1
|
Pietras R, Sarewicz M, Osyczka A. Distinct properties of semiquinone species detected at the ubiquinol oxidation Qo site of cytochrome bc1 and their mechanistic implications. J R Soc Interface 2017; 13:rsif.2016.0133. [PMID: 27194483 PMCID: PMC4892266 DOI: 10.1098/rsif.2016.0133] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 04/18/2016] [Indexed: 12/23/2022] Open
Abstract
The two-electron ubiquinol oxidation or ubiquinone reduction typically involves semiquinone (SQ) intermediates. Natural engineering of ubiquinone binding sites of bioenergetic enzymes secures that SQ is sufficiently stabilized, so that it does not leave the site to membranous environment before full oxidation/reduction is completed. The ubiquinol oxidation Qo site of cytochrome bc1 (mitochondrial complex III, cytochrome b6f in plants) has been considered an exception with catalytic reactions assumed to involve highly unstable SQ or not to involve any SQ intermediate. This view seemed consistent with long-standing difficulty in detecting any reaction intermediates at the Qo site. New perspective on this issue is now offered by recent, independent reports on detection of SQ in this site. Each of the described SQs seems to have different spectroscopic properties leaving space for various interpretations and mechanistic considerations. Here, we comparatively reflect on those properties and their consequences on the SQ stabilization, the involvement of SQ in catalytic reactions, including proton transfers, and the reactivity of SQ with oxygen associated with superoxide generation activity of the Qo site.
Collapse
Affiliation(s)
- Rafał Pietras
- Department of Molecular Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland
| | - Marcin Sarewicz
- Department of Molecular Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland
| | - Artur Osyczka
- Department of Molecular Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland
| |
Collapse
|
2
|
Szabó T, Csekő R, Hajdu K, Nagy K, Sipos O, Galajda P, Garab G, Nagy L. Sensing photosynthetic herbicides in an electrochemical flow cell. PHOTOSYNTHESIS RESEARCH 2017; 132:127-134. [PMID: 27709414 DOI: 10.1007/s11120-016-0314-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 09/26/2016] [Indexed: 06/06/2023]
Abstract
Specific inhibitory reactions of herbicides with photosynthetic reaction centers bound to working electrodes were monitored in a conventional electrochemical cell and a newly designed microfluidic electrochemical flow cell. In both cases, the bacterial reaction centers were bound to a transparent conductive metal oxide, indium-tin-oxide, electrode through carbon nanotubes. In the conventional cell, photocurrent densities of up to a few μA/cm2 could be measured routinely. The photocurrent could be blocked by the photosynthetic inhibitor terbutryn (I 50 = 0.38 ± 0.14 μM) and o-phenanthroline (I 50 = 63.9 ± 12.2 μM). The microfluidic flow cell device enabled us to reduce the sample volume and to simplify the electrode arrangement. The useful area of the electrodes remained the same (ca. 2 cm2), similar to the classical electrochemical cell; however, the size of the cell was reduced considerably. The microfluidic flow control enabled us monitoring in real time the binding/unbinding of the inhibitor and cofactor molecules at the secondary quinone site.
Collapse
Affiliation(s)
- Tibor Szabó
- Department of Medical Physics and Informatics, University of Szeged, H-6720, Rerrich B. tér 1, Szeged, Hungary
| | - Richárd Csekő
- Department of Medical Physics and Informatics, University of Szeged, H-6720, Rerrich B. tér 1, Szeged, Hungary
| | - Kata Hajdu
- Department of Medical Physics and Informatics, University of Szeged, H-6720, Rerrich B. tér 1, Szeged, Hungary
| | - Krisztina Nagy
- Biological Research Centre, Institue of Biophysics, Hungarian Academy of Sciences, Szeged, Hungary
| | - Orsolya Sipos
- Biological Research Centre, Institue of Biophysics, Hungarian Academy of Sciences, Szeged, Hungary
| | - Péter Galajda
- Biological Research Centre, Institue of Biophysics, Hungarian Academy of Sciences, Szeged, Hungary
| | - Győző Garab
- Biological Research Centre, Institue of Plant Biology, Hungarian Academy of Sciences, Szeged, Hungary
- Biofotonika R&D Ltd., Szeged, Hungary
| | - László Nagy
- Department of Medical Physics and Informatics, University of Szeged, H-6720, Rerrich B. tér 1, Szeged, Hungary.
| |
Collapse
|
3
|
Kaminskaya OP, Shuvalov VA. New interpretation of the redox properties of cytochrome b559 in photosystem II. DOKL BIOCHEM BIOPHYS 2016; 466:39-42. [PMID: 27025485 DOI: 10.1134/s1607672916010117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Indexed: 11/23/2022]
Abstract
A model of heme-quinone redox interaction has been developed for cytochrome b559 in photosystem II. The quinone QC in the singly protonated form may function as an interacting quinone. The electrostatic effect between the charges on the heme iron of the cytochrome and QCH leads to appearance of three forms of the cytochrome with different redox potentials. A simple and effective mechanism of redox regulation of the electron transfer pathways in photosystem II is proposed.
Collapse
Affiliation(s)
- O P Kaminskaya
- Institute of Basic Biological Problems, Russian Academy of Sciences, ul. Institutskaya 2, Pushchino, Moscow oblast, 142290, Russia.
| | - V A Shuvalov
- Institute of Basic Biological Problems, Russian Academy of Sciences, ul. Institutskaya 2, Pushchino, Moscow oblast, 142290, Russia
| |
Collapse
|
4
|
Kaminskaya OP, Shuvalov VA. Towards an understanding of redox heterogeneity of the photosystem II cytochrome b559 in the native membrane. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2015; 45:129-38. [DOI: 10.1007/s00249-015-1082-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Revised: 09/07/2015] [Accepted: 09/16/2015] [Indexed: 11/29/2022]
|
5
|
Vennam PR, Fisher N, Krzyaniak MD, Kramer DM, Bowman MK. A caged, destabilized, free radical intermediate in the q-cycle. Chembiochem 2013; 14:1745-53. [PMID: 24009094 PMCID: PMC3951126 DOI: 10.1002/cbic.201300265] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2013] [Indexed: 11/12/2022]
Abstract
The Rieske/cytochrome b complexes, also known as cytochrome bc complexes, catalyze a unique oxidant-induced reduction reaction at their quinol oxidase (Qo ) sites, in which substrate hydroquinone reduces two distinct electron transfer chains, one through a series of high-potential electron carriers, the second through low-potential cytochrome b. This reaction is a critical step in energy storage by the Q-cycle. The semiquinone intermediate in this reaction can reduce O2 to produce deleterious superoxide. It is yet unknown how the enzyme controls this reaction, though numerous models have been proposed. In previous work, we trapped a Q-cycle semiquinone anion intermediate, termed SQo , in bacterial cytochrome bc1 by rapid freeze-quenching. In this work, we apply pulsed-EPR techniques to determine the location and properties of SQo in the mitochondrial complex. In contrast to semiquinone intermediates in other enzymes, SQo is not thermodynamically stabilized, and can even be destabilized with respect to solution. It is trapped in Qo at a site that is distinct from previously described inhibitor-binding sites, yet sufficiently close to cytochrome bL to allow rapid electron transfer. The binding site and EPR analyses show that SQo is not stabilized by hydrogen bonds to proteins. The formation of SQo involves "stripping" of both substrate -OH protons during the initial oxidation step, as well as conformational changes of the semiquinone and Qo proteins. The resulting charged radical is kinetically trapped, rather than thermodynamically stabilized (as in most enzymatic semiquinone species), conserving redox energy to drive electron transfer to cytochrome bL while minimizing certain Q-cycle bypass reactions, including oxidation of prereduced cytochrome b and reduction of O2 .
Collapse
Affiliation(s)
- Preethi R. Vennam
- Chemistry Department University of Alabama Box 870336, Tuscaloosa, AL 35487, United States
| | - Nicholas Fisher
- Biochemistry and Molecular Biology and the MSU-DOE Plant Research Laboratory Michigan State University East Lansing, MI 48824, United States
| | - Matthew D. Krzyaniak
- Chemistry Department University of Alabama Box 870336, Tuscaloosa, AL 35487, United States
| | - David M. Kramer
- Biochemistry and Molecular Biology and the MSU-DOE Plant Research Laboratory Michigan State University East Lansing, MI 48824, United States
| | - Michael K. Bowman
- Chemistry Department University of Alabama Box 870336, Tuscaloosa, AL 35487, United States
| |
Collapse
|
6
|
Moore AL, Shiba T, Young L, Harada S, Kita K, Ito K. Unraveling the heater: new insights into the structure of the alternative oxidase. ANNUAL REVIEW OF PLANT BIOLOGY 2013; 64:637-63. [PMID: 23638828 DOI: 10.1146/annurev-arplant-042811-105432] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
The alternative oxidase is a membrane-bound ubiquinol oxidase found in the majority of plants as well as many fungi and protists, including pathogenic organisms such as Trypanosoma brucei. It catalyzes a cyanide- and antimycin-A-resistant oxidation of ubiquinol and the reduction of oxygen to water, short-circuiting the mitochondrial electron-transport chain prior to proton translocation by complexes III and IV, thereby dramatically reducing ATP formation. In plants, it plays a key role in cellular metabolism, thermogenesis, and energy homeostasis and is generally considered to be a major stress-induced protein. We describe recent advances in our understanding of this protein's structure following the recent successful crystallization of the alternative oxidase from T. brucei. We focus on the nature of the active site and ubiquinol-binding channels and propose a mechanism for the reduction of oxygen to water based on these structural insights. We also consider the regulation of activity at the posttranslational and retrograde levels and highlight challenges for future research.
Collapse
Affiliation(s)
- Anthony L Moore
- Biochemistry and Molecular Biology, School of Life Sciences, University of Sussex, Brighton BN1 9QG, United Kingdom.
| | | | | | | | | | | |
Collapse
|
7
|
Albury MS, Elliott C, Moore AL. Ubiquinol-binding site in the alternative oxidase: Mutagenesis reveals features important for substrate binding and inhibition. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2010; 1797:1933-9. [DOI: 10.1016/j.bbabio.2010.01.013] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2009] [Revised: 01/11/2010] [Accepted: 01/12/2010] [Indexed: 11/16/2022]
|
8
|
Albury MS, Elliott C, Moore AL. Towards a structural elucidation of the alternative oxidase in plants. PHYSIOLOGIA PLANTARUM 2009; 137:316-27. [PMID: 19719482 DOI: 10.1111/j.1399-3054.2009.01270.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
In addition to the conventional cytochrome c oxidase, mitochondria of all plants studied to date contain a second cyanide-resistant terminal oxidase or alternative oxidase (AOX). The AOX is located in the inner mitochondrial membrane and branches from the cytochrome pathway at the level of the quinone pool. It is non-protonmotive and couples the oxidation of ubiquinone to the reduction of oxygen to water. For many years, the AOX was considered to be confined to plants, fungi and a small number of protists. Recently, it has become apparent that the AOX occurs in wide range of organisms including prokaryotes and a moderate number of animal species. In this paper, we provide an overview of general features and current knowledge available about the AOX with emphasis on structure, the active site and quinone-binding site. Characterisation of the AOX has advanced considerably over recent years with information emerging about the role of the protein, regulatory regions and functional sites. The large number of sequences available is now enabling us to obtain a clearer picture of evolutionary origins and diversity.
Collapse
Affiliation(s)
- Mary S Albury
- Division of Biochemistry and Biomedical Sciences, School of Life Sciences, University of Sussex, Falmer, Brighton BN19QG, UK
| | | | | |
Collapse
|
9
|
The Cytochrome bc 1 and Related bc Complexes: The Rieske/Cytochrome b Complex as the Functional Core of a Central Electron/Proton Transfer Complex. THE PURPLE PHOTOTROPHIC BACTERIA 2009. [DOI: 10.1007/978-1-4020-8815-5_23] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
|
10
|
Kocherginsky N. Acidic lipids, H(+)-ATPases, and mechanism of oxidative phosphorylation. Physico-chemical ideas 30 years after P. Mitchell's Nobel Prize award. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2008; 99:20-41. [PMID: 19049812 DOI: 10.1016/j.pbiomolbio.2008.10.013] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Peter D. Mitchell, who was awarded the Nobel Prize in Chemistry 30 years ago, in 1978, formulated the chemiosmotic theory of oxidative phosphorylation. This review initially analyzes the major aspects of this theory, its unresolved problems, and its modifications. A new physico-chemical mechanism of energy transformation and coupling of oxidation and phosphorylation is then suggested based on recent concepts regarding proteins, including ATPases that work as molecular motors, and acidic lipids that act as hydrogen ion (H(+)) carriers. According to this proposed mechanism, the chemical energy of a redox substrate is transformed into nonequilibrium states of electron-transporting chain (ETC) coupling proteins. This leads to nonequilibrium pumping of H(+) into the membrane. An acidic lipid, cardiolipin, binds with this H(+) and carries it to the ATP-synthase along the membrane surface. This transport generates gradients of surface tension or electric field along the membrane surface. Hydrodynamic effects on a nanolevel lead to rotation of ATP-synthase and finally to the release of ATP into aqueous solution. This model also explains the generation of a transmembrane protonmotive force that is used for regulation of transmembrane transport, but is not necessary for the coupling of electron transport and ATP synthesis.
Collapse
|
11
|
Mutations in cytochrome b that affect kinetics of the electron transfer reactions at center N in the yeast cytochrome bc1 complex. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2008; 1777:239-49. [DOI: 10.1016/j.bbabio.2007.08.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2007] [Revised: 08/15/2007] [Accepted: 08/17/2007] [Indexed: 11/24/2022]
|
12
|
Kern J, Renger G. Photosystem II: structure and mechanism of the water:plastoquinone oxidoreductase. PHOTOSYNTHESIS RESEARCH 2007; 94:183-202. [PMID: 17634752 DOI: 10.1007/s11120-007-9201-1] [Citation(s) in RCA: 107] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2006] [Accepted: 05/16/2007] [Indexed: 05/07/2023]
Abstract
This mini-review briefly summarizes our current knowledge on the reaction pattern of light-driven water splitting and the structure of Photosystem II that acts as a water:plastoquinone oxidoreductase. The overall process comprises three types of reaction sequences: (a) light-induced charge separation leading to formation of the radical ion pair P680+*QA(-*) ; (b) reduction of plastoquinone to plastoquinol at the QB site via a two-step reaction sequence with QA(-*) as reductant and (c) oxidative water splitting into O2 and four protons at a manganese-containing catalytic site via a four-step sequence driven by P680+* as oxidant and a redox active tyrosine YZ acting as mediator. Based on recent progress in X-ray diffraction crystallographic structure analysis the array of the cofactors within the protein matrix is discussed in relation to the functional pattern. Special emphasis is paid on the structure of the catalytic sites of PQH2 formation (QB-site) and oxidative water splitting (Mn4OxCa cluster). The energetics and kinetics of the reactions taking place at these sites are presented only in a very concise manner with reference to recent up-to-date reviews. It is illustrated that several questions on the mechanism of oxidative water splitting and the structure of the catalytic sites are far from being satisfactorily answered.
Collapse
Affiliation(s)
- Jan Kern
- Institut für Chemie, Max-Volmer-Laboratorium für Biophysikalische Chemie, Technische Universität Berlin, Strasse des 17. Juni 135, 10623, Berlin, Germany.
| | | |
Collapse
|