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Thind S, Lima D, Booy E, Trinh D, McKenna SA, Kuss S. Cytochrome c oxidase deficiency detection in human fibroblasts using scanning electrochemical microscopy. Proc Natl Acad Sci U S A 2024; 121:e2310288120. [PMID: 38154062 PMCID: PMC10769844 DOI: 10.1073/pnas.2310288120] [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: 06/20/2023] [Accepted: 11/17/2023] [Indexed: 12/30/2023] Open
Abstract
Cytochrome c oxidase deficiency (COXD) is an inherited disorder characterized by the absence or mutation in the genes encoding for the cytochrome c oxidase protein (COX). COX deficiency results in severe muscle weakness, heart, liver, and kidney disorders, as well as brain damage in infants and adolescents, leading to death in many cases. With no cure for this disorder, finding an efficient, inexpensive, and early means of diagnosis is essential to minimize symptoms and long-term disabilities. Furthermore, muscle biopsy, the traditional detection method, is invasive, expensive, and time-consuming. This study demonstrates the applicability of scanning electrochemical microscopy to quantify COX activity in living human fibroblast cells. Taking advantage of the interaction between the redox mediator N, N, N', N'-tetramethyl-para-phenylene-diamine, and COX, the enzymatic activity was successfully quantified by monitoring current changes using a platinum microelectrode and determining the apparent heterogeneous rate constant k0 using numerical modeling. This study provides a foundation for developing a diagnostic method for detecting COXD in infants, which has the potential to increase treatment effectiveness and improve the quality of life of affected individuals.
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Affiliation(s)
- Shubhneet Thind
- Laboratory for Bioanalytics and Electrochemical Sensing, Department of Chemistry, University of Manitoba, Winnipeg, MBR3T 2N2, Canada
| | - Dhésmon Lima
- Laboratory for Bioanalytics and Electrochemical Sensing, Department of Chemistry, University of Manitoba, Winnipeg, MBR3T 2N2, Canada
| | - Evan Booy
- Department of Chemistry, University of Manitoba, Winnipeg, MBR3T 2N2, Canada
| | - Dao Trinh
- Laboratoire des Sciences de l’Ingénieur Pour l’Environnement, UMR CNRS 7356, Université de La Rochelle, Pôle Sciences et Technologie17042, La Rochelle, Cedex 1, France
| | - Sean A. McKenna
- Department of Chemistry, University of Manitoba, Winnipeg, MBR3T 2N2, Canada
| | - Sabine Kuss
- Laboratory for Bioanalytics and Electrochemical Sensing, Department of Chemistry, University of Manitoba, Winnipeg, MBR3T 2N2, Canada
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Lee CY, Chen KW, Chiang CL, Kao HY, Yu HC, Lee HC, Chen WL. Improved production of β-carotene in light-powered Escherichia coli by co-expression of Gloeobacter rhodopsin expression. Microb Cell Fact 2023; 22:207. [PMID: 37817206 PMCID: PMC10563301 DOI: 10.1186/s12934-023-02212-0] [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: 05/25/2023] [Accepted: 09/25/2023] [Indexed: 10/12/2023] Open
Abstract
BACKGROUND Providing sufficient and usable energy for the cell factory has long been a heated issue in biosynthesis as solar energy has never been rooted out from the strategy for improvement, and turning Escherichia coli (E. coli) into a phototrophic host has multiple captivating qualities for biosynthesis. In this study, β-carotene was a stable compound for production in E. coli with the expression of four enzymes (CrtE, CrtB, CrtI, CrtY) for production due to its light-harvesting feature as an antenna pigment and as an antioxidant and important precursor for human health. The expression of Gloeobacter rhodopsin (GR) in microbial organisms was proved to have potential for application. RESULTS The expression of fusion protein, GR-GFP, in E. coli showed visible GFP signal under fluorescent microscopy, and its in vivo proton pumping activity signal can be detected in induced photocurrent by electrodes on the chip under intervals of illumination. To assess the phototrophic synthesis ability of the host strain compared to wild-type and vector control strain in chemostat batch with illumination, the expression of red fluorescent protein (RFP) as a target protein showed its yield improvement in protein assay and also reflected its early dominance in RFP fluorescence signal during the incubation, whereas the synthesis of β-carotene also showed yield increase by 1.36-fold and 2.32-fold compared with its wildtype and vector control strain. To investigate the effect of GR-GFP on E. coli, the growth of the host showed early rise into the exponential phase compared to the vector control strain and glucose turnover rate was elevated in increased glucose intake rate and upregulation of ATP-related genes in glycolysis (PtsG, Pgk, Pyk). CONCLUSION We reported the first-time potential application of GR in the form of fusion protein GR-GFP. Expression of GR-GFP in E. coli improved the production of β-carotene and RFP. Our work provides a strain of E. coli harboring phototrophic metabolism, thus paving path to a more sustainable and scalable production of biosynthesis.
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Affiliation(s)
- Chao-Yu Lee
- Institute of Molecular Medicine and Bioengineering, Department of Biological Science & Technology, National Yang Ming Chiao Tung University, Hsinchu, 300093, Taiwan
| | - Kai-Wen Chen
- Institute of Molecular Medicine and Bioengineering, Department of Biological Science & Technology, National Yang Ming Chiao Tung University, Hsinchu, 300093, Taiwan
| | - Chih-Lu Chiang
- Department of Civil Engineering, National Yang Ming Chiao Tung University, Hsinchu, 300093, Taiwan
| | - Hsuan-Yu Kao
- Department of Mechanical Engineering, National Yang Ming Chiao Tung University, Hsinchu, 300093, Taiwan
- Department of Civil Engineering, National Yang Ming Chiao Tung University, Hsinchu, 300093, Taiwan
| | - Hao-Cheng Yu
- Institute of Molecular Medicine and Bioengineering, Department of Biological Science & Technology, National Yang Ming Chiao Tung University, Hsinchu, 300093, Taiwan
| | - Hsiao-Ching Lee
- Institute of Molecular Medicine and Bioengineering, Department of Biological Science & Technology, National Yang Ming Chiao Tung University, Hsinchu, 300093, Taiwan
| | - Wen-Liang Chen
- Institute of Molecular Medicine and Bioengineering, Department of Biological Science & Technology, National Yang Ming Chiao Tung University, Hsinchu, 300093, Taiwan.
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Arima H, Nakazono T, Wada T. Proton Relay Effects on Oxygen Reduction Reaction Catalyzed by Dinuclear Cobalt Polypyridyl Complexes with OH Groups on Bipyridine Ligands. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2022. [DOI: 10.1246/bcsj.20220104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Hiroaki Arima
- Department of Chemistry, College of Science, Rikkyo University, 3-34-1 Nishi-Ikebukuro, Toshima-ku, Tokyo 171-8501, Japan
| | - Takashi Nakazono
- Research Center for Artificial Photosynthesis (ReCAP), Osaka City University, 3-3-138 Sugimoto, Sumiyoshi-ku, Osaka 558-8585, Japan
| | - Tohru Wada
- Department of Chemistry, College of Science, Rikkyo University, 3-34-1 Nishi-Ikebukuro, Toshima-ku, Tokyo 171-8501, Japan
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Wang J, Horwitz MA, Dürr AB, Ibba F, Pupo G, Gao Y, Ricci P, Christensen KE, Pathak TP, Claridge TDW, Lloyd-Jones GC, Paton RS, Gouverneur V. Asymmetric Azidation under Hydrogen Bonding Phase-Transfer Catalysis: A Combined Experimental and Computational Study. J Am Chem Soc 2022; 144:4572-4584. [PMID: 35230845 PMCID: PMC8931729 DOI: 10.1021/jacs.1c13434] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
![]()
Asymmetric catalytic
azidation has increased in importance to access
enantioenriched nitrogen containing molecules, but methods that employ
inexpensive sodium azide remain scarce. This encouraged us to undertake
a detailed study on the application of hydrogen bonding phase-transfer
catalysis (HB-PTC) to enantioselective azidation with sodium azide.
So far, this phase-transfer manifold has been applied exclusively
to insoluble metal alkali fluorides for carbon–fluorine bond
formation. Herein, we disclose the asymmetric ring opening of meso aziridinium electrophiles derived from β-chloroamines
with sodium azide in the presence of a chiral bisurea catalyst. The
structure of novel hydrogen bonded azide complexes was analyzed computationally,
in the solid state by X-ray diffraction, and in solution phase by 1H and 14N/15N NMR spectroscopy. With N-isopropylated BINAM-derived bisurea, end-on binding of
azide in a tripodal fashion to all three NH bonds is energetically
favorable, an arrangement reminiscent of the corresponding dynamically
more rigid trifurcated hydrogen-bonded fluoride complex. Computational
analysis informs that the most stable transition state leading to
the major enantiomer displays attack from the hydrogen-bonded end
of the azide anion. All three H-bonds are retained in the transition
state; however, as seen in asymmetric HB-PTC fluorination, the H-bond
between the nucleophile and the monodentate urea lengthens most noticeably
along the reaction coordinate. Kinetic studies corroborate with the
turnover rate limiting event resulting in a chiral ion pair containing
an aziridinium cation and a catalyst-bound azide anion, along with
catalyst inhibition incurred by accumulation of NaCl. This study demonstrates
that HB-PTC can serve as an activation mode for inorganic salts other
than metal alkali fluorides for applications in asymmetric synthesis.
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Affiliation(s)
- Jimmy Wang
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, U.K
| | - Matthew A Horwitz
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, U.K
| | - Alexander B Dürr
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, U.K
| | - Francesco Ibba
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, U.K
| | - Gabriele Pupo
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, U.K
| | - Yuan Gao
- School of Chemistry, University of Edinburgh, Edinburgh EH9 3FJ, U.K
| | - Paolo Ricci
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, U.K
| | - Kirsten E Christensen
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, U.K
| | - Tejas P Pathak
- Novartis Institutes for Biomedical Research, 22 Windsor Street, Cambridge, Massachusetts 02139, United States
| | - Timothy D W Claridge
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, U.K
| | - Guy C Lloyd-Jones
- School of Chemistry, University of Edinburgh, Edinburgh EH9 3FJ, U.K
| | - Robert S Paton
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80528, United States
| | - Véronique Gouverneur
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, U.K
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Updates and Original Case Studies Focused on the NMR-Linked Metabolomics Analysis of Human Oral Fluids Part I: Emerging Platforms and Perspectives. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12031235] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
1H NMR-based metabolomics analysis of human saliva, other oral fluids, and/or tissue biopsies serves as a valuable technique for the exploration of metabolic processes, and when associated with ’state-of-the-art’ multivariate (MV) statistical analysis strategies, provides a powerful means of examining the identification of characteristic metabolite patterns, which may serve to differentiate between patients with oral health conditions (e.g., periodontitis, dental caries, and oral cancers) and age-matched heathy controls. This approach may also be employed to explore such discriminatory signatures in the salivary 1H NMR profiles of patients with systemic diseases, and to date, these have included diabetes, Sjörgen’s syndrome, cancers, neurological conditions such as Alzheimer’s disease, and viral infections. However, such investigations are complicated in view of quite a large number of serious inconsistencies between the different studies performed by independent research groups globally; these include differing protocols and routes for saliva sample collection (e.g., stimulated versus unstimulated samples), their timings (particularly the oral activity abstention period involved, which may range from one to 12 h or more), and methods for sample transport, storage, and preparation for NMR analysis, not to mention a very wide variety of demographic variables that may influence salivary metabolite concentrations, notably the age, gender, ethnic origin, salivary flow-rate, lifestyles, diets, and smoking status of participant donors, together with their exposure to any other possible convoluting environmental factors. In view of the explosive increase in reported salivary metabolomics investigations, in this update, we critically review a wide range of critical considerations for the successful performance of such experiments. These include the nature, composite sources, and biomolecular status of human saliva samples; the merits of these samples as media for the screening of disease biomarkers, notably their facile, unsupervised collection; and the different classes of such metabolomics investigations possible. Also encompassed is an account of the history of NMR-based salivary metabolomics; our recommended regimens for the collection, transport, and storage of saliva samples, along with their preparation for NMR analysis; frequently employed pulse sequences for the NMR analysis of these samples; the supreme resonance assignment benefits offered by homo- and heteronuclear two-dimensional NMR techniques; deliberations regarding salivary biomolecule quantification approaches employed for such studies, including the preprocessing and bucketing of multianalyte salivary NMR spectra, and the normalization, transformation, and scaling of datasets therefrom; salivary phenotype analysis, featuring the segregation of a range of different metabolites into ‘pools’ grouped according to their potential physiological sources; and lastly, future prospects afforded by the applications of LF benchtop NMR spectrometers for direct evaluations of the oral or systemic health status of patients at clinical ‘point-of-contact’ sites, e.g., dental surgeries. This commentary is then concluded with appropriate recommendations for the conduct of future salivary metabolomics studies. Also included are two original case studies featuring investigations of (1) the 1H NMR resonance line-widths of selected biomolecules and their possible dependence on biomacromolecular binding equilibria, and (2) the combined univariate (UV) and MV analysis of saliva specimens collected from a large group of healthy control participants in order to potentially delineate the possible origins of biomolecules therein, particularly host- versus oral microbiome-derived sources. In a follow-up publication, Part II of this series, we conduct censorious reviews of reported observations acquired from a diversity of salivary metabolomics investigations performed to evaluate both localized oral and non-oral diseases. Perplexing problems encountered with these again include those arising from sample collection and preparation protocols, along with 1H NMR spectral misassignments.
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Boursiac Y, Protto V, Rishmawi L, Maurel C. Experimental and conceptual approaches to root water transport. PLANT AND SOIL 2022; 478:349-370. [PMID: 36277078 PMCID: PMC9579117 DOI: 10.1007/s11104-022-05427-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 04/03/2022] [Indexed: 05/05/2023]
Abstract
BACKGROUND Root water transport, which critically contributes to the plant water status and thereby plant productivity, has been the object of extensive experimental and theoretical studies. However, root systems represent an intricate assembly of cells in complex architectures, including many tissues at distinct developmental stages. Our comprehension of where and how molecular actors integrate their function in order to provide the root with its hydraulic properties is therefore still limited. SCOPE Based on current literature and prospective discussions, this review addresses how root water transport can be experimentally measured, what is known about the underlying molecular actors, and how elementary water transport processes are scaled up in numerical/mathematical models. CONCLUSIONS The theoretical framework and experimental procedures on root water transport that are in use today have been established a few decades ago. However, recent years have seen the appearance of new techniques and models with enhanced resolution, down to a portion of root or to the tissue level. These advances pave the way for a better comprehension of the dynamics of water uptake by roots in the soil.
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Affiliation(s)
- Yann Boursiac
- IPSiM, Univ Montpellier, CNRS, INRAE, Institut Agro, 34060 Montpellier, France
| | - Virginia Protto
- IPSiM, Univ Montpellier, CNRS, INRAE, Institut Agro, 34060 Montpellier, France
| | - Louai Rishmawi
- IPSiM, Univ Montpellier, CNRS, INRAE, Institut Agro, 34060 Montpellier, France
| | - Christophe Maurel
- IPSiM, Univ Montpellier, CNRS, INRAE, Institut Agro, 34060 Montpellier, France
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Rahi D, Dzyuba B, Policar T, Malinovskyi O, Rodina M, Dzyuba V. Bioenergetic Pathways in the Sperm of an Under-Ice Spawning Fish, Burbot ( Lota lota): The Role of Mitochondrial Respiration in a Varying Thermal Environment. BIOLOGY 2021; 10:biology10080739. [PMID: 34439971 PMCID: PMC8389567 DOI: 10.3390/biology10080739] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 07/18/2021] [Accepted: 07/27/2021] [Indexed: 01/19/2023]
Abstract
Regarding the sperm of cold-water fish, the contributions of different bioenergetic pathways, including mitochondrial respiration, to energy production at the spawning temperature and its adaptation at the maximum critical temperature (CTmax) are unclear. The roles of glycolysis, fatty acid oxidation, oxidative phosphorylation (OXPHOS) at 4 °C, and OXPHOS at 15 °C for energy production in burbot (Lota lota) spermatozoa were studied by motility and the oxygen consumption rate (OCR) (with and without pathway inhibitors and the OXPHOS uncoupler). At both temperatures, the effects of the inhibitors and the uncoupler on the motility duration, curvilinear velocity, and track linearity were insignificant; in addition, the OCRs in activation and non-activation media differed insignificantly and were not enhanced after uncoupler treatment. After inhibitor treatment in both media, OXPHOS was insignificantly different at the 2, 30, and 60 s time points at 4 °C but was reduced significantly at the 30 and 60 s time points after treatment with sodium azide at 15 °C. In conclusion, for burbot sperm at both the spawning temperature and the CTmax, the energy synthesized via OXPHOS during motility was insufficient. Therefore, the majority of the energy required to sustain motility was derived from pre-accumulated energy produced and stored during the quiescent state of the spermatozoa.
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8
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Arima H, Wada M, Nakazono T, Wada T. Tuning Oxygen Reduction Catalysis of Dinuclear Cobalt Polypyridyl Complexes by the Bridging Structure. Inorg Chem 2021; 60:9402-9415. [PMID: 33988979 DOI: 10.1021/acs.inorgchem.1c00293] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The four-electron oxygen reduction reaction (4e--ORR) is the mainstay in chemical energy conversion. Elucidation of factors influencing the catalyst's reaction rate and selectivity is important in the development of more active catalysts of 4e--ORR. In this study, we investigated chemical and electrochemical 4e--ORR catalyzed by Co2(μ-O2) complexes bridged by xanthene (1) and anthracene (3) and by a Co2(OH)2 complex bridged by anthraquinone (2). In the chemical ORR using Fe(CpMe)2 as a reductant in acidic PhCN, we found that 1 showed the highest initial turnover frequency (TOFinit = 6.8 × 102 s-1) and selectivity for 4e--ORR (96%) in three complexes. The detailed kinetic analyses have revealed that the rate-determining steps (RDSs) in the catalytic cycles of 1-3 have the O2 addition to [CoII2(OH2)2]4+ as an intermediate in common. In the only case that complex 1 was used as a catalyst, kcat depended on proton concentration because the reaction rate of the O2 addition to [CoII2(OH2)2]4+ was so fast as compared to that of the concerted PCET process of 1. Through X-ray, Raman, and electrochemical analyses and stoichiometric reactions, we found the face-to-face structure of 1 characterized by a slightly flexible xanthene was advantageous in capturing O2 and stabilizing the Co2(μ-O2) structure, thus increasing both the reaction rate and selectivity for 4e--ORR.
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Affiliation(s)
- Hiroaki Arima
- Department of Chemistry, College of Science, Rikkyo University, 3-34-1, Nishi-Ikebukuro, Toshima, Tokyo 171-8501, Japan
| | - Misato Wada
- Department of Chemistry, College of Science, Rikkyo University, 3-34-1, Nishi-Ikebukuro, Toshima, Tokyo 171-8501, Japan
| | - Takashi Nakazono
- Department of Chemistry, College of Science, Rikkyo University, 3-34-1, Nishi-Ikebukuro, Toshima, Tokyo 171-8501, Japan
| | - Tohru Wada
- Department of Chemistry, College of Science, Rikkyo University, 3-34-1, Nishi-Ikebukuro, Toshima, Tokyo 171-8501, Japan
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9
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Kruse F, Nguyen AD, Dragelj J, Schlesinger R, Heberle J, Mroginski MA, Weidinger IM. Characterisation of the Cyanate Inhibited State of Cytochrome c Oxidase. Sci Rep 2020; 10:3863. [PMID: 32123230 PMCID: PMC7052191 DOI: 10.1038/s41598-020-60801-0] [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: 03/22/2019] [Accepted: 02/17/2020] [Indexed: 12/22/2022] Open
Abstract
Heme-copper oxygen reductases are terminal respiratory enzymes, catalyzing the reduction of dioxygen to water and the translocation of protons across the membrane. Oxygen consumption is inhibited by various substances. Here we tested the relatively unknown inhibition of cytochrome c oxidase (CcO) with isocyanate. In contrast to other more common inhibitors like cyanide, inhibition with cyanate was accompanied with the rise of a metal to ligand charge transfer (MLCT) band around 638 nm. Increasing the cyanate concentration furthermore caused selective reduction of heme a. The presence of the CT band allowed for the first time to directly monitor the nature of the ligand via surface-enhanced resonance Raman (SERR) spectroscopy. Analysis of isotope sensitive SERR spectra in comparison with Density Functional Theory (DFT) calculations identified not only the cyanate monomer as an inhibiting ligand but suggested also presence of an uretdion ligand formed upon dimerization of two cyanate ions. It is therefore proposed that under high cyanate concentrations the catalytic site of CcO promotes cyanate dimerization. The two excess electrons that are supplied from the uretdion ligand lead to the observed physiologically inverse electron transfer from heme a3 to heme a.
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Affiliation(s)
- Fabian Kruse
- Technische Universität Dresden, Department of Chemistry and Food Chemistry, 01069, Dresden, Germany
| | - Anh Duc Nguyen
- Technische Universität Berlin, Department of Chemistry, Strasse des 17. Juni 135, 10623, Berlin, Germany
| | - Jovan Dragelj
- Technische Universität Berlin, Department of Chemistry, Strasse des 17. Juni 135, 10623, Berlin, Germany
| | - Ramona Schlesinger
- Freie Universität Berlin, Department of Physics, Arnimallee 14, 14195, Berlin, Germany
| | - Joachim Heberle
- Freie Universität Berlin, Department of Physics, Arnimallee 14, 14195, Berlin, Germany
| | - Maria Andrea Mroginski
- Technische Universität Berlin, Department of Chemistry, Strasse des 17. Juni 135, 10623, Berlin, Germany
| | - Inez M Weidinger
- Technische Universität Dresden, Department of Chemistry and Food Chemistry, 01069, Dresden, Germany.
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Measuring the functionality of the mitochondrial pumping complexes with multi-wavelength spectroscopy. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2019; 1860:89-101. [DOI: 10.1016/j.bbabio.2018.11.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Revised: 10/04/2018] [Accepted: 11/07/2018] [Indexed: 12/24/2022]
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Richaud M, Galas S. Defining the viability of tardigrades with a molecular sensor related to death. PLoS One 2018; 13:e0206444. [PMID: 30365540 PMCID: PMC6203378 DOI: 10.1371/journal.pone.0206444] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 10/13/2018] [Indexed: 11/19/2022] Open
Abstract
The design of experimental protocols that use animal models to assess the impact of a stress on a population or to determine the life span expectancy impact can be time-consuming due to the need for direct observations of dead and living animals. These experiments are usually based on the detectable activity of animals such as food intake or mobility and can sometimes produce either under- or overestimated results. The tardigrade Hypsibius exemplaris is an emerging model for the evolutionary biology of the tardigrade phylum because of its convenient laboratory breeding and the recent introduction of new molecular tools. In this report, we describe the use of a new fluorescent dye that can specifically stain dead tardigrades. Furthermore, we also monitored the absence of a toxic side effect of the death-linked fluorescent dye on tardigrade populations. Finally, we conclude that tardigrade experiments that require survival counting of the Hypsibius exemplaris species can be greatly improved by using this technique in order to limit underestimation of alive animals.
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Affiliation(s)
- Myriam Richaud
- IBMM, University of Montpellier, CNRS, ENSCM, Montpellier, France
| | - Simon Galas
- IBMM, University of Montpellier, CNRS, ENSCM, Montpellier, France
- * E-mail:
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Shimada A, Hatano K, Tadehara H, Yano N, Shinzawa-Itoh K, Yamashita E, Muramoto K, Tsukihara T, Yoshikawa S. X-ray structural analyses of azide-bound cytochrome c oxidases reveal that the H-pathway is critically important for the proton-pumping activity. J Biol Chem 2018; 293:14868-14879. [PMID: 30077971 PMCID: PMC6153300 DOI: 10.1074/jbc.ra118.003123] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2018] [Revised: 07/31/2018] [Indexed: 01/07/2023] Open
Abstract
Cytochrome c oxidase (CcO) is the terminal oxidase of cellular respiration, reducing O2 to water and pumping protons. X-ray structural features have suggested that CcO pumps protons via a mechanism involving electrostatic repulsions between pumping protons in the hydrogen-bond network of a proton-conducting pathway (the H-pathway) and net positive charges created upon oxidation of an iron site, heme a (Fe a2+), for reduction of O2 at another iron site, heme a3 (Fe a32+). The protons for pumping are transferred to the hydrogen-bond network from the N-side via the water channel of the H-pathway. Back-leakage of protons to the N-side is thought to be blocked by closure of the water channel. To experimentally test this, we examined X-ray structures of the azide-bound, oxidized bovine CcO and found that an azide derivative (N3--Fe a33+, CuB2+-N3-) induces a translational movement of the heme a3 plane. This was accompanied by opening of the water channel, revealing that Fe a3 and the H-pathway are tightly coupled. The channel opening in the oxidized state is likely to induce back-leakage of pumping protons, which lowers the proton level in the hydrogen-bond network during enzymatic turnover. The proton level decrease weakens the electron affinity of Fe a , if Fe a electrostatically interacts with protons in the hydrogen-bond network. The previously reported azide-induced redox-potential decrease in Fe a supports existence of the electrostatic interaction. In summary, our results indicate that the H-pathway is critical for CcO's proton-pumping function.
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Affiliation(s)
| | | | | | | | | | - Eiki Yamashita
- the Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, and
| | - Kazumasa Muramoto
- Department of Life Science, Graduate School of Life Science, University of Hyogo, 3-2-1 Koto, Kamigori, Akoh, Hyogo 678-1297, , To whom correspondence may be addressed:
Dept. of Life Science, Graduate School of Life Science, University of Hyogo, 3-2-1 Koto, Kamigori, Akoh, Hyogo 678-1297, Japan. E-mail:
| | - Tomitake Tsukihara
- From the Picobiology Institute and ,the Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, and ,the Japan Science and Technology Agency, CREST, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan, To whom correspondence may be addressed:
Picobiology Institute, Graduate School of Life Science, University of Hyogo, 3-2-1 Koto, Kamigori, Akoh, Hyogo 678-1297, Japan. E-mail:
| | - Shinya Yoshikawa
- From the Picobiology Institute and , To whom correspondence may be addressed:
Picobiology Institute, Graduate School of Life Science, University of Hyogo, 3-2-1 Koto, Kamigori, Akoh, Hyogo 678-1297, Japan. Tel.:
81-791-58-0189; E-mail:
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Rocha MC, Springett R. Spectral components of detergent-solubilized bovine cytochrome oxidase. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2018; 1859:555-566. [PMID: 29704499 DOI: 10.1016/j.bbabio.2018.04.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Revised: 03/21/2018] [Accepted: 04/23/2018] [Indexed: 11/27/2022]
Abstract
Cytochrome oxidase is the terminal oxidase of the mitochondrial electron transport chain and pumps 4 protons per oxygen reduced to water. Spectral shifts in the α-band of heme a have been observed in multiple studies and these shifts have the potential to shed light on the proton pumping intermediates. Previously we found that heme a had two spectral components in the α-band during redox titrations in living RAW 264.7 mouse macrophage cells, the classical 605 nm form and a blue-shifted 602 nm form. To confirm these spectral changes were not an artifact due to the complex milieu of the living cell, redox titrations were performed in the isolated detergent-solubilized bovine enzyme from both the Soret- and α-band using precise multiwavelength spectroscopy. This data verified the presence of the 602 nm form in the α-band, revealed a similar shift of heme a in the Soret-band and ruled out the reversal of calcium binding as the origin of the blue shift. The 602 nm form was found to be stabilized at high pH or by binding of azide, which is known to blue shift the α-band of heme a. Azide also stabilized the 602 nm form in the living cells. It is concluded there is a form of cytochrome oxidase in which heme a undergoes a blue shift to a 602 nm form and that redox titrations can be successfully performed in living cells where the oxidase operates in its authentic environment and in the presence of a proton motive force.
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Affiliation(s)
- Mariana C Rocha
- Cardiovascular Division, King's College London, British Heart Foundation Centre of Excellence, 125 Coldharbour Lane, London SE5 9NU, United Kingdom
| | - Roger Springett
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Wellcome Trust/MRC Building, Hills Road, Cambridge CB2 0XY, United Kingdom.
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Unraveling Synaptic GCaMP Signals: Differential Excitability and Clearance Mechanisms Underlying Distinct Ca 2+ Dynamics in Tonic and Phasic Excitatory, and Aminergic Modulatory Motor Terminals in Drosophila. eNeuro 2018; 5:eN-NWR-0362-17. [PMID: 29464198 PMCID: PMC5818553 DOI: 10.1523/eneuro.0362-17.2018] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Revised: 01/27/2018] [Accepted: 02/02/2018] [Indexed: 11/21/2022] Open
Abstract
GCaMP is an optogenetic Ca2+ sensor widely used for monitoring neuronal activities but the precise physiological implications of GCaMP signals remain to be further delineated among functionally distinct synapses. The Drosophila neuromuscular junction (NMJ), a powerful genetic system for studying synaptic function and plasticity, consists of tonic and phasic glutamatergic and modulatory aminergic motor terminals of distinct properties. We report a first simultaneous imaging and electric recording study to directly contrast the frequency characteristics of GCaMP signals of the three synapses for physiological implications. Different GCaMP variants were applied in genetic and pharmacological perturbation experiments to examine the Ca2+ influx and clearance processes underlying the GCaMP signal. Distinct mutational and drug effects on GCaMP signals indicate differential roles of Na+ and K+ channels, encoded by genes including paralytic (para), Shaker (Sh), Shab, and ether-a-go-go (eag), in excitability control of different motor terminals. Moreover, the Ca2+ handling properties reflected by the characteristic frequency dependence of the synaptic GCaMP signals were determined to a large extent by differential capacity of mitochondria-powered Ca2+ clearance mechanisms. Simultaneous focal recordings of synaptic activities further revealed that GCaMPs were ineffective in tracking the rapid dynamics of Ca2+ influx that triggers transmitter release, especially during low-frequency activities, but more adequately reflected cytosolic residual Ca2+ accumulation, a major factor governing activity-dependent synaptic plasticity. These results highlight the vast range of GCaMP response patterns in functionally distinct synaptic types and provide relevant information for establishing basic guidelines for the physiological interpretations of presynaptic GCaMP signals from in situ imaging studies.
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15
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Hikita M, Yamamoto A, Shinzawa-Itoh K, Ogura T, Yoshikawa S. Stepwise Binding of Two Azide Ions to the O 2-reduction Site of Bovine Heart Cytochrome cOxidase Shown by Resonance Raman Analyses. CHEM LETT 2015. [DOI: 10.1246/cl.150384] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Masahide Hikita
- Picobiology Institute, Graduate School of Life Science, University of Hyogo
| | - Akima Yamamoto
- Picobiology Institute, Graduate School of Life Science, University of Hyogo
| | | | - Takashi Ogura
- Picobiology Institute, Graduate School of Life Science, University of Hyogo
- Department of Life Science and Picobiology Institute, Graduate School of Life Science, University of Hyogo
| | - Shinya Yoshikawa
- Picobiology Institute, Graduate School of Life Science, University of Hyogo
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16
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Luz AL, Rooney JP, Kubik LL, Gonzalez CP, Song DH, Meyer JN. Mitochondrial Morphology and Fundamental Parameters of the Mitochondrial Respiratory Chain Are Altered in Caenorhabditis elegans Strains Deficient in Mitochondrial Dynamics and Homeostasis Processes. PLoS One 2015; 10:e0130940. [PMID: 26106885 PMCID: PMC4480853 DOI: 10.1371/journal.pone.0130940] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Accepted: 05/27/2015] [Indexed: 12/28/2022] Open
Abstract
Mitochondrial dysfunction has been linked to myriad human diseases and toxicant exposures, highlighting the need for assays capable of rapidly assessing mitochondrial health in vivo. Here, using the Seahorse XFe24 Analyzer and the pharmacological inhibitors dicyclohexylcarbodiimide and oligomycin (ATP-synthase inhibitors), carbonyl cyanide 4-(trifluoromethoxy) phenylhydrazone (mitochondrial uncoupler) and sodium azide (cytochrome c oxidase inhibitor), we measured the fundamental parameters of mitochondrial respiratory chain function: basal oxygen consumption, ATP-linked respiration, maximal respiratory capacity, spare respiratory capacity and proton leak in the model organism Caenhorhabditis elegans. Since mutations in mitochondrial homeostasis genes cause mitochondrial dysfunction and have been linked to human disease, we measured mitochondrial respiratory function in mitochondrial fission (drp-1)-, fusion (fzo-1)-, mitophagy (pdr-1, pink-1)-, and electron transport chain complex III (isp-1)-deficient C. elegans. All showed altered function, but the nature of the alterations varied between the tested strains. We report increased basal oxygen consumption in drp-1; reduced maximal respiration in drp-1, fzo-1, and isp-1; reduced spare respiratory capacity in drp-1 and fzo-1; reduced proton leak in fzo-1 and isp-1; and increased proton leak in pink-1 nematodes. As mitochondrial morphology can play a role in mitochondrial energetics, we also quantified the mitochondrial aspect ratio for each mutant strain using a novel method, and for the first time report increased aspect ratios in pdr-1- and pink-1-deficient nematodes.
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Affiliation(s)
- Anthony L. Luz
- Nicholas School of the Environment, Duke University, Durham, North Carolina, United States of America
| | - John P. Rooney
- Nicholas School of the Environment, Duke University, Durham, North Carolina, United States of America
| | - Laura L. Kubik
- Nicholas School of the Environment, Duke University, Durham, North Carolina, United States of America
| | - Claudia P. Gonzalez
- Nicholas School of the Environment, Duke University, Durham, North Carolina, United States of America
| | - Dong Hoon Song
- Simulation Group, Samsung SDI, Suwon-si, Gyeonggi-do, Republic of Korea
| | - Joel N. Meyer
- Nicholas School of the Environment, Duke University, Durham, North Carolina, United States of America
- * E-mail:
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17
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Gabison L, Colloc’h N, Prangé T. Azide inhibition of urate oxidase. Acta Crystallogr F Struct Biol Commun 2014; 70:896-902. [PMID: 25005084 PMCID: PMC4089527 DOI: 10.1107/s2053230x14011753] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Accepted: 05/21/2014] [Indexed: 02/04/2023] Open
Abstract
The inhibition of urate oxidase (UOX) by azide was investigated by X-ray diffraction techniques and compared with cyanide inhibition. Two well characterized sites for reagents are present in the enzyme: the dioxygen site and the substrate-binding site. To examine the selectivity of these sites towards azide inhibition, several crystallization conditions were developed. UOX was co-crystallized with azide (N3) in the presence or absence of either uric acid (UA, the natural substrate) or 8-azaxanthine (8AZA, a competitive inhibitor). In a second set of experiments, previously grown orthorhombic crystals of the UOX-UA or UOX-8AZA complexes were soaked in sodium azide solutions. In a third set of experiments, orthorhombic crystals of UOX with the exchangeable ligand 8-nitroxanthine (8NXN) were soaked in a solution containing uric acid and azide simultaneously (competitive soaking). In all assays, the soaking periods were either short (a few hours) or long (one or two months). These different experimental conditions showed that one or other of the sites, or the two sites together, could be inhibited. This also demonstrated that azide not only competes with dioxygen as cyanide does but also competes with the substrate for its enzymatic site. A model in agreement with experimental data would be an azide in equilibrium between two sites, kinetically in favour of the dioxygen site and thermodynamically in favour of the substrate-binding site.
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Affiliation(s)
- Laure Gabison
- Faculty of Pharmacy, UMR 8015 CNRS Laboratoire de Cristallographie et RMN Biologiques, 4 Avenue de l’Observatoire, 75006 Paris, France
| | - Nathalie Colloc’h
- ISTCT, UMR 6301–CNRS–Université de Caen–Normandie Université–CEA, Centre Cyceron, Boulevard Becquerel, 14074 Caen CEDEX, France
| | - Thierry Prangé
- Faculty of Pharmacy, UMR 8015 CNRS Laboratoire de Cristallographie et RMN Biologiques, 4 Avenue de l’Observatoire, 75006 Paris, France
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18
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Ishii H, Shirai T, Makino C, Nishikata T. Mitochondrial inhibitor sodium azide inhibits the reorganization of mitochondria-rich cytoplasm and the establishment of the anteroposterior axis in ascidian embryo. Dev Growth Differ 2014; 56:175-88. [DOI: 10.1111/dgd.12117] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2013] [Revised: 12/04/2013] [Accepted: 12/04/2013] [Indexed: 11/30/2022]
Affiliation(s)
- Hirokazu Ishii
- Frontiers of Innovative Research in Science and Technology (FIRST); Konan University; Kobe Hyogo 650-0047 Japan
| | - Takuma Shirai
- Frontiers of Innovative Research in Science and Technology (FIRST); Konan University; Kobe Hyogo 650-0047 Japan
| | - Chisato Makino
- Frontiers of Innovative Research in Science and Technology (FIRST); Konan University; Kobe Hyogo 650-0047 Japan
| | - Takahito Nishikata
- Frontiers of Innovative Research in Science and Technology (FIRST); Konan University; Kobe Hyogo 650-0047 Japan
- Frontier Institute for Biomolecular Engineering Research (FIBER); Konan University; Kobe Hyogo 650-0047 Japan
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19
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20
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Pramanik D, Ghosh C, Mukherjee S, Dey SG. Interaction of amyloid β peptides with redox active heme cofactor: Relevance to Alzheimer's disease. Coord Chem Rev 2013. [DOI: 10.1016/j.ccr.2012.02.025] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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21
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Pramanik D, Ghosh C, Dey SG. Heme–Cu Bound Aβ Peptides: Spectroscopic Characterization, Reactivity, and Relevance to Alzheimer’s Disease. J Am Chem Soc 2011; 133:15545-52. [DOI: 10.1021/ja204628b] [Citation(s) in RCA: 102] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Debajyoti Pramanik
- Department of Inorganic Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata, India 700032
| | - Chandradeep Ghosh
- Department of Inorganic Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata, India 700032
| | - Somdatta Ghosh Dey
- Department of Inorganic Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata, India 700032
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22
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Ghosh Dey S, Dey A. NO and O2 reactivities of synthetic functional models of nitric oxide reductase and cytochrome c oxidase. Dalton Trans 2011; 40:12633-47. [DOI: 10.1039/c1dt10451a] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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23
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Yang Y, Dey A, Decréau RA. Spectroscopic Characterization and Competitive Inhibition Studies of Azide Binding to a Functional NOR Model. Eur J Inorg Chem 2010. [DOI: 10.1002/ejic.201000566] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Ying Yang
- Department of Chemistry, University of Toronto, Toronto, ON M5S 3H6, Canada, Fax: +1‐416‐978‐8775
| | - Abhishek Dey
- Department of Chemistry, Stanford University, Stanford, CA 94305‐5080, USA
| | - Richard A. Decréau
- Department of Chemistry, Stanford University, Stanford, CA 94305‐5080, USA
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24
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Parul D, Palmer G, Fabian M. Ligand trapping by cytochrome c oxidase: implications for gating at the catalytic center. J Biol Chem 2009; 285:4536-43. [PMID: 20037139 DOI: 10.1074/jbc.m109.078618] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Cytochrome c oxidase is a member of the heme-copper family of oxygen reductases in which electron transfer is linked to the pumping of protons across the membrane. Neither the redox center(s) associated with proton pumping nor the pumping mechanism presumably common to all heme-copper oxidases has been established. A possible conformational coupling between the catalytic center (Fe(a3)(3+)-Cu(B)(2+)) and a protein site has been identified earlier from ligand binding studies, whereas a structural change initiated by azide binding to the protein has been proposed to facilitate the access of cyanide to the catalytic center of the oxidized bovine enzyme. Here we show that cytochrome oxidase pretreated with a low concentration of azide exhibits a significant increase in the apparent rate of cyanide binding relative to that of free enzyme. However, this increase in rate does not reflect a conformational change enhancing the rapid formation of a Fe(a3)(3+)-CN-Cu(B)(2+) complex. Instead the cyanide-induced transition of a preformed Fe(a3)(3+)-N(3)-Cu(B)(2+) to the ternary complex of Fe(a3)(3+)-N(3) Cu(B)(2+)-CN is the most likely reason for the observed acceleration. Significantly, the slow rate of azide release from the ternary complex indicates that cyanide ligated to Cu(B) blocks a channel between the catalytic site and the solvent. The results suggest that there is a pathway that originates at Cu(B) and that, during catalysis, ligands present at this copper center control access to the iron of heme a(3) from the bulk medium.
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Affiliation(s)
- Dzmitry Parul
- Department of Biochemistry and Cell Biology, Rice University, Houston, Texas 77005, USA
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25
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Collman JP, Ghosh S, Dey A, Decréau RA, Yang Y. Catalytic reduction of O2 by cytochrome C using a synthetic model of cytochrome C oxidase. J Am Chem Soc 2009; 131:5034-5. [PMID: 19317484 DOI: 10.1021/ja9001579] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cytochrome c oxidase (CcO) catalyzes the four-electron reduction of oxygen to water, the one-electron reductant Cytochrome c (Cytc) being the source of electrons. Recently we reported a functional model of CcO that electrochemically catalyzes the four-electron reduction of O(2) to H(2)O (Collman et al. Science 2007, 315, 1565). The current paper shows that the same functional CcO model catalyzes the four-electron reduction of O(2) using the actual biological reductant Cytc in a homogeneous solution. Both single and steady-state turnover kinetics studies indicate that O(2) binding is rate-determining and that O-O bond cleavage and electron transfer from reduced Cytc to the oxidized model complex are relatively fast.
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Affiliation(s)
- James P Collman
- Department of Chemistry, Stanford University, Stanford, California 94305, USA.
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26
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Collman JP, Dey A, Decréau RA, Yang Y. Model studies of azide binding to functional analogues of CcO. Inorg Chem 2008; 47:2916-8. [PMID: 18361486 DOI: 10.1021/ic702294n] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
N3- binding to a functional model of CcO is investigated in its Fe3+, Fe3+Cu+, and Fe3+Cu2+ forms. A combination of EPR and FTIR indicates that N3- binds in a bridging mode in the bimetallic sites and signature N3- bands are identified for several forms of N3- binding to the site. The presence of the distal metal increases the binding affinity of N3-. This bridging enables antiferromagnetic interaction between the two metal centers in the Fe3+Cu2+ state, which results in an EPR-silent ground state.
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Affiliation(s)
- James P Collman
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA.
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27
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Bowler MW, Montgomery MG, Leslie AGW, Walker JE. How azide inhibits ATP hydrolysis by the F-ATPases. Proc Natl Acad Sci U S A 2006; 103:8646-9. [PMID: 16728506 PMCID: PMC1469772 DOI: 10.1073/pnas.0602915103] [Citation(s) in RCA: 181] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In the structure of bovine F1-ATPase determined at 1.95-A resolution with crystals grown in the presence of ADP, 5'-adenylyl-imidodiphosphate, and azide, the azide anion interacts with the beta-phosphate of ADP and with residues in the ADP-binding catalytic subunit, betaDP. It occupies a position between the catalytically essential amino acids, beta-Lys-162 in the P loop and the "arginine finger" residue, alpha-Arg-373, similar to the site occupied by the gamma-phosphate in the ATP-binding subunit, betaTP. Its presence in the betaDP-subunit tightens the binding of the side chains to the nucleotide, enhancing its affinity and thereby stabilizing the state with bound ADP. This mechanism of inhibition appears to be common to many other ATPases, including ABC transporters, SecA, and DNA topoisomerase IIalpha. It also explains the stimulatory effect of azide on ATP-sensitive potassium channels by enhancing the binding of ADP.
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Affiliation(s)
- Matthew W. Bowler
- *Dunn Human Nutrition Unit, Medical Research Council, Hills Road, Cambridge CB2 2XY, United Kingdom; and
| | - Martin G. Montgomery
- *Dunn Human Nutrition Unit, Medical Research Council, Hills Road, Cambridge CB2 2XY, United Kingdom; and
| | - Andrew G. W. Leslie
- Laboratory of Molecular Biology, Medical Research Council, Hills Road, Cambridge CB2 2QH, United Kingdom
| | - John E. Walker
- *Dunn Human Nutrition Unit, Medical Research Council, Hills Road, Cambridge CB2 2XY, United Kingdom; and
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28
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Liu W, Rogge CE, Bambai B, Palmer G, Tsai AL, Kulmacz RJ. Characterization of the heme environment in Arabidopsis thaliana fatty acid alpha-dioxygenase-1. J Biol Chem 2004; 279:29805-15. [PMID: 15100225 PMCID: PMC2862001 DOI: 10.1074/jbc.m401779200] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Plant alpha-dioxygenases (PADOX) are hemoproteins in the myeloperoxidase family. We have used a variety of spectroscopic, mutagenic, and kinetic approaches to characterize the heme environment in Arabidopsis thaliana PADOX-1. Recombinant PADOX-1 purified to homogeneity contained 1 mol of heme bound tightly but noncovalently per protein monomer. Electronic absorbance, electron paramagnetic resonance, and magnetic circular dichroism spectra showed a high spin ferric heme that could be reduced to the ferrous state by dithionite. Cyanide bound relatively weakly in the ferric PADOX-1 heme vicinity (K(d) approximately 10 mm) but did not shift the heme to the low spin state. Cyanide was a very strong inhibitor of the fatty acid oxygenase activity (K(i) approximately 5 microm) and increased the K(m) value for oxygen but not that for fatty acid. Spectroscopic analyses indicated that carbon monoxide, azide, imidazole, and a variety of substituted imidazoles did not bind appreciably in the ferric PADOX-1 heme vicinity. Substitution of His-163 and His-389 with cysteine, glutamine, tyrosine, or methionine resulted in variable degrees of perturbation of the heme absorbance spectrum and oxygenase activity, consistent with His-389 serving as the proximal heme ligand and indicating that the heme has a functional role in catalysis. Overall, A. thaliana PADOX-1 resembles a b-type cytochrome, although with much more restricted access to the distal face of the heme than seen in most other myeloperoxidase family members, explaining the previously puzzling lack of peroxidase activity in the plant protein. PADOX-1 is unusual in that it has a high affinity, inhibitory cyanide-binding site distinct from the distal heme face and the fatty acid site.
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Affiliation(s)
- Wen Liu
- Department of Internal Medicine, University of Texas Health Science Center, Houston, Texas 77030
| | - Corina E. Rogge
- Department of Internal Medicine, University of Texas Health Science Center, Houston, Texas 77030
| | - Bijan Bambai
- Department of Internal Medicine, University of Texas Health Science Center, Houston, Texas 77030
| | - Graham Palmer
- Department of Biochemistry and Cell Biology, Rice University, Houston, Texas 77005
| | - Ah-Lim Tsai
- Department of Internal Medicine, University of Texas Health Science Center, Houston, Texas 77030
| | - Richard J. Kulmacz
- Department of Internal Medicine, University of Texas Health Science Center, Houston, Texas 77030
- To whom correspondence should be addressed: Dept. of Internal Medicine, University of Texas Health Science Center, MSB 5.284, 6431 Fannin St., Houston, TX 77030. Tel.: 713-500-6772; Fax: 713-500-6810;
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29
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Fabian M, Skultety L, Jancura D, Palmer G. Implications of ligand binding studies for the catalytic mechanism of cytochrome c oxidase. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2004; 1655:298-305. [PMID: 15100045 DOI: 10.1016/j.bbabio.2003.07.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2003] [Accepted: 07/17/2003] [Indexed: 11/28/2022]
Abstract
The reaction of oxidized bovine heart cytochrome c oxidase (CcO) with one equivalent of hydrogen peroxide results in the formation of two spectrally distinct species. The yield of these two forms is controlled by the ionization of a group with a pK(a) of 6.6. At basic pH, where this group is deprotonated, an intermediate called P dominates (P, because it was initially believed to be a peroxy compound). At acidic pH where the group is protonated, a different species, called F (ferryl intermediate) is obtained. We previously proposed that the only difference between these two species is the presence of one proton in the catalytic center of F that is absent in P. It is now suggested that the catalytic center of this F form has the same redox and protonation state as a second ferryl intermediate produced at basic pH by two equivalents of hydrogen peroxide; the role of the second equivalent of H(2)O(2) is that of a proton donor in the conversion of P to F. Two chloride-binding sites have been detected in oxidized CcO. One site is located at the binuclear center; the second site was identified from the sensitivity of g=3 signal of cytochrome a to chloride in the EPR spectra of oxidized CcO. Turnover of CcO releases chloride from the catalytic center into the medium probably by one of the hydrophobic channels, proposed for oxygen access, with an orientation parallel to the membrane plane. Chloride in the binuclear center is most likely not involved in CcO catalysis. The influence of the second chloride site upon several reactions of CcO has been assessed. No correlation was found between chloride binding to the second site and the reactions that were examined.
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Affiliation(s)
- Marian Fabian
- Department of Biochemistry and Cell Biology, Rice University MS 140, P.O. Box 1892, 6100 Main, Houston TX 77005, USA.
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Fabian M, Jancura D, Palmer G. Two Sites of Interaction of Anions with Cytochrome a in Oxidized Bovine Cytochrome c Oxidase. J Biol Chem 2004; 279:16170-7. [PMID: 14766756 DOI: 10.1074/jbc.m311834200] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
An interaction between cytochrome a in oxidized cytochrome c oxidase (CcO) and anions has been characterized by EPR spectroscopy. Those anions that affect the EPR g = 3 signal of cytochrome a can be divided into two groups. One group consists of halides (Cl-, Br-, and I-) and induces an upfield shift of the g = 3 signal. Nitrogen-containing anions (CN-, NO2-, N3-, NO3-) are in the second group and shift the g = 3 signal downfield. The shifts in the EPR spectrum of CcO are unrelated to ligand binding to the binuclear center. The binding properties of one representative from each group, azide and chloride, were characterized in detail. The dependence of the shift on chloride concentration is consistent with a single binding site in the isolated oxidized enzyme with a Kd of approximately 3 mm. In mitochondria, the apparent Kd was found to be about four times larger than that of the isolated enzyme. The data indicate it is the chloride anion that is bound to CcO, and there is a hydrophilic size-selective access channel to this site from the cytosolic side of the mitochondrial membrane. An observed competition between azide and chloride is interpreted by azide binding to three sites: two that are apparent in the x-ray structure plus the chloride-binding site. It is suggested that either Mg2+ or Arg-438/Arg-439 is the chloride-binding site, and a mechanism for the ligand-induced shift of the g = 3 signal is proposed.
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Affiliation(s)
- Marian Fabian
- Department of Biochemistry and Cell Biology, Rice University, Houston, Texas 77005, USA.
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31
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Bento I, Teixeira VH, Baptista AM, Soares CM, Matias PM, Carrondo MA. Redox-Bohr and other cooperativity effects in the nine-heme cytochrome C from Desulfovibrio desulfuricans ATCC 27774: crystallographic and modeling studies. J Biol Chem 2003; 278:36455-69. [PMID: 12750363 DOI: 10.1074/jbc.m301745200] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The nine-heme cytochrome c is a monomeric multiheme cytochrome found in Desulfovibrio desulfuricans ATCC 27774. The polypeptide chain comprises 296 residues and wraps around nine hemes of type c. It is believed to take part in the periplasmic assembly of proteins involved in the mechanism of hydrogen cycling, receiving electrons from the tetraheme cytochrome c3. With the purpose of understanding the molecular basis of electron transfer processes in this cytochrome, we have determined the crystal structures of its oxidized and reduced forms at pH 7.5 and performed theoretical calculations of the binding equilibrium of protons and electrons in these structures. This integrated study allowed us to observe that the reduction process induced relevant conformational changes in several residues, as well as protonation changes in some protonatable residues. In particular, the surroundings of hemes I and IV constitute two areas of special interest. In addition, we were able to ascertain the groups involved in the redox-Bohr effect present in this cytochrome and the conformational changes that may underlie the redox-cooperativity effects on different hemes. Furthermore, the thermodynamic simulations provide evidence that the N- and C-terminal domains function in an independent manner, with the hemes belonging to the N-terminal domain showing, in general, a lower redox potential than those found in the C-terminal domain. In this way, electrons captured by the N-terminal domain could easily flow to the C-terminal domain, allowing the former to capture more electrons. A notable exception is heme IX, which has low redox potential and could serve as the exit path for electrons toward other proteins in the electron transfer pathway.
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Affiliation(s)
- Isabel Bento
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, 2781-901 Oeiras, Portugal
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Affiliation(s)
- Shinya Yoshikawa
- Department of Life Science, Himeji Institute of Technology, and CREST, Japan Science and Technology Corporation (JST), Kamigohri Akoh, Hyogo 678-1297, Japan
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Wasser IM, de Vries S, Moënne-Loccoz P, Schröder I, Karlin KD. Nitric oxide in biological denitrification: Fe/Cu metalloenzyme and metal complex NO(x) redox chemistry. Chem Rev 2002; 102:1201-34. [PMID: 11942794 DOI: 10.1021/cr0006627] [Citation(s) in RCA: 355] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ian M Wasser
- Department of Chemistry, The Johns Hopkins University, Charles and 34th Streets, Baltimore, MD 21218, USA
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