1
|
Belay A, Joy EJM, Lark RM, Ander EL, Young SD, Bailey EH, Broadley MR, Gashu D. Micronutrients and socio-demographic factors were major predictors of anaemia among the Ethiopian population. Br J Nutr 2023; 130:2123-2135. [PMID: 37424305 PMCID: PMC10657751 DOI: 10.1017/s0007114523001472] [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: 11/05/2022] [Revised: 06/27/2023] [Accepted: 07/01/2023] [Indexed: 07/11/2023]
Abstract
Anaemia is characterised by low hemoglobin (Hb) concentration. Despite being a public health concern in Ethiopia, the role of micronutrients and non-nutritional factors as a determinant of Hb concentrations has been inadequately explored. This study focused on the assessment of serum micronutrient and Hb concentrations and a range of non-nutritional factors, to evaluate their associations with the risk of anaemia among the Ethiopian population (n 2046). It also explored the mediation effect of Zn on the relation between se and Hb. Bivariate and multivariate regression analyses were performed to identify the relationship between serum micronutrients concentration, inflammation biomarkers, nutritional status, presence of parasitic infection and socio-demographic factors with Hb concentration (n 2046). Sobel-Goodman test was applied to investigate the mediation of Zn on relations between serum se and Hb. In total, 18·6 % of participants were anaemic, 5·8 % had iron deficiency (ID), 2·6 % had ID anaemia and 0·6 % had tissue ID. Younger age, household head illiteracy and low serum concentrations of ferritin, Co, Cu and folate were associated with anaemia. Serum se had an indirect effect that was mediated by Zn, with a significant effect of se on Zn (P < 0·001) and Zn on Hb (P < 0·001). The findings of this study suggest the need for designing a multi-sectorial intervention to address anaemia based on demographic group.
Collapse
Affiliation(s)
- Adamu Belay
- Center for Food Science and Nutrition, Addis Ababa University, Addis Ababa, Ethiopia
- Food Science and Nutrition Research Directorate, Ethiopian Public Health Institute, Gulele Sub City, Addis Ababa, Ethiopia
| | - Edward J. M. Joy
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, UK
| | - R. Murray Lark
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, UK
| | - E. Louise Ander
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, UK
| | - Scott D. Young
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, UK
| | - Elizabeth H. Bailey
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, UK
| | - Martin R. Broadley
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, UK
- Rothamsted Research, West Common, Harpenden, Hertfordshire, UK
| | - Dawd Gashu
- Center for Food Science and Nutrition, Addis Ababa University, Addis Ababa, Ethiopia
| |
Collapse
|
2
|
Rajbongshi J, Das DK, Mazumdar S. Spectroscopic and electrochemical studies of the pH-Induced transition in the CuA centre from Thermus thermophilus. Inorganica Chim Acta 2022. [DOI: 10.1016/j.ica.2021.120749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
3
|
Brotto AC, Annavajhala MK, Chandran K. Metatranscriptomic Investigation of Adaptation in NO and N 2O Production From a Lab-Scale Nitrification Process Upon Repeated Exposure to Anoxic-Aerobic Cycling. Front Microbiol 2018; 9:3012. [PMID: 30574136 PMCID: PMC6291752 DOI: 10.3389/fmicb.2018.03012] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 11/21/2018] [Indexed: 11/13/2022] Open
Abstract
The molecular mechanisms of microbial adaptation to repeated anoxic-aerobic cycling were investigated by integrating whole community gene expression (metatranscriptomics) and physiological responses, including the production of nitric (NO) and nitrous (N2O) oxides. Anoxic-aerobic cycling was imposed for 17 days in a lab-scale full-nitrification mixed culture system. Prior to cycling, NO and N2O levels were sustained at 0.097 ± 0.006 and 0.054 ± 0.019 ppmv, respectively. Once the anoxic-aerobic cycling was initiated, peak emissions were highest on the first day (9.8 and 1.3 ppmv, respectively). By the end of day 17, NO production returned to pre-cycling levels (a peak of 0.12 ± 0.007 ppmv), while N2O production reached a new baseline (a peak of 0.32 ± 0.05 ppmv), one order of magnitude higher than steady-state conditions. Concurrently, post-cycling transcription of norBQ and nosZ returned to pre-cycling levels after an initial 5.7- and 9.5-fold increase, while nirK remained significantly expressed (1.6-fold) for the duration of and after cycling conditions. The imbalance in nirK and nosZ mRNA abundance coupled with continuous conversion of NO to N2O might explain the elevated post-cycling baseline for N2O. Metatranscriptomic investigation notably indicated possible NO production by NOB under anoxic-aerobic cycling through a significant increase in nirK expression. Opposing effects on AOB (down-regulation) and NOB (up-regulation) CO2 fixation were observed, suggesting that nitrifying bacteria are differently impacted by anoxic-aerobic cycling. Genes encoding the terminal oxidase of the electron transport chain (ccoNP, coxBC) were the most significantly transcribed, highlighting a hitherto unexplored pathway to manage high electron fluxes resulting from increased ammonia oxidation rates, and leading to overall, increased NO and N2O production. In sum, this study identified underlying metabolic processes and mechanisms contributing to NO and N2O production through a systems-level interrogation, which revealed the differential ability of specific microbial groups to adapt to sustained operational conditions in engineered biological nitrogen removal processes.
Collapse
Affiliation(s)
| | | | - Kartik Chandran
- Department of Earth and Environmental Engineering, Columbia University, New York, NY, United States
| |
Collapse
|
4
|
Kroneck PMH. Walking the seven lines: binuclear copper A in cytochrome c oxidase and nitrous oxide reductase. J Biol Inorg Chem 2017; 23:27-39. [PMID: 29218634 DOI: 10.1007/s00775-017-1510-z] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Accepted: 10/20/2017] [Indexed: 01/19/2023]
Abstract
The enzymes nitrous oxide reductase (N2OR) and cytochrome c oxidase (COX) are constituents of important biological processes. N2OR is the terminal reductase in a respiratory chain converting N2O to N2 in denitrifying bacteria; COX is the terminal oxidase of the aerobic respiratory chain of certain bacteria and eukaryotic organisms transforming O2 to H2O accompanied by proton pumping. Different spectroscopies including magnetic resonance techniques, were applied to show that N2OR has a mixed-valent Cys-bridged [Cu1.5+(CyS)2Cu1.5+] copper site, and that such a binuclear center, called CuA, does also exist in COX. A sequence motif shared between the CuA center of N2OR and the subunit II of COX raises the issue of a putative evolutionary relationship of the two enzymes. The suggestion of a binuclear CuA in COX, with one unpaired electron delocalized between two equivalent Cu nuclei, was difficult to accept originally, even though regarded as a clever solution to many experimental observations. This minireview in honor of Helmut Sigel traces several of the critical steps forward in understanding the nature of CuA in N2OR and COX, and discusses its unique electronic features to some extent including the contributions made by the development of methodology and the discovery of a novel multi-copper enzyme. Left: X-band (9.130 GHz) and C-band (4.530 GHz, 1st harmonic display of experimental spectrum) EPR spectra of bovine heart cytochrome c oxidase, recorded at 20K. Right: Ribbon presentation of the CuA domain in cytochrome c oxidase and nitrous oxide reductase.
Collapse
Affiliation(s)
- Peter M H Kroneck
- Department of Biology, University of Konstanz, Universitätsstrasse 10, 78457, Konstanz, Germany.
| |
Collapse
|
5
|
In situ characterization of cofacial Co(IV) centers in Co 4O 4 cubane: Modeling the high-valent active site in oxygen-evolving catalysts. Proc Natl Acad Sci U S A 2017; 114:3855-3860. [PMID: 28348217 DOI: 10.1073/pnas.1701816114] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
The Co4O4 cubane is a representative structural model of oxidic cobalt oxygen-evolving catalysts (Co-OECs). The Co-OECs are active when residing at two oxidation levels above an all-Co(III) resting state. This doubly oxidized Co(IV)2 state may be captured in a Co(III)2(IV)2 cubane. We demonstrate that the Co(III)2(IV)2 cubane may be electrochemically generated and the electronic properties of this unique high-valent state may be probed by in situ spectroscopy. Intervalence charge-transfer (IVCT) bands in the near-IR are observed for the Co(III)2(IV)2 cubane, and spectroscopic analysis together with electrochemical kinetics measurements reveal a larger reorganization energy and a smaller electron transfer rate constant for the doubly versus singly oxidized cubane. Spectroelectrochemical X-ray absorption data further reveal systematic spectral changes with successive oxidations from the cubane resting state. Electronic structure calculations correlated to experimental data suggest that this state is best represented as a localized, antiferromagnetically coupled Co(IV)2 dimer. The exchange coupling in the cofacial Co(IV)2 site allows for parallels to be drawn between the electronic structure of the Co4O4 cubane model system and the high-valent active site of the Co-OEC, with specific emphasis on the manifestation of a doubly oxidized Co(IV)2 center on O-O bond formation.
Collapse
|
6
|
|
7
|
Liu J, Chakraborty S, Hosseinzadeh P, Yu Y, Tian S, Petrik I, Bhagi A, Lu Y. Metalloproteins containing cytochrome, iron-sulfur, or copper redox centers. Chem Rev 2014; 114:4366-469. [PMID: 24758379 PMCID: PMC4002152 DOI: 10.1021/cr400479b] [Citation(s) in RCA: 560] [Impact Index Per Article: 56.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Indexed: 02/07/2023]
Affiliation(s)
- Jing Liu
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Saumen Chakraborty
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Parisa Hosseinzadeh
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Yang Yu
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Shiliang Tian
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Igor Petrik
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Ambika Bhagi
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Yi Lu
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| |
Collapse
|
8
|
Radzi Noor M, Soulimane T. Bioenergetics at extreme temperature: Thermus thermophilus ba(3)- and caa(3)-type cytochrome c oxidases. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2012; 1817:638-49. [PMID: 22385645 DOI: 10.1016/j.bbabio.2011.08.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2011] [Revised: 08/11/2011] [Accepted: 08/12/2011] [Indexed: 10/28/2022]
Abstract
Seven years into the completion of the genome sequencing projects of the thermophilic bacterium Thermus thermophilus strains HB8 and HB27, many questions remain on its bioenergetic mechanisms. A key fact that is occasionally overlooked is that oxygen has a very limited solubility in water at high temperatures. The HB8 strain is a facultative anaerobe whereas its relative HB27 is strictly aerobic. This has been attributed to the absence of nitrate respiration genes from the HB27 genome that are carried on a mobilizable but highly-unstable plasmid. In T. thermophilus, the nitrate respiration complements the primary aerobic respiration. It is widely known that many organisms encode multiple biochemically-redundant components of the respiratory complexes. In this minireview, the presence of the two cytochrome c oxidases (CcO) in T. thermophilus, the ba(3)- and caa(3)-types, is outlined along with functional considerations. We argue for the distinct evolutionary histories of these two CcO including their respective genetic and molecular organizations, with the caa(3)-oxidase subunits having been initially 'fused'. Coupled with sequence analysis, the ba(3)-oxidase crystal structure has provided evolutionary and functional information; for example, its subunit I is more closely related to archaeal sequences than bacterial and the substrate-enzyme interaction is hydrophobic as the elevated growth temperature weakens the electrostatic interactions common in mesophiles. Discussion on the role of cofactors in intra- and intermolecular electron transfer and proton pumping mechanism is also included.
Collapse
Affiliation(s)
- Mohamed Radzi Noor
- Department of Chemical and Environmental Sciences, University of Limerick, Limerick, Ireland
| | | |
Collapse
|
9
|
Papa S, Martino PL, Capitanio G, Gaballo A, De Rasmo D, Signorile A, Petruzzella V. The oxidative phosphorylation system in mammalian mitochondria. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2012; 942:3-37. [PMID: 22399416 DOI: 10.1007/978-94-007-2869-1_1] [Citation(s) in RCA: 169] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The chapter provides a review of the state of art of the oxidative phosphorylation system in mammalian mitochondria. The sections of the paper deal with: (i) the respiratory chain as a whole: redox centers of the chain and protonic coupling in oxidative phosphorylation (ii) atomic structure and functional mechanism of protonmotive complexes I, III, IV and V of the oxidative phosphorylation system (iii) biogenesis of oxidative phosphorylation complexes: mitochondrial import of nuclear encoded subunits, assembly of oxidative phosphorylation complexes, transcriptional factors controlling biogenesis of the complexes. This advanced knowledge of the structure, functional mechanism and biogenesis of the oxidative phosphorylation system provides a background to understand the pathological impact of genetic and acquired dysfunctions of mitochondrial oxidative phosphorylation.
Collapse
Affiliation(s)
- Sergio Papa
- Department of Basic Medical Sciences, University of Bari, Bari, Italy.
| | | | | | | | | | | | | |
Collapse
|
10
|
Shah F, Kazi TG, Afridi HI, Kazi N, Baig JA, Shah AQ, Khan S, Kolachi NF, Wadhwa SK. Evaluation of status of trace and toxic metals in biological samples (scalp hair, blood, and urine) of normal and anemic children of two age groups. Biol Trace Elem Res 2011; 141:131-49. [PMID: 20526751 DOI: 10.1007/s12011-010-8736-8] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/15/2010] [Accepted: 05/14/2010] [Indexed: 10/19/2022]
Abstract
Anemia affects a substantial portion of the world's population, provoking severe health problems as well as important economic losses to the region in which this condition is found. This study was designed to compare the levels of essential trace and toxic elements in scalp hair, blood, and urine samples of anemic children (n = 132) with age range 1-5 and 6-10 years of both genders. For a comparative study, 134 non-anemic age- and sex-matched children as control subjects, residing in the same city, were selected. The metals in the biological samples were measured by flame atomic absorption spectrophotometry/electrothermal atomic absorption spectrometry prior to microwave-assisted acid digestion. The proposed method was validated using certified reference samples of hair, blood, and urine. The results indicated significantly lower levels of iron, copper, and zinc in the biological samples as compared to the control children of both genders (p = 0.01-0.008). The mean values of lead and cadmium were significantly high in all three biological samples of anemic children as compared to non-anemic children of both age groups (p = 0.005-0.001). The ratios of essential metal to toxic metals in the biological samples of anemic children of both age groups were significantly lower than that of controls. Deficiency of essential trace metals and high level of toxic metals may play a role in the development of anemia in the subjects under study.
Collapse
Affiliation(s)
- Faheem Shah
- National Center of Excellence in Analytical Chemistry, University of Sindh, Jamshoro, 76080, Pakistan.
| | | | | | | | | | | | | | | | | |
Collapse
|
11
|
Bleackley MR, Macgillivray RTA. Transition metal homeostasis: from yeast to human disease. Biometals 2011; 24:785-809. [PMID: 21479832 DOI: 10.1007/s10534-011-9451-4] [Citation(s) in RCA: 162] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2011] [Accepted: 03/28/2011] [Indexed: 12/16/2022]
Abstract
Transition metal ions are essential nutrients to all forms of life. Iron, copper, zinc, manganese, cobalt and nickel all have unique chemical and physical properties that make them attractive molecules for use in biological systems. Many of these same properties that allow these metals to provide essential biochemical activities and structural motifs to a multitude of proteins including enzymes and other cellular constituents also lead to a potential for cytotoxicity. Organisms have been required to evolve a number of systems for the efficient uptake, intracellular transport, protein loading and storage of metal ions to ensure that the needs of the cells can be met while minimizing the associated toxic effects. Disruptions in the cellular systems for handling transition metals are observed as a number of diseases ranging from hemochromatosis and anemias to neurodegenerative disorders including Alzheimer's and Parkinson's disease. The yeast Saccharomyces cerevisiae has proved useful as a model organism for the investigation of these processes and many of the genes and biological systems that function in yeast metal homeostasis are conserved throughout eukaryotes to humans. This review focuses on the biological roles of iron, copper, zinc, manganese, nickel and cobalt, the homeostatic mechanisms that function in S. cerevisiae and the human diseases in which these metals have been implicated.
Collapse
Affiliation(s)
- Mark R Bleackley
- Department of Biochemistry and Molecular Biology, Centre for Blood Research, Life Sciences Institute, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC, V6T1Z3, Canada
| | | |
Collapse
|
12
|
|
13
|
Rajbongshi J, Das DK, Mazumdar S. Direct electrochemistry of dinuclear CuA fragment from cytochrome c oxidase of Thermus thermophilus at surfactant modified glassy carbon electrode. Electrochim Acta 2010. [DOI: 10.1016/j.electacta.2010.02.045] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
|
14
|
Savelieff MG, Lu Y. CuA centers and their biosynthetic models in azurin. J Biol Inorg Chem 2010; 15:461-83. [DOI: 10.1007/s00775-010-0625-2] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2009] [Accepted: 01/20/2010] [Indexed: 11/28/2022]
|
15
|
Smirnov AY, Mourokh LG, Nori F. Kinetics of proton pumping in cytochrome c oxidase. J Chem Phys 2009; 130:235105. [DOI: 10.1063/1.3155213] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
16
|
Xie X, Gorelsky SI, Sarangi R, Garner DK, Hwang HJ, Hodgson KO, Hedman B, Lu Y, Solomon EI. Perturbations to the geometric and electronic structure of the CuA site: factors that influence delocalization and their contributions to electron transfer. J Am Chem Soc 2008; 130:5194-205. [PMID: 18348522 DOI: 10.1021/ja7102668] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Using a combination of electronic spectroscopies and DFT calculations, the effect of pH perturbation on the geometric and electronic structure of the CuA site has been defined. Descriptions are developed for high pH (pH = 7) and low pH (pH = 4) forms of CuA azurin and its H120A mutant which address the discrepancies concerning the extent of delocalization indicated by multifrequency EPR and ENDOR data (J. Am. Chem. Soc. 2005, 127, 7274; Biophys. J. 2002, 82, 2758). Our resonance Raman and MCD spectra demonstrate that the low pH and H120A mutant forms are essentially identical and are the perturbed forms of the completely delocalized high pH CuA site. However, in going from high pH to low pH, a seven-line hyperfine coupling pattern associated with complete delocalization of the electron (S = 1/2) over two Cu coppers (I(Cu) = 3/2) changes into a four-line pattern reflecting apparent localization. DFT calculations show that the unpaired electron is delocalized in the low pH form and reveal that its four-line hyperfine pattern results from the large EPR spectral effects of approximately 1% 4s orbital contribution of one Cu to the ground-state spin wave function upon protonative loss of its His ligand. The contribution of the Cu-Cu interaction to electron delocalization in this low symmetry protein site is evaluated, and the possible functional significance of the pH-dependent transition in regulating proton-coupled electron transfer in cytochrome c oxidase is discussed.
Collapse
Affiliation(s)
- Xiangjin Xie
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
| | | | | | | | | | | | | | | | | |
Collapse
|
17
|
Zumft WG, Kroneck PMH. Respiratory transformation of nitrous oxide (N2O) to dinitrogen by Bacteria and Archaea. Adv Microb Physiol 2006; 52:107-227. [PMID: 17027372 DOI: 10.1016/s0065-2911(06)52003-x] [Citation(s) in RCA: 203] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
N2O is a potent greenhouse gas and stratospheric reactant that has been steadily on the rise since the beginning of industrialization. It is an obligatory inorganic metabolite of denitrifying bacteria, and some production of N2O is also found in nitrifying and methanotrophic bacteria. We focus this review on the respiratory aspect of N2O transformation catalysed by the multicopper enzyme nitrous oxide reductase (N2OR) that provides the bacterial cell with an electron sink for anaerobic growth. Two types of Cu centres discovered in N2OR were both novel structures among the Cu proteins: the mixed-valent dinuclear Cu(A) species at the electron entry site of the enzyme, and the tetranuclear Cu(Z) centre as the first catalytically active Cu-sulfur complex known. Several accessory proteins function as Cu chaperone and ABC transporter systems for the biogenesis of the catalytic centre. We describe here the paradigm of Z-type N2OR, whose characteristics have been studied in most detail in the genera Pseudomonas and Paracoccus. Sequenced bacterial genomes now provide an invaluable additional source of information. New strains harbouring nos genes and capability of N2O utilization are being uncovered. This reveals previously unknown relationships and allows pattern recognition and predictions. The core nos genes, nosZDFYL, share a common phylogeny. Most principal taxonomic lineages follow the same biochemical and genetic pattern and share the Z-type enzyme. A modified N2OR is found in Wolinella succinogenes, and circumstantial evidence also indicates for certain Archaea another type of N2OR. The current picture supports the view of evolution of N2O respiration prior to the separation of the domains Bacteria and Archaea. Lateral nos gene transfer from an epsilon-proteobacterium as donor is suggested for Magnetospirillum magnetotacticum and Dechloromonas aromatica. In a few cases, nos gene clusters are plasmid borne. Inorganic N2O metabolism is associated with a diversity of physiological traits and biochemically challenging metabolic modes or habitats, including halorespiration, diazotrophy, symbiosis, pathogenicity, psychrophily, thermophily, extreme halophily and the marine habitat down to the greatest depth. Components for N2O respiration cover topologically the periplasm and the inner and outer membranes. The Sec and Tat translocons share the task of exporting Nos components to their functional sites. Electron donation to N2OR follows pathways with modifications depending on the host organism. A short chronology of the field is also presented.
Collapse
Affiliation(s)
- Walter G Zumft
- Institute of Applied Biosciences, Division of Molecular Microbiology, University of Karlsruhe, D-76128 Karlsruhe, Germany
| | | |
Collapse
|
18
|
Khalimonchuk O, Rödel G. Biogenesis of cytochrome c oxidase. Mitochondrion 2005; 5:363-88. [PMID: 16199211 DOI: 10.1016/j.mito.2005.08.002] [Citation(s) in RCA: 102] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2005] [Accepted: 08/10/2005] [Indexed: 11/20/2022]
Abstract
Cytochrome c oxidase (COX), the terminal enzyme of electron transport chains in some prokaryotes and in mitochondria, has been characterized in detail over many years. Recently, a number of new data on structural and functional aspects as well as on COX biogenesis emerged. COX biogenesis includes a variety of steps starting from translation to the formation of the mature complex. Each step involves a set of specific factors that assist translation of subunits, their translocation across membranes, insertion of essential cofactors, assembly and final maturation of the enzyme. In this review, we focus on the organization and biogenesis of COX.
Collapse
Affiliation(s)
- Oleh Khalimonchuk
- Institut für Genetik, Technische Universität Dresden, 01062 Dresden, Germany
| | | |
Collapse
|
19
|
Paumann M, Bernroitner M, Lubura B, Peer M, Jakopitsch C, Furtmüller PG, Peschek GA, Obinger C. Kinetics of electron transfer between plastocyanin and the soluble CuAdomain of cyanobacterial cytochromecoxidase. FEMS Microbiol Lett 2004; 239:301-7. [PMID: 15476980 DOI: 10.1016/j.femsle.2004.09.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2004] [Revised: 08/30/2004] [Accepted: 09/02/2004] [Indexed: 11/24/2022] Open
Abstract
It has been shown that efficient functioning of photosynthesis and respiration in the cyanobacterium Synechocystis PCC 6803 requires the presence of either cytochrome c6 or plastocyanin. In order to check whether the blue copper protein plastocyanin can act as electron donor to cytochrome c oxidase, we investigated the intermolecular electron transfer kinetics between plastocyanin and the soluble CuA domain (i.e. the donor binding and electron entry site) of subunit II of the aa3-type cytochrome c oxidase from Synechocystis. Both copper proteins were expressed heterologously in Escherichia coli. The forward and the reverse electron transfer reactions were studied yielding apparent bimolecular rate constants of (5.1+/-0.2) x 10(4) M(-1) s(-1) and (8.5+/-0.4) x 10(5) M(-1) s(-1), respectively (20 mM phosphate buffer, pH 7). This corresponds to an apparent equilibrium constant of 0.06 in the physiological direction (reduction of CuA), which is similar to Keq values calculated for the reaction between c-type cytochromes and the soluble fragments of other CuA domains. The potential physiological role of plastocyanin in cyanobacterial respiration is discussed.
Collapse
Affiliation(s)
- Martina Paumann
- Department of Physical Chemistry, Molecular Bioenergetics Group, University of Vienna, Althanstrasse 14, A-1090 Vienna, Austria
| | | | | | | | | | | | | | | |
Collapse
|
20
|
Paumann M, Lubura B, Regelsberger G, Feichtinger M, Köllensberger G, Jakopitsch C, Furtmüller PG, Peschek GA, Obinger C. Soluble CuA Domain of Cyanobacterial Cytochrome c Oxidase. J Biol Chem 2004; 279:10293-303. [PMID: 14672950 DOI: 10.1074/jbc.m308903200] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The genomes of several cyanobacteria show the existence of gene clusters encoding subunits I, II, and III of aa(3)-type cytochrome c oxidase. The enzyme occurs on both plasma and thylakoid membranes of these oxygenic phototrophic prokaryotes. Here we report the expression and purification of a truncated subunit II copper A (Cu(A)) domain (i.e. the electron entry and donor binding site) of cytochrome c oxidase from the cyanobacterium Synechocystis PCC 6803 in high yield. The water-soluble purple redox-active bimetallic center displays a relatively low standard reduction potential of 216 mV. Its absorption spectrum at pH 7 is similar to that of other soluble fragments from aa(3)-type oxidases, but the insensitivity of both absorbance and circular dichroism spectra to pH suggests that it is less exposed to the aqueous milieu compared with other Cu(A) domains. Oxidation of horse heart cytochrome c by the bimetallic center follows monophasic kinetics. At pH 7 and low ionic strength the bimolecular rate constant is (2.1 +/- 0.3) x 10(4) m-1 s(-1), and the rates decrease upon the increase of ionic strength. Sequence alignment and modeling of cyanobacterial Cu(A) domains show several peculiarities such as: (i) a large insertion located between the second transmembrane region and the putative hydrophobic cytochrome c docking site, (ii) the lack of acidic residues shown to be important in the interaction between cytochrome c and Paracoccus Cu(A) domain, and (iii) an extended C terminus similar to Escherichia coli ubiquinol oxidase.
Collapse
Affiliation(s)
- Martina Paumann
- Institute of Physical Chemistry, Molecular Bioenergetics Group, University of Vienna, Austria
| | | | | | | | | | | | | | | | | |
Collapse
|
21
|
Olsson MH, Ryde U. Geometry, reduction potential, and reorganization energy of the binuclear Cu(A) site, studied by density functional theory. J Am Chem Soc 2001; 123:7866-76. [PMID: 11493060 DOI: 10.1021/ja010315u] [Citation(s) in RCA: 87] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The dimeric Cu(A) site found in cytochrome c oxidase and nitrous oxide reductase has been studied with the density functional B3LYP method. We have optimized the structure of the realistic (Im)(S(CH(3))(2))Cu(SCH(3))(2)Cu(Im)(CH(3)CONHCH(3)) model in the fully reduced, mixed-valence, and fully oxidized states. The optimized structures are very similar to crystal structures of the protein, which shows that the protein does not strain the site significantly. Instead, inorganic model complexes of the protein site are strained by the macrocyclic connections between the ligand models. For the mixed-valence (Cu(I)+Cu(II)) state, two distinct equilibrium structures were found, one with a short Cu-Cu distance, 248 pm, similar to the protein structure, and one with a longer distance, 310 pm, similar to what is found in inorganic models. In the first state, the unpaired electron is delocalized over both copper ions, whereas in the latter, it is more localized to one of the ions. The two states are nearly degenerate. The potential energy surfaces for the Cu-Cu, Cu-S(Met), and Cu-O interactions are extremely flat. In fact, all three distances can be varied between 230 and 310 pm at an expense in energy of less than 8 kJ/mol, which explains the large variation observed in crystal structures for these interactions. Inclusion of solvation effects does not change this significantly. Therefore, we can conclude that a variation in these distances can change the reduction potential of the Cu(A) site by at most 100 mV. The model complex has a reorganization energy of 43 kJ/mol, 20 kJ/mol lower than for a monomeric blue-copper site. This lowering is caused by the delocalization of the unpaired electron in the mixed-valence state.
Collapse
Affiliation(s)
- M H Olsson
- Contribution from the Department of Theoretical Chemistry, Lund University, Chemical Centre, P.O. Box 124, S-221 00 Lund, Sweden
| | | |
Collapse
|
22
|
Pereira MM, Santana M, Teixeira M. A novel scenario for the evolution of haem-copper oxygen reductases. BIOCHIMICA ET BIOPHYSICA ACTA 2001; 1505:185-208. [PMID: 11334784 DOI: 10.1016/s0005-2728(01)00169-4] [Citation(s) in RCA: 339] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
The increasing sequence information on oxygen reductases of the haem-copper superfamily, together with the available three-dimensional structures, allows a clear identification of their common, functionally important features. Taking into consideration both the overall amino acid sequences of the core subunits and key residues involved in proton transfer, a novel hypothesis for the molecular evolution of these enzymes is proposed. Three main families of oxygen reductases are identified on the basis of common features of the core subunits, constituting three lines of evolution: (i) type A (mitochondrial-like oxidases), (ii) type B (ba3-like oxidases) and (iii) type C (cbb3-type oxidases). The first group can be further divided into two subfamilies, according to the helix VI residues at the hydrophobic end of one of the proton pathways (the so-called D-channel): (i) type A1, comprising the enzymes with a glutamate residue in the motif -XGHPEV-, and (ii) type A2, enzymes having instead a tyrosine and a serine in the alternative motif -YSHPXV-. This second subfamily of oxidases is shown to be ancestor to the one containing the glutamate residue, which in the Bacteria domain is only present in oxidases from Gram-positive or purple bacteria. It is further proposed that the Archaea domain acquired terminal oxidases by gene transfer from the Gram-positive bacteria, implying that these enzymes were not present in the last common ancestor before the divergence between Archaea and Bacteria. In fact, most oxidases from archaea have a higher amino acid sequence identity and similarity with those from bacteria, mainly from the Gram-positive group, than with oxidases from other archaea. Finally, a possible relation between the dihaemic subunit (FixP) of the cbb3 oxidases and subunit II of caa3 oxidases is discussed. As the families of haem-copper oxidases can also be identified by their subunit II, a parallel evolution of subunits I and II is suggested.
Collapse
Affiliation(s)
- M M Pereira
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Rua da Quinta Grande 6, 2780-156, Oeiras, Portugal.
| | | | | |
Collapse
|
23
|
Sigfridsson E, Olsson MH, Ryde U. Inner-Sphere Reorganization Energy of Iron−Sulfur Clusters Studied with Theoretical Methods. Inorg Chem 2001; 40:2509-19. [PMID: 11350228 DOI: 10.1021/ic000752u] [Citation(s) in RCA: 91] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Models of several types of iron-sulfur clusters (e.g., Fe(4)S(4)(SCH(3))(4)(2-/3-/4-)) have been studied with the density functional B3LYP method and medium-sized basis sets. In a vacuum, the inner-sphere reorganization energies are 40, 76, 40, 62, 43, and 42 kJ/mol for the rubredoxin, [2Fe-2S] ferredoxin, Rieske, [4Fe-4S] ferredoxin, high-potential iron protein, and desulfoferrodoxin models, respectively. The first two types of clusters were also studied in the protein, where the reorganization energy was approximately halved. This change is caused by the numerous NH.S(Cys) hydrogen bonds to the negatively charged iron-sulfur cluster, giving rise to a polar local environment. The reorganization energy of the iron-sulfur clusters is low because the iron ions retain the same geometry and coordination number in both oxidation states. Cysteine ligands give approximately the same reorganization energy as imidazole, but they have the advantage of stabilizing a lower coordination number and giving more covalent bonds and therefore more effective electron-transfer paths.
Collapse
Affiliation(s)
- E Sigfridsson
- Department of Theoretical Chemistry, Lund University, Chemical Centre, P.O. Box 124, S-221 00 Lund, Sweden
| | | | | |
Collapse
|
24
|
|
25
|
Abstract
The CuA center is a dinuclear Cu2S2(Cys) electron transfer center found in cytochrome c oxidase and nitrous oxide reductase. In a previous investigation of the equatorial histidine ligands' effect on the reduction potential, electron transfer and spectroscopic properties of the CuA center, His120 in the engineered CuA azurin was mutated to Asn, Asp, and Ala. The identical absorption and EPR spectra of these mutants indicate that a common ligand is bound to the copper center. To identify this replacement ligand, the His120Gly CuA azurin mutant was constructed and purified. Absorption and X-band EPR spectra show that His120Gly is similar to the other His120X (X = Asn, Asp, Ala) mutant proteins. Titrations with chloride, imidazole, and azide suggest that the replacement ligand is not exchangeable with exogenous ligands. The possibility of an internal amino acid acting as the replacement ligand for His120 in the His120X mutant proteins was investigated by analyzing the CuA azurin crystal structure and then converting the likely internal ligand, Asn 119, to Asp, Ser, or Ala in the His120Gly mutant. The double mutants H120G/Asn 119X (X = Asp, Ser, or Ala) displayed UV-Vis absorption and EPR spectra that are identical to His120Gly and the other His120X mutants, indicating that Asn119 is not the internal ligand replacing His120 in the His120X mutant proteins. These results demonstrate the remarkable stability of the dinuclear His120 mutants of CuA azurin.
Collapse
Affiliation(s)
- S M Berry
- Department of Chemistry, The University of Illinois at Urbana-Champaign, Urbana 61801, USA
| | | | | |
Collapse
|
26
|
Wang K, Zhen Y, Sadoski R, Grinnell S, Geren L, Ferguson-Miller S, Durham B, Millett F. Definition of the interaction domain for cytochrome c on cytochrome c oxidase. Ii. Rapid kinetic analysis of electron transfer from cytochrome c to Rhodobacter sphaeroides cytochrome oxidase surface mutants. J Biol Chem 1999; 274:38042-50. [PMID: 10608873 DOI: 10.1074/jbc.274.53.38042] [Citation(s) in RCA: 63] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The reaction between cytochrome c (Cc) and Rhodobacter sphaeroides cytochrome c oxidase (CcO) was studied using a cytochrome c derivative labeled with ruthenium trisbipyridine at lysine 55 (Ru-55-Cc). Flash photolysis of a 1:1 complex between Ru-55-Cc and CcO at low ionic strength results in electron transfer from photoreduced heme c to Cu(A) with an intracomplex rate constant of k(a) = 4 x 10(4) s(-1), followed by electron transfer from Cu(A) to heme a with a rate constant of k(b) = 9 x 10(4) s(-1). The effects of CcO surface mutations on the kinetics follow the order D214N > E157Q > E148Q > D195N > D151N/E152Q approximately D188N/E189Q approximately wild type, indicating that the acidic residues Asp(214), Glu(157), Glu(148), and Asp(195) on subunit II interact electrostatically with the lysines surrounding the heme crevice of Cc. Mutating the highly conserved tryptophan residue, Trp(143), to Phe or Ala decreased the intracomplex electron transfer rate constant k(a) by 450- and 1200-fold, respectively, without affecting the dissociation constant K(D). It therefore appears that the indole ring of Trp(143) mediates electron transfer from the heme group of Cc to Cu(A). These results are consistent with steady-state kinetic results (Zhen, Y., Hoganson, C. W., Babcock, G. T., and Ferguson-Miller, S. (1999) J. Biol. Chem. 274, 38032-38041) and a computational docking analysis (Roberts, V. A., and Pique, M. E. (1999) J. Biol. Chem. 274, 38051-38060).
Collapse
Affiliation(s)
- K Wang
- Department of Chemistry, University of Arkansas, Fayetteville, Arkansas 72701, USA
| | | | | | | | | | | | | | | |
Collapse
|
27
|
Kannt A, Pfitzner U, Ruitenberg M, Hellwig P, Ludwig B, Mäntele W, Fendler K, Michel H. Mutation of Arg-54 strongly influences heme composition and rate and directionality of electron transfer in Paracoccus denitrificans cytochrome c oxidase. J Biol Chem 1999; 274:37974-81. [PMID: 10608865 DOI: 10.1074/jbc.274.53.37974] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The effect of a single site mutation of Arg-54 to methionine in Paracoccus denitrificans cytochrome c oxidase was studied using a combination of optical spectroscopy, electrochemical and rapid kinetics techniques, and time-resolved measurements of electrical membrane potential. The mutation resulted in a blue-shift of the heme a alpha-band by 15 nm and partial occupation of the low-spin heme site by heme O. Additionally, there was a marked decrease in the midpoint potential of the low-spin heme, resulting in slow reduction of this heme species. A stopped-flow investigation of the reaction with ferrocytochrome c yielded a kinetic difference spectrum resembling that of heme a(3). This observation, and the absence of transient absorbance changes at the corresponding wavelength of the low-spin heme, suggests that, in the mutant enzyme, electron transfer from Cu(A) to the binuclear center may not occur via heme a but that instead direct electron transfer to the high-spin heme is the dominating process. This was supported by charge translocation measurements where Deltapsi generation was completely inhibited in the presence of KCN. Our results thus provide an example for how the interplay between protein and cofactors can modulate the functional properties of the enzyme complex.
Collapse
Affiliation(s)
- A Kannt
- Max-Planck-Institut für Biophysik, Abteilung Molekulare Membranbiologie, Heinrich-Hoffmann-Strasse 7, D-60528, Germany
| | | | | | | | | | | | | | | |
Collapse
|
28
|
Kolczak U, Salgado J, Siegal G, Saraste M, Canters GW. Paramagnetic NMR studies of blue and purple copper proteins. BIOSPECTROSCOPY 1999; 5:S19-32. [PMID: 10512535 DOI: 10.1002/(sici)1520-6343(1999)5:5+3.0.co;2-h] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
1H- and 13C-NMR spectroscopy is applied to investigate the CU(A) and type 1 active sites of copper proteins in solution. The analysis of hyperfine shifted 1H resonances allows the comparison of the electron spin density delocalization in the CU(A) site of the wild-type soluble domains of various cytochrome c oxidases (Thermus thermophilus, Paracoccus denitrificans, and Paracoccus versutus) and genetically engineered constructs (soluble domain of quinol oxidase from Escherichia coli and Thiobacillus versutus amicyanin). Comparable spin densities are found on the two terminal His ligands for the wild-type constructs as opposed to the engineered proteins where the spin is more unevenly distributed on the two His residues. A reevaluation of the Cys H(beta) chemical shifts that is in agreement with the data published for both the P. denitrificans and the P. versutus Cu(A) soluble domains confirms the thermal accessibility of the 2B(3u) electronic excited state and indicates the existence of slightly different spin densities on the two bridging Cys ligands. The 13C-NMR spectrum of isotopically enriched oxidized azurin from Pseudomonas aeruginosa reveals six fast relaxing signals, which can be partially identified by 1- and 2-dimensional (1-D, 2-D) direct detection techniques combined with 3-D triple resonance experiments. The observed contact shifts suggest the presence of direct spin density transfer and spin polarization mechanisms for the delocalization of the unpaired electron.
Collapse
Affiliation(s)
- U Kolczak
- Leiden Institute of Chemistry, Leiden University, Gorlaeus Laboratories, The Netherlands
| | | | | | | | | |
Collapse
|
29
|
Bominaar EL, Achim C, Borshch SA. Theory for electron transfer from a mixed-valence dimer with paramagnetic sites to a mononuclear acceptor. J Chem Phys 1999. [DOI: 10.1063/1.479082] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
30
|
Effects of protein folding on metalloprotein redox-active sites: electron-transfer properties of blue and purple copper proteins. Coord Chem Rev 1999. [DOI: 10.1016/s0010-8545(98)00257-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
31
|
Wang X, Ang MC, Lu Y. Kinetics of Copper Incorporation into an Engineered Purple Azurin. J Am Chem Soc 1999. [DOI: 10.1021/ja982636k] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Xiaotang Wang
- Department of Chemistry University of Illinois at Urbana-Champaign Urbana, Illinois 61801
| | - Marjorie C. Ang
- Department of Chemistry University of Illinois at Urbana-Champaign Urbana, Illinois 61801
| | - Yi Lu
- Department of Chemistry University of Illinois at Urbana-Champaign Urbana, Illinois 61801
| |
Collapse
|
32
|
Farver O, Lu Y, Ang MC, Pecht I. Enhanced rate of intramolecular electron transfer in an engineered purple CuA azurin. Proc Natl Acad Sci U S A 1999; 96:899-902. [PMID: 9927665 PMCID: PMC15322 DOI: 10.1073/pnas.96.3.899] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The recent expression of an azurin mutant where the blue type 1 copper site is replaced by the purple CuA site of Paracoccus denitrificans cytochrome c oxidase has yielded an optimal system for examining the unique electron mediation properties of the binuclear CuA center, because both type 1 and CuA centers are placed in the same location in the protein while all other structural elements remain the same. Long-range electron transfer is induced between the disulfide radical anion, produced pulse radiolytically, and the oxidized binuclear CuA center in the purple azurin mutant. The rate constant of this intramolecular process, kET = 650 +/- 60 s-1 at 298 K and pH 5.1, is almost 3-fold faster than for the same process in the wild-type single blue copper azurin from Pseudomonas aeruginosa (250 +/- 20 s-1), in spite of a smaller driving force (0.69 eV for purple CuA azurin vs. 0.76 eV for blue copper azurin). The reorganization energy of the CuA center is calculated to be 0.4 eV, which is only 50% of that found for the wild-type azurin. These results represent a direct comparison of electron transfer properties of the blue and purple CuA sites in the same protein framework and provide support for the notion that the binuclear purple CuA center is a more efficient electron transfer agent than the blue single copper center because reactivity of the former involves a lower reorganization energy.
Collapse
Affiliation(s)
- O Farver
- Institute of Analytical and Pharmaceutical Chemistry, The Royal Danish School of Pharmacy, DK-2100 Copenhagen, Denmark
| | | | | | | |
Collapse
|
33
|
Wittung-Stafshede P, Gomez E, Ohman A, Aasa R, Villahermosa RM, Leckner J, Karlsson BG, Sanders D, Fee JA, Winkler JR, Malmström BG, Gray HB, Hill MG. High-potential states of blue and purple copper proteins. BIOCHIMICA ET BIOPHYSICA ACTA 1998; 1388:437-43. [PMID: 9858778 DOI: 10.1016/s0167-4838(98)00205-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Electrochemical measurements show that there are high-potential states of two copper proteins, Pseudomonas aeruginosa azurin and Thermus thermophilus CuA domain; these perturbed states are formed in guanidine hydrochloride (GuHCl) solution in which the proteins are still blue (azurin) and purple (CuA). In each case, the high-potential state forms reversibly. Absorption (azurin, CuA), visible circular dichroism (azurin, CuA), resonance-Raman (CuA), and EPR (CuA) spectra indicate that the structure of the oxidized copper site of each high-potential form is very similar to that of the native protein. It is proposed that GuHCl perturbs one or more H-bonds in the blue or purple copper active site, thereby allowing Cu(I) to adopt a more favorable coordination structure than that in the rigid cavity of the native protein.
Collapse
Affiliation(s)
- P Wittung-Stafshede
- Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA.
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
34
|
Michel H, Behr J, Harrenga A, Kannt A. Cytochrome c oxidase: structure and spectroscopy. ANNUAL REVIEW OF BIOPHYSICS AND BIOMOLECULAR STRUCTURE 1998; 27:329-56. [PMID: 9646871 DOI: 10.1146/annurev.biophys.27.1.329] [Citation(s) in RCA: 341] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Cytochrome c oxidase, the terminal enzyme of the respiratory chains of mitochondria and aerobic bacteria, catalyzes electron transfer from cytochrome c to molecular oxygen, reducing the latter to water. Electron transfer is coupled to proton translocation across the membrane, resulting in a proton and charge gradient that is then employed by the F0F1-ATPase to synthesize ATP. Over the last years, substantial progress has been made in our understanding of the structure and function of this enzyme. Spectroscopic techniques such as EPR, absorbance and resonance Raman spectroscopy, in combination with site-directed mutagenesis work, have been successfully applied to elucidate the nature of the cofactors and their ligands, to identify key residues involved in proton transfer, and to gain insight into the catalytic cycle and the structures of its intermediates. Recently, the crystal structures of a bacterial and a mitochondrial cytochrome c oxidase have been determined. In this review, we provide an overview of the crystal structures, summarize recent spectroscopic work, and combine structural and spectroscopic data in discussing mechanistic aspects of the enzyme. For the latter, we focus on the structure of the oxygen intermediates, proton-transfer pathways, and the much-debated issue of how electron transfer in the enzyme might be coupled to proton translocation.
Collapse
Affiliation(s)
- H Michel
- Max-Planck-Institut für Biophysik, Frankfurt/Main, Germany.
| | | | | | | |
Collapse
|
35
|
Gamelin DR, Randall DW, Hay MT, Houser RP, Mulder TC, Canters GW, de Vries S, Tolman WB, Lu Y, Solomon EI. Spectroscopy of Mixed-Valence CuA-Type Centers: Ligand-Field Control of Ground-State Properties Related to Electron Transfer. J Am Chem Soc 1998. [DOI: 10.1021/ja973161k] [Citation(s) in RCA: 138] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
36
|
Hay MT, Ang MC, Gamelin DR, Solomon EI, Antholine WE, Ralle M, Blackburn NJ, Massey PD, Wang X, Kwon AH, Lu Y. Spectroscopic Characterization of an Engineered Purple CuA Center in Azurin. Inorg Chem 1998. [DOI: 10.1021/ic971232a] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Michael T. Hay
- Department of Chemistry, University of Illinois at UrbanaChampaign, Urbana, Illinois 61801, Department of Chemistry, Stanford University, Stanford, California 94305, National Biomedical ESR Center, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, and Department of Chemistry, Biochemistry, and Molecular Biology, Oregon Graduate Institute of Science and Technology, P.O. Box 91000, Portland, Oregon 97291
| | - Marjorie C. Ang
- Department of Chemistry, University of Illinois at UrbanaChampaign, Urbana, Illinois 61801, Department of Chemistry, Stanford University, Stanford, California 94305, National Biomedical ESR Center, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, and Department of Chemistry, Biochemistry, and Molecular Biology, Oregon Graduate Institute of Science and Technology, P.O. Box 91000, Portland, Oregon 97291
| | - Daniel R. Gamelin
- Department of Chemistry, University of Illinois at UrbanaChampaign, Urbana, Illinois 61801, Department of Chemistry, Stanford University, Stanford, California 94305, National Biomedical ESR Center, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, and Department of Chemistry, Biochemistry, and Molecular Biology, Oregon Graduate Institute of Science and Technology, P.O. Box 91000, Portland, Oregon 97291
| | - Edward I. Solomon
- Department of Chemistry, University of Illinois at UrbanaChampaign, Urbana, Illinois 61801, Department of Chemistry, Stanford University, Stanford, California 94305, National Biomedical ESR Center, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, and Department of Chemistry, Biochemistry, and Molecular Biology, Oregon Graduate Institute of Science and Technology, P.O. Box 91000, Portland, Oregon 97291
| | - William E. Antholine
- Department of Chemistry, University of Illinois at UrbanaChampaign, Urbana, Illinois 61801, Department of Chemistry, Stanford University, Stanford, California 94305, National Biomedical ESR Center, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, and Department of Chemistry, Biochemistry, and Molecular Biology, Oregon Graduate Institute of Science and Technology, P.O. Box 91000, Portland, Oregon 97291
| | - Martina Ralle
- Department of Chemistry, University of Illinois at UrbanaChampaign, Urbana, Illinois 61801, Department of Chemistry, Stanford University, Stanford, California 94305, National Biomedical ESR Center, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, and Department of Chemistry, Biochemistry, and Molecular Biology, Oregon Graduate Institute of Science and Technology, P.O. Box 91000, Portland, Oregon 97291
| | - Ninian J. Blackburn
- Department of Chemistry, University of Illinois at UrbanaChampaign, Urbana, Illinois 61801, Department of Chemistry, Stanford University, Stanford, California 94305, National Biomedical ESR Center, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, and Department of Chemistry, Biochemistry, and Molecular Biology, Oregon Graduate Institute of Science and Technology, P.O. Box 91000, Portland, Oregon 97291
| | - Priscilla D. Massey
- Department of Chemistry, University of Illinois at UrbanaChampaign, Urbana, Illinois 61801, Department of Chemistry, Stanford University, Stanford, California 94305, National Biomedical ESR Center, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, and Department of Chemistry, Biochemistry, and Molecular Biology, Oregon Graduate Institute of Science and Technology, P.O. Box 91000, Portland, Oregon 97291
| | - Xiaotang Wang
- Department of Chemistry, University of Illinois at UrbanaChampaign, Urbana, Illinois 61801, Department of Chemistry, Stanford University, Stanford, California 94305, National Biomedical ESR Center, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, and Department of Chemistry, Biochemistry, and Molecular Biology, Oregon Graduate Institute of Science and Technology, P.O. Box 91000, Portland, Oregon 97291
| | - Angela H. Kwon
- Department of Chemistry, University of Illinois at UrbanaChampaign, Urbana, Illinois 61801, Department of Chemistry, Stanford University, Stanford, California 94305, National Biomedical ESR Center, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, and Department of Chemistry, Biochemistry, and Molecular Biology, Oregon Graduate Institute of Science and Technology, P.O. Box 91000, Portland, Oregon 97291
| | - Yi Lu
- Department of Chemistry, University of Illinois at UrbanaChampaign, Urbana, Illinois 61801, Department of Chemistry, Stanford University, Stanford, California 94305, National Biomedical ESR Center, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, and Department of Chemistry, Biochemistry, and Molecular Biology, Oregon Graduate Institute of Science and Technology, P.O. Box 91000, Portland, Oregon 97291
| |
Collapse
|
37
|
Abstract
Denitrification is a distinct means of energy conservation, making use of N oxides as terminal electron acceptors for cellular bioenergetics under anaerobic, microaerophilic, and occasionally aerobic conditions. The process is an essential branch of the global N cycle, reversing dinitrogen fixation, and is associated with chemolithotrophic, phototrophic, diazotrophic, or organotrophic metabolism but generally not with obligately anaerobic life. Discovered more than a century ago and believed to be exclusively a bacterial trait, denitrification has now been found in halophilic and hyperthermophilic archaea and in the mitochondria of fungi, raising evolutionarily intriguing vistas. Important advances in the biochemical characterization of denitrification and the underlying genetics have been achieved with Pseudomonas stutzeri, Pseudomonas aeruginosa, Paracoccus denitrificans, Ralstonia eutropha, and Rhodobacter sphaeroides. Pseudomonads represent one of the largest assemblies of the denitrifying bacteria within a single genus, favoring their use as model organisms. Around 50 genes are required within a single bacterium to encode the core structures of the denitrification apparatus. Much of the denitrification process of gram-negative bacteria has been found confined to the periplasm, whereas the topology and enzymology of the gram-positive bacteria are less well established. The activation and enzymatic transformation of N oxides is based on the redox chemistry of Fe, Cu, and Mo. Biochemical breakthroughs have included the X-ray structures of the two types of respiratory nitrite reductases and the isolation of the novel enzymes nitric oxide reductase and nitrous oxide reductase, as well as their structural characterization by indirect spectroscopic means. This revealed unexpected relationships among denitrification enzymes and respiratory oxygen reductases. Denitrification is intimately related to fundamental cellular processes that include primary and secondary transport, protein translocation, cytochrome c biogenesis, anaerobic gene regulation, metalloprotein assembly, and the biosynthesis of the cofactors molybdopterin and heme D1. An important class of regulators for the anaerobic expression of the denitrification apparatus are transcription factors of the greater FNR family. Nitrate and nitric oxide, in addition to being respiratory substrates, have been identified as signaling molecules for the induction of distinct N oxide-metabolizing enzymes.
Collapse
Affiliation(s)
- W G Zumft
- Lehrstuhl für Mikrobiologie, Universität Fridericiana, Karlsruhe, Germany
| |
Collapse
|
38
|
Luchinat C, Soriano A, Djinovic-Carugo K, Saraste M, Malmström BG, Bertini I. Electronic and Geometric Structure of the CuA Site Studied by 1H NMR in a Soluble Domain of Cytochrome c Oxidase from Paracoccus denitrificans. J Am Chem Soc 1997. [DOI: 10.1021/ja9715399] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Claudio Luchinat
- Contribution from the Department of Chemistry, University of Florence, Via Gino Capponi 7, 50121 Florence, Italy, Department of Soil Science and Plant Nutrition, University of Florence, P.le delle Cascine 28, 50144 Florence, Italy, European Molecular Biology Laboratory, 69012 Heidelberg, Germany, and Department of Biochemistry and Biophysics, Göteborg University, Göteborg, Sweden
| | - Aileen Soriano
- Contribution from the Department of Chemistry, University of Florence, Via Gino Capponi 7, 50121 Florence, Italy, Department of Soil Science and Plant Nutrition, University of Florence, P.le delle Cascine 28, 50144 Florence, Italy, European Molecular Biology Laboratory, 69012 Heidelberg, Germany, and Department of Biochemistry and Biophysics, Göteborg University, Göteborg, Sweden
| | - Kristina Djinovic-Carugo
- Contribution from the Department of Chemistry, University of Florence, Via Gino Capponi 7, 50121 Florence, Italy, Department of Soil Science and Plant Nutrition, University of Florence, P.le delle Cascine 28, 50144 Florence, Italy, European Molecular Biology Laboratory, 69012 Heidelberg, Germany, and Department of Biochemistry and Biophysics, Göteborg University, Göteborg, Sweden
| | - Matti Saraste
- Contribution from the Department of Chemistry, University of Florence, Via Gino Capponi 7, 50121 Florence, Italy, Department of Soil Science and Plant Nutrition, University of Florence, P.le delle Cascine 28, 50144 Florence, Italy, European Molecular Biology Laboratory, 69012 Heidelberg, Germany, and Department of Biochemistry and Biophysics, Göteborg University, Göteborg, Sweden
| | - Bo G. Malmström
- Contribution from the Department of Chemistry, University of Florence, Via Gino Capponi 7, 50121 Florence, Italy, Department of Soil Science and Plant Nutrition, University of Florence, P.le delle Cascine 28, 50144 Florence, Italy, European Molecular Biology Laboratory, 69012 Heidelberg, Germany, and Department of Biochemistry and Biophysics, Göteborg University, Göteborg, Sweden
| | - Ivano Bertini
- Contribution from the Department of Chemistry, University of Florence, Via Gino Capponi 7, 50121 Florence, Italy, Department of Soil Science and Plant Nutrition, University of Florence, P.le delle Cascine 28, 50144 Florence, Italy, European Molecular Biology Laboratory, 69012 Heidelberg, Germany, and Department of Biochemistry and Biophysics, Göteborg University, Göteborg, Sweden
| |
Collapse
|
39
|
Di Bilio AJ, Hill MG, Bonander N, Karlsson BG, Villahermosa RM, Malmström BG, Winkler JR, Gray HB. Reorganization Energy of Blue Copper: Effects of Temperature and Driving Force on the Rates of Electron Transfer in Ruthenium- and Osmium-Modified Azurins. J Am Chem Soc 1997. [DOI: 10.1021/ja971518e] [Citation(s) in RCA: 123] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Angel J. Di Bilio
- Beckman Institute, California Institute of Technology Pasadena, California 91125 Department of Biochemistry and Biophysics Göteborg University, Medicinaregatan 9C S-413 90 Göteborg, Sweden
| | - Michael G. Hill
- Beckman Institute, California Institute of Technology Pasadena, California 91125 Department of Biochemistry and Biophysics Göteborg University, Medicinaregatan 9C S-413 90 Göteborg, Sweden
| | - Nicklas Bonander
- Beckman Institute, California Institute of Technology Pasadena, California 91125 Department of Biochemistry and Biophysics Göteborg University, Medicinaregatan 9C S-413 90 Göteborg, Sweden
| | - B. Göran Karlsson
- Beckman Institute, California Institute of Technology Pasadena, California 91125 Department of Biochemistry and Biophysics Göteborg University, Medicinaregatan 9C S-413 90 Göteborg, Sweden
| | - Randy M. Villahermosa
- Beckman Institute, California Institute of Technology Pasadena, California 91125 Department of Biochemistry and Biophysics Göteborg University, Medicinaregatan 9C S-413 90 Göteborg, Sweden
| | - Bo G. Malmström
- Beckman Institute, California Institute of Technology Pasadena, California 91125 Department of Biochemistry and Biophysics Göteborg University, Medicinaregatan 9C S-413 90 Göteborg, Sweden
| | - Jay R. Winkler
- Beckman Institute, California Institute of Technology Pasadena, California 91125 Department of Biochemistry and Biophysics Göteborg University, Medicinaregatan 9C S-413 90 Göteborg, Sweden
| | - Harry B. Gray
- Beckman Institute, California Institute of Technology Pasadena, California 91125 Department of Biochemistry and Biophysics Göteborg University, Medicinaregatan 9C S-413 90 Göteborg, Sweden
| |
Collapse
|
40
|
Bominaar EL, Achim C, Borshch SA, Girerd JJ, Münck E. Analysis of Exchange Interaction and Electron Delocalization as Intramolecular Determinants of Intermolecular Electron-Transfer Kinetics. Inorg Chem 1997; 36:3689-3701. [PMID: 11670061 DOI: 10.1021/ic961298q] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
During the past decades, spectroscopic characterization of exchange interactions and electron delocalization has developed into a powerful tool for the recognition of metal clusters in metalloproteins. By contrast, the biological relevance of these interactions has received little attention thus far. This paper presents a theoretical study in which this problem is addressed. The rate constant for intermolecular electron-transfer reactions which are essential in many biological processes is investigated. An expression is derived for the dependence of the rate constant for self-exchange on the delocalization degree of the mixed-valence species. This result allows us to rationalize published kinetic data. In the simplest case of electron transfer from an exchange-coupled binuclear mixed-valence donor to a diamagnetic acceptor, the rate constant is evaluated, taking into account spin factors and exchange energies in the initial and final state. The theoretical analysis indicates that intramolecular spin-dependent electron delocalization (double exchange) and Heisenberg-Dirac-van Vleck (HDvV) exchange have an important impact on the rate constant for intermolecular electron transfer. This correlation reveals a novel relationship between magnetochemistry and electrochemistry. Contributions to the electron transfer from the ground and excited states of the exchange-coupled dimer have been evaluated. For clusters in which these states have different degrees of delocalization, the excited-state contributions to electron transfer may become dominant at potentials which are less reductive than the potential at which the rate constant for the transfer from the ground state is maximum. The rate constant shows a steep dependence on HDvV exchange, which suggests that an exchange-coupled cluster can act as a molecular switch for exchange-controlled electron gating. The relevance of this result is discussed in the context of substrate specificity of electron-transfer reactions in biology. Our theoretical analysis points toward a possible biological role of the spin-state variability in iron-sulfur clusters depending on cluster environment.
Collapse
Affiliation(s)
- E. L. Bominaar
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, Institut de Recherches sur la Catalyse, CNRS, 69626 Villeurbanne cedex, France, and Laboratoire de Chimie Inorganique, URA CNRS 420, Université de Paris-Sud, 91405 Orsay, France
| | | | | | | | | |
Collapse
|
41
|
Abstract
During the past two years, the crystal structures of beef heart cytochrome c oxidase with 13 subunits and the bacterial enzyme with four subunits have been reported at atomic resolution, ushering in a new era for cytochrome c oxidase research. Different proton pumping mechanisms have been proposed for the two organisms.
Collapse
Affiliation(s)
- S Yoshikawa
- Department of Life Science, Himeji Institute of Technology, Akoh Hyogo, Japan.
| |
Collapse
|
42
|
Beinert H. Copper A of cytochrome c oxidase, a novel, long-embattled, biological electron-transfer site. EUROPEAN JOURNAL OF BIOCHEMISTRY 1997; 245:521-32. [PMID: 9182986 DOI: 10.1111/j.1432-1033.1997.t01-1-00521.x] [Citation(s) in RCA: 107] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
This review traces the history of understanding of the CuA site in cytochrome c oxidase (COX) from the beginnings, when few believed that there was any significant Cu in COX, to the verification of three atoms Cu/monomer and to the final identification of the site as a dinuclear, Cys-bridged average valence Cu1.5+ ... Cu1.5+ structure through spectroscopy, recombinant DNA techniques, and crystallography. The critical steps forward in understanding the nature of the CuA site are recounted and the present state (as of the end of 1996) of our knowledge of the molecular and electronic structure is discussed in some detail. The contributions made through the years by the development of methodology and concepts for solving the enigma of CuA are emphasized and impediments, often rooted in contemporary preconceptions and attitudes rather than solid data, are mentioned, which discouraged the exploitation of early valuable clues. Finally, analogies in construction principles of polynuclear Cu-S and Fe-S proteins are pointed out.
Collapse
Affiliation(s)
- H Beinert
- Institute for Enzyme Research, Graduate School, and Department of Biochemistry, College of Agricultural and Life Sciences, University of Wisconsin, Madison 53705-4098, USA
| |
Collapse
|
43
|
Bertini I, Bren KL, Clemente A, Fee JA, Gray HB, Luchinat C, Malmström BG, Richards JH, Sanders D, Slutter CE. The CuA Center of a Soluble Domain from Thermus Cytochrome ba3. An NMR Investigation of the Paramagnetic Protein. J Am Chem Soc 1996. [DOI: 10.1021/ja9621410] [Citation(s) in RCA: 68] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ivano Bertini
- Department of Chemistry, University of Florence Via G. Capponi 7, I-50121 Florence, Italy Division of Chemistry and Chemical Engineering California Institute of Technology Pasadena, California 91125 Department of Biology University of California at San Diego La Jolla, California 92093 Institute of Agricultural Chemistry University of Bologna, Bologna, Italy Department of Biochemistry and Biophysics Göteborg University, Göteborg, Sweden
| | - Kara L. Bren
- Department of Chemistry, University of Florence Via G. Capponi 7, I-50121 Florence, Italy Division of Chemistry and Chemical Engineering California Institute of Technology Pasadena, California 91125 Department of Biology University of California at San Diego La Jolla, California 92093 Institute of Agricultural Chemistry University of Bologna, Bologna, Italy Department of Biochemistry and Biophysics Göteborg University, Göteborg, Sweden
| | - Antonio Clemente
- Department of Chemistry, University of Florence Via G. Capponi 7, I-50121 Florence, Italy Division of Chemistry and Chemical Engineering California Institute of Technology Pasadena, California 91125 Department of Biology University of California at San Diego La Jolla, California 92093 Institute of Agricultural Chemistry University of Bologna, Bologna, Italy Department of Biochemistry and Biophysics Göteborg University, Göteborg, Sweden
| | - James A. Fee
- Department of Chemistry, University of Florence Via G. Capponi 7, I-50121 Florence, Italy Division of Chemistry and Chemical Engineering California Institute of Technology Pasadena, California 91125 Department of Biology University of California at San Diego La Jolla, California 92093 Institute of Agricultural Chemistry University of Bologna, Bologna, Italy Department of Biochemistry and Biophysics Göteborg University, Göteborg, Sweden
| | - Harry B. Gray
- Department of Chemistry, University of Florence Via G. Capponi 7, I-50121 Florence, Italy Division of Chemistry and Chemical Engineering California Institute of Technology Pasadena, California 91125 Department of Biology University of California at San Diego La Jolla, California 92093 Institute of Agricultural Chemistry University of Bologna, Bologna, Italy Department of Biochemistry and Biophysics Göteborg University, Göteborg, Sweden
| | - Claudio Luchinat
- Department of Chemistry, University of Florence Via G. Capponi 7, I-50121 Florence, Italy Division of Chemistry and Chemical Engineering California Institute of Technology Pasadena, California 91125 Department of Biology University of California at San Diego La Jolla, California 92093 Institute of Agricultural Chemistry University of Bologna, Bologna, Italy Department of Biochemistry and Biophysics Göteborg University, Göteborg, Sweden
| | - Bo G. Malmström
- Department of Chemistry, University of Florence Via G. Capponi 7, I-50121 Florence, Italy Division of Chemistry and Chemical Engineering California Institute of Technology Pasadena, California 91125 Department of Biology University of California at San Diego La Jolla, California 92093 Institute of Agricultural Chemistry University of Bologna, Bologna, Italy Department of Biochemistry and Biophysics Göteborg University, Göteborg, Sweden
| | - John H. Richards
- Department of Chemistry, University of Florence Via G. Capponi 7, I-50121 Florence, Italy Division of Chemistry and Chemical Engineering California Institute of Technology Pasadena, California 91125 Department of Biology University of California at San Diego La Jolla, California 92093 Institute of Agricultural Chemistry University of Bologna, Bologna, Italy Department of Biochemistry and Biophysics Göteborg University, Göteborg, Sweden
| | - Donita Sanders
- Department of Chemistry, University of Florence Via G. Capponi 7, I-50121 Florence, Italy Division of Chemistry and Chemical Engineering California Institute of Technology Pasadena, California 91125 Department of Biology University of California at San Diego La Jolla, California 92093 Institute of Agricultural Chemistry University of Bologna, Bologna, Italy Department of Biochemistry and Biophysics Göteborg University, Göteborg, Sweden
| | - Claire E. Slutter
- Department of Chemistry, University of Florence Via G. Capponi 7, I-50121 Florence, Italy Division of Chemistry and Chemical Engineering California Institute of Technology Pasadena, California 91125 Department of Biology University of California at San Diego La Jolla, California 92093 Institute of Agricultural Chemistry University of Bologna, Bologna, Italy Department of Biochemistry and Biophysics Göteborg University, Göteborg, Sweden
| |
Collapse
|
44
|
Farrar JA, Neese F, Lappalainen P, Kroneck PMH, Saraste M, Zumft WG, Thomson AJ. The Electronic Structure of CuA: A Novel Mixed-Valence Dinuclear Copper Electron-Transfer Center. J Am Chem Soc 1996. [DOI: 10.1021/ja9618715] [Citation(s) in RCA: 145] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- J. A. Farrar
- Contribution from the School of Chemical Sciences, University of East Anglia, Norwich NR4 7TJ, U.K., Fakultät für Biologie, Universität Konstanz, D-78434 Konstanz, Germany, European Molecular Biology Laboratory, D-69012 Heidelberg, Germany, and Lehrstuhl für Mikrobiologie, Universität Fridericiana, D-76128 Karlsruhe, Germany
| | - F. Neese
- Contribution from the School of Chemical Sciences, University of East Anglia, Norwich NR4 7TJ, U.K., Fakultät für Biologie, Universität Konstanz, D-78434 Konstanz, Germany, European Molecular Biology Laboratory, D-69012 Heidelberg, Germany, and Lehrstuhl für Mikrobiologie, Universität Fridericiana, D-76128 Karlsruhe, Germany
| | - P. Lappalainen
- Contribution from the School of Chemical Sciences, University of East Anglia, Norwich NR4 7TJ, U.K., Fakultät für Biologie, Universität Konstanz, D-78434 Konstanz, Germany, European Molecular Biology Laboratory, D-69012 Heidelberg, Germany, and Lehrstuhl für Mikrobiologie, Universität Fridericiana, D-76128 Karlsruhe, Germany
| | - P. M. H. Kroneck
- Contribution from the School of Chemical Sciences, University of East Anglia, Norwich NR4 7TJ, U.K., Fakultät für Biologie, Universität Konstanz, D-78434 Konstanz, Germany, European Molecular Biology Laboratory, D-69012 Heidelberg, Germany, and Lehrstuhl für Mikrobiologie, Universität Fridericiana, D-76128 Karlsruhe, Germany
| | - M. Saraste
- Contribution from the School of Chemical Sciences, University of East Anglia, Norwich NR4 7TJ, U.K., Fakultät für Biologie, Universität Konstanz, D-78434 Konstanz, Germany, European Molecular Biology Laboratory, D-69012 Heidelberg, Germany, and Lehrstuhl für Mikrobiologie, Universität Fridericiana, D-76128 Karlsruhe, Germany
| | - W. G. Zumft
- Contribution from the School of Chemical Sciences, University of East Anglia, Norwich NR4 7TJ, U.K., Fakultät für Biologie, Universität Konstanz, D-78434 Konstanz, Germany, European Molecular Biology Laboratory, D-69012 Heidelberg, Germany, and Lehrstuhl für Mikrobiologie, Universität Fridericiana, D-76128 Karlsruhe, Germany
| | - A. J. Thomson
- Contribution from the School of Chemical Sciences, University of East Anglia, Norwich NR4 7TJ, U.K., Fakultät für Biologie, Universität Konstanz, D-78434 Konstanz, Germany, European Molecular Biology Laboratory, D-69012 Heidelberg, Germany, and Lehrstuhl für Mikrobiologie, Universität Fridericiana, D-76128 Karlsruhe, Germany
| |
Collapse
|
45
|
Templeton AR. Contingency tests of neutrality using intra/interspecific gene trees: the rejection of neutrality for the evolution of the mitochondrial cytochrome oxidase II gene in the hominoid primates. Genetics 1996; 144:1263-70. [PMID: 8913766 PMCID: PMC1207617 DOI: 10.1093/genetics/144.3.1263] [Citation(s) in RCA: 95] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Contingency tests of neutrality are performed using mitochondrial cytochrome oxidase II (COII) DNA sequences from hominoid primates, including humans. An intra-/interspecific haplotype tree is estimated, including a statistical assessment of ambiguities in tree topology and branch lengths. Four functional mutational categories are considered: silent and replacement substitutions in the transmembrane portion of the COII molecule, and silent and replacement substitutions in the cytosolic portion. Three tree topological mutational categories are used: intraspecific tips, intraspecific interiors, and interspecific fixed mutations. A full contingency analysis is performed, followed by nested contingency analyses. The analyses indicate that replacement mutations in the cytosolic portion are deleterious, and replacement mutations in the transmembrane portion and silent mutations throughout tend to be neutral. These conclusions are robust to ambiguities in tree topology and branch lengths. These inferences would have been impossible with an analysis that only contrasts silent and replacement vs. polymorphic and fixed. Also, intraspecific interior mutations have similar evolutionary dynamics to fixed mutations, so pooling tip and interior mutations into a single "polymorphic" class reduces power. Finally, the detected deleterious selection causes lowered inbreeding effective sizes, so arguments for small effective sizes in recent human evolutionary history based upon mitochondrial DNA may be invalid.
Collapse
Affiliation(s)
- A R Templeton
- Department of Biology, Washington University, St. Louis, Missouri 63130-4899, USA.
| |
Collapse
|
46
|
Neese F, Zumft WG, Antholine WE, Kroneck PMH. The Purple Mixed-Valence CuA Center in Nitrous-oxide Reductase: EPR of the Copper-63-, Copper-65-, and Both Copper-65- and [15N]Histidine-Enriched Enzyme and a Molecular Orbital Interpretation. J Am Chem Soc 1996. [DOI: 10.1021/ja960125x] [Citation(s) in RCA: 137] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Frank Neese
- Contribution from the Fakultät für Biologie, Universität Konstanz, D-78434 Konstanz, Germany, Lehrstuhl für Mikrobiologie, Universität Fridericiana, D-76128 Karlsruhe, Germany, and Biophysics Research Institute, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, Wisconsin 53226
| | - Walter G. Zumft
- Contribution from the Fakultät für Biologie, Universität Konstanz, D-78434 Konstanz, Germany, Lehrstuhl für Mikrobiologie, Universität Fridericiana, D-76128 Karlsruhe, Germany, and Biophysics Research Institute, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, Wisconsin 53226
| | - William E. Antholine
- Contribution from the Fakultät für Biologie, Universität Konstanz, D-78434 Konstanz, Germany, Lehrstuhl für Mikrobiologie, Universität Fridericiana, D-76128 Karlsruhe, Germany, and Biophysics Research Institute, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, Wisconsin 53226
| | - Peter M. H. Kroneck
- Contribution from the Fakultät für Biologie, Universität Konstanz, D-78434 Konstanz, Germany, Lehrstuhl für Mikrobiologie, Universität Fridericiana, D-76128 Karlsruhe, Germany, and Biophysics Research Institute, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, Wisconsin 53226
| |
Collapse
|
47
|
Weghorn SJ, Sessler JL, Lynch V, Baumann TF, Sibert JW. Bis[(&mgr;-chloro)copper(II)] Amethyrin: A Bimetallic Copper(II) Complex of an Expanded Porphyrin. Inorg Chem 1996; 35:1089-1090. [PMID: 11666292 DOI: 10.1021/ic9509692] [Citation(s) in RCA: 75] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Steven J. Weghorn
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208
| | | | | | | | | |
Collapse
|
48
|
Hay M, Richards JH, Lu Y. Construction and characterization of an azurin analog for the purple copper site in cytochrome c oxidase. Proc Natl Acad Sci U S A 1996; 93:461-4. [PMID: 8552661 PMCID: PMC40258 DOI: 10.1073/pnas.93.1.461] [Citation(s) in RCA: 108] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
A protein analog of a purple copper center has been constructed from a recombinant blue copper protein (Pseudomonas aeruginosa azurin) by replacing the loop containing the three ligands to the blue copper center with the corresponding loop of the CuA center in cytochrome c oxidase (COX) from Paracoccus denitrificans. The electronic absorption in the UV and visible region (UV-vis) and electron paramagnetic resonance (EPR) spectra of this analog are remarkably similar to those of the native CuA center in COX from Paracoccus denitrificans. The above spectra can be obtained upon addition of a mixture of Cu2+ and Cu+. Addition of Cu2+ only results in a UV-vis spectrum consisting of absorptions from both a purple copper center and a blue copper center. This spectrum can be converted to the spectrum of a pure purple copper by a prolonged incubation in the air, or by addition of excess ascorbate. The azurin mutant reported here is an example of an engineered purple copper center with the A480/A530 ratio greater than 1 and with no detectable hyperfines, similar to those of the CuA sites in COX of bovine heart and of Paracoccus denitrificans.
Collapse
Affiliation(s)
- M Hay
- Department of Chemistry, University of Illinois, Urbana 61801, USA
| | | | | |
Collapse
|
49
|
Ramirez BE, Malmström BG, Winkler JR, Gray HB. The currents of life: the terminal electron-transfer complex of respiration. Proc Natl Acad Sci U S A 1995; 92:11949-51. [PMID: 8618820 PMCID: PMC40272 DOI: 10.1073/pnas.92.26.11949] [Citation(s) in RCA: 133] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Affiliation(s)
- B E Ramirez
- Beckman Institute, California Institute of Technology, Pasadena 91125, USA
| | | | | | | |
Collapse
|