1
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Lopes J, Marques-da-Silva D, Videira PA, Samhan-Arias AK, Lagoa R. Cardiolipin Membranes Promote Cytochrome c Transformation of Polycyclic Aromatic Hydrocarbons and Their In Vivo Metabolites. Molecules 2024; 29:1129. [PMID: 38474641 DOI: 10.3390/molecules29051129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 02/25/2024] [Accepted: 02/28/2024] [Indexed: 03/14/2024] Open
Abstract
The catalytic properties of cytochrome c (Cc) have captured great interest in respect to mitochondrial physiology and apoptosis, and hold potential for novel enzymatic bioremediation systems. Nevertheless, its contribution to the metabolism of environmental toxicants remains unstudied. Human exposure to polycyclic aromatic hydrocarbons (PAHs) has been associated with impactful diseases, and animal models have unveiled concerning signs of PAHs' toxicity to mitochondria. In this work, a series of eight PAHs with ionization potentials between 7.2 and 8.1 eV were used to challenge the catalytic ability of Cc and to evaluate the effect of vesicles containing cardiolipin mimicking mitochondrial membranes activating the peroxidase activity of Cc. With moderate levels of H2O2 and at pH 7.0, Cc catalyzed the oxidation of toxic PAHs, such as benzo[a]pyrene, anthracene, and benzo[a]anthracene, and the cardiolipin-containing membranes clearly increased the PAH conversions. Our results also demonstrate for the first time that Cc and Cc-cardiolipin complexes efficiently transformed the PAH metabolites 2-hydroxynaphthalene and 1-hydroxypyrene. In comparison to horseradish peroxidase, Cc was shown to reach more potent oxidizing states and react with PAHs with ionization potentials up to 7.70 eV, including pyrene and acenaphthene. Spectral assays indicated that anthracene binds to Cc, and docking simulations proposed possible binding sites positioning anthracene for oxidation. The results give support to the participation of Cc in the metabolism of PAHs, especially in mitochondria, and encourage further investigation of the molecular interaction between PAHs and Cc.
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Affiliation(s)
- João Lopes
- School of Technology and Management, Polytechnic Institute of Leiria, Morro do Lena-Alto do Vieiro, 2411-901 Leiria, Portugal
- Laboratory of Separation and Reaction Engineering-Laboratory of Catalysis and Materials (LSRE-LCM), School of Management and Technology, Polytechnic Institute of Leiria, 2411-901 Leiria, Portugal
- Associate Laboratory in Chemical Engineering (ALiCE), Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
| | - Dorinda Marques-da-Silva
- School of Technology and Management, Polytechnic Institute of Leiria, Morro do Lena-Alto do Vieiro, 2411-901 Leiria, Portugal
- Laboratory of Separation and Reaction Engineering-Laboratory of Catalysis and Materials (LSRE-LCM), School of Management and Technology, Polytechnic Institute of Leiria, 2411-901 Leiria, Portugal
- Associate Laboratory in Chemical Engineering (ALiCE), Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
| | - Paula A Videira
- Applied Molecular Biosciences Unit (UCIBIO), NOVA School of Science and Technology, NOVA University of Lisbon, 2829-516 Caparica, Portugal
- Institute for Health and Bioeconomy (i4HB), NOVA School of Science and Technology, NOVA University of Lisbon, 2829-516 Caparica, Portugal
| | - Alejandro K Samhan-Arias
- Department of Biochemistry, Autonoma University of Madrid (UAM), C/Arturo Duperier 4, 28029 Madrid, Spain
- Institute for Biomedical Research 'Sols-Morreale' (CSIC-UAM), C/Arturo Duperier 4, 28029 Madrid, Spain
| | - Ricardo Lagoa
- School of Technology and Management, Polytechnic Institute of Leiria, Morro do Lena-Alto do Vieiro, 2411-901 Leiria, Portugal
- Laboratory of Separation and Reaction Engineering-Laboratory of Catalysis and Materials (LSRE-LCM), School of Management and Technology, Polytechnic Institute of Leiria, 2411-901 Leiria, Portugal
- Associate Laboratory in Chemical Engineering (ALiCE), Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
- Applied Molecular Biosciences Unit (UCIBIO), NOVA School of Science and Technology, NOVA University of Lisbon, 2829-516 Caparica, Portugal
- Institute for Health and Bioeconomy (i4HB), NOVA School of Science and Technology, NOVA University of Lisbon, 2829-516 Caparica, Portugal
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2
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Proskurnin MA, Proskurnina EV, Galimova VR, Alekseev AV, Mikheev IV, Vladimirov YA. Composition of the Cytochrome c Complex with Cardiolipin by Thermal Lens Spectrometry. Molecules 2023; 28:molecules28062692. [PMID: 36985664 PMCID: PMC10057424 DOI: 10.3390/molecules28062692] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 03/07/2023] [Accepted: 03/14/2023] [Indexed: 03/19/2023] Open
Abstract
Thermal lens spectrometry along with spectrophotometric titration were used to assess the composition of the complex of oxidized cytochrome c (ferricytochrome c) with 1,1′,2,2′-tetraoleyl cardiolipin, which plays a key role in the initiation of apoptosis. Spectrophotometric titration was carried out for micromolar concentrations at which the complex is mainly insoluble, to assess the residual concentration in the solution and to estimate the solubility of the complex. Thermal lens spectrometry was used as a method of molecular absorption spectroscopy, which has two advantages over conventional optical transmission spectroscopy: the higher sensitivity of absorbance measurements and the possibility of studying the light absorption by chromophores and heat transfer in complex systems, such as living cells or tissues. Thermal lens measurements were carried out at nanomolar concentrations, where the complex is mainly in solution, i.e., under the conditions of its direct measurements. From the thermal lens measurements, the ratios of cytochrome c and cardiolipin in the complex were 50 at pH 7.4; 30 at pH 6.8; and 10 at pH 5.5, which fit well to the spectrophotometric data. The molecular solubility of the complex at pH 6.8–7.4 was estimated as 30 µmol/L.
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Affiliation(s)
- Mikhail A. Proskurnin
- Analytical Chemistry Division, Chemistry Department, M.V. Lomonosov Moscow State University, d. 1, Str. 3, Lenin Hills, GSP-1 V-234, 119991 Moscow, Russia;
- Correspondence: (M.A.P.); (I.V.M.); Tel.: +7-495-939-15-68 (I.V.M.)
| | - Elena V. Proskurnina
- Laboratory of Molecular Biology, Research Centre for Medical Genetics, 1 Moskvorechye St, 115522 Moscow, Russia;
| | - Viktoriya R. Galimova
- Analytical Chemistry Division, Chemistry Department, M.V. Lomonosov Moscow State University, d. 1, Str. 3, Lenin Hills, GSP-1 V-234, 119991 Moscow, Russia;
| | - Andrei V. Alekseev
- Russian Research Institute of Aviation Materials, ul. Radio 17, 105005 Moscow, Russia;
| | - Ivan V. Mikheev
- Analytical Chemistry Division, Chemistry Department, M.V. Lomonosov Moscow State University, d. 1, Str. 3, Lenin Hills, GSP-1 V-234, 119991 Moscow, Russia;
- Correspondence: (M.A.P.); (I.V.M.); Tel.: +7-495-939-15-68 (I.V.M.)
| | - Yuri A. Vladimirov
- Faculty of Basic Medicine, M.V. Lomonosov Moscow State University, Leninskie Gory, A, 119991 Moscow, Russia;
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3
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Bian H, Ma D, Pan F, Zhang X, Xin K, Zhang X, Yang Y, Peng X, Xiao Y. Cardiolipin-Targeted NIR-II Fluorophore Causes "Avalanche Effects" for Re-Engaging Cancer Apoptosis and Inhibiting Metastasis. J Am Chem Soc 2022; 144:22562-22573. [PMID: 36445324 DOI: 10.1021/jacs.2c08602] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Restoring innate apoptosis and simultaneously inhibiting metastasis by a molecular drug is an effective cancer therapeutic approach. Herein, a large rigid and V-shaped NIR-II dye, DUT850, is rationally designed for potential cardiolipin (CL)-targeted chemo-phototheranostic application. DUT850 displays moderate NIR-II fluorescence, excellent photodynamic therapy (PDT) and photothermal therapy (PTT) performance, and ultra-high photostability. More importantly, the unique rigid V-shaped backbone, positive charge, and lipophilicity of DUT850 afford its specific recognition and efficient binding to CL; such an interaction of DUT850-CL induced a spectrum of physiological disruptions, including translocation of cytochrome c, Ca2+ overload, reactive oxygen species burst, and ATP depletion, which not only activated cancer cell apoptosis but also inhibited tumor metastasis both in vitro and in vivo. Furthermore, the tight binding of DUT850-CL improves the phototoxicity of DUT850 toward cancer cells (IC50 as low as 90 nM) under safe 808 nm laser irradiation (330 mW cm-2). Upon encapsulation into bovine serum albumin (BSA), DUT850@BSA exerted a synergetic chemo-PDT-PTT effect on the 4T1 tumor mouse model, eventually leading to solid tumor annihilation and metastasis inhibition, which could be followed in real time with the NIR-II fluorescence of DUT850. This work contributed a promising approach for simultaneously re-engaging cancer cell apoptotic networks and activating the anti-metastasis pathway by targeting a pivotal upstream effector, which will bring a medical boon for inhibition of tumor proliferation and metastasis.
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Affiliation(s)
- Hui Bian
- State Key Laboratory of Fine Chemicals, Frontiers Science Center for Smart Materials Oriented Chemical Engineering, Dalian University of Technology, 2 Linggong Road, Dalian 116024, P. R. China
| | - Dandan Ma
- State Key Laboratory of Fine Chemicals, Frontiers Science Center for Smart Materials Oriented Chemical Engineering, Dalian University of Technology, 2 Linggong Road, Dalian 116024, P. R. China
| | - Fei Pan
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing 100093, P. R. China
| | - Xiaodong Zhang
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, P. R. China
| | - Kai Xin
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, P. R. China
| | - Xinfu Zhang
- State Key Laboratory of Fine Chemicals, Frontiers Science Center for Smart Materials Oriented Chemical Engineering, Dalian University of Technology, 2 Linggong Road, Dalian 116024, P. R. China
| | - Youjun Yang
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, P. R. China
| | - Xiaojun Peng
- State Key Laboratory of Fine Chemicals, Frontiers Science Center for Smart Materials Oriented Chemical Engineering, Dalian University of Technology, 2 Linggong Road, Dalian 116024, P. R. China
| | - Yi Xiao
- State Key Laboratory of Fine Chemicals, Frontiers Science Center for Smart Materials Oriented Chemical Engineering, Dalian University of Technology, 2 Linggong Road, Dalian 116024, P. R. China
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4
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Corey RA, Harrison N, Stansfeld PJ, Sansom MSP, Duncan AL. Cardiolipin, and not monolysocardiolipin, preferentially binds to the interface of complexes III and IV. Chem Sci 2022; 13:13489-13498. [PMID: 36507170 PMCID: PMC9682889 DOI: 10.1039/d2sc04072g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 10/25/2022] [Indexed: 12/15/2022] Open
Abstract
The mitochondrial electron transport chain comprises a series of protein complexes embedded in the inner mitochondrial membrane that generate a proton motive force via oxidative phosphorylation, ultimately generating ATP. These protein complexes can oligomerize to form larger structures called supercomplexes. Cardiolipin (CL), a conical lipid, unique within eukaryotes to the inner mitochondrial membrane, has proven essential in maintaining the stability and function of supercomplexes. Monolysocardiolipin (MLCL) is a CL variant that accumulates in people with Barth syndrome (BTHS). BTHS is caused by defects in CL biosynthesis and characterised by abnormal mitochondrial bioenergetics and destabilised supercomplexes. However, the mechanisms by which MLCL causes pathogenesis remain unclear. Here, multiscale molecular dynamics characterise the interactions of CL and MLCL with yeast and mammalian mitochondrial supercomplexes containing complex III (CIII) and complex IV (CIV). Coarse-grained simulations reveal that both CL and MLCL bind to sites at the interface between CIII and CIV of the supercomplex. Free energy perturbation calculations show that MLCL interaction is weaker than that of CL and suggest that interaction with CIV drives this difference. Atomistic contact analyses show that, although interaction with CIII is similar for CL and MLCL, CIV makes more contacts with CL than MLCL, demonstrating that CL is a more successful "glue" between the two complexes. Simulations of the human CIII2CIV supercomplex show that this interface site is maintained between species. Our study suggests that MLCL accumulation in people with BTHS disrupts supercomplex stability by formation of relatively weak interactions at the interface lipid binding site.
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Affiliation(s)
- Robin A Corey
- Department of Biochemistry, University of Oxford South Parks Road Oxford OX1 3QU UK
| | - Noah Harrison
- Department of Biochemistry, University of Oxford South Parks Road Oxford OX1 3QU UK
| | - Philllp J Stansfeld
- School of Life Sciences & Department of Chemistry, University of Warwick Coventry CV4 7AL UK
| | - Mark S P Sansom
- Department of Biochemistry, University of Oxford South Parks Road Oxford OX1 3QU UK
| | - Anna L Duncan
- Department of Biochemistry, University of Oxford South Parks Road Oxford OX1 3QU UK
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5
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Kleinwächter I, Mohr B, Joppe A, Hellmann N, Bereau T, Osiewacz HD, Schneider D. CLiB - a novel cardiolipin-binder isolated via data-driven and in vitro screening. RSC Chem Biol 2022; 3:941-954. [PMID: 35866160 PMCID: PMC9257654 DOI: 10.1039/d2cb00125j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 06/01/2022] [Indexed: 11/21/2022] Open
Abstract
Cardiolipin, the mitochondria marker lipid, is crucially involved in stabilizing the inner mitochondrial membrane and is vital for the activity of mitochondrial proteins and protein complexes. Directly targeting cardiolipin by a chemical-biology approach and thereby altering the cellular concentration of "available" cardiolipin eventually allows to systematically study the dependence of cellular processes on cardiolipin availability. In the present study, physics-based coarse-grained free energy calculations allowed us to identify the physical and chemical properties indicative of cardiolipin selectivity and to apply these to screen a compound database for putative cardiolipin-binders. The membrane binding properties of the 22 most promising molecules identified in the in silico approach were screened in vitro, using model membrane systems finally resulting in the identification of a single molecule, CLiB (CardioLipin-Binder). CLiB clearly affects respiration of cardiolipin-containing intact bacterial cells as well as of isolated mitochondria. Thus, the structure and function of mitochondrial membranes and membrane proteins might be (indirectly) targeted and controlled by CLiB for basic research and, potentially, also for therapeutic purposes.
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Affiliation(s)
- Isabel Kleinwächter
- Department of Chemistry, Biochemistry, Johannes Gutenberg University Mainz Hanns-Dieter-Hüsch-Weg 17 55128 Mainz Germany
| | - Bernadette Mohr
- Van 't Hoff Institute for Molecular Sciences and Informatics Institute, University of Amsterdam Amsterdam The Netherlands
| | - Aljoscha Joppe
- Institute for Molecular Biosciences, J. W. Goethe University Frankfurt am Main Germany
| | - Nadja Hellmann
- Department of Chemistry, Biochemistry, Johannes Gutenberg University Mainz Hanns-Dieter-Hüsch-Weg 17 55128 Mainz Germany
| | - Tristan Bereau
- Van 't Hoff Institute for Molecular Sciences and Informatics Institute, University of Amsterdam Amsterdam The Netherlands
| | - Heinz D Osiewacz
- Institute for Molecular Biosciences, J. W. Goethe University Frankfurt am Main Germany
| | - Dirk Schneider
- Department of Chemistry, Biochemistry, Johannes Gutenberg University Mainz Hanns-Dieter-Hüsch-Weg 17 55128 Mainz Germany
- Institute of Molecular Physiology, Johannes Gutenberg University Mainz Hanns-Dieter-Hüsch-Weg 17 55128 Mainz Germany
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6
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Cytochrome c Interaction with Cardiolipin Plays a Key Role in Cell Apoptosis: Implications for Human Diseases. Symmetry (Basel) 2022. [DOI: 10.3390/sym14040767] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
In the cell cytochrome, c performs different functions depending on the environment in which it acts; therefore, it has been classified as a multifunction protein. When anchored to the outer side of the inner mitochondrial membrane, native cytochrome c acts as a Schweitzer-StennerSchweitzer-Stenner that transfers electrons from cytochrome c reductase to cytochrome c oxidase in the respiratory chain. On the other hand, to interact with cardiolipin (one of the phospholipids making up the mitochondrial membrane) and form the cytochrome c/cardiolipin complex in the apoptotic process, the protein reorganizes its structure into a non-native state characterized by different asymmetry. The formation of the cytochrome c/cardiolipin complex is a fundamental step of the apoptotic pathway, since the structural rearrangement induces peroxidase activity in cytochrome c, the subsequent permeabilization of the membrane, and the release of the free protein into the cytoplasm, where cytochrome c activates the apoptotic process. Apoptosis is closely related to the pathogenesis of neoplastic, neurodegenerative and cardiovascular diseases; in this contest, the biosynthesis and remodeling of cardiolipin are crucial for the regulation of the apoptotic process. Since the role of cytochrome c as a promoter of apoptosis strictly depends on the non-native conformation(s) that the protein acquires when bound to the cardiolipin and such event leads to cytochrome c traslocation into the cytosol, the structural and functional properties of the cytochrome c/cardiolipin complex in cell fate will be the focus of the present review.
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7
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NMR Reveals the Conformational Changes of Cytochrome C upon Interaction with Cardiolipin. Life (Basel) 2021; 11:life11101031. [PMID: 34685404 PMCID: PMC8540660 DOI: 10.3390/life11101031] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 09/22/2021] [Accepted: 09/27/2021] [Indexed: 01/06/2023] Open
Abstract
Conformational change of cytochrome c (cyt c) caused by interaction with cardiolipin (CL) is an important step during apoptosis, but the underlying mechanism is controversial. To comprehensively clarify the structural transformations of cyt c upon interaction with CL and avoid the unpredictable alias that might come from protein labeling or mutations, the conformation of purified yeast iso–1 cyt c with natural isotopic abundance in different contents of CL was measured by using NMR spectroscopy, in which the trimethylated group of the protein was used as a natural probe. The data demonstrate that cyt c has two partially unfolded conformations when interacted with CL: one with Fe–His33 coordination and the other with a penta–coordination heme. The Fe–His33 coordination conformation can be converted into a penta–coordination heme conformation in high content of CL. The structure of cyt c becomes partially unfolded with more exposed heme upon interaction with CL, suggesting that cyt c prefers a high peroxidase activity state in the mitochondria, which, in turn, makes CL easy to be oxidized, and causes the release of cyt c into the cytoplasm as a trigger in apoptosis.
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8
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Di Rocco G, Bighi B, Borsari M, Bortolotti CA, Ranieri A, Sola M, Battistuzzi G. Electron Transfer and Electrocatalytic Properties of the Immobilized Met80Ala Cytochrome
c
Variant in Dimethylsulfoxide. ChemElectroChem 2021. [DOI: 10.1002/celc.202100499] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Giulia Di Rocco
- Department of Life Sciences University of Modena and Reggio Emilia via Campi 103 41125 Modena Italy
| | - Beatrice Bighi
- Department of Chemistry and Geology University of Modena and Reggio Emilia via Campi 103 41125 Modena Italy
| | - Marco Borsari
- Department of Chemistry and Geology University of Modena and Reggio Emilia via Campi 103 41125 Modena Italy
| | - Carlo Augusto Bortolotti
- Department of Life Sciences University of Modena and Reggio Emilia via Campi 103 41125 Modena Italy
| | - Antonio Ranieri
- Department of Life Sciences University of Modena and Reggio Emilia via Campi 103 41125 Modena Italy
| | - Marco Sola
- Department of Life Sciences University of Modena and Reggio Emilia via Campi 103 41125 Modena Italy
| | - Gianantonio Battistuzzi
- Department of Chemistry and Geology University of Modena and Reggio Emilia via Campi 103 41125 Modena Italy
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9
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Wilkinson JA, Silvera S, LeBlanc PJ. The effect of cardiolipin side chain composition on cytochrome c protein conformation and peroxidase activity. Physiol Rep 2021; 9:e14772. [PMID: 33667034 PMCID: PMC7934914 DOI: 10.14814/phy2.14772] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 01/21/2021] [Accepted: 02/01/2021] [Indexed: 12/26/2022] Open
Abstract
Skeletal muscle, a highly active tissue, makes up 40% of the total body weight. This tissue relies on mitochondria for ATP production, calcium homeostasis, and programed cell death. Mitochondrial phospholipid composition, namely, cardiolipin (CL), influences the functional efficiency of mitochondrial proteins, specifically cytochrome c. The interaction of CL with cytochrome c in the presence of free radicals induces structural and functional changes promoting peroxidase activity and cytochrome c release, a key event in the initiation of apoptosis. The CL acyl chain degree of saturation has been implicated in the cytochrome c to cytochrome c peroxidase transition in liposomal models. However, mitochondrial membranes are composed of differing CL acyl chain composition. Currently, it is unclear how differing CL acyl chain composition utilizing liposomes will influence the cytochrome c form and function as a peroxidase. Thus, this study examined the role of CL acyl chain saturation within liposomes broadly reflecting the relative CL composition of mitochondrial membranes from healthy and dystrophic mouse muscle on cytochrome c conformation and function. Despite no differences in protein conformation or function between healthy and dystrophic liposomes, cytochrome c's affinity to CL increased with greater unsaturation. These findings suggest that increasing CL acyl chain saturation, as implicated in muscle wasting diseases, may not influence cytochrome c transformation and function as a peroxidase but may alter its interaction with CL, potentially impacting further downstream effects.
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Affiliation(s)
- Jennifer A Wilkinson
- Center for Bone and Muscle Health, Faculty of Applied Health Sciences, Brock University, 1812 Sir Isaac Brock Way, St. Catharines, Ontario, L2S 3A1, Canada
| | - Sebastian Silvera
- Center for Bone and Muscle Health, Faculty of Applied Health Sciences, Brock University, 1812 Sir Isaac Brock Way, St. Catharines, Ontario, L2S 3A1, Canada
| | - Paul J LeBlanc
- Center for Bone and Muscle Health, Faculty of Applied Health Sciences, Brock University, 1812 Sir Isaac Brock Way, St. Catharines, Ontario, L2S 3A1, Canada
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10
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Rice M, Wong B, Oja M, Samuels K, Williams AK, Fong J, Sapse AM, Maran U, Korobkova EA. A role of flavonoids in cytochrome c-cardiolipin interactions. Bioorg Med Chem 2021; 33:116043. [PMID: 33530021 DOI: 10.1016/j.bmc.2021.116043] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 01/13/2021] [Accepted: 01/20/2021] [Indexed: 11/26/2022]
Abstract
The processes preceding the detachment of cytochrome c (cyt c) from the inner mitochondrial membrane in intrinsic apoptosis involve peroxidation of cardiolipin (CL) catalyzed by cyt c-CL complex. In the present work, we studied the effect of 17 dietary flavonoids on the peroxidase activity of cyt c bound to liposomes. Specifically, we explored the relationship between peroxidase activity and flavonoids' (1) potential to modulate cyt c unfolding, (2) effect on the oxidation state of heme iron, (3) membrane permeability, (4) membrane binding energy, and (5) structure. The measurements revealed that flavones, flavonols, and flavanols were the strongest, while isoflavones were the weakest inhibitors of the oxidation. Flavonoids' peroxidase inhibition activity correlated positively with their potential to suppress Trp-59 fluorescence in cyt c as well as the number of OH groups. Hydrophilic flavonoids, such as catechin, having the lowest membrane permeability and the strongest binding with phosphocholine (PC) based on the quantum chemical calculations exhibited the strongest inhibition of Amplex Red (AR) peroxidation, suggesting a membrane-protective function of flavonoids at the surface. The results of the present research specify basic principles for the design of molecules that will control the catalytic oxidation of lipids in mitochondrial membranes. These principles take into account the number of hydroxyl groups and hydrophilicity of flavonoids.
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Affiliation(s)
- Malaysha Rice
- Department of Sciences, John Jay College of Criminal Justice, City University of New York, 524 W 59th St., NY 10019, USA
| | - Bokey Wong
- Department of Sciences, John Jay College of Criminal Justice, City University of New York, 524 W 59th St., NY 10019, USA
| | - Mare Oja
- Institute of Chemistry, University of Tartu, Ravila 14A, Tartu 50411, Estonia
| | - Kelley Samuels
- Department of Sciences, John Jay College of Criminal Justice, City University of New York, 524 W 59th St., NY 10019, USA
| | - Alicia K Williams
- Department of Sciences, John Jay College of Criminal Justice, City University of New York, 524 W 59th St., NY 10019, USA
| | - Jenny Fong
- Department of Sciences, John Jay College of Criminal Justice, City University of New York, 524 W 59th St., NY 10019, USA
| | - Anne-Marie Sapse
- Department of Sciences, John Jay College of Criminal Justice, City University of New York, 524 W 59th St., NY 10019, USA; The Graduate Center at the City University of New York, 365 5th Ave, New York, NY 10016, USA
| | - Uko Maran
- Institute of Chemistry, University of Tartu, Ravila 14A, Tartu 50411, Estonia
| | - Ekaterina A Korobkova
- Department of Sciences, John Jay College of Criminal Justice, City University of New York, 524 W 59th St., NY 10019, USA.
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11
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Elmer-Dixon MM, Xie Z, Alverson JB, Priestley ND, Bowler BE. Curvature-Dependent Binding of Cytochrome c to Cardiolipin. J Am Chem Soc 2020; 142:19532-19539. [PMID: 33156621 DOI: 10.1021/jacs.0c07301] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Cytochrome c binds cardiolipin on the concave surface of the inner mitochondrial membrane, before oxidizing the lipid and initiating the apoptotic pathway. This interaction has been studied in vitro, where mimicking the membrane curvature of the binding environment is difficult. Here we report binding to concave, cardiolipin-containing, membrane surfaces and compare findings to convex binding under the same conditions. For binding to the convex outer surface of cardiolipin-containing vesicles, a two-step structural rearrangement is observed with a small rearrangement detectable by Soret circular dichroism (CD) occurring at an exposed lipid-to-protein ratio (LPR) near 10 and partial unfolding detectable by Trp59 fluorescence occurring at an exposed LPR near 23. On the concave inner surface of cardiolipin-containing vesicles, the structural transitions monitored by Soret CD and Trp59 fluorescence are coincident and occur at an exposed LPR near 58. On the concave inner surface of mitochondrial cristae, we estimate the LPR of cardiolipin to cytochrome c is between 50 and 100. Thus, cytochrome c may have adapted to its native environment so that it can undergo a conformational change that switches on its peroxidase activity when it binds to CL-containing membranes in the cristae early in apoptosis. Our results show that membrane curvature qualitatively affects peripheral protein-lipid interactions and also highlights the disparity between in vitro binding studies and their physiological counterparts where cone-shaped lipids, like cardiolipin, are involved.
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Affiliation(s)
- Margaret M Elmer-Dixon
- Department of Chemistry and Biochemistry, University of Montana, Missoula, Montana 59812, United States.,Center for Biomolecular Structure and Dynamics, University of Montana, Missoula, Montana 59812, United States
| | - Ziqing Xie
- Department of Chemistry and Biochemistry, University of Montana, Missoula, Montana 59812, United States
| | - Jeremy B Alverson
- Department of Chemistry and Biochemistry, University of Montana, Missoula, Montana 59812, United States
| | - Nigel D Priestley
- Department of Chemistry and Biochemistry, University of Montana, Missoula, Montana 59812, United States
| | - Bruce E Bowler
- Department of Chemistry and Biochemistry, University of Montana, Missoula, Montana 59812, United States.,Center for Biomolecular Structure and Dynamics, University of Montana, Missoula, Montana 59812, United States
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12
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Cytochrome c modification and oligomerization induced by cardiolipin hydroperoxides in a membrane mimetic model. Arch Biochem Biophys 2020; 693:108568. [DOI: 10.1016/j.abb.2020.108568] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Revised: 08/10/2020] [Accepted: 08/27/2020] [Indexed: 12/31/2022]
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13
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Steele HBB, Elmer-Dixon MM, Rogan JT, Ross JBA, Bowler BE. The Human Cytochrome c Domain-Swapped Dimer Facilitates Tight Regulation of Intrinsic Apoptosis. Biochemistry 2020; 59:2055-2068. [PMID: 32428404 PMCID: PMC7291863 DOI: 10.1021/acs.biochem.0c00326] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Oxidation of cardiolipin (CL) by cytochrome c (cytc) has been proposed to initiate the intrinsic pathway of apoptosis. Domain-swapped dimer (DSD) conformations of cytc have been reported both by our laboratory and by others. The DSD is an alternate conformer of cytc that could oxygenate CL early in apoptosis. We demonstrate here that the cytc DSD has a set of properties that would provide tighter regulation of the intrinsic pathway. We show that the human DSD is kinetically more stable than horse and yeast DSDs. Circular dichroism data indicate that the DSD has a less asymmetric heme environment, similar to that seen when the monomeric protein binds to CL vesicles at high lipid:protein ratios. The dimer undergoes the alkaline conformational transition near pH 7.0, 2.5 pH units lower than that of the monomer. Data from fluorescence correlation spectroscopy and fluorescence anisotropy suggest that the alkaline transition of the DSD may act as a switch from a high affinity for CL nanodiscs at pH 7.4 to a much lower affinity at pH 8.0. Additionally, the peroxidase activity of the human DSD increases 7-fold compared to that of the monomer at pH 7 and 8, but by 14-fold at pH 6 when mixed Met80/H2O ligation replaces the lysine ligation of the alkaline state. We also present data that indicate that cytc binding shows a cooperative effect as the concentration of cytc is increased. The DSD appears to have evolved into a pH-inducible switch that provides a means to control activation of apoptosis near pH 7.0.
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Affiliation(s)
- Harmen B. B. Steele
- Department of Chemistry & Biochemistry, University of Montana, Missoula, Montana 59812, United States
- Center for Biomolecular Structure & Dynamics, University of Montana, Missoula, Montana 59812, United States
| | - Margaret M. Elmer-Dixon
- Department of Chemistry & Biochemistry, University of Montana, Missoula, Montana 59812, United States
- Center for Biomolecular Structure & Dynamics, University of Montana, Missoula, Montana 59812, United States
| | - James T. Rogan
- Department of Chemistry & Biochemistry, University of Montana, Missoula, Montana 59812, United States
| | - J. B. Alexander Ross
- Department of Chemistry & Biochemistry, University of Montana, Missoula, Montana 59812, United States
- Center for Biomolecular Structure & Dynamics, University of Montana, Missoula, Montana 59812, United States
| | - Bruce E. Bowler
- Department of Chemistry & Biochemistry, University of Montana, Missoula, Montana 59812, United States
- Center for Biomolecular Structure & Dynamics, University of Montana, Missoula, Montana 59812, United States
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14
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Wheel and Deal in the Mitochondrial Inner Membranes: The Tale of Cytochrome c and Cardiolipin. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2020; 2020:6813405. [PMID: 32377304 PMCID: PMC7193304 DOI: 10.1155/2020/6813405] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 02/28/2020] [Indexed: 12/15/2022]
Abstract
Cardiolipin oxidation and degradation by different factors under severe cell stress serve as a trigger for genetically encoded cell death programs. In this context, the interplay between cardiolipin and another mitochondrial factor—cytochrome c—is a key process in the early stages of apoptosis, and it is a matter of intense research. Cytochrome c interacts with lipid membranes by electrostatic interactions, hydrogen bonds, and hydrophobic effects. Experimental conditions (including pH, lipid composition, and post-translational modifications) determine which specific amino acid residues are involved in the interaction and influence the heme iron coordination state. In fact, up to four binding sites (A, C, N, and L), driven by different interactions, have been reported. Nevertheless, key aspects of the mechanism for cardiolipin oxidation by the hemeprotein are well established. First, cytochrome c acts as a pseudoperoxidase, a process orchestrated by tyrosine residues which are crucial for peroxygenase activity and sensitivity towards oxidation caused by protein self-degradation. Second, flexibility of two weakest folding units of the hemeprotein correlates with its peroxidase activity and the stability of the iron coordination sphere. Third, the diversity of the mode of interaction parallels a broad diversity in the specific reaction pathway. Thus, current knowledge has already enabled the design of novel drugs designed to successfully inhibit cardiolipin oxidation.
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15
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Paradisi A, Bellei M, Paltrinieri L, Bortolotti CA, Di Rocco G, Ranieri A, Borsari M, Sola M, Battistuzzi G. Binding of S. cerevisiae iso-1 cytochrome c and its surface lysine-to-alanine variants to cardiolipin: charge effects and the role of the lipid to protein ratio. J Biol Inorg Chem 2020; 25:467-487. [DOI: 10.1007/s00775-020-01776-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 03/06/2020] [Indexed: 11/30/2022]
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16
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El-Hafidi M, Correa F, Zazueta C. Mitochondrial dysfunction in metabolic and cardiovascular diseases associated with cardiolipin remodeling. Biochim Biophys Acta Mol Basis Dis 2020; 1866:165744. [PMID: 32105822 DOI: 10.1016/j.bbadis.2020.165744] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 01/21/2020] [Accepted: 02/20/2020] [Indexed: 02/07/2023]
Abstract
Cardiolipin (CL) is an acidic phospholipid almost exclusively found in the inner mitochondrial membrane, that not only stabilizes the structure and function of individual components of the mitochondrial electron transport chain, but regulates relevant mitochondrial processes, like mitochondrial dynamics and cristae structure maintenance among others. Alterations in CL due to peroxidation, correlates with loss of such mitochondrial activities and disease progression. In this review it is recapitulated the current state of knowledge of the role of cardiolipin remodeling associated with mitochondrial dysfunction in metabolic and cardiovascular diseases.
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Affiliation(s)
- Mohammed El-Hafidi
- Departamento de Biomedicina Cardiovascular, Instituto Nacional de Cardiología I. Ch. 14080, Ciudad de México, México
| | - Francisco Correa
- Departamento de Biomedicina Cardiovascular, Instituto Nacional de Cardiología I. Ch. 14080, Ciudad de México, México
| | - Cecilia Zazueta
- Departamento de Biomedicina Cardiovascular, Instituto Nacional de Cardiología I. Ch. 14080, Ciudad de México, México.
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17
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Paradisi A, Lancellotti L, Borsari M, Bellei M, Bortolotti CA, Di Rocco G, Ranieri A, Sola M, Battistuzzi G. Met80 and Tyr67 affect the chemical unfolding of yeast cytochrome c: comparing the solution vs.immobilized state. RSC Chem Biol 2020. [DOI: 10.1039/d0cb00115e] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The motional regime affects the unfolding propensity and axial heme coordination of the Met80Ala and Met80Ala/Tyr67Ala variants of yeast iso-1 cytochromec.
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Affiliation(s)
| | - Lidia Lancellotti
- Department of Chemistry and Geology
- University of Modena and Reggio Emilia
- 41126 Modena
- Italy
| | - Marco Borsari
- Department of Chemistry and Geology
- University of Modena and Reggio Emilia
- 41126 Modena
- Italy
| | - Marzia Bellei
- Department of Life Sciences
- University of Modena and Reggio Emilia
- 41126 Modena
- Italy
| | | | - Giulia Di Rocco
- Department of Life Sciences
- University of Modena and Reggio Emilia
- 41126 Modena
- Italy
| | - Antonio Ranieri
- Department of Life Sciences
- University of Modena and Reggio Emilia
- 41126 Modena
- Italy
| | - Marco Sola
- Department of Life Sciences
- University of Modena and Reggio Emilia
- 41126 Modena
- Italy
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18
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Elmer-Dixon MM, Hoody J, Steele HBB, Becht DC, Bowler BE. Cardiolipin Preferentially Partitions to the Inner Leaflet of Mixed Lipid Large Unilamellar Vesicles. J Phys Chem B 2019; 123:9111-9122. [DOI: 10.1021/acs.jpcb.9b07690] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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19
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Cytochrome c: An extreme multifunctional protein with a key role in cell fate. Int J Biol Macromol 2019; 136:1237-1246. [DOI: 10.1016/j.ijbiomac.2019.06.180] [Citation(s) in RCA: 88] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 06/24/2019] [Accepted: 06/24/2019] [Indexed: 01/25/2023]
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20
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Parui PP, Sarakar Y, Majumder R, Das S, Yang H, Yasuhara K, Hirota S. Determination of proton concentration at cardiolipin-containing membrane interfaces and its relation with the peroxidase activity of cytochrome c. Chem Sci 2019; 10:9140-9151. [PMID: 31827756 PMCID: PMC6889831 DOI: 10.1039/c9sc02993a] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 08/03/2019] [Indexed: 01/04/2023] Open
Abstract
The interface –log[H+] defined as pH′ of a mimic inner mitochondrial membrane is ∼3.9 at bulk pH ∼ 6.8, which affects cytochrome c activity.
The activities of biomolecules are affected by the proton concentrations at biological membranes. Here, we succeeded in evaluating the interface proton concentration (–log[H+] defined as pH′) of cardiolipin (CL)-enriched membrane models of the inner mitochondrial membrane (IMM) using a spiro-rhodamine-glucose molecule (RHG). According to fluorescence microscopy and 1H-NMR studies, RHG interacted with the Stern layer of the membrane. The acid/base equilibrium of RHG between its protonated open form (o-RHG) and deprotonated closed spiro-form (c-RHG) at the membrane interface was monitored with UV-vis absorption and fluorescence spectra. The interface pH′ of 25% cardiolipin (CL)-containing large unilamellar vesicles (LUVs), which possess similar lipid properties to those of the IMM, was estimated to be ∼3.9, when the bulk pH was similar to the mitochondrial intermembrane space pH (6.8). However, for the membranes containing mono-anionic lipids, the interface pH′ was estimated to be ∼5.3 at bulk pH 6.8, indicating that the local negative charges of the lipid headgroups in the lipid membranes are responsible for the deviation of the interface pH′ from the bulk pH. The peroxidase activity of cyt c increased 5–7 fold upon lowering the pH to 3.9–4.3 or adding CL-containing (10–25% of total lipids) LUVs compared to that at bulk pH 6.8, indicating that the pH′ decrease at the IMM interface from the bulk pH enhances the peroxidase activity of cyt c. The peroxidase activity of cyt c at the membrane interface of tetraoleoyl CL (TOCL)-enriched (50% of total lipids) LUVs was higher than that estimated from the interface pH′, while the peroxidase activity was similar to that estimated from the interface pH′ for tetramyristoyl CL (TMCL)-enriched LUVs, supporting the hypothesis that when interacting with TOCL (not TMCL), cyt c opens the heme crevice to substrates. The present simple methodology allows us to estimate the interface proton concentrations of complex biological membranes.
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Affiliation(s)
- Partha Pratim Parui
- Department of Chemistry , Jadavpur University , Kolkata 700032 , India . ; ; Tel: +91-9433490492.,Division of Materials Science , Nara Institute of Science and Technology , Nara 630-0192 , Japan
| | - Yeasmin Sarakar
- Department of Chemistry , Jadavpur University , Kolkata 700032 , India . ; ; Tel: +91-9433490492
| | - Rini Majumder
- Department of Chemistry , Jadavpur University , Kolkata 700032 , India . ; ; Tel: +91-9433490492
| | - Sanju Das
- Department of Chemistry , Jadavpur University , Kolkata 700032 , India . ; ; Tel: +91-9433490492.,Department of Chemistry , Maulana Azad College , Kolkata 700013 , India
| | - Hongxu Yang
- Division of Materials Science , Nara Institute of Science and Technology , Nara 630-0192 , Japan
| | - Kazuma Yasuhara
- Division of Materials Science , Nara Institute of Science and Technology , Nara 630-0192 , Japan
| | - Shun Hirota
- Division of Materials Science , Nara Institute of Science and Technology , Nara 630-0192 , Japan
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21
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Muller MP, Jiang T, Sun C, Lihan M, Pant S, Mahinthichaichan P, Trifan A, Tajkhorshid E. Characterization of Lipid-Protein Interactions and Lipid-Mediated Modulation of Membrane Protein Function through Molecular Simulation. Chem Rev 2019; 119:6086-6161. [PMID: 30978005 PMCID: PMC6506392 DOI: 10.1021/acs.chemrev.8b00608] [Citation(s) in RCA: 133] [Impact Index Per Article: 26.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The cellular membrane constitutes one of the most fundamental compartments of a living cell, where key processes such as selective transport of material and exchange of information between the cell and its environment are mediated by proteins that are closely associated with the membrane. The heterogeneity of lipid composition of biological membranes and the effect of lipid molecules on the structure, dynamics, and function of membrane proteins are now widely recognized. Characterization of these functionally important lipid-protein interactions with experimental techniques is however still prohibitively challenging. Molecular dynamics (MD) simulations offer a powerful complementary approach with sufficient temporal and spatial resolutions to gain atomic-level structural information and energetics on lipid-protein interactions. In this review, we aim to provide a broad survey of MD simulations focusing on exploring lipid-protein interactions and characterizing lipid-modulated protein structure and dynamics that have been successful in providing novel insight into the mechanism of membrane protein function.
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Affiliation(s)
- Melanie P. Muller
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- Center for Biophysics and Quantitative Biology
- College of Medicine
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Tao Jiang
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- Center for Biophysics and Quantitative Biology
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Chang Sun
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Muyun Lihan
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- Center for Biophysics and Quantitative Biology
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Shashank Pant
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- Center for Biophysics and Quantitative Biology
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Paween Mahinthichaichan
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Anda Trifan
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- Center for Biophysics and Quantitative Biology
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Emad Tajkhorshid
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- Center for Biophysics and Quantitative Biology
- College of Medicine
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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22
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Li M, Mandal A, Tyurin VA, DeLucia M, Ahn J, Kagan VE, van der Wel PCA. Surface-Binding to Cardiolipin Nanodomains Triggers Cytochrome c Pro-apoptotic Peroxidase Activity via Localized Dynamics. Structure 2019; 27:806-815.e4. [PMID: 30879887 DOI: 10.1016/j.str.2019.02.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 01/16/2019] [Accepted: 02/15/2019] [Indexed: 02/06/2023]
Abstract
The peroxidation of cardiolipins by reactive oxygen species, which is regulated and enhanced by cytochrome c (cyt c), is a critical signaling event in mitochondrial apoptosis. We probe the molecular underpinnings of this mitochondrial death signal through structural and functional studies of horse heart cyt c binding to mixed-lipid membranes containing cardiolipin with mono- and polyunsaturated acyl chains. Lipidomics reveal the selective oxidation of polyunsaturated fatty acid (PUFA) cardiolipin (CL), while multidimensional solid-state NMR probes the structure and dynamics of the membrane and the peripherally bound protein. The hydrophilic milieu at the membrane interface stabilizes a native-like fold, but also leads to localized flexibility at the membrane-interacting protein face. PUFA CL acts as both a preferred substrate and a dynamic regulator by affecting the dynamics of the cyt c N70-I85 Ω loop, which covers the heme cavity.
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Affiliation(s)
- Mingyue Li
- Department of Structural Biology, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Abhishek Mandal
- Department of Structural Biology, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Vladimir A Tyurin
- Department of Environmental and Occupational Health, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Maria DeLucia
- Department of Structural Biology, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Jinwoo Ahn
- Department of Structural Biology, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Valerian E Kagan
- Department of Environmental and Occupational Health, University of Pittsburgh, Pittsburgh, PA 15213, USA; Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15213, USA; Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA 15213, USA; Department of Radiation Oncology, University of Pittsburgh, Pittsburgh, PA 15213, USA; Center for Free Radical and Antioxidant Health, University of Pittsburgh, Pittsburgh, PA 15213, USA; Laboratory of Navigational Redox Lipidomics, IM Sechenov Moscow State Medical University, Moscow 119146, Russian Federation
| | - Patrick C A van der Wel
- Department of Structural Biology, University of Pittsburgh, Pittsburgh, PA 15213, USA; Zernike Institute for Advanced Materials, University of Groningen, 9747 AG Groningen, The Netherlands.
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23
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Enkavi G, Javanainen M, Kulig W, Róg T, Vattulainen I. Multiscale Simulations of Biological Membranes: The Challenge To Understand Biological Phenomena in a Living Substance. Chem Rev 2019; 119:5607-5774. [PMID: 30859819 PMCID: PMC6727218 DOI: 10.1021/acs.chemrev.8b00538] [Citation(s) in RCA: 173] [Impact Index Per Article: 34.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
![]()
Biological
membranes are tricky to investigate. They are complex
in terms of molecular composition and structure, functional
over a wide range of time scales, and characterized
by nonequilibrium conditions. Because of all of these
features, simulations are a great technique to study biomembrane
behavior. A significant part of the functional processes
in biological membranes takes place at the molecular
level; thus computer simulations are the method of
choice to explore how their properties emerge from specific
molecular features and how the interplay among the numerous
molecules gives rise to function over spatial and
time scales larger than the molecular ones. In this
review, we focus on this broad theme. We discuss the current
state-of-the-art of biomembrane simulations that, until
now, have largely focused on a rather narrow picture
of the complexity of the membranes. Given this, we
also discuss the challenges that we should unravel in the
foreseeable future. Numerous features such as the actin-cytoskeleton
network, the glycocalyx network, and nonequilibrium
transport under ATP-driven conditions have so far
received very little attention; however, the potential
of simulations to solve them would be exceptionally high. A
major milestone for this research would be that one day
we could say that computer simulations genuinely research
biological membranes, not just lipid bilayers.
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Affiliation(s)
- Giray Enkavi
- Department of Physics , University of Helsinki , P.O. Box 64, FI-00014 Helsinki , Finland
| | - Matti Javanainen
- Department of Physics , University of Helsinki , P.O. Box 64, FI-00014 Helsinki , Finland.,Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences , Flemingovo naḿesti 542/2 , 16610 Prague , Czech Republic.,Computational Physics Laboratory , Tampere University , P.O. Box 692, FI-33014 Tampere , Finland
| | - Waldemar Kulig
- Department of Physics , University of Helsinki , P.O. Box 64, FI-00014 Helsinki , Finland
| | - Tomasz Róg
- Department of Physics , University of Helsinki , P.O. Box 64, FI-00014 Helsinki , Finland.,Computational Physics Laboratory , Tampere University , P.O. Box 692, FI-33014 Tampere , Finland
| | - Ilpo Vattulainen
- Department of Physics , University of Helsinki , P.O. Box 64, FI-00014 Helsinki , Finland.,Computational Physics Laboratory , Tampere University , P.O. Box 692, FI-33014 Tampere , Finland.,MEMPHYS-Center for Biomembrane Physics
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24
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Ciambellotti S, Turano P. Structural Biology of Iron‐Binding Proteins by NMR Spectroscopy. Eur J Inorg Chem 2019. [DOI: 10.1002/ejic.201801261] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Silvia Ciambellotti
- Resonance Magnetic Center (CERM) University of Florence via Luigi Sacconi 6 50019 Sesto Fiorentino Italy
- Department of Chemistry University of Florence via della Lastruccia 3 50019 Sesto Fiorentino, Italy
| | - Paola Turano
- Resonance Magnetic Center (CERM) University of Florence via Luigi Sacconi 6 50019 Sesto Fiorentino Italy
- Department of Chemistry University of Florence via della Lastruccia 3 50019 Sesto Fiorentino, Italy
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25
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Barayeu U, Lange M, Méndez L, Arnhold J, Shadyro OI, Fedorova M, Flemmig J. Cytochrome c autocatalyzed carbonylation in the presence of hydrogen peroxide and cardiolipins. J Biol Chem 2018; 294:1816-1830. [PMID: 30541920 DOI: 10.1074/jbc.ra118.004110] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 12/05/2018] [Indexed: 11/06/2022] Open
Abstract
Cytochrome c (cyt c) is a small hemoprotein involved in electron shuttling in the mitochondrial respiratory chain and is now also recognized as an important mediator of apoptotic cell death. Its role in inducing programmed cell death is closely associated with the formation of a complex with the mitochondrion-specific phospholipid cardiolipin (CL), leading to a gain of peroxidase activity. However, the molecular mechanisms behind this gain and eventual cyt c autoinactivation via its release from mitochondrial membranes remain largely unknown. Here, we examined the kinetics of the H2O2-mediated peroxidase activity of cyt c both in the presence and absence of tetraoleoyl cardiolipin (TOCL)- and tetralinoleoyl cardiolipin (TLCL)-containing liposomes to evaluate the role of cyt c-CL complex formation in the induction and stimulation of cyt c peroxidase activity. Moreover, we examined peroxide-mediated cyt c heme degradation to gain insights into the mechanisms by which cyt c self-limits its peroxidase activity. Bottom-up proteomics revealed >50 oxidative modifications on cyt c upon peroxide reduction. Of note, one of these by-products was the Tyr-based "cofactor" trihydroxyphenylalanine quinone (TPQ) capable of inducing deamination of Lys ϵ-amino groups and formation of the carbonylated product aminoadipic semialdehyde. In view of these results, we propose that autoinduced carbonylation, and thus removal of a positive charge in Lys, abrogates binding of cyt c to negatively charged CL. The proposed mechanism may be responsible for release of cyt c from mitochondrial membranes and ensuing inactivation of its peroxidase activity.
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Affiliation(s)
- Uladzimir Barayeu
- From the Institute of Bioanalytical Chemistry, Faculty of Chemistry and Mineralogy, and.,Center for Biotechnology and Biomedicine, University of Leipzig, 04103 Leipzig, Germany.,Institute for Medical Physics and Biophysics, Medical Faculty, University of Leipzig, 04107 Leipzig, Germany
| | - Mike Lange
- From the Institute of Bioanalytical Chemistry, Faculty of Chemistry and Mineralogy, and.,Center for Biotechnology and Biomedicine, University of Leipzig, 04103 Leipzig, Germany
| | - Lucía Méndez
- From the Institute of Bioanalytical Chemistry, Faculty of Chemistry and Mineralogy, and.,Center for Biotechnology and Biomedicine, University of Leipzig, 04103 Leipzig, Germany.,Institute of Marine Research, Spanish Council for Scientific Research (IIM-CSIC), 36208 Vigo, Spain, and
| | - Jürgen Arnhold
- Institute for Medical Physics and Biophysics, Medical Faculty, University of Leipzig, 04107 Leipzig, Germany
| | - Oleg I Shadyro
- Department of Chemistry, Belarusian State University, 220030 Minsk, Belarus
| | - Maria Fedorova
- From the Institute of Bioanalytical Chemistry, Faculty of Chemistry and Mineralogy, and .,Center for Biotechnology and Biomedicine, University of Leipzig, 04103 Leipzig, Germany
| | - Jörg Flemmig
- Institute for Medical Physics and Biophysics, Medical Faculty, University of Leipzig, 04107 Leipzig, Germany,
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26
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Elmer-Dixon MM, Bowler BE. Electrostatic Constituents of the Interaction of Cardiolipin with Site A of Cytochrome c. Biochemistry 2018; 57:5683-5695. [DOI: 10.1021/acs.biochem.8b00704] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Margaret M. Elmer-Dixon
- Department of Chemistry and Biochemistry, Center for Bimolecular Structure and Dynamics, University of Montana, Missoula, Montana 59812, United States
| | - Bruce E. Bowler
- Department of Chemistry and Biochemistry, Center for Bimolecular Structure and Dynamics, University of Montana, Missoula, Montana 59812, United States
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27
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How cardiolipin peroxidation alters the properties of the inner mitochondrial membrane? Chem Phys Lipids 2018; 214:15-23. [DOI: 10.1016/j.chemphyslip.2018.04.005] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 04/29/2018] [Indexed: 01/16/2023]
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28
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Oxidative stress is tightly regulated by cytochrome c phosphorylation and respirasome factors in mitochondria. Proc Natl Acad Sci U S A 2018; 115:7955-7960. [PMID: 30018060 PMCID: PMC6077723 DOI: 10.1073/pnas.1806833115] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Dysfunction of mitochondria, the powerhouses of living cells, favors the onset of human diseases, namely neurodegenerative diseases, cardiovascular pathologies, and cancer. Actually, respiratory cytochrome c has been found to be phosphorylated at tyrosine 97 during the insulin-induced neuroprotection response following a brain ischemic injury. Here, we report that the decrease in neuronal death could be directly ascribed to changes in mitochondrial metabolism—including lower production of reactive oxygen species—and cell homeostasis induced by cytochrome c phosphorylation. Our findings thus provide the basis for understanding the molecular mechanism and potential use of phosphomimetic species of cytochrome c, thereby yielding new opportunities to develop more efficient therapies against acute pathologies. Respiratory cytochrome c has been found to be phosphorylated at tyrosine 97 in the postischemic brain upon neuroprotective insulin treatment, but how such posttranslational modification affects mitochondrial metabolism is unclear. Here, we report the structural features and functional behavior of a phosphomimetic cytochrome c mutant, which was generated by site-specific incorporation at position 97 of p-carboxymethyl-l-phenylalanine using the evolved tRNA synthetase method. We found that the point mutation does not alter the overall folding and heme environment of cytochrome c, but significantly affects the entire oxidative phosphorylation process. In fact, the electron donation rate of the mutant heme protein to cytochrome c oxidase, or complex IV, within respiratory supercomplexes was higher than that of the wild-type species, in agreement with the observed decrease in reactive oxygen species production. Direct contact of cytochrome c with the respiratory supercomplex factor HIGD1A (hypoxia-inducible domain family member 1A) is reported here, with the mutant heme protein exhibiting a lower affinity than the wild-type species. Interestingly, phosphomimetic cytochrome c also exhibited a lower caspase-3 activation activity. Altogether, these findings yield a better understanding of the molecular basis for mitochondrial metabolism in acute diseases, such as brain ischemia, and thus could allow the use of phosphomimetic cytochrome c as a neuroprotector with therapeutic applications.
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