
- Institut de Minéralogie, de Physique des Matériaux et Cosmochimie (IMPMC), Sorbonne Universités, France—Muséum National d’Histoire Naturelle, Paris, France
| | | | - Lubos Polerecky
- Department of Earth Sciences, Utrecht University, Utrecht, Netherlands
| | - Gert Nuyts
- Department of Bioscience Engineering, University of Antwerp, Antwerp, Belgium
- Department of Physics, University of Antwerp, Antwerp, Belgium
| | - Karolien De Wael
- Department of Bioscience Engineering, University of Antwerp, Antwerp, Belgium
| | - Filip J. R. Meysman
- Department of Biology, University of Antwerp, Antwerp, Belgium
- Department of Biotechnology, Delft University of Technology, Delft, Netherlands
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2
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Chen H, Shi H, Chen C, Jiao Y, Wang P, Chen C, Li J, Wu LF, Song T. Effects of static magnetic field on the sulfate metabolic pathway involved in Magnetospirillum magneticum AMB-1 cell growth and magnetosome formation. J Appl Microbiol 2023; 134:lxad302. [PMID: 38066686 DOI: 10.1093/jambio/lxad302] [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: 11/10/2023] [Accepted: 12/08/2023] [Indexed: 12/27/2023]
Abstract
AIMS Magnetotactic bacteria (MTB) can use their unique intracellular magnetosome organelles to swim along the Earth's magnetic field. They play important roles in the biogeochemical cycles of iron and sulfur. Previous studies have shown that the applied magnetic fields could affect the magnetosome formation and antioxidant defense systems in MTB. However, the molecular mechanisms by which magnetic fields affect MTB cells remain unclear. We aim to better understand the dark at 28°C-29°C for 20 h, as shownthe interactions between magnetic fields and cells, and the mechanism of MTB adaptation to magnetic field at molecular levels. METHODS AND RESULTS We performed microbiological, transcriptomic, and genetic experiments to analyze the effects of a weak static magnetic field (SMF) exposure on the cell growth and magnetosome formation in the MTB strain Magnetospirillum magneticum AMB-1. The results showed that a 1.5 mT SMF significantly promoted the cell growth but reduced magnetosome formation in AMB-1, compared to the geomagnetic field. Transcriptomic analysis revealed decreased expression of genes primarily involved in the sulfate reduction pathway. Consistently, knockout mutant lacking adenylyl-sulfate kinase CysC did no more react to the SMF and the differences in growth and Cmag disappeared. Together with experimental findings of increased reactive oxidative species in the SMF-treated wild-type strain, we proposed that cysC, as a key gene, can participate in the cell growth and mineralization in AMB-1 by SMF regulation. CONCLUSIONS This study suggests that the magnetic field exposure can trigger a bacterial oxidative stress response involved in AMB-1 growth and magnetosome mineralization by regulating the sulfur metabolism pathway. CysC may serve as a pivotal enzyme in mediating sulfur metabolism to synchronize the impact of SMF on both growth and magnetization of AMB-1.
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Affiliation(s)
- Haitao Chen
- Beijing Key Laboratory of Biological Electromagnetism, Institute of Electrical Engineering, Chinese Academy of Sciences, Beijing 100190, China
- France-China International Laboratory of Evolution and Development of Magnetotactic Multicellular Organisms, Chinese Academy of Sciences, Beijing 100190, China
| | - Hongkai Shi
- Beijing Key Laboratory of Biological Electromagnetism, Institute of Electrical Engineering, Chinese Academy of Sciences, Beijing 100190, China
- France-China International Laboratory of Evolution and Development of Magnetotactic Multicellular Organisms, Chinese Academy of Sciences, Beijing 100190, China
- School of Electronics, Electrical and Communication Engineering, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Changyou Chen
- Beijing Key Laboratory of Biological Electromagnetism, Institute of Electrical Engineering, Chinese Academy of Sciences, Beijing 100190, China
- France-China International Laboratory of Evolution and Development of Magnetotactic Multicellular Organisms, Chinese Academy of Sciences, Beijing 100190, China
| | - Yangkun Jiao
- Beijing Key Laboratory of Biological Electromagnetism, Institute of Electrical Engineering, Chinese Academy of Sciences, Beijing 100190, China
- France-China International Laboratory of Evolution and Development of Magnetotactic Multicellular Organisms, Chinese Academy of Sciences, Beijing 100190, China
- School of Electronics, Electrical and Communication Engineering, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Pingping Wang
- Beijing Key Laboratory of Biological Electromagnetism, Institute of Electrical Engineering, Chinese Academy of Sciences, Beijing 100190, China
- France-China International Laboratory of Evolution and Development of Magnetotactic Multicellular Organisms, Chinese Academy of Sciences, Beijing 100190, China
| | - Chuanfang Chen
- Beijing Key Laboratory of Biological Electromagnetism, Institute of Electrical Engineering, Chinese Academy of Sciences, Beijing 100190, China
- France-China International Laboratory of Evolution and Development of Magnetotactic Multicellular Organisms, Chinese Academy of Sciences, Beijing 100190, China
| | - Jinhua Li
- France-China International Laboratory of Evolution and Development of Magnetotactic Multicellular Organisms, Chinese Academy of Sciences, Beijing 100190, China
- Key Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Chinese Academy of Sciences, Beijing 100029, China
| | - Long-Fei Wu
- France-China International Laboratory of Evolution and Development of Magnetotactic Multicellular Organisms, CNRS, F-13402 Marseille, France
- Aix Marseille University, CNRS, LCB, F-13402 Marseille, France
| | - Tao Song
- Beijing Key Laboratory of Biological Electromagnetism, Institute of Electrical Engineering, Chinese Academy of Sciences, Beijing 100190, China
- France-China International Laboratory of Evolution and Development of Magnetotactic Multicellular Organisms, Chinese Academy of Sciences, Beijing 100190, China
- School of Electronics, Electrical and Communication Engineering, University of Chinese Academy of Sciences, Beijing 100049, China
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3
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Barreiro DS, Oliveira RN, Pauleta SR. Bacterial peroxidases – Multivalent enzymes that enable the use of hydrogen peroxide for microaerobic and anaerobic proliferation. Coord Chem Rev 2023. [DOI: 10.1016/j.ccr.2023.215114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/01/2023]
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4
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Manesis AC, Slater JW, Cantave K, Martin Bollinger J, Krebs C, Rosenzweig AC. Capturing a bis-Fe(IV) State in Methylosinus trichosporium OB3b MbnH. Biochemistry 2023; 62:1082-1092. [PMID: 36812111 PMCID: PMC10083075 DOI: 10.1021/acs.biochem.3c00021] [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] [Indexed: 02/24/2023]
Abstract
The diheme bacterial cytochrome c peroxidase (bCcP)/MauG superfamily is a diverse set of enzymes that remains largely uncharacterized. One recently discovered member, MbnH, converts a tryptophan residue in its substrate protein, MbnP, to kynurenine. Here we show that upon reaction with H2O2, MbnH forms a bis-Fe(IV) intermediate, a state previously detected in just two other enzymes, MauG and BthA. Using absorption, Mössbauer, and electron paramagnetic resonance (EPR) spectroscopies coupled with kinetic analysis, we characterized the bis-Fe(IV) state of MbnH and determined that this intermediate decays back to the diferric state in the absence of MbnP substrate. In the absence of MbnP substrate, MbnH can also detoxify H2O2 to prevent oxidative self damage, unlike MauG, which has long been viewed as the prototype for bis-Fe(IV) forming enzymes. MbnH performs a different reaction from MauG, while the role of BthA remains unclear. All three enzymes can form a bis-Fe(IV) intermediate but within distinct kinetic regimes. The study of MbnH significantly expands our knowledge of enzymes that form this species. Computational and structural analyses indicate that electron transfer between the two heme groups in MbnH and between MbnH and the target tryptophan in MbnP likely occurs via a hole-hopping mechanism involving intervening tryptophan residues. These findings set the stage for discovery of additional functional and mechanistic diversity within the bCcP/MauG superfamily.
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Affiliation(s)
- Anastasia C Manesis
- Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Jeffrey W Slater
- Department of Chemistry and Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Kenny Cantave
- Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - J Martin Bollinger
- Department of Chemistry and Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Carsten Krebs
- Department of Chemistry and Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Amy C Rosenzweig
- Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
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5
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Nims C, Johnson JE. Exploring the secondary mineral products generated by microbial iron respiration in Archean ocean simulations. GEOBIOLOGY 2022; 20:743-763. [PMID: 36087062 PMCID: PMC9826415 DOI: 10.1111/gbi.12523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 05/17/2022] [Accepted: 07/02/2022] [Indexed: 06/15/2023]
Abstract
Marine chemical sedimentary deposits known as Banded Iron Formations (BIFs) archive Archean ocean chemistry and, potentially, signs of ancient microbial life. BIFs contain a diversity of iron- and silica-rich minerals in disequilibrium, and thus many interpretations of these phases suggest they formed secondarily during early diagenetic processes. One such hypothesis posits that the early diagenetic microbial respiration of primary iron(III) oxides in BIFs resulted in the formation of other iron phases, including the iron-rich silicates, carbonates, and magnetite common in BIF assemblages. Here, we simulated this proposed pathway in laboratory incubations combining a model dissimilatory iron-reducing (DIR) bacterium, Shewanella putrefaciens CN32, and the ferric oxyhydroxide mineral ferrihydrite under conditions mimicking the predicted Archean seawater geochemistry. We assessed the impact of dissolved silica, calcium, and magnesium on the bioreduced precipitates. After harvesting the solid products from these experiments, we analyzed the reduced mineral phases using Raman spectroscopy, electron microscopy, powder x-ray diffraction, and spectrophotometric techniques to identify mineral precipitates and track the bulk distributions of Fe(II) and Fe(III). These techniques detected a diverse range of calcium carbonate morphologies and polymorphism in incubations with calcium, as well as secondary ferric oxide phases like goethite in silica-free experiments. We also identified aggregates of curling, iron- and silica-rich amorphous precipitates in all incubations amended with silica. Although ferric oxides persist even in our electron acceptor-limited incubations, our observations indicate that microbial iron reduction of ferrihydrite is a viable pathway for the formation of early iron silicate phases. This finding allows us to draw parallels between our experimental proto-silicates and the recently characterized iron silicate nanoinclusions in BIF chert deposits, suggesting that early iron silicates could possibly be signatures of iron-reducing metabolisms on early Earth.
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Affiliation(s)
- Christine Nims
- Department of Earth and Environmental SciencesUniversity of MichiganAnn ArborMichiganUSA
| | - Jena E. Johnson
- Department of Earth and Environmental SciencesUniversity of MichiganAnn ArborMichiganUSA
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6
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Abendroth J, Buchko GW, Liew FN, Nguyen JN, Kim HJ. Structural Characterization of Cytochrome c'β-Met from an Ammonia-Oxidizing Bacterium. Biochemistry 2022; 61:563-574. [PMID: 35315646 DOI: 10.1021/acs.biochem.1c00640] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The ammonia-oxidizing bacterium Nitrosomonas europaea expresses two cytochromes in the P460 superfamily that are predicted to be structurally similar. In one, cytochrome (cyt) P460, the substrate hydroxylamine (NH2OH) is converted to nitric oxide (NO) and nitrous oxide (N2O) requiring a unique heme-lysyl cross-link in the catalytic cofactor. In the second, cyt c'β-Met, the cross-link is absent, and the cytochrome instead binds H2O2 forming a ferryl species similar to compound II of peroxidases. Here, we report the 1.80 Å crystal structure of cyt c'β-Met─a well-expressed protein in N. europaea with a lysine to a methionine replacement at the cross-linking position. The structure of cyt c'β-Met is characterized by a large β-sheet typical of P460 members; however, several localized structural differences render cyt c'β-Met distinct. This includes a large lasso-like loop at the "top" of the cytochrome that is not observed in other structurally characterized members. Active site variation is also observed, especially in comparison to its closest homologue cyt c'β from the methane-oxidizing Methylococcus capsulatus Bath, which also lacks the cross-link. The phenylalanine "cap" which is presumed to control small ligand access to the distal heme iron is replaced with an arginine, reminiscent of the strictly conserved distal arginine in peroxidases and to the NH2OH-oxidizing cytochromes P460. A critical proton-transferring glutamate residue required for NH2OH oxidation is nevertheless missing in the active site. This in part explains the inability of cyt c'β-Met to oxidize NH2OH. Our structure also rationalizes the absence of a methionyl cross-link, although the side chain's spatial position in the structure does not eliminate the possibility that it could form under certain conditions.
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Affiliation(s)
- Jan Abendroth
- Seattle Structural Genomics Center for Infectious Diseases, Seattle, Washington 98105, United States.,UCB Biosciences, Bainbridge Island, Washington 98110, United States
| | - Garry W Buchko
- Seattle Structural Genomics Center for Infectious Diseases, Seattle, Washington 98105, United States.,Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 98354, United States.,School of Molecular Biosciences, Washington State University, Pullman, Washington 99164, United States
| | - Fong Ning Liew
- Division of Physical Sciences, Chemistry, University of Washington-Bothell, Bothell, Washington 98011, United States
| | - Joline N Nguyen
- Division of Physical Sciences, Chemistry, University of Washington-Bothell, Bothell, Washington 98011, United States
| | - Hyung J Kim
- Division of Physical Sciences, Chemistry, University of Washington-Bothell, Bothell, Washington 98011, United States
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7
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Lehnert N, Kim E, Dong HT, Harland JB, Hunt AP, Manickas EC, Oakley KM, Pham J, Reed GC, Alfaro VS. The Biologically Relevant Coordination Chemistry of Iron and Nitric Oxide: Electronic Structure and Reactivity. Chem Rev 2021; 121:14682-14905. [PMID: 34902255 DOI: 10.1021/acs.chemrev.1c00253] [Citation(s) in RCA: 96] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Nitric oxide (NO) is an important signaling molecule that is involved in a wide range of physiological and pathological events in biology. Metal coordination chemistry, especially with iron, is at the heart of many biological transformations involving NO. A series of heme proteins, nitric oxide synthases (NOS), soluble guanylate cyclase (sGC), and nitrophorins, are responsible for the biosynthesis, sensing, and transport of NO. Alternatively, NO can be generated from nitrite by heme- and copper-containing nitrite reductases (NIRs). The NO-bearing small molecules such as nitrosothiols and dinitrosyl iron complexes (DNICs) can serve as an alternative vehicle for NO storage and transport. Once NO is formed, the rich reaction chemistry of NO leads to a wide variety of biological activities including reduction of NO by heme or non-heme iron-containing NO reductases and protein post-translational modifications by DNICs. Much of our understanding of the reactivity of metal sites in biology with NO and the mechanisms of these transformations has come from the elucidation of the geometric and electronic structures and chemical reactivity of synthetic model systems, in synergy with biochemical and biophysical studies on the relevant proteins themselves. This review focuses on recent advancements from studies on proteins and model complexes that not only have improved our understanding of the biological roles of NO but also have provided foundations for biomedical research and for bio-inspired catalyst design in energy science.
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Affiliation(s)
- Nicolai Lehnert
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Eunsuk Kim
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, United States
| | - Hai T Dong
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Jill B Harland
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Andrew P Hunt
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Elizabeth C Manickas
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Kady M Oakley
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, United States
| | - John Pham
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, United States
| | - Garrett C Reed
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Victor Sosa Alfaro
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
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8
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Karnaukh EA, Bravaya KB. The redox potential of a heme cofactor in Nitrosomonas europaea cytochrome c peroxidase: a polarizable QM/MM study. Phys Chem Chem Phys 2021; 23:16506-16515. [PMID: 34017969 PMCID: PMC11178132 DOI: 10.1039/d0cp06632j] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Redox reactions are crucial to biological processes that protect organisms against oxidative stress. Metalloenzymes, such as peroxidases which reduce excess reactive oxygen species into water, play a key role in detoxification mechanisms. Here we present the results of a polarizable QM/MM study of the reduction potential of the electron transfer heme in the cytochrome c peroxidase of Nitrosomonas europaea. We have found that environment polarization does not substantially affect the computed value of the redox potential. Particular attention has been given to analyzing the role of electrostatic interactions within the protein environment and the solvent on tuning the redox potential of the heme co-factor. We have found that the electrostatic interactions predominantly explain the fluctuations of the vertical ionization/attachment energies of the heme for the sampled configurations, and that the long range electrostatic interactions (up to 40 Å) contribute substantially to the absolute values of the vertical energy gaps.
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9
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Silveira CM, Zuccarello L, Barbosa C, Caserta G, Zebger I, Hildebrandt P, Todorovic S. Molecular Details on Multiple Cofactor Containing Redox Metalloproteins Revealed by Infrared and Resonance Raman Spectroscopies. Molecules 2021; 26:4852. [PMID: 34443440 PMCID: PMC8398457 DOI: 10.3390/molecules26164852] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 08/06/2021] [Accepted: 08/07/2021] [Indexed: 12/12/2022] Open
Abstract
Vibrational spectroscopy and in particular, resonance Raman (RR) spectroscopy, can provide molecular details on metalloproteins containing multiple cofactors, which are often challenging for other spectroscopies. Due to distinct spectroscopic fingerprints, RR spectroscopy has a unique capacity to monitor simultaneously and independently different metal cofactors that can have particular roles in metalloproteins. These include e.g., (i) different types of hemes, for instance hemes c, a and a3 in caa3-type oxygen reductases, (ii) distinct spin populations, such as electron transfer (ET) low-spin (LS) and catalytic high-spin (HS) hemes in nitrite reductases, (iii) different types of Fe-S clusters, such as 3Fe-4S and 4Fe-4S centers in di-cluster ferredoxins, and (iv) bi-metallic center and ET Fe-S clusters in hydrogenases. IR spectroscopy can provide unmatched molecular details on specific enzymes like hydrogenases that possess catalytic centers coordinated by CO and CN- ligands, which exhibit spectrally well separated IR bands. This article reviews the work on metalloproteins for which vibrational spectroscopy has ensured advances in understanding structural and mechanistic properties, including multiple heme-containing proteins, such as nitrite reductases that house a notable total of 28 hemes in a functional unit, respiratory chain complexes, and hydrogenases that carry out the most fundamental functions in cells.
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Affiliation(s)
- Célia M. Silveira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Av. da República, 2780-157 Oeiras, Portugal; (C.M.S.); (L.Z.); (C.B.)
| | - Lidia Zuccarello
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Av. da República, 2780-157 Oeiras, Portugal; (C.M.S.); (L.Z.); (C.B.)
| | - Catarina Barbosa
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Av. da República, 2780-157 Oeiras, Portugal; (C.M.S.); (L.Z.); (C.B.)
| | - Giorgio Caserta
- Institut fur Chemie, Sekr. PC14, Technische Universitat Berlin, Strasse des 17. Juni 135, D-10623 Berlin, Germany; (G.C.); (I.Z.); (P.H.)
| | - Ingo Zebger
- Institut fur Chemie, Sekr. PC14, Technische Universitat Berlin, Strasse des 17. Juni 135, D-10623 Berlin, Germany; (G.C.); (I.Z.); (P.H.)
| | - Peter Hildebrandt
- Institut fur Chemie, Sekr. PC14, Technische Universitat Berlin, Strasse des 17. Juni 135, D-10623 Berlin, Germany; (G.C.); (I.Z.); (P.H.)
| | - Smilja Todorovic
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Av. da República, 2780-157 Oeiras, Portugal; (C.M.S.); (L.Z.); (C.B.)
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10
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Patel AY, Jonnalagadda KS, Paradis N, Vaden TD, Wu C, Caputo GA. Effects of Ionic Liquids on Metalloproteins. Molecules 2021; 26:514. [PMID: 33478102 PMCID: PMC7835893 DOI: 10.3390/molecules26020514] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 01/04/2021] [Accepted: 01/08/2021] [Indexed: 01/28/2023] Open
Abstract
In the past decade, innovative protein therapies and bio-similar industries have grown rapidly. Additionally, ionic liquids (ILs) have been an area of great interest and rapid development in industrial processes over a similar timeline. Therefore, there is a pressing need to understand the structure and function of proteins in novel environments with ILs. Understanding the short-term and long-term stability of protein molecules in IL formulations will be key to using ILs for protein technologies. Similarly, ILs have been investigated as part of therapeutic delivery systems and implicated in numerous studies in which ILs impact the activity and/or stability of protein molecules. Notably, many of the proteins used in industrial applications are involved in redox chemistry, and thus often contain metal ions or metal-associated cofactors. In this review article, we focus on the current understanding of protein structure-function relationship in the presence of ILs, specifically focusing on the effect of ILs on metal containing proteins.
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Affiliation(s)
- Aashka Y. Patel
- Department of Chemistry and Biochemistry, Rowan University, Glassboro, NJ 08028, USA; (A.Y.P.); (N.P.); (T.D.V.); (C.W.)
| | | | - Nicholas Paradis
- Department of Chemistry and Biochemistry, Rowan University, Glassboro, NJ 08028, USA; (A.Y.P.); (N.P.); (T.D.V.); (C.W.)
| | - Timothy D. Vaden
- Department of Chemistry and Biochemistry, Rowan University, Glassboro, NJ 08028, USA; (A.Y.P.); (N.P.); (T.D.V.); (C.W.)
| | - Chun Wu
- Department of Chemistry and Biochemistry, Rowan University, Glassboro, NJ 08028, USA; (A.Y.P.); (N.P.); (T.D.V.); (C.W.)
- Department of Molecular and Cellular Biosciences, Rowan University, Glassboro, NJ 08028, USA
| | - Gregory A. Caputo
- Department of Chemistry and Biochemistry, Rowan University, Glassboro, NJ 08028, USA; (A.Y.P.); (N.P.); (T.D.V.); (C.W.)
- Department of Molecular and Cellular Biosciences, Rowan University, Glassboro, NJ 08028, USA
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11
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Wolford NJ, Radovic A, Neidig ML. C-Term magnetic circular dichroism (MCD) spectroscopy in paramagnetic transition metal and f-element organometallic chemistry. Dalton Trans 2021; 50:416-428. [PMID: 33315022 DOI: 10.1039/d0dt03730c] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Magnetic circular dichroism (MCD) spectroscopy is a powerful experiment used to probe the electronic structure and bonding in paramagnetic metal-based complexes. While C-term MCD spectroscopy has been utilized in many areas of chemistry, it has been underutilized in studying paramagnetic organometallic transition metal and f-element complexes. From the analysis of isolated organometallic complexes to the study of in situ generated species, MCD can provide information regarding ligand interactions, oxidation and spin state, and geometry and coordination environment of paramagnetic species. The pratical aspects of this technique, such as air-free sample preparation and cryogenic experimental temperatures, allow for the study of highly unstable species, something that is often difficult with other spectroscopic techniques. This perspective highlights MCD studies of both transition metal and f-element organometallic complexes, including in situ generated reactive intermediates, to demonstrate the utility of this technique in probing electronic structure, bonding and mechanism in paramagnetic organometallic chemistry.
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Affiliation(s)
- Nikki J Wolford
- Department of Chemistry, University of Rochester, Rochester, New York 14627, USA.
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12
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Rizzolo K, Weitz AC, Cohen SE, Drennan CL, Hendrich MP, Elliott SJ. A Stable Ferryl Porphyrin at the Active Site of Y463M BthA. J Am Chem Soc 2020; 142:11978-11982. [PMID: 32564595 DOI: 10.1021/jacs.0c04023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
BthA is a diheme enzyme that is a member of the bacterial cytochrome c peroxidase superfamily, capable of generating a highly unusual Fe(IV)Fe(IV)═O oxidation state, known to be responsible for long-range oxidative chemistry in the enzyme MauG. Here, we show that installing a canonical Met ligand in lieu of the Tyr found at the heme of MauG associated with electron transfer, results in a construct that yields an unusually stable Fe(IV)═O porphyrin at the peroxidatic heme. This state is spontaneously formed at ambient conditions using either molecular O2 or H2O2. The resulting data illustrate how a ferryl iron, with unforeseen stability, may be achieved in biology.
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Affiliation(s)
- Kimberly Rizzolo
- Boston University, Department of Chemistry, Boston, Massachusetts 02215, United States
| | - Andrew C Weitz
- Boston University, Department of Chemistry, Boston, Massachusetts 02215, United States.,Carnegie Mellon University, Department of Chemistry, Pittsburgh, Pennsylvania 15213, United States
| | - Steven E Cohen
- Massachusetts Institute of Technology, Department of Chemistry, Cambridge, Massachusetts 02139, United States
| | - Catherine L Drennan
- Massachusetts Institute of Technology, Department of Chemistry, Cambridge, Massachusetts 02139, United States.,Massachusetts Institute of Technology, Department of Biology, Cambridge, Massachusetts 02139, United States.,Howard Hughes Medical Institute, Cambridge, Massachusetts 02139, United States
| | - Michael P Hendrich
- Carnegie Mellon University, Department of Chemistry, Pittsburgh, Pennsylvania 15213, United States
| | - Sean J Elliott
- Boston University, Department of Chemistry, Boston, Massachusetts 02215, United States
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Liew FN, Brandys MA, Biswas S, Nguyen JN, Rahmawati M, Nevala M, Elmore BO, Hendrich MP, Kim HJ. Cytochrome c' β-Met Is a Variant in the P460 Superfamily Lacking the Heme-Lysyl Cross-Link: A Peroxidase Mimic Generating a Ferryl Intermediate. Biochemistry 2020; 59:704-716. [PMID: 31887031 DOI: 10.1021/acs.biochem.9b00810] [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
A defining characteristic of bacterial cytochromes (cyt's) in the P460 family is an unusual cross-link connecting the heme porphyrin to the side chain of a lysyl residue in the protein backbone. Here, via proteomics of the periplasmic fraction of the ammonia-oxidizing bacterium (AOB) Nitrosomonas europaea, we report the identification of a variant member of the P460 family that contains a methionyl residue in place of the cross-linking lysine. We formally designate this protein cytochrome "c'β-Met" to distinguish it from other members bearing different residues at this position (e.g., cyt c'β-Phe from the methane-oxidizing Methylococcus capsulatus Bath). As isolated, the monoheme cyt c'β-Met is high-spin (S = 5/2). Optical spectroscopy suggests that a cross-link is absent. Hydroxylamine, the substrate for the cross-linked cyt P460 from N. europaea, did not appreciably alter the optical spectrum of cyt c'β with up to 1000-fold excess at pH 7.5. Cyt c'β-Met did however bind 1 equiv of H2O2, and with a slight excess, Mössbauer spectroscopy indicated the formation of a semistable ferryl (FeIV═O) Compound II-like species. The corresponding electron paramagnetic resonance showed a very low intensity signal indicative of a radical at g = 2.0. Furthermore, cyt c'β-Met exhibited guaiacol-dependent peroxidase activity (kcat = 20.0 ± 1.2 s-1; KM = 2.6 ± 0.4 mM). Unlike cyt c'β-Met, cyt P460 showed evidence of heme inactivation in the presence of 2 equiv of H2O2 with no appreciable guaiacol-dependent peroxidase activity. Mutagenesis of the cross-linking lysyl residue to an alanine in cyt P460, however, reversed this lack of activity.
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Affiliation(s)
- Fong Ning Liew
- Division of Physical Sciences, Chemistry , University of Washington Bothell , Bothell , Washington 98012 , United States
| | - Marisa A Brandys
- Division of Physical Sciences, Chemistry , University of Washington Bothell , Bothell , Washington 98012 , United States
| | - Saborni Biswas
- Department of Chemistry , Carnegie Mellon University , Pittsburgh , Pennsylvania 15213 , United States
| | - Joline N Nguyen
- Division of Physical Sciences, Chemistry , University of Washington Bothell , Bothell , Washington 98012 , United States
| | - Mustika Rahmawati
- Division of Physical Sciences, Chemistry , University of Washington Bothell , Bothell , Washington 98012 , United States
| | - Michael Nevala
- Division of Physical Sciences, Chemistry , University of Washington Bothell , Bothell , Washington 98012 , United States.,Veolia Nuclear Solutions Federal Solutions , Richland , Washington 99354 , United States
| | - Bradley O Elmore
- Newport Laboratories , Worthington , Minnesota 56187 , United States
| | - Michael P Hendrich
- Department of Chemistry , Carnegie Mellon University , Pittsburgh , Pennsylvania 15213 , United States
| | - Hyung J Kim
- Division of Physical Sciences, Chemistry , University of Washington Bothell , Bothell , Washington 98012 , United States
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