1
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Havens J, Su T, Wang Q, Yu CA, Yu L, Durham B, Millett F. Photoinduced electron transfer in cytochrome bc 1: Dynamics of rotation of the Iron-sulfur protein during bifurcated electron transfer from ubiquinol to cytochrome c 1 and cytochrome b L. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2023; 1864:148957. [PMID: 36709837 DOI: 10.1016/j.bbabio.2023.148957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Revised: 01/12/2023] [Accepted: 01/20/2023] [Indexed: 01/27/2023]
Abstract
The electron transfer reactions within wild-type Rhodobacter sphaeroides cytochrome bc1 (cyt bc1) were studied using a binuclear ruthenium complex to rapidly photooxidize cyt c1. When cyt c1, the iron‑sulfur center Fe2S2, and cyt bH were reduced before the reaction, photooxidation of cyt c1 led to electron transfer from Fe2S2 to cyt c1 with a rate constant of ka = 80,000 s-1, followed by bifurcated reduction of both Fe2S2 and cyt bL by QH2 in the Qo site with a rate constant of k2 = 3000 s-1. The resulting Q then traveled from the Qo site to the Qi site and oxidized one equivalent each of cyt bL and cyt bH with a rate constant of k3 = 340 s-1. The rate constant ka was decreased in a nonlinear fashion by a factor of 53 as the viscosity was increased to 13.7. A mechanism that is consistent with the effect of viscosity involves rotational diffusion of the iron‑sulfur protein from the b state with reduced Fe2S2 close to cyt bL to one or more intermediate states, followed by rotation to the final c1 state with Fe2S2 close to cyt c1, and rapid electron transfer to cyt c1.
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Affiliation(s)
- Jeffrey Havens
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, United States of America; Vaccines and Therapeutics Division, Chemical and Biological Technologies, Defense Threat Reduction Agency, Fort Belvoir, VA 22060, United States of America
| | - Ting Su
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078, United States of America; ABclonal Technology Woburn, MA 01801, United States of America
| | - Qiyu Wang
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078, United States of America; Vesigen Therapeutics Cambridge, MA 02139, United States of America
| | - Chang-An Yu
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078, United States of America
| | - Linda Yu
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078, United States of America
| | - Bill Durham
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, United States of America
| | - Francis Millett
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, United States of America.
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2
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Sarewicz M, Pintscher S, Pietras R, Borek A, Bujnowicz Ł, Hanke G, Cramer WA, Finazzi G, Osyczka A. Catalytic Reactions and Energy Conservation in the Cytochrome bc1 and b6f Complexes of Energy-Transducing Membranes. Chem Rev 2021; 121:2020-2108. [PMID: 33464892 PMCID: PMC7908018 DOI: 10.1021/acs.chemrev.0c00712] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Indexed: 12/16/2022]
Abstract
This review focuses on key components of respiratory and photosynthetic energy-transduction systems: the cytochrome bc1 and b6f (Cytbc1/b6f) membranous multisubunit homodimeric complexes. These remarkable molecular machines catalyze electron transfer from membranous quinones to water-soluble electron carriers (such as cytochromes c or plastocyanin), coupling electron flow to proton translocation across the energy-transducing membrane and contributing to the generation of a transmembrane electrochemical potential gradient, which powers cellular metabolism in the majority of living organisms. Cytsbc1/b6f share many similarities but also have significant differences. While decades of research have provided extensive knowledge on these enzymes, several important aspects of their molecular mechanisms remain to be elucidated. We summarize a broad range of structural, mechanistic, and physiological aspects required for function of Cytbc1/b6f, combining textbook fundamentals with new intriguing concepts that have emerged from more recent studies. The discussion covers but is not limited to (i) mechanisms of energy-conserving bifurcation of electron pathway and energy-wasting superoxide generation at the quinol oxidation site, (ii) the mechanism by which semiquinone is stabilized at the quinone reduction site, (iii) interactions with substrates and specific inhibitors, (iv) intermonomer electron transfer and the role of a dimeric complex, and (v) higher levels of organization and regulation that involve Cytsbc1/b6f. In addressing these topics, we point out existing uncertainties and controversies, which, as suggested, will drive further research in this field.
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Affiliation(s)
- Marcin Sarewicz
- Department
of Molecular Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
| | - Sebastian Pintscher
- Department
of Molecular Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
| | - Rafał Pietras
- Department
of Molecular Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
| | - Arkadiusz Borek
- Department
of Molecular Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
| | - Łukasz Bujnowicz
- Department
of Molecular Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
| | - Guy Hanke
- School
of Biological and Chemical Sciences, Queen
Mary University of London, London E1 4NS, U.K.
| | - William A. Cramer
- Department
of Biological Sciences, Purdue University, West Lafayette, Indiana 47907 United States
| | - Giovanni Finazzi
- Laboratoire
de Physiologie Cellulaire et Végétale, Université Grenoble Alpes, Centre National Recherche Scientifique,
Commissariat Energie Atomique et Energies Alternatives, Institut National
Recherche l’agriculture, l’alimentation et l’environnement, 38054 Grenoble Cedex 9, France
| | - Artur Osyczka
- Department
of Molecular Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
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3
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Francia F, Khalfaoui-Hassani B, Lanciano P, Musiani F, Noodleman L, Venturoli G, Daldal F. The cytochrome b lysine 329 residue is critical for ubihydroquinone oxidation and proton release at the Q o site of bacterial cytochrome bc 1. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2018; 1860:167-179. [PMID: 30550726 DOI: 10.1016/j.bbabio.2018.12.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Revised: 12/06/2018] [Accepted: 12/07/2018] [Indexed: 11/16/2022]
Abstract
The ubihydroquinone:cytochrome (cyt) c oxidoreductase (or cyt bc1) is an important enzyme for photosynthesis and respiration. In bacteria like Rhodobacter capsulatus, this membrane complex has three subunits, the iron‑sulfur protein (ISP) with its Fe2S2 cluster, cyt c1 and cyt b, forming two catalytic domains, the Qo (hydroquinone (QH2) oxidation) and Qi (quinone (Q) reduction) sites. At the Qo site, the electron transfer pathways originating from QH2 oxidation are known, but their associated proton release routes are less well defined. Earlier, we demonstrated that the His291 of cyt b is important for this latter process. In this work, using the bacterial cyt bc1 and site directed mutagenesis, we show that Lys329 of cyt b is also critical for electron and proton transfer at the Qo site. Of the mutants examined, Lys329Arg was photosynthesis proficient and had quasi-wild type cyt bc1 activity. In contrast, the Lys329Ala and Lys329Asp were photosynthesis-impaired and contained defective but assembled cyt bc1. In particular, the bifurcated electron transfer and associated proton(s) release reactions occurring during QH2 oxidation were drastically impaired in Lys329Asp mutant. Furthermore, in silico docking studies showed that in this mutant the location and the H-bonding network around the Fe2S2 cluster of ISP on cyt b surface was different than the wild type enzyme. Based on these experimental findings and theoretical considerations, we propose that the presence of a positive charge at position 329 of cyt b is critical for efficient electron transfer and proton release for QH2 oxidation at the Qo site of cyt bc1.
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Affiliation(s)
- Francesco Francia
- Dipartimento di Farmacia e Biotecnologie, FaBiT, Università di Bologna, 40126 Bologna, Italy
| | | | - Pascal Lanciano
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Francesco Musiani
- Dipartimento di Farmacia e Biotecnologie, FaBiT, Università di Bologna, 40126 Bologna, Italy
| | - Louis Noodleman
- The Scripps Research Institute, Department of Integrative Structural and Computational Biology, La Jolla, CA 92037, USA
| | - Giovanni Venturoli
- Dipartimento di Farmacia e Biotecnologie, FaBiT, Università di Bologna, 40126 Bologna, Italy; Consorzio Nazionale Interuniversitario per le Scienze Fisiche della Materia (CNISM), Dipartimento di Fisica, Università di Bologna, 40127 Bologna, Italy
| | - Fevzi Daldal
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA.
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4
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Gorczyński A, Harrowfield JM, Patroniak V, Stefankiewicz AR. Quaterpyridines as Scaffolds for Functional Metallosupramolecular Materials. Chem Rev 2016; 116:14620-14674. [DOI: 10.1021/acs.chemrev.6b00377] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Adam Gorczyński
- Faculty
of Chemistry, Adam Mickiewicz University, Umultowska 89b, 61614 Poznań, Poland
| | - Jack M. Harrowfield
- Institut
de Science et d’Ingénierie Supramoléculaires
(ISIS), Université de Strasbourg, 8 allée Gaspard Monge, 67083 Strasbourg, France
| | - Violetta Patroniak
- Faculty
of Chemistry, Adam Mickiewicz University, Umultowska 89b, 61614 Poznań, Poland
| | - Artur R. Stefankiewicz
- Faculty
of Chemistry, Adam Mickiewicz University, Umultowska 89b, 61614 Poznań, Poland
- Centre
for Advanced Technologies, Adam Mickiewicz University, Umultowska
89c, 61-614 Poznań, Poland
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5
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Vladkova R. Chlorophyllais the crucial redox sensor and transmembrane signal transmitter in the cytochromeb6fcomplex. Components and mechanisms of state transitions from the hydrophobic mismatch viewpoint. J Biomol Struct Dyn 2015; 34:824-54. [DOI: 10.1080/07391102.2015.1056551] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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6
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Chen F, Han P, Liu P, Si N, Liu J, Liu X. Activity of the novel fungicide SYP-Z048 against plant pathogens. Sci Rep 2014; 4:6473. [PMID: 25253681 PMCID: PMC4174571 DOI: 10.1038/srep06473] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Accepted: 08/19/2014] [Indexed: 11/09/2022] Open
Abstract
In in vitro tests with 18 plant pathogens, the fungicide 3-[5-(4-chlorophenyl)-2,3-dimethyl-3-isoxazolidinyl] pyridine (SYP-Z048) was highly effective on inhibiting mycelial growth of various ascomycota and basidiomycota, with EC50 values ranging from 0.008 to 1.140 μg/ml. SYP-Z048 had much weaker activity against growth of oomycota with EC50 values > 100 μg/ml. In a second in vitro test with Monilinia fructicola isolates, SYP-Z048 inhibited mycelial growth (EC50 = 0.013 μg/ml), germ tube elongation (EC50 = 0.007 μg/ml), and sporulation but did not affect spore germination. In a detached pear fruit assay inoculated with M. fructicola isolates, SYP-Z048 showed protective and curative activity. Field tests indicated that SYP-Z048 was an efficacious fungicide for control of brown rot disease in two peach orchards. When applied to a single spot on a tomato leaflet in a compound leaf, SYP-Z048 suppressed the growth of Botrytis cinerea isolates on the rest 4 leaflets, indicating that the fungicide has systemic movement in plant tissues. These results indicate that SYP-Z048 has potential for management of brown rot causing by M. fructicola and other diseases caused by ascomycota and basidiomycota.
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Affiliation(s)
- Fengping Chen
- Key Laboratory of Plant Virology of Fujian Province, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou. 350002, China
- Department of Plant Pathology, China Agricultural University, Beijing 100193, China
| | - Ping Han
- Department of Plant Pathology, China Agricultural University, Beijing 100193, China
- Beijing Research Center for Agricultural Standards and Testing, Beijing 100097, China
| | - Pengfei Liu
- Department of Plant Pathology, China Agricultural University, Beijing 100193, China
| | - Naiguo Si
- State Key Laboratory of the Discovery and Development of Novel Pesticide, China ShenYang Research Institute of Chemical Industry, Shenyang 110021, China
| | - Junli Liu
- State Key Laboratory of the Discovery and Development of Novel Pesticide, China ShenYang Research Institute of Chemical Industry, Shenyang 110021, China
| | - Xili Liu
- Department of Plant Pathology, China Agricultural University, Beijing 100193, China
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7
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Zhang X, Wu D, Duan Y, Ge C, Wang J, Zhou M, Chen C. Biological characteristics and resistance analysis of the novel fungicide SYP-1620 against Botrytis cinerea. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2014; 114:72-78. [PMID: 25175653 DOI: 10.1016/j.pestbp.2014.06.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Revised: 06/29/2014] [Accepted: 06/29/2014] [Indexed: 06/03/2023]
Abstract
SYP-1620, a quinone-outside-inhibitor (QoI), is a novel broad-spectrum fungicide. In this study, 108 isolates of Botrytis cinerea from different geographical regions in Jiangsu Province of China were characterized for baseline sensitivity to SYP-1620. The curves of baseline sensitivity were unimodal with a mean EC50 value of 0.0130±0.0109 μg/mL for mycelial growth, 0.01147±0.0062 μg/mL for spore germination, respectively. The biological characterization of SYP-1620 against B. cinerea was determined in vitro. The results indicated that SYP-1620 has a strong inhibiting effect on spore germination, mycelial growth, and respiration. The protective and curative test of SYP-1620 suggested that protective effect was better than curative either on strawberry leaves or on cucumber leaves in vivo. In addition, the biological characterization of SYP-1620-resistant mutants of B. cinerea was investigated. SYP-1620 has no cross-resistance with other types of fungicide. Compared to the sensitive isolates, the resistant mutants had lower mycelial growth and virulence but not differ in mycelial dry weight. Sequencing indicated that SYP-1620 resistance was associated with a single point mutation (G143A) in the cytochrome b gene.
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Affiliation(s)
- Xiaoke Zhang
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, Jiangsu Province, China; Key Laboratory of Monitoring and Management of Crop Diseases and Pest Insects, Ministry of Agriculture, Nanjing 210095, Jiangsu Province, China; Key Laboratory of Pesticide, Nanjing 210095, Jiangsu Province, China.
| | - Dongxia Wu
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, Jiangsu Province, China; Key Laboratory of Monitoring and Management of Crop Diseases and Pest Insects, Ministry of Agriculture, Nanjing 210095, Jiangsu Province, China; Key Laboratory of Pesticide, Nanjing 210095, Jiangsu Province, China
| | - Yabing Duan
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, Jiangsu Province, China; Key Laboratory of Monitoring and Management of Crop Diseases and Pest Insects, Ministry of Agriculture, Nanjing 210095, Jiangsu Province, China; Key Laboratory of Pesticide, Nanjing 210095, Jiangsu Province, China
| | - Changyan Ge
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, Jiangsu Province, China; Key Laboratory of Monitoring and Management of Crop Diseases and Pest Insects, Ministry of Agriculture, Nanjing 210095, Jiangsu Province, China; Key Laboratory of Pesticide, Nanjing 210095, Jiangsu Province, China
| | - Jianxin Wang
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, Jiangsu Province, China; Key Laboratory of Monitoring and Management of Crop Diseases and Pest Insects, Ministry of Agriculture, Nanjing 210095, Jiangsu Province, China; Key Laboratory of Pesticide, Nanjing 210095, Jiangsu Province, China
| | - Mingguo Zhou
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, Jiangsu Province, China; Key Laboratory of Monitoring and Management of Crop Diseases and Pest Insects, Ministry of Agriculture, Nanjing 210095, Jiangsu Province, China; Key Laboratory of Pesticide, Nanjing 210095, Jiangsu Province, China
| | - Changjun Chen
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, Jiangsu Province, China; Key Laboratory of Monitoring and Management of Crop Diseases and Pest Insects, Ministry of Agriculture, Nanjing 210095, Jiangsu Province, China; Key Laboratory of Pesticide, Nanjing 210095, Jiangsu Province, China.
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8
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Cooley JW. Protein conformational changes involved in the cytochrome bc1 complex catalytic cycle. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2013; 1827:1340-5. [PMID: 23876289 DOI: 10.1016/j.bbabio.2013.07.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2013] [Revised: 05/23/2013] [Accepted: 07/15/2013] [Indexed: 11/28/2022]
Abstract
Early structures of the cytochrome bc1 complex revealed heterogeneity in the position of the soluble portion of the Rieske iron sulfur protein subunit, implicating a movement of this domain during function. Subsequent biochemical and biophysical works have firmly established that the motion of this subunit acts in the capacity of a conformationally assisted electron transfer step during the already complicated catalytic mechanism described within the modified version of Peter Mitchells Q cycle. How the movement of this subunit is initiated or how the frequency of its motion is controlled as a function of other steps during the catalysis remain topics of debate within the active research communities. This review addresses the historical aspects of the discovery and description of this movement, while attempting to provide a context for the involvement of conformational motion in the catalysis and efficiency of the enzyme. This article is part of a Special Issue entitled: Respiratory complex III and related bc complexes.
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Affiliation(s)
- Jason W Cooley
- Department of Chemistry, University of Missouri, Columbia, MO 65211-7600, USA.
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9
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Millett F, Havens J, Rajagukguk S, Durham B. Design and use of photoactive ruthenium complexes to study electron transfer within cytochrome bc1 and from cytochrome bc1 to cytochrome c. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2012; 1827:1309-19. [PMID: 22985600 DOI: 10.1016/j.bbabio.2012.09.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2012] [Revised: 08/29/2012] [Accepted: 09/03/2012] [Indexed: 10/27/2022]
Abstract
The cytochrome bc1 complex (ubiquinone:cytochrome c oxidoreductase) is the central integral membrane protein in the mitochondrial respiratory chain as well as the electron-transfer chains of many respiratory and photosynthetic prokaryotes. Based on X-ray crystallographic studies of cytochrome bc1, a mechanism has been proposed in which the extrinsic domain of the iron-sulfur protein first binds to cytochrome b where it accepts an electron from ubiquinol in the Qo site, and then rotates by 57° to a position close to cytochrome c1 where it transfers an electron to cytochrome c1. This review describes the development of a ruthenium photooxidation technique to measure key electron transfer steps in cytochrome bc1, including rapid electron transfer from the iron-sulfur protein to cytochrome c1. It was discovered that this reaction is rate-limited by the rotational dynamics of the iron-sulfur protein rather than true electron transfer. A conformational linkage between the occupant of the Qo ubiquinol binding site and the rotational dynamics of the iron-sulfur protein was discovered which could play a role in the bifurcated oxidation of ubiquinol. A ruthenium photoexcitation method is also described for the measurement of electron transfer from cytochrome c1 to cytochrome c. This article is part of a Special Issue entitled: Respiratory Complex III and related bc complexes.
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Key Words
- 2,2′-bipyrazine
- 2,2′-bipyridine
- 2,2′:4′,4″:2″,2‴-quaterpyridine
- 2Fe2S
- 3,3′-bipyridazine
- 4,4′-dimethyl-2,2′-bipridine
- Cc
- CcO
- Cytochrome bc(1)
- Cytochrome c
- Electron transfer
- ISP
- JG144
- MOAS
- P(f)
- P(m)
- Q
- Q(i)
- Q(o)
- Q(o) site inhibitor which fixes ISP in b state
- Q(o) site inhibitor which promotes mobile state of ISP
- QH(2)
- R. sphaeroides
- Rhodobacter sphaeroides
- Rieske iron–sulfur center
- Ru(2)D
- Ruthenium
- S-3-anilino-5-methyl-5-(4,6-difluorophenyl)-1,3-oxazolidine-2,4-dione
- [Ru(bpy)(2)](2)qpy(4+)
- bpd
- bpy
- bpz
- cyt bc(1)
- cytochrome bc(1)
- cytochrome c
- cytochrome c oxidase
- dmb
- inside ubiquinone binding site
- iron–sulfur protein
- methoxyacrylate stilbene
- outside ubiquinol binding site
- qpy
- ubiquinol
- ubiquionone
- yCc
- yeast Cc
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Affiliation(s)
- Francis Millett
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, USA.
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10
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Havens J, Castellani M, Kleinschroth T, Ludwig B, Durham B, Millett F. Photoinitiated electron transfer within the Paracoccus denitrificans cytochrome bc1 complex: mobility of the iron-sulfur protein is modulated by the occupant of the Q(o) site. Biochemistry 2011; 50:10462-72. [PMID: 22026826 DOI: 10.1021/bi200453r] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Domain rotation of the Rieske iron-sulfur protein (ISP) between the cytochrome (cyt) b and cyt c(1) redox centers plays a key role in the mechanism of the cyt bc(1) complex. Electron transfer within the cyt bc(1) complex of Paracoccus denitrificans was studied using a ruthenium dimer to rapidly photo-oxidize cyt c(1) within 1 μs and initiate the reaction. In the absence of any added quinol or inhibitor of the bc(1) complex at pH 8.0, electron transfer from reduced ISP to cyt c(1) was biphasic with rate constants of k(1f) = 6300 ± 3000 s(-1)and k(1s) = 640 ± 300 s(-1) and amplitudes of 10 ± 3% and 16 ± 4% of the total amount of cyt c(1) photooxidized. Upon addition of any of the P(m) type inhibitors MOA-stilbene, myxothiazol, or azoxystrobin to cyt bc(1) in the absence of quinol, the total amplitude increased 2-fold, consistent with a decrease in redox potential of the ISP. In addition, the relative amplitude of the fast phase increased significantly, consistent with a change in the dynamics of the ISP domain rotation. In contrast, addition of the P(f) type inhibitors JG-144 and famoxadone decreased the rate constant k(1f) by 5-10-fold and increased the amplitude over 2-fold. Addition of quinol substrate in the absence of inhibitors led to a 2-fold increase in the amplitude of the k(1f) phase. The effect of QH(2) on the kinetics of electron transfer from reduced ISP to cyt c(1) was thus similar to that of the P(m) inhibitors and very different from that of the P(f) inhibitors. The current results indicate that the species occupying the Q(o) site has a significant conformational influence on the dynamics of the ISP domain rotation.
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Affiliation(s)
- Jeffrey Havens
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas 72701, United States
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11
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Berry EA, Huang LS. Conformationally linked interaction in the cytochrome bc(1) complex between inhibitors of the Q(o) site and the Rieske iron-sulfur protein. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2011; 1807:1349-63. [PMID: 21575592 DOI: 10.1016/j.bbabio.2011.04.005] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2011] [Revised: 04/01/2011] [Accepted: 04/01/2011] [Indexed: 10/18/2022]
Abstract
The modified Q cycle mechanism accounts for the proton and charge translocation stoichiometry of the bc(1) complex, and is now widely accepted. However the mechanism by which the requisite bifurcation of electron flow at the Q(o) site reaction is enforced is not clear. One of several proposals involves conformational gating of the docking of the Rieske ISP at the Q(o) site, controlled by the stage of the reaction cycle. Effects of different Q(o)-site inhibitors on the position of the ISP seen in crystals may reflect the same conformational mechanism, in which case understanding how different inhibitors control the position of the ISP may be a key to understanding the enforcement of bifurcation at the Q(o) site (Table 1). Here we examine the available structures of cytochrome bc(1) with different Q(o)-site inhibitors and different ISP positions to look for clues to this mechanism. The effect of ISP removal on binding affinity of the inhibitors stigmatellin and famoxadone suggest a "mutual stabilization" of inhibitor binding and ISP docking, however this thermodynamic observation sheds little light on the mechanism. The cd(1) helix of cytochrome b moves in such a way as to accommodate docking when inhibitors favoring docking are bound, but it is impossible with the current structures to say whether this movement of α-cd(1) is a cause or result of ISP docking. One component of the movement of the linker between E and F helices also correlates with the type of inhibitor and ISP position, and seems to be related to the H-bonding pattern of Y279 of cytochrome b. An H-bond from Y279 to the ISP, and its possible modulation by movement of F275 in the presence of famoxadone and related inhibitors, or its competition with an alternate H-bond to I269 of cytochrome b that may be destabilized by bound famoxadone, suggest other possible mechanisms. This article is part of a Special Issue entitled: Allosteric cooperativity in respiratory proteins.
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Affiliation(s)
- Edward A Berry
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, USA.
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12
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13
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Millett F, Durham B. Chapter 5 Use of ruthenium photooxidation techniques to study electron transfer in the cytochrome bc1 complex. Methods Enzymol 2009; 456:95-109. [PMID: 19348884 PMCID: PMC2761082 DOI: 10.1016/s0076-6879(08)04405-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Ruthenium photooxidation methods are presented to study electron transfer between the cytochrome bc(1) complex and cytochrome c and within the cytochrome bc(1) complex. Methods are described to prepare a ruthenium cytochrome c derivative, Ru(z)-39-Cc, by labeling the single sulfhydryl on yeast H39C;C102T iso-1-Cc with the reagent Ru(bpz)(2)(4-bromomethyl-4'-methylbipyridine). The ruthenium complex attached to Cys-39 on the opposite side of Cc from the heme crevice does not affect the interaction with cyt bc(1). Laser excitation of reduced Ru(z)-39-Cc results in photooxidation of heme c within 1 microsec with a yield of 20%. Flash photolysis of a 1:1 complex between reduced yeast cytochrome bc(1) and Ru(z)-39-Cc leads to electron transfer from heme c(1) to heme c with a rate constant of 1.4 x 10(4) s(-1). Methods are described for the use of the ruthenium dimer, Ru(2)D, to photooxidize cyt c(1) in the cytochrome bc(1) complex within 1 microsec with a yield of 20%. Electron transfer from the Rieske iron-sulfur center [2Fe2S] to cyt c(1) was detected with a rate constant of 6 x 10(4) s(-1) in R. sphaeroides cyt bc(1) with this method. This electron transfer step is rate-limited by the rotation of the Rieske iron-sulfur protein in a conformational gating mechanism. This method provides critical information on the dynamics of rotation of the iron-sulfur protein (ISP) as it transfers electrons from QH(2) in the Q(o) site to cyt c(1). These ruthenium photooxidation methods can be used to measure many of the electron transfer reactions in cytochrome bc(1) complexes from any source.
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Rajagukguk S, Yang S, Yu CA, Yu L, Durham B, Millett F. Effect of mutations in the cytochrome b ef loop on the electron-transfer reactions of the Rieske iron-sulfur protein in the cytochrome bc1 complex. Biochemistry 2007; 46:1791-8. [PMID: 17253777 PMCID: PMC2527182 DOI: 10.1021/bi062094g] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Long-range movement of the Rieske iron-sulfur protein (ISP) between the cytochrome (cyt) b and cyt c1 redox centers plays a key role in electron transfer within the cyt bc1 complex. A series of 21 mutants in the cyt b ef loop of Rhodobacter sphaeroides cyt bc1 were prepared to examine the role of this loop in controlling the capture and release of the ISP from cyt b. Electron transfer in the cyt bc1 complex was studied using a ruthenium dimer to rapidly photo-oxidize cyt c1 within 1 mus and initiate the reaction. The rate constant for electron transfer from the Rieske iron-sulfur center [2Fe2S] to cyt c1 was k1 = 60 000 s-1. Famoxadone binding to the Qo site decreases k1 to 5400 s-1, indicating that a conformational change on the surface of cyt b decreases the rate of release of the ISP from cyt b. The mutation I292A on the surface of the ISP-binding crater decreased k1 to 4400 s-1, while the addition of famoxadone further decreased it to 3000 s-1. The mutation L286A at the tip of the ef loop decreased k1 to 33 000 s-1, but famoxadone binding caused no further decrease, suggesting that this mutation blocked the conformational change induced by famoxadone. Studies of all of the mutants provide further evidence that the ef loop plays an important role in regulating the domain movement of the ISP to facilitate productive electron transfer and prevent short-circuit reactions.
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Affiliation(s)
- Sany Rajagukguk
- Department of Chemistry and Biochemistry University of Arkansas Fayetteville, Arkansas 72701
| | - Shaoqing Yang
- Department of Biochemistry and Molecular Biology Oklahoma State University Stillwater, Oklahoma 74078
| | - Chang-An Yu
- Department of Biochemistry and Molecular Biology Oklahoma State University Stillwater, Oklahoma 74078
| | - Linda Yu
- Department of Biochemistry and Molecular Biology Oklahoma State University Stillwater, Oklahoma 74078
| | - Bill Durham
- Department of Chemistry and Biochemistry University of Arkansas Fayetteville, Arkansas 72701
| | - Francis Millett
- Department of Chemistry and Biochemistry University of Arkansas Fayetteville, Arkansas 72701
- To whom correspondence should be addressed FAX: 479−575−4049, Phone: 479−575−4999, E-mail:
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Szaciłowski K, Macyk W, Drzewiecka-Matuszek A, Brindell M, Stochel G. Bioinorganic photochemistry: frontiers and mechanisms. Chem Rev 2005; 105:2647-94. [PMID: 15941225 DOI: 10.1021/cr030707e] [Citation(s) in RCA: 561] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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Pember SO, Fleck LC, Moberg WK, Walker MP. Mechanistic differences in inhibition of ubiquinol cytochrome c reductase by the proximal Qo-site inhibitors famoxadone and methoxyacrylate stilbene. Arch Biochem Biophys 2005; 435:280-90. [PMID: 15708371 DOI: 10.1016/j.abb.2004.12.013] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2004] [Revised: 12/09/2004] [Indexed: 11/22/2022]
Abstract
Famoxadone (FAM) is a newly commercialized antibiotic for use against plant pathogenic fungi. It inhibits mitochondria ubiquinol:cytochrome c oxidoreductase (EC 1.10.2.2, bc(1) complex) function by binding to the proximal niche of the quinol oxidation site on the enzyme. FAM has effects on the enzyme characteristic of both type Ia (E-beta-methoxyacrylates) and type Ic (stigmatellin) inhibitors. Steady-state and tight-binding inhibition kinetics; as well as direct binding measurements with famoxadone (FAM) and methoxyacrylate stilbene (MOAS), indicated that FAM is a non-competitive inhibitor of the enzyme while methoxyacrylate stilbene (MOAS) is better described as a mixed-competitive inhibitor with respect to substrate. Mixed-competitive and non-competitive inhibition kinetics predicts a ternary enzyme-substrate-inhibitor (ESI) intermediate in the reaction sequence. Current views of the Qo domain architecture propose substrate binding niches in both distal and proximal regions of the domain. Since both inhibitors bind within the proximal niche, the formation of an ESI complex implicates substrate binding within the distal niche near the iron-sulfur protein (ISP) and cytochrome c(1) (C1). In the presence of saturating FAM, addition of substrate led to a slow, nearly stoichiometric reduction of C1 that was enzyme dependent, and independent of O(2)(-) production. Similar experiments with saturating MOAS led to a slow, sub-stoichiometric reduction of C1 by substrate. A comparison of the stoichiometries of reduction, and the apparent second order rate constants (K(cat)/K(m)) indicated that saturating MOAS elicits two distinct enzyme-inhibitor (EI) intermediates. One form does not bind substrate, but the other does. In contrast, saturating FAM leads to a predominant EI form capable of binding substrate. We suggest that these differences can be correlated to the respective effects of each inhibitor on the position of the ISP, and the integrity of a distal substrate binding site. The results also indicate that binding of these inhibitory substrate analogues to the proximal niche of the Qo domain significantly increases the DeltaG(double dagger) for reduction of C1.
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Affiliation(s)
- Stephen O Pember
- E.I. Dupont Company, Division of Agriculture and Nutrition, Stine Haskell Research Center, 1094 Elkton Rd., Newark, DE 19711-3507, USA.
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Abstract
The bc1 complexes are intrinsic membrane proteins that catalyze the oxidation of ubihydroquinone and the reduction of cytochrome c in mitochondrial respiratory chains and bacterial photosynthetic and respiratory chains. The bc1 complex operates through a Q-cycle mechanism that couples electron transfer to generation of the proton gradient that drives ATP synthesis. Genetic defects leading to mutations in proteins of the respiratory chain, including the subunits of the bc1 complex, result in mitochondrial myopathies, many of which are a direct result of dysfunction at catalytic sites. Some myopathies, especially those in the cytochrome b subunit, exacerbate free-radical damage by enhancing superoxide production at the ubihydroquinone oxidation site. This bypass reaction appears to be an unavoidable feature of the reaction mechanism. Cellular aging is largely attributable to damage to DNA and proteins from the reactive oxygen species arising from superoxide and is a major contributing factor in many diseases of old age. An understanding of the mechanism of the bc1 complex is therefore central to our understanding of the aging process. In addition, a wide range of inhibitors that mimic the quinone substrates are finding important applications in clinical therapy and agronomy. Recent structural studies have shown how many of these inhibitors bind, and have provided important clues to the mechanism of action and the basis of resistance through mutation. This paper reviews recent advances in our understanding of the mechanism of the bc1 complex and their relation to these physiologically important issues in the context of the structural information available.
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Affiliation(s)
- Antony R Crofts
- Department of Biochemistry, and Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA.
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