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Schweitzer-Stenner R. Heme-Protein Interactions and Functional Relevant Heme Deformations: The Cytochrome c Case. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27248751. [PMID: 36557884 PMCID: PMC9781506 DOI: 10.3390/molecules27248751] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 11/28/2022] [Accepted: 11/29/2022] [Indexed: 12/14/2022]
Abstract
Heme proteins are known to perform a plethora of biologically important functions. This article reviews work that has been conducted on various class I cytochrome c proteins over a period of nearly 50 years. The article focuses on the relevance of symmetry-lowering heme-protein interactions that affect the function of the electron transfer protein cytochrome c. The article provides an overview of various, mostly spectroscopic studies that explored the electronic structure of the heme group in these proteins and how it is affected by symmetry-lowering deformations. In addition to discussing a large variety of spectroscopic studies, the article provides a theoretical framework that should enable a comprehensive understanding of the physical chemistry that underlies the function not only of cytochrome c but of all heme proteins.
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2
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Mitochondrial COA7 is a heme-binding protein with disulfide reductase activity, which acts in the early stages of complex IV assembly. Proc Natl Acad Sci U S A 2022; 119:2110357119. [PMID: 35210360 PMCID: PMC8892353 DOI: 10.1073/pnas.2110357119] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/11/2022] [Indexed: 12/12/2022] Open
Abstract
Assembly factors play key roles in the biogenesis of mitochondrial protein complexes, regulating their stabilities, activities, and incorporation of essential cofactors. Cytochrome c oxidase assembly factor 7 (COA7) is a metazoan-specific assembly factor, the absence or mutation of which in humans accompanies complex IV assembly defects and neurological conditions. Here, we report the crystal structure of COA7 to 2.4 Å resolution, revealing a banana-shaped molecule composed of five helix-turn-helix (α/α) repeats. COA7 binds heme with micromolar affinity, even though the protein structure does not resemble previously characterized heme-binding proteins. The heme-bound COA7 can redox cycle between oxidation states Fe(II) and Fe(III) and shows disulfide reductase activity toward copper binding assembly factors. We propose that COA7 functions to facilitate the biogenesis of the binuclear copper site (CuA) of complex IV. Cytochrome c oxidase (COX) assembly factor 7 (COA7) is a metazoan-specific assembly factor, critical for the biogenesis of mitochondrial complex IV (cytochrome c oxidase). Although mutations in COA7 have been linked to complex IV assembly defects and neurological conditions such as peripheral neuropathy, ataxia, and leukoencephalopathy, the precise role COA7 plays in the biogenesis of complex IV is not known. Here, we show that loss of COA7 blocks complex IV assembly after the initial step where the COX1 module is built, progression from which requires the incorporation of copper and addition of the COX2 and COX3 modules. The crystal structure of COA7, determined to 2.4 Å resolution, reveals a banana-shaped molecule composed of five helix-turn-helix (α/α) repeats, tethered by disulfide bonds. COA7 interacts transiently with the copper metallochaperones SCO1 and SCO2 and catalyzes the reduction of disulfide bonds within these proteins, which are crucial for copper relay to COX2. COA7 binds heme with micromolar affinity, through axial ligation to the central iron atom by histidine and methionine residues. We therefore propose that COA7 is a heme-binding disulfide reductase for regenerating the copper relay system that underpins complex IV assembly.
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3
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Sedlák E, Žár T, Varhač R, Musatov A, Tomášková N. Anion-Specific Effects on the Alkaline State of Cytochrome c. BIOCHEMISTRY (MOSCOW) 2021; 86:59-73. [PMID: 33705282 DOI: 10.1134/s0006297921010065] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Specific effects of anions on the structure, thermal stability, and peroxidase activity of native (state III) and alkaline (state IV) cytochrome c (cyt c) have been studied by the UV-VIS absorbance spectroscopy, intrinsic tryptophan fluorescence, and circular dichroism. Thermal and isothermal denaturation monitored by the tryptophan fluorescence and circular dichroism, respectively, implied lower stability of cyt c state IV in comparison with the state III. The pKa value of alkaline isomerization of cyt c depended on the present salts, i.e., kosmotropic anions increased and chaotropic anions decreased pKa (Hofmeister effect on protein stability). The peroxidase activity of cyt c in the state III, measured by oxidation of guaiacol, showed clear dependence on the salt position in the Hofmeister series, while cyt c in the alkaline state lacked the peroxidase activity regardless of the type of anions present in the solution. The alkaline isomerization of cyt c in the presence of 8 M urea, measured by Trp59 fluorescence, implied an existence of a high-affinity non-native ligand for the heme iron even in a partially denatured protein conformation. The conformation of the cyt c alkaline state in 8 M urea was considerably modulated by the specific effect of anions. Based on the Trp59 fluorescence quenching upon titration to alkaline pH in 8 M urea and molecular dynamics simulation, we hypothesize that the Lys79 conformer is most likely the predominant alkaline conformer of cyt c. The high affinity of the sixth ligand for the heme iron is likely a reason of the lack of peroxidase activity of cyt c in the alkaline state.
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Affiliation(s)
- Erik Sedlák
- Department of Biochemistry, Faculty of Science, P. J. Šafárik University in Košice, Košice, 04154, Slovakia. .,Centre for Interdisciplinary Biosciences, P. J. Šafárik University in Košice, Košice, 04154, Slovakia
| | - Tibor Žár
- Centre for Interdisciplinary Biosciences, P. J. Šafárik University in Košice, Košice, 04154, Slovakia.
| | - Rastislav Varhač
- Department of Biochemistry, Faculty of Science, P. J. Šafárik University in Košice, Košice, 04154, Slovakia.
| | - Andrej Musatov
- Department of Biophysics, Institute of Experimental Physics, Slovak Academy of Sciences, Košice, 040 01, Slovakia.
| | - Nataša Tomášková
- Department of Biochemistry, Faculty of Science, P. J. Šafárik University in Košice, Košice, 04154, Slovakia.
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4
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Vogt S, Irqsusi M, Naraghi H, Sattler A, Ruppert V, Weber P, Rhiel A, Ramzan R. Mitochondrial active and relaxed state respiration after heat shock mRNA response in the heart. J Therm Biol 2019; 80:106-112. [PMID: 30784473 DOI: 10.1016/j.jtherbio.2019.01.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 01/02/2019] [Accepted: 01/06/2019] [Indexed: 12/11/2022]
Abstract
Induction of Heat Shock Proteins results in cytoprotection. Beneficial effect results from transcription and translational cellular components' involvement that defends metabolism and thus induce ischemic protection of the tissue. Mitochondrial respiration is also involved in stress- induced conditions. It is not a uniform process. Cytochrome c Oxidase (CytOx) representing complex IV of the Electron Transfer Chain (ETC) has a regulatory role for mitochondrial respiratory activity, which is tested in our study after hsp induction. Moreover, protein translation for mitochondrial components was probed by the detection of MT-CO1 for Subunit 1 of CytOx neosynthesis. Wistar rats were subjected to whole-body hyperthermia at 42.0-42.5 °C for 15 min followed by a normothermic recovery period. Heat shock response was monitored time dependent from LV biopsies of all control and heat treated animals with PCR-analysis for hsp 32, 60, 70.1, 70.2, 90 and MT-CO1 expression at 15, 30, 45, 60, 120 and 360 min recovery (n = 5 in each group), respectively. Enzymatic activity of CytOx were evaluated polarographically. High energy phosphates were detected by chromatographic analysis. The mRNA expression of MT-CO1 peaked at 60 min and was accompanied by hsp 32 (r = 0.457; p = 0.037) and hsp 70.2 (r = 0.615; p = 0.003) upregulation. With hsp induction, mitochondrial respiration was increased initially. Enzymatic activity reconciled from active into relaxed status wherein CytOx activity was completely inhibited by ATP. Myocardial ATP content increased from stress induced point i.e. < 1 µmol g-1 protein w/w to finally 1.5 ± 0.53 µmol g-1 protein w/w at 120 min recovery interval. Hyperthermic, myocardial hsp- induction goes along with increased CytOx activity representing an increased "active" mitochondrial respiration. In parallel, de -novo holoenzyme assembly of CytOx begins as shown by MT-CO1 upregulation at 60 min recovery time crossing with a final return to the physiological "relaxed" state and ATP -inhibited respiration.
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Affiliation(s)
- Sebastian Vogt
- Cardiovascular Surgery, Universitätsklinikum Marburg und Giessen GmbH, Germany; Cardiovascular Research Lab, Biochemical Pharmacological Center, Philipps, University Marburg, Germany.
| | - Marc Irqsusi
- Cardiovascular Surgery, Universitätsklinikum Marburg und Giessen GmbH, Germany
| | - Hamid Naraghi
- Cardiovascular Surgery, Universitätsklinikum Marburg und Giessen GmbH, Germany
| | - Alexander Sattler
- Center for Internal Medicine, Cardiology, Universitätsklinikum Marburg und Giessen GmbH, Germany
| | - Volker Ruppert
- Center for Internal Medicine, Cardiology, Universitätsklinikum Marburg und Giessen GmbH, Germany
| | - Petra Weber
- Cardiovascular Surgery, Universitätsklinikum Marburg und Giessen GmbH, Germany; Cardiovascular Research Lab, Biochemical Pharmacological Center, Philipps, University Marburg, Germany
| | - Annika Rhiel
- Cardiovascular Surgery, Universitätsklinikum Marburg und Giessen GmbH, Germany; Cardiovascular Research Lab, Biochemical Pharmacological Center, Philipps, University Marburg, Germany
| | - Rabia Ramzan
- Cardiovascular Surgery, Universitätsklinikum Marburg und Giessen GmbH, Germany; Cardiovascular Research Lab, Biochemical Pharmacological Center, Philipps, University Marburg, Germany
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5
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Deng Y, Zhong F, Alden SL, Hoke KR, Pletneva EV. The K79G Mutation Reshapes the Heme Crevice and Alters Redox Properties of Cytochrome c. Biochemistry 2018; 57:5827-5840. [PMID: 30142276 DOI: 10.1021/acs.biochem.8b00650] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The two roles of cytochrome c (cyt c), in oxidative phosphorylation and apoptosis, critically depend on redox properties of its heme iron center. The K79G mutant has served as a parent protein for a series of mutants of yeast iso-1 cyt c. The mutation preserves the Met80 coordination to the heme iron, as found in WT* (K72A/C102S), and many spectroscopic properties of K79G and WT* are indistinguishable. The K79G mutation does not alter the global stability, fold, rate of Met80 dissociation, or thermodynamics of the alkaline transition (p Ka) of the protein. However, the reduction potential of the heme iron decreases; further, the p KH of the trigger group and the rate of the Met-to-Lys ligand exchange associated with the alkaline transition decrease, suggesting changes in the environment of the heme. The rates of electron self-exchange and bimolecular electron transfer (ET) with positively charged inorganic complexes increase, as does the intrinsic peroxidase activity. Analysis of the reaction rates suggests that there is increased accessibility of the heme edge in K79G and supports the importance of the Lys79 site for bimolecular ET reactions of cyt c, including those with some of its native redox partners. Structural modeling rationalizes the observed effects to arise from changes in the volume of the heme pocket and solvent accessibility of the heme group. Kinetic and structural analyses of WT* characterize the properties of the heme crevice of this commonly employed reference variant. This study highlights the important role of Lys79 for defining functional redox properties of cyt c.
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Affiliation(s)
- Yunling Deng
- Department of Chemistry , Dartmouth College , Hanover , New Hampshire 03755 , United States
| | - Fangfang Zhong
- Department of Chemistry , Dartmouth College , Hanover , New Hampshire 03755 , United States
| | - Stephanie L Alden
- Department of Chemistry , Dartmouth College , Hanover , New Hampshire 03755 , United States
| | - Kevin R Hoke
- Department of Chemistry and Biochemistry , Berry College , Mount Berry , Georgia 30149 , United States
| | - Ekaterina V Pletneva
- Department of Chemistry , Dartmouth College , Hanover , New Hampshire 03755 , United States
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6
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Alvarez-Paggi D, Hannibal L, Castro MA, Oviedo-Rouco S, Demicheli V, Tórtora V, Tomasina F, Radi R, Murgida DH. Multifunctional Cytochrome c: Learning New Tricks from an Old Dog. Chem Rev 2017; 117:13382-13460. [DOI: 10.1021/acs.chemrev.7b00257] [Citation(s) in RCA: 135] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Damián Alvarez-Paggi
- Departamento
de Química Inorgánica, Analítica y Química
Física and INQUIMAE (CONICET-UBA), Facultad de Ciencias Exactas
y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. 2, piso 1, Buenos Aires C1428EHA, Argentina
| | - Luciana Hannibal
- Department
of Pediatrics, Universitätsklinikum Freiburg, Mathildenstrasse 1, Freiburg 79106, Germany
- Departamento
de Bioquímica and Center for Free Radical and Biomedical Research,
Facultad de Medicina, Universidad de la República, Av.
Gral. Flores 2125, Montevideo 11800, Uruguay
| | - María A. Castro
- Departamento
de Química Inorgánica, Analítica y Química
Física and INQUIMAE (CONICET-UBA), Facultad de Ciencias Exactas
y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. 2, piso 1, Buenos Aires C1428EHA, Argentina
| | - Santiago Oviedo-Rouco
- Departamento
de Química Inorgánica, Analítica y Química
Física and INQUIMAE (CONICET-UBA), Facultad de Ciencias Exactas
y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. 2, piso 1, Buenos Aires C1428EHA, Argentina
| | - Veronica Demicheli
- Departamento
de Bioquímica and Center for Free Radical and Biomedical Research,
Facultad de Medicina, Universidad de la República, Av.
Gral. Flores 2125, Montevideo 11800, Uruguay
| | - Veronica Tórtora
- Departamento
de Bioquímica and Center for Free Radical and Biomedical Research,
Facultad de Medicina, Universidad de la República, Av.
Gral. Flores 2125, Montevideo 11800, Uruguay
| | - Florencia Tomasina
- Departamento
de Bioquímica and Center for Free Radical and Biomedical Research,
Facultad de Medicina, Universidad de la República, Av.
Gral. Flores 2125, Montevideo 11800, Uruguay
| | - Rafael Radi
- Departamento
de Bioquímica and Center for Free Radical and Biomedical Research,
Facultad de Medicina, Universidad de la República, Av.
Gral. Flores 2125, Montevideo 11800, Uruguay
| | - Daniel H. Murgida
- Departamento
de Química Inorgánica, Analítica y Química
Física and INQUIMAE (CONICET-UBA), Facultad de Ciencias Exactas
y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. 2, piso 1, Buenos Aires C1428EHA, Argentina
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7
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Chenge JT, Duyet LV, Swami S, McLean KJ, Kavanagh ME, Coyne AG, Rigby SEJ, Cheesman MR, Girvan HM, Levy CW, Rupp B, von Kries JP, Abell C, Leys D, Munro AW. Structural Characterization and Ligand/Inhibitor Identification Provide Functional Insights into the Mycobacterium tuberculosis Cytochrome P450 CYP126A1. J Biol Chem 2016; 292:1310-1329. [PMID: 27932461 PMCID: PMC5270475 DOI: 10.1074/jbc.m116.748822] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2016] [Revised: 12/02/2016] [Indexed: 12/12/2022] Open
Abstract
The Mycobacterium tuberculosis H37Rv genome encodes 20 cytochromes P450, including P450s crucial to infection and bacterial viability. Many M. tuberculosis P450s remain uncharacterized, suggesting that their further analysis may provide new insights into M. tuberculosis metabolic processes and new targets for drug discovery. CYP126A1 is representative of a P450 family widely distributed in mycobacteria and other bacteria. Here we explore the biochemical and structural properties of CYP126A1, including its interactions with new chemical ligands. A survey of azole antifungal drugs showed that CYP126A1 is inhibited strongly by azoles containing an imidazole ring but not by those tested containing a triazole ring. To further explore the molecular preferences of CYP126A1 and search for probes of enzyme function, we conducted a high throughput screen. Compounds containing three or more ring structures dominated the screening hits, including nitroaromatic compounds that induce substrate-like shifts in the heme spectrum of CYP126A1. Spectroelectrochemical measurements revealed a 155-mV increase in heme iron potential when bound to one of the newly identified nitroaromatic drugs. CYP126A1 dimers were observed in crystal structures of ligand-free CYP126A1 and for CYP126A1 bound to compounds discovered in the screen. However, ketoconazole binds in an orientation that disrupts the BC-loop regions at the P450 dimer interface and results in a CYP126A1 monomeric crystal form. Structural data also reveal that nitroaromatic ligands "moonlight" as substrates by displacing the CYP126A1 distal water but inhibit enzyme activity. The relatively polar active site of CYP126A1 distinguishes it from its most closely related sterol-binding P450s in M. tuberculosis, suggesting that further investigations will reveal its diverse substrate selectivity.
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Affiliation(s)
- Jude T Chenge
- From the Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Le Van Duyet
- From the Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Shalini Swami
- From the Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Kirsty J McLean
- From the Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Madeline E Kavanagh
- the Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Anthony G Coyne
- the Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Stephen E J Rigby
- From the Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Myles R Cheesman
- the School of Chemistry, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, United Kingdom, and
| | - Hazel M Girvan
- From the Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Colin W Levy
- From the Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Bernd Rupp
- the Leibniz-Institut für Molekulare Pharmakologie, Robert-Rössle-Strasse 10, 13125 Berlin, Germany
| | - Jens P von Kries
- the Leibniz-Institut für Molekulare Pharmakologie, Robert-Rössle-Strasse 10, 13125 Berlin, Germany
| | - Chris Abell
- the Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - David Leys
- From the Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Andrew W Munro
- From the Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom,
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8
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Met104 is the CO-replaceable ligand at Fe(II) heme in the CO-sensing transcription factor BxRcoM-1. J Biol Inorg Chem 2016; 21:559-69. [DOI: 10.1007/s00775-016-1368-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Accepted: 06/01/2016] [Indexed: 10/21/2022]
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9
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Lavrinenko IA, Vashanov GA, Artyukhov VG. Decomposition of the hemoglobin UV absorption spectrum into the absorption spectra of a prosthetic group and apoprotein using an additive model. Biophysics (Nagoya-shi) 2015. [DOI: 10.1134/s0006350915020098] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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10
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Pandiscia LA, Schweitzer-Stenner R. Coexistence of Native-like and Non-Native Partially Unfolded Ferricytochrome c on the Surface of Cardiolipin-Containing Liposomes. J Phys Chem B 2015; 119:1334-49. [DOI: 10.1021/jp5104752] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Leah A. Pandiscia
- Department
of Chemistry, Drexel University, Philadelphia, PA 19104, United States
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11
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Cytochrome c: A Multifunctional Protein Combining Conformational Rigidity with Flexibility. ACTA ACUST UNITED AC 2014. [DOI: 10.1155/2014/484538] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Cytochrome has served as a model system for studying redox reactions, protein folding, and more recently peroxidase activity induced by partial unfolding on membranes. This review illuminates some important aspects of the research on this biomolecule. The first part summarizes the results of structural analyses of its active site. Owing to heme-protein interactions the heme group is subject to both in-plane and out-of-plane deformations. The unfolding of the protein as discussed in detail in the second part of this review can be induced by changes of pH and temperature and most prominently by the addition of denaturing agents. Both the kinetic and thermodynamic folding and unfolding involve intermediate states with regard to all unfolding conditions. If allowed to sit at alkaline pH (11.5) for a week, the protein does not return to its folding state when the solvent is switched back to neutral pH. It rather adopts a misfolded state that is prone to aggregation via domain swapping. On the surface of cardiolipin containing liposomes, the protein can adopt a variety of partially unfolded states. Apparently, ferricytochrome c can perform biological functions even if it is only partially folded.
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12
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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: 549] [Impact Index Per Article: 54.9] [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
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13
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Sakamoto K, Kamiya M, Uchida T, Kawano K, Ishimori K. Redox-controlled backbone dynamics of human cytochrome c revealed by 15N NMR relaxation measurements. Biochem Biophys Res Commun 2010; 398:231-6. [DOI: 10.1016/j.bbrc.2010.06.065] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2010] [Accepted: 06/16/2010] [Indexed: 11/26/2022]
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14
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Verbaro D, Hagarman A, Soffer J, Schweitzer-Stenner R. The pH Dependence of the 695 nm Charge Transfer Band Reveals the Population of an Intermediate State of the Alkaline Transition of Ferricytochrome c at Low Ion Concentrations. Biochemistry 2009; 48:2990-6. [DOI: 10.1021/bi802208f] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Daniel Verbaro
- Department of Chemistry and Department of Biology, Drexel University, 3141 Chestnut Street, Philadelphia, Pennsylvania 19104
| | - Andrew Hagarman
- Department of Chemistry and Department of Biology, Drexel University, 3141 Chestnut Street, Philadelphia, Pennsylvania 19104
| | - Jonathan Soffer
- Department of Chemistry and Department of Biology, Drexel University, 3141 Chestnut Street, Philadelphia, Pennsylvania 19104
| | - Reinhard Schweitzer-Stenner
- Department of Chemistry and Department of Biology, Drexel University, 3141 Chestnut Street, Philadelphia, Pennsylvania 19104
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15
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Schweitzer-Stenner R, Hagarman A, Verbaro D, Soffer JB. Conformational Stability of Cytochrome c Probed by Optical Spectroscopy. Methods Enzymol 2009; 466:109-53. [DOI: 10.1016/s0076-6879(09)66006-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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16
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Dadak V, Holik M. Electrostatic attraction between cytochrome bc 1 and cytochrome c affects kinetics of cytochrome c reduction. BIOCHEMISTRY (MOSCOW) 2008; 73:870-80. [DOI: 10.1134/s000629790808004x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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17
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Takahashi I, Inomata T, Funahashi Y, Ozawa T, Masuda H. Electron-Transfer Reactions through the Associated Interaction between Cytochromec and Self-Assembled Monolayers of Optically Active Cobalt(III) Complexes: Molecular Recognition Ability Induced by the Chirality of the Cobalt(III) Units. Chemistry 2007; 13:8007-17. [PMID: 17616958 DOI: 10.1002/chem.200700155] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Self-assembled monolayers (SAMs) of optically active Co(III) complexes ((S)-2/(R)-2) that contain (S)- or (R)-phenylalanine derivatives as a molecular recognition site were constructed on Au electrodes ((S)-2-Au/(R)-2-Au). Molecular recognition characteristics induced by the S and R configurations were investigated by measurements of electron-transfer reactions with horse heart cytochrome c (cyt c). The electrochemical studies indicate that the maximum current of cyt c reduction is obtained when the Au electrode is modified by 2 with a moderate coverage of approximately 4.0 x 10(-11) mol cm(-2). Since the Au electrode is not densely packed with the Co(III) units at this concentration, we conclude that the penetrative association process between cyt c and the Co(III) unit plays an important role in this electron-transfer system. The differences in the electron-transfer rates of (S)-2-Au and (R)-2-Au increase with increasing scan rates, a result indicating that the chiral ligand has an influence on the rate of association of the complexes with cyt c. 3-Au has a mixed monolayer composed of 2 and hexanethiol and exhibits electron-transfer behavior comparable to 2-Au. The difference in the association rates of (S)-3-Au and (R)-3-Au is larger than that between (S)-2-Au and (R)-2-Au, which indicates that the molecular recognition ability of 3-Au has been enhanced by filling the gap between molecules of 2 with hexanethiols. The differences in the oxidation rates of cyt c(II) between (S)-2-Au and (R)-2-Au and between (S)-3-Au and (R)-3-Au were larger than the differences in the rates of the reduction of cyt c(III); this suggests that the size of the heme crevice varies according to the oxidation state of cyt c.
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Affiliation(s)
- Isao Takahashi
- Department of Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
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18
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Asakura N, Kamachi T, Okura I. Direct monitoring of the electron pool effect of cytochrome c3 by highly sensitive EQCM measurements. J Biol Inorg Chem 2004; 9:1007-16. [PMID: 15517437 DOI: 10.1007/s00775-004-0604-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2004] [Accepted: 09/28/2004] [Indexed: 10/26/2022]
Abstract
Cytochrome c(3) from Desulfovibrio vulgaris has four hemes per molecule, and a redox change at the hemes alters the conformation of the protein, leading to a redox-dependent change in the interaction of cytochrome c(3) with redox partners (an electron acceptor or an electron donor). The redox-dependent change in this interaction was directly monitored by the high-performance electrochemical quartz crystal microbalance (EQCM) technique that has been improved to give high sensitivity in solution. In this method, cytochrome c(3) molecules in solution associate electrostatically with a viologen-immobilized quartz crystal electrode as a monolayer, and redox of the associating cytochrome c(3) is controlled by the immobilized viologen. This technique makes it possible to measure the access of cytochrome c(3) to the electrode or repulsion from the electrode, and hence interconversion between an electrostatic complex and an electron transfer complex on the cytochrome c(3) and the viologen as a mass change accompanying a potential sweep is monitored. In addition, simultaneous measurement of a mass change and a potential step reveals that the cytochrome c(3) stores electrons when the four hemes are reduced (an electron pool effect), that is, the oxidized cytochrome c(3) facilitates acceptance of electrons from the immobilized viologen molecule, but the reduced cytochrome c(3) donates the accepted electrons to the viologen with difficulty.
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Affiliation(s)
- Noriyuki Asakura
- Department of Bioengineering, Tokyo Institute of Technology, 4259 Nagatsuta-cho, 226-8501, Yokohama, Japan
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19
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Bonincontro A, Risuleo G. Dielectric spectroscopy as a probe for the investigation of conformational properties of proteins. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2003; 59:2677-2684. [PMID: 14499827 DOI: 10.1016/s1386-1425(03)00085-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
In this brief paper, we review recent and significant results obtained in our laboratory by dielectric spectroscopy (DS). This is a multi purpose and very sensitive approach to investigate structural features of biological systems. DS at radiofrequencies is particularly powerful in the study of structural and conformational properties of proteins. We report on results obtained on three well-known proteins: lysozyme, cytochrome-c and metmyoglobin, which represent very useful models for folding/unfolding studies. The influence of pH and temperature as well as presence of trehalose as a co-solvent, was determined by estimation of the effective hydrodynamic radius and electric dipole moment of the protein in solution. In particular, trehalose was shown to affect the alkaline transition of cytochrome. Conformational effects on the three above-mentioned proteins were observed in a temperature range near the physiological ones. Dynamical properties of lysozyme in mixtures water-glycerol are also discussed. Parallel measurements of photon correlation spectroscopy (PCS) and DS indicated that both translational and rotational diffusive behavior are coherent with the Debye-Stokes-Einstein hydrodynamic model.
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Affiliation(s)
- Adalberto Bonincontro
- INFM-Dipartimento di Fisica, Università 'La Sapienza', P le A Moro 2, 00185 Rome, Italy
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20
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Yao Y, Tang W. NMR investigation of the alkaline-like conformational transition of horse heart cytochrome c in the presence of exogenous thiazole. Biophys Chem 2003; 104:459-68. [PMID: 12878313 DOI: 10.1016/s0301-4622(03)00031-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The conformational transition of horse heart cyt c in the presence of exogenous thiazole is investigated by NMR spectroscopy. Surprisingly, besides the native form and the ligand-bound form, another species (species A) exists at neutral pH. Titration of thiazole at alkaline condition indicates that this form has Lys as the axial ligands and in fact is one of alkaline cyt c conformers. At a high concentration of thiazole, species A has a dominant population at a pH of approximately 7. It is the first time that a pure alkaline conformer of cyt c is obtained at neutral pH. The observed NOEs show that species A maintains the overall protein fold although large structural rearrangements are expected in the distal pocket. Furthermore, the different effect of imidazole, pyridine and thiazole on the alkaline transformation of cyt c is discussed.
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Affiliation(s)
- Yong Yao
- State Key Laboratory of Coordination Chemistry, Nanjing University, 210093, Nanjing, PR China
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21
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Blouin C, Guillemette JG, Wallace CJA. Probing electrostatic interactions in cytochrome c using site-directed chemical modification. Biochem Cell Biol 2002; 80:197-203. [PMID: 11989715 DOI: 10.1139/o01-238] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
This communication reports the generation of an electrostatic probe using chemical modification of methionine side chains. The alkylation of methionine by iodoacetamide was achieved in a set of Saccharomyces cerevisiae iso-1-cytochrome c mutants, introducing the nontitratable, nondelocalized positive charge of a carboxyamidomethylmethionine sulfonium (CAMMS) ion at five surface and one buried site in the protein. Changes in redox potential and its variation with temperature were used to calculate microscopic effective dielectric constants operating between the probe and the heme iron. Dielectric constants (epsilon) derived from deltadeltaG values were not useful due to entropic effects, but epsilon(deltadeltaH) gave results that supported the theory. The effect on biological activity of surface derivatization was interpreted in terms of protein-protein interactions. The introduction of an electrostatic probe in cytochrome c often resulted in marked effects on activity with one of two physiological partners: cytochrome c reductase, especially if introduced at position 65, and cytochrome c oxidase, if at position 28.
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Affiliation(s)
- Christian Blouin
- Department of Biochemistry, Dalhousie University, Halifax, NS, Canada
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22
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Oellerich S, Wackerbarth H, Hildebrandt P. Spectroscopic Characterization of Nonnative Conformational States of Cytochrome c. J Phys Chem B 2002. [DOI: 10.1021/jp013841g] [Citation(s) in RCA: 199] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Silke Oellerich
- Max-Planck-Institut für Strahlenchemie, Stiftstrasse 34-36, D-45470 Mülheim, Germany, and Instituto de Tecnologia Química e Biológica, Apartado 127, Av. da República, 2781-901 Oeiras, Portugal
| | - Hainer Wackerbarth
- Max-Planck-Institut für Strahlenchemie, Stiftstrasse 34-36, D-45470 Mülheim, Germany, and Instituto de Tecnologia Química e Biológica, Apartado 127, Av. da República, 2781-901 Oeiras, Portugal
| | - Peter Hildebrandt
- Max-Planck-Institut für Strahlenchemie, Stiftstrasse 34-36, D-45470 Mülheim, Germany, and Instituto de Tecnologia Química e Biológica, Apartado 127, Av. da República, 2781-901 Oeiras, Portugal
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23
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Dadák V, Janiczek O, Vrána O. Cytochrome c forms complexes and is partly reduced at interaction with GPI-anchored alkaline phosphatase. BIOCHIMICA ET BIOPHYSICA ACTA 2002; 1570:9-18. [PMID: 11960683 DOI: 10.1016/s0304-4165(02)00145-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Cytochrome (cyt) c forms complexes, undergoes a conformational change and becomes partly reduced at interaction with membrane anchored alkaline phosphatase (AP), a glycoprotein which is released into the body fluid in forms differing in hydrophobicity. The proportion of products formed in the mixtures depends on pH, ionic strength, temperature and the buffer composition. The reaction terminates in an equilibrium between cyt c(FeII) and other cyt c conformers. Optimal conditions for the rate of the reaction are 100 mM glycine/NaOH, pH 9.7-9.9, at which 68-74% of cyt c is found in the reduced state. The interaction affects compactness of the haem cleft as shown by changes induced in CD spectra of the Soret region and changes in optical characteristics of phenylalanine, tyrosine and tryptophan residues. Differential scanning calorimetry of AP+cyt c mixtures revealed a creation of at least two types of complexes. A complex formed by non-coulombic binding prevails at substoichiometric AP/cyt c ratios, at higher ratios more electrostatic attraction is involved and at 1:1 molar ratio an apparent complexity of binding forces occurs. The rapid phase of the cyt c(FeII) formation depends on the presence of the hydrophobic alkylacylphosphoinositol (glycosylphosphatidylinositol) moiety, the protein part of the enzyme participates in an electrostatic and much slower phase of cyt c(FeII) creation. The results show that non-coulombic interaction may participate at interaction of cyt c with cellular proteins.
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Affiliation(s)
- Vladimír Dadák
- Department of Biochemistry, Faculty of Science, Masaryk University, 61137, Brno, Czech Republic
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24
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Cinelli S, Spinozzi F, Itri R, Finet S, Carsughi F, Onori G, Mariani P. Structural characterization of the pH-denatured states of ferricytochrome-c by synchrotron small angle X-ray scattering. Biophys J 2001; 81:3522-33. [PMID: 11721013 PMCID: PMC1301807 DOI: 10.1016/s0006-3495(01)75983-8] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
The ferricytochrome-c (cyt-c) shows a complex unfolding pathway characterized by a series of stable partially folded states. When titrated with HCl at low ionic strength, two transitions are detected. At pH 2, cyt-c assumes the U1 unfolded state, whereas the successive addition of Cl(-) ion from either HCl or NaCl induces the recompaction to a molten globule conformation (A1 and A2 states, respectively). A second unfolded state (U2) is also observed at pH 12. Recent data evidence different features for the local structure of the heme in the different states. To derive relationships between local and overall conformations, we analyzed the structural characteristics of the different states by synchrotron small angle X-ray scattering. The results show that in the acidic-unfolded U1 form the protein assumes a worm-like conformation, whereas in the alkaline-unfolded U2 state, the cyt-c is globular. Moreover, the molten globule states induced by adding HCl or NaCl to U1 appear structurally different: in the A1 state cyt-c is dimeric and less compact, whereas in the A2 form the protein reverts to a globular-like conformation. According to the local heme structure, a molecular model for the different forms is derived.
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Affiliation(s)
- S Cinelli
- Dipartimento di Fisica and INFM, Università di Perugia, Via Pascoli, I-06123 Perugia, Italy
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25
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26
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Conformational stability of ferricytochrome c near the heme in its complex with heparin in alkaline pH. Carbohydr Polym 2001. [DOI: 10.1016/s0144-8617(00)00253-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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27
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Murgida DH, Hildebrandt P. Heterogeneous Electron Transfer of Cytochrome c on Coated Silver Electrodes. Electric Field Effects on Structure and Redox Potential. J Phys Chem B 2001. [DOI: 10.1021/jp003742n] [Citation(s) in RCA: 155] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Daniel H. Murgida
- Max-Planck-Institut für Strahlenchemie, Stiftstrasse 34-36, D-45470 Mülheim, Germany
| | - Peter Hildebrandt
- Max-Planck-Institut für Strahlenchemie, Stiftstrasse 34-36, D-45470 Mülheim, Germany
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28
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Battistuzzi G, Borsari M, Ranieri A, Sola M. Effects of Specific Anion-Protein Binding on the Alkaline Transition of Cytochrome c. Arch Biochem Biophys 2001; 386:117-22. [PMID: 11360995 DOI: 10.1006/abbi.2000.2183] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The thermodynamic parameters of the alkaline transition of beef heart ferricytochrome c have been measured through direct electrochemistry experiments carried out at variable pH and temperature in the presence of different sulfate concentrations. Sulfate is known to bind specifically to cytochrome c in a sequential manner at two surface sites. The effects of such a specific binding reflect on the thermodynamics of the transition and can be satisfactorily interpreted within the frame of the Debye-Hückel theory with simple electrostatic considerations. In particular, the increase in the thermodynamic pKa values (extrapolated to I = 0) upon sulfate binding turns out to be a fully enthalpic effect which can be accounted for by considering the coulombic effects of the formation of ionic couple(s) on the protein surface. This study also shows that the apparent pKa values at finite ionic strength are only moderately affected by the nature of the anion in solution, and differences tend to vanish at high ionic strength.
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Affiliation(s)
- G Battistuzzi
- Department of Chemistry, University of Modena and Reggio Emilia, Italy
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29
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Döpner S, Hudecek J, Ludwig B, Witt H, Hildebrandt P. Structural changes in cytochrome c oxidase induced by cytochrome c binding. A resonance raman study. BIOCHIMICA ET BIOPHYSICA ACTA 2000; 1480:57-64. [PMID: 11004555 DOI: 10.1016/s0167-4838(00)00103-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Electrostatically stabilized complexes of fully oxidized cytochrome c oxidase from Paracoccus denitrificans and horse heart cytochrome c were studied by resonance Raman spectroscopy. The experiments were carried out with the wild-type oxidase and a variant in which a negatively charged amino acid in the binding domain (D257) is replaced by an asparagine. It is shown that cytochrome c induces structural changes at heme a and heme a(3) which are reminiscent to those found in mammalian cytochrome c oxidase-cytochrome c complex. The spectral changes are attributed to subtle changes in the heme-protein interactions implying that there is a structural communication from the binding domain even to the remote catalytic center. Only for the heme a modes minor spectral differences were found in the response of the wild-type and the D257N variant oxidase upon cytochrome c binding indicating that electrostatic interactions of aspartate 257 are not crucial for the perturbation of the catalytic site structure in the complex. On the other hand, in none of the complexes, structural changes were detected in the bound cytochrome c. These findings are in contrast to previous results obtained with beef heart cytochrome c oxidase which triggers the formation of a new conformational state of cytochrome c assumed to be involved in the biological electron transfer process.
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Affiliation(s)
- S Döpner
- Max-Planck-Institut für Strahlenchemie, Mülheim an der Ruhr, Germany
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30
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Bonincontro A, Bultrini E, Calandrini V, Cinelli S, Onori G. Effect of Trehalose on Alkaline Transition of Cytochrome-c. J Phys Chem B 2000. [DOI: 10.1021/jp993948s] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Adalberto Bonincontro
- INFM-Dipartimento di Fisica, Università “ La Sapienza “, Piazzale A. Moro 2, 00185 Roma, Italy, and INFM-Dipartimento di Fisica, Università di Perugia, Via A. Pascoli, I-06123 Perugia, Italy
| | - Emanuele Bultrini
- INFM-Dipartimento di Fisica, Università “ La Sapienza “, Piazzale A. Moro 2, 00185 Roma, Italy, and INFM-Dipartimento di Fisica, Università di Perugia, Via A. Pascoli, I-06123 Perugia, Italy
| | - Vania Calandrini
- INFM-Dipartimento di Fisica, Università “ La Sapienza “, Piazzale A. Moro 2, 00185 Roma, Italy, and INFM-Dipartimento di Fisica, Università di Perugia, Via A. Pascoli, I-06123 Perugia, Italy
| | - Stefania Cinelli
- INFM-Dipartimento di Fisica, Università “ La Sapienza “, Piazzale A. Moro 2, 00185 Roma, Italy, and INFM-Dipartimento di Fisica, Università di Perugia, Via A. Pascoli, I-06123 Perugia, Italy
| | - Giuseppe Onori
- INFM-Dipartimento di Fisica, Università “ La Sapienza “, Piazzale A. Moro 2, 00185 Roma, Italy, and INFM-Dipartimento di Fisica, Università di Perugia, Via A. Pascoli, I-06123 Perugia, Italy
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31
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Döpner S, Hildebrandt P, Rosell FI, Mauk AG, von Walter M, Buse G, Soulimane T. The structural and functional role of lysine residues in the binding domain of cytochrome c in the electron transfer to cytochrome c oxidase. EUROPEAN JOURNAL OF BIOCHEMISTRY 1999; 261:379-91. [PMID: 10215847 DOI: 10.1046/j.1432-1327.1999.00249.x] [Citation(s) in RCA: 92] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The interactions of yeast iso-1 cytochrome c with bovine cytochrome c oxidase were studied using cytochrome c variants in which lysines of the binding domain were substituted by alanines. Resonance Raman spectra of the fully oxidized complexes of both proteins reveal structural changes of both the heme c and the hemes a and a3. The structural changes in cytochrome c are the same as those observed upon binding to phospholipid vesicles where the bound protein exists in two conformers, B1 and B2. Whereas the structure of B1 is the same as that of the unbound cytochrome c, the formation of B2 is associated with substantial alterations of the heme pocket. In cytochrome c oxidase, the structural changes in both hemes refer to more subtle perturbations of the immediate protein environment and may be a result of a conformational equilibrium involving two states. These changes are qualitatively different to those observed for cytochrome c oxidase upon poly-l-lysine binding. The resonance Raman spectra of the various cytochrome c/cytochrome c oxidase complexes were analyzed quantitatively. The spectroscopic studies were paralleled by steady-state kinetic measurements of the same protein combinations. The results of the spectra analysis and the kinetic studies were used to determine the stability of the complexes and the conformational equilibria B2/B1 for all cytochrome c variants. The complex stability decreases in the order: wild-type WT > J72K > K79A > K73A > K87A > J72A > K86A > K73A/K79A (where J is the natural trimethyl lysine). This order is not exhibited by the conformational equilibria. The electrostatic control of state B2 formation does not depend on individual intermolecular salt bridges, but on the charge distribution in a specific region of the front surface of cytochrome c that is defined by the lysyl residues at positions 72, 73 and 79. On the other hand, the conformational changes in cytochrome c oxidase were found to be independent of the identity of the bound cytochrome c variant. The maximum rate constants determined from steady-state kinetic measurements could be related to the conformational equilibria of the bound cytochrome c using a simple model that assumes that the conformational transitions are faster than product formation. Within this model, the data analysis leads to the conclusion that the interprotein electron transfer rate constant is around two times higher in state B2 than in B1. These results can be interpreted in terms of an increase of the driving force in state B2 as a result of the large negative shift of the reduction potential.
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Affiliation(s)
- S Döpner
- Max-Planck-Institut für Strahlenchemie, Mülheim an der Ruhr, Germany
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32
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Abstract
The properties of the complexes of ferricytochrome c with two different polyanions--poly(vinylsulfate) and poly(4-styrene-sulfonate)--with a comparable charge density but with the different size of the uncharged part of their molecules have been studied by means of optical spectroscopy, differential scanning colorimetry, and gel chromatography. Ferriccytochrome c formed a complex with the former one through coulombic interactions and remained in a native-like state. The addition of the second polyanion to a solution of ferric cytochrome c at a low ionic strength, pH 7.0, resulted in profound conformational change in the hydrophobic core of protein (opening of the heme crevice with a perturbation of the methionine 80-heme iron bond and the hydrophobic core of the protein). These may be understood as an involvement of noncoulombic (hydrophobic, H-bonding) interactions of the uncharged part of the polyanion molecule. Conformational changes and the observed shift in acidic transition from low spin to high spin state of ferric cytochrome c detected in the presence of the polyanions may have biological implication in understanding the origin of conformational changes in proteins induced in the course of their interaction with membrane lipids and membrane proteins.
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Affiliation(s)
- E Sedlák
- Department of Biochemistry, Faculty of Science, P. J. Safárik University, Kosice, Slovakia
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33
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Moench SJ, Satterlee JD. A comparison of spectral and physicochemical properties of yeast iso-1 cytochrome c and Cys 102-modified derivatives of the protein. JOURNAL OF PROTEIN CHEMISTRY 1995; 14:567-82. [PMID: 8561853 DOI: 10.1007/bf01886883] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Derivatives of yeast iso-1 cytochrome c, chemically modified at Cys-102 (Cys-102 acetamide-derivatized monomer, Cys-102 thionitrobenzoate-derivatized monomer, Cys-102 S-methylated monomer, and the disulfide dimer), exhibit different spectral and physicochemical properties relative to the native, unmodified protein, depending on the nature of the modifying group. The results of proton NMR studies on the Cys-102 acetamide-derivatized monomer of iso-1 ferricytochrome c indicate that the conformational characteristics of the heme environment in this protein derivative are intermediate between those of the unmodified monomer and disulfide dimer forms of the protein. Measurements of the pKa of the alkaline transitions of the five forms of iso-1 ferricytochrome c provided values of 8.89, 8.82, 8.67, 8.47, and 8.50 for the unmodified monomer, S-methylated monomer, acetamide-derivatized monomer, thionitrobenzoate-derivatized monomer, and disulfide dimer, respectively. The results of proton NMR studies of the reduced form of these proteins suggest that the heme environments of the unmodified monomer and disulfide dimer derivatives of iso-1 ferrocytochrome c are similar and indicate that treatment of the thionitrobenzoate-derivatized and disulfide dimer forms of the protein with sodium dithionite results in cleavage of the disulfide bonds at position 102. Circular dichroism studies reveal that only the disulfide dimer form of iso-1 ferricytochrome c exhibits a Soret CD spectrum which differs from the native, unmodified monomer in that the intensity of the negative band at approximately 420 nm is diminished in the spectrum of the dimer relative to the spectrum of the monomer. Soret CD spectra of the ascorbate-reduced form of all protein derivatives are similar. The process of "autoreduction" of yeast iso-1 ferricytochrome c is shown to occur in the absence of a free sulfhydryl group at position 102 and is exacerbated under moderately high pH conditions. These results are suggestive of the presence of a redox-active amino acid, perhaps a tyrosine, in yeast iso-1 cytochrome c.
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Affiliation(s)
- S J Moench
- Department of Chemistry, Washington State Chemistry, Pullman 99164-4630, USA
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34
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Ubbink M, Canters GW. Mutagenesis of the conserved lysine 14 of cytochrome c-550 from Thiobacillus versutus affects the protein structure and the electron self-exchange rate. Biochemistry 1993; 32:13893-901. [PMID: 7903553 DOI: 10.1021/bi00213a019] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The lysine residue K14 of cytochrome c-550 of Thiobacillus versutus has been mutated to a glutamine (Q) and a glutamate (E) residue. These mutations have a minimal effect on the pKa for replacement of the methionine ligand (the "alkaline transition"), indicating that a presumptive salt bridge between K14 and E11 does not help stabilize the native form. This is in contrast with mitochondrial cytochrome c, where the homologous K13 forms a structurally important salt bridge with glutamate 90. The NMR signals of protons close to the heme iron in wild-type and mutant ferricytochrome c-550 shift considerably with increasing ionic strength. These effects resemble those seen in mitochondrial cytochrome c upon addition of salt and upon complex formation with redox partners. It is likely that electrostatic screening of positive charges near the heme crevice leads to a slight redistribution of the electron density in the heme. At low ionic strength the NMR spectrum of wild-type cytochrome c-550 shows broad peaks. Line widths decrease upon addition of salt up to 200 mM. In K14Q and K14E cytochrome c-550 the line widths are much smaller at low ionic strength. Wild-type cytochrome c-550 may exist in two exchanging conformations, one of which may represent a more open (non-native) form, in analogy with cytochrome c. However, in the case of cytochrome c-550 this non-native form does not show ligand replacement. The electron self-exchange rates of wild type and mutants have been determined as a function of the ionic strength.(ABSTRACT TRUNCATED AT 250 WORDS)
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Affiliation(s)
- M Ubbink
- Gorlaeus Laboratories, Department of Chemistry, Leiden University, The Netherlands
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35
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Lynch SR, Copeland RA. Electronic and vibrational spectroscopy of the cytochrome c:cytochrome c oxidase complexes from bovine and Paracoccus denitrificans. Protein Sci 1992; 1:1428-34. [PMID: 1338946 PMCID: PMC2142114 DOI: 10.1002/pro.5560011104] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The 1:1 complex between horse heart cytochrome c and bovine cytochrome c oxidase, and between yeast cytochrome c and Paracoccus denitrificans cytochrome c oxidase have been studied by a combination of second derivative absorption, circular dichroism (CD), and resonance Raman spectroscopy. The second derivative absorption and CD spectra reveal changes in the electronic transitions of cytochrome a upon complex formation. These results could reflect changes in ground state heme structure or changes in the protein environment surrounding the chromophore that affect either the ground or excited electronic states. The resonance Raman spectrum, on the other hand, reflects the heme structure in the ground electronic state only and shows no significant difference between cytochrome a vibrations in the complex or free enzyme. The only major difference between the Raman spectra of the free enzyme and complex is a broadening of the cytochrome a3 formyl band of the complex that is relieved upon complex dissociation at high ionic strength. These data suggest that the differences observed in the second derivative and CD spectra are the result of changes in the protein environment around cytochrome a that affect the electronic excited state. By analogy to other protein-chromophore systems, we suggest that the energy of the Soret pi* state of cytochrome a may be affected by (1) changes in the local dielectric, possibly brought about by movement of a charged amino acid side chain in proximity to the heme group, or (2) pi-pi interactions between the heme and aromatic amino acid residues.
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Affiliation(s)
- S R Lynch
- Department of Biochemistry and Molecular Biology, University of Chicago, Illinois 60637
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Dong AC, Huang P, Caughey WS. Redox-dependent changes in beta-extended chain and turn structures of cytochrome c in water solution determined by second derivative amide I infrared spectra. Biochemistry 1992; 31:182-9. [PMID: 1310028 DOI: 10.1021/bi00116a027] [Citation(s) in RCA: 136] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The redox-dependent changes in secondary structure of cytochromes c from horse, cow, and dog hearts in water at 20 degrees C have been determined by amide I infrared spectroscopy. Second derivative amide I spectra were obtained by use of a procedure that includes a convenient method for the effective subtraction of the spectrum of water vapor in the system. The band at 1657 cm-1 representing the helix structure was unaffected by a change in redox state whereas changes in bands due to turns at 1680, 1672, and 1666 cm-1, unordered structure at 1650 cm-1, and beta-structures at 1632 and 1627 cm-1 occurred. About one-fourth of the beta-extended chain spectral region and one-fifth of the beta-turn region (involving a total of approximately 9-13 residues) were sensitive to the oxidation state of heme iron. No significant changes in the secondary structure of either the reduced or oxidized protein due to changes in ionic strength were detected. The localized structural rearrangements triggered by the changes in oxidation state of heme iron are consistent with differences in the binding of heme iron to a histidine imidazole nitrogen and a methionine sulfur atom from the beta-extended chain. The demonstrated ability to obtain highly reproducible second derivative amide I infrared spectra confirms the unique utility of such spectral measurements for localization of subtle changes in secondary structure within a protein, especially for changes among the multiple turns and beta-structures.
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Affiliation(s)
- A C Dong
- Department of Biochemistry, Colorado State University, Fort Collins 80523
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Lynch SR, Sherman D, Copeland RA. Cytochrome c binding affects the conformation of cytochrome a in cytochrome c oxidase. J Biol Chem 1992. [DOI: 10.1016/s0021-9258(18)48493-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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Hildebrandt P, Heimburg T, Marsh D, Powell GL. Conformational changes in cytochrome c and cytochrome oxidase upon complex formation: a resonance Raman study. Biochemistry 1990; 29:1661-8. [PMID: 2159343 DOI: 10.1021/bi00458a044] [Citation(s) in RCA: 58] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The fully oxidized complex of cytochrome c and cytochrome oxidase formed at low ionic strength was studied by resonance Raman spectroscopy. The spectra of the complex and of the individual components were compared over a wide frequency range using Soret band excitation. In both partners of the complex, structural changes occur in the heme groups and in their immediate protein environment. The spectra of the complex in the 1600-1700 cm-1 frequency range were dominated by bands from the cytochrome oxidase component, whereas those in the 300-500 cm-1 range were dominated by bands from the cytochrome c component, hence allowing separation of the contributions from the two individual species. For cytochrome c, spectral changes were observed which correspond to the induction of the conformational state I and the six-coordinated low-spin configuration of state II on binding to cytochrome oxidase. While in state I the structure of cytochrome c is essentially the same as in solution, state II is characterized by a structural rearrangement of the heme pocket, leading to a weakening of the axial iron-methionine bond and an opening of the heme crevice which is situated in the center of the binding domain for cytochrome oxidase. The relative contributions of the two cytochrome c states were estimated to be approximately in the ratio 1:1 in the complex.(ABSTRACT TRUNCATED AT 250 WORDS)
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Affiliation(s)
- P Hildebrandt
- Max-Planck-Institut für biophysikalische Chemie, Abteilung Spektroskopie, Göttingen, FRG
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Saad B, Bosshard HR. Antigenic sites on cytochrome c2 from Rhodospirillum rubrum. EUROPEAN JOURNAL OF BIOCHEMISTRY 1990; 187:425-30. [PMID: 1688799 DOI: 10.1111/j.1432-1033.1990.tb15321.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The antigenic determinants for three monoclonal antibodies against cytochrome c2 from Rhodospirillum rubrum were partially characterized by differential chemical modification of free and antibody-bound cytochrome c2 and by cross-reactivity analysis with different antigens. Circular dichroism spectroscopy was used to probe the effect of antibody binding on the conformation of cytochrome c2. The binding of two antibodies was strongly dependent on the native folding of the antigen. The first antibody bound to a determinant around the exposed heme edge on the 'front side' of the molecule which is not antigenic in mitochondrial cytochrome c2. Binding of this antibody to cytochrome c increased the induced CD of the ferric heme in a manner similar to that observed previously when mitochondrial cytochrome-c oxidase bound to the front side of cytochrome c. This observation points to a subtle conformational adaptation of the antigen induced by the antibody. The determinant for the second antibody, which also affected the heme CD spectrum of the antigen, was on a polypeptide loop where cytochrome c2 differs from mitochondrial cytochrome c by an eight-residue insertion. The third antibody, which did not induce a change in CD, bound to a sequential determinant near the amino end of cytochrome c2. Only this antibody cross-reacted with isolated cytochrome-c-derived peptides and with apo-cytochrome c2. A preliminary analysis of the polyclonal immune response of five rats against cytochrome c2 indicates that, unlike in eukaryotic cytochrome c, antigenic determinants are distributed over the whole polypeptide chain of the prokaryotic immunogen.
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Affiliation(s)
- B Saad
- Biochemisches Institut, Universität Zürich, Switzerland
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Soussi B, Bylund-Fellenius AC, Scherstén T, Angström J. 1H-n.m.r. evaluation of the ferricytochrome c-cardiolipin interaction. Effect of superoxide radicals. Biochem J 1990; 265:227-32. [PMID: 2154181 PMCID: PMC1136634 DOI: 10.1042/bj2650227] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The interaction between ferricytochrome c and cardiolipin was investigated by 1H n.m.r. at 270 MHz. From the phospholipid-induced changes of the protein spectral features it is concluded that the first 2 equivalents of cardiolipin cause a conformational change at the lower part of the solvent-exposed haem edge, involving a rearrangement of the hydrogen-bond interactions of propionate 6, thus partly accounting for the lowered redox potential of cytochrome c in the presence of cardiolipin. The increased value for the pK of the alkaline isomerization of ferricytochrome c shows that cardiolipin stabilizes the native structure of the protein, indicating that the oxidized form assumes ferrocytochrome c-like properties. Peroxidation of cardiolipin by superoxide radical ions drastically decreases the protein binding to this phospholipid. The implications of this finding, and the likelihood of the ternary cytochrome c-cardiolipin-cytochrome c oxidase complex, for the binding of cytochrome c to cytochrome c oxidase in vivo, are discussed in relation to peroxidative damage following ischaemia and reperfusion.
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Affiliation(s)
- B Soussi
- Wallenberg Laboratory, Department of Surgery, University of Gothenburg, Sweden
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Wallace CJA, Mascagni P, Chait BT, Collawn JF, Paterson Y, Proudfoot AEI, Kent SBH. Substitutions engineered by chemical synthesis at three conserved sites in mitochondrial cytochrome c. J Biol Chem 1989. [DOI: 10.1016/s0021-9258(19)84810-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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Abstract
Mutation of conserved Phe-82 of yeast iso-1 cytochrome c to Tyr, Gly, Ser, Leu, or Ile affects binding to and reaction with cytochrome-c oxidase from beef heart. The observed changes of binding and kinetic constants reflect mutation-induced rearrangements in the heme vicinity brought about by the replacement of Phe-82. Such conformational rearrangements are also revealed by altered circular dichroism spectra of the oxidase-bound mutant cytochromes c. Variations in Km for cytochrome c oxidation do not parallel variations in Kd, the dissociation constant for binding of cytochrome c to the oxidase. This observation does not support an enzymatic mechanism in which the rate of cytochrome c oxidation is governed by product dissociation.
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Affiliation(s)
- B Michel
- Department of Biochemistry, University of Zürich, Switzerland
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Wilson MT, Alleyne T, Clague M, Conroy K, el-Agez B. Electron transfer and conformation states in bovine cytochrome c oxidase. Ann N Y Acad Sci 1988; 550:167-76. [PMID: 2854389 DOI: 10.1111/j.1749-6632.1988.tb35333.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The fluorophores 1,5-I-AEDANS and eosin maleimide bind to subunit III of bovine cytochrome c oxidase. Fluorescence lifetime measurements have been made of bound AEDANS under a number of conditions. It appears that the spatial relationship between this bound probe and metal centers is unaffected by the redox changes in the enzyme. Cyanide binding to CuA-modified cytochrome c oxidase during turnover suggests that reduction of cytochrome a leads to exposure of the cytochrome a3-CuB binuclear center to incoming ligands. These results are discussed in terms of a model describing the roles of cytochrome a and CuA in triggering the "closed" to "open" transition.
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Affiliation(s)
- M T Wilson
- Department of Chemistry and Biological Chemistry, University of Essex, United Kingdom
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Rush JD, Koppenol WH, Garber EA, Margoliash E. Conformational stability of ferrocytochrome c. Electrostatic aspects of the oxidation by tris(1,10-phenanthroline)cobalt(III) at low ionic strength. J Biol Chem 1988. [DOI: 10.1016/s0021-9258(18)68528-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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