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Frederick AK, Bowler BE. Binding of yeast and human cytochrome c to cardiolipin nanodiscs at physiological ionic strength. J Inorg Biochem 2024; 260:112699. [PMID: 39181020 PMCID: PMC11404356 DOI: 10.1016/j.jinorgbio.2024.112699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2024] [Revised: 08/05/2024] [Accepted: 08/12/2024] [Indexed: 08/27/2024]
Abstract
Binding of cytochrome c (Cytc) to membranes containing cardiolipin (CL) is of considerable interest because of the importance of this interaction in the early stages of apoptosis. The molecular-level determinants of this interaction are still not well defined and there appear to be species-specific differences in Cytc affinity for CL-containing membranes. Many studies are carried out at low ionic strength far from the 100-150 mM ionic strength within mitochondria. Similarly, most binding studies are done at Cytc concentrations of 10 μM or less, much lower that the estimated range of 0.1 to 5 mM Cytc present in mitochondria. In this study, we evaluate binding of human and yeast Cytc to CL nanodiscs using size exclusion chromatography at 25 μM Cytc concentration and 100 mM ionic strength. We find that yeast Cytc affinity for CL nanodiscs is much stronger than that of human Cytc. Mutational analysis of the site A binding surface shows that lysines 86 and 87 are more important for yeast Cytc binding to CL nanodiscs than lysines 72 and 73, counter to results at lower ionic strength. Analysis of the electrostatic surface potential of human versus yeast Cytc shows that the positive potential due to lysines 86 and 87 and other nearby lysines (4, 5, 11, 89) is stronger than that due to lysines 72 and 73. In the case of human Cytc the positive potential around site A is less uniform and likely weakens electrostatic binding to CL membranes through site A.
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Affiliation(s)
- Ariel K Frederick
- Department of Chemistry & Biochemistry, University of Montana, Missoula, MT 59812, United States
| | - Bruce E Bowler
- Department of Chemistry & Biochemistry, University of Montana, Missoula, MT 59812, United States; Center for Biomolecular Structure & Dynamics, University of Montana, Missoula, MT 59812, United States.
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2
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Kanzaki Y, Minami R, Ota K, Adachi J, Hori Y, Ohtani R, Le Ouay B, Ohba M. Enhancing Performances of Enzyme/Metal-Organic Polyhedra Composites by Mixed-Protein Co-Immobilization. ACS APPLIED MATERIALS & INTERFACES 2024; 16:54423-54434. [PMID: 39315760 DOI: 10.1021/acsami.4c10146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/25/2024]
Abstract
Protein immobilization using water-soluble ionic metal-organic polyhedra (MOPs) acting as porous spacers has recently been demonstrated as a potent strategy for the preparation of biocatalysts. In this article, we describe a mixed-protein approach to achieve biocomposites with adjustable enzyme contents and excellent immobilization efficiencies, in a systematic and well-controlled manner. Self-assembly of either cationic or anionic MOPs with bovine serum albumin or egg white lysozyme combined with enzymes (alkaline phosphatase, laccase or cytochrome c) led to solid-state catalysts with a high retention of enzyme activity. Furthermore, for all these systems, the dilution of enzymes within the solid-state composite led to noticeably improved catalytic performances, with both higher specific activity and affinity for substrate.
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Affiliation(s)
- Yuri Kanzaki
- Department of Chemistry, Faculty of Science, Kyushu University, Fukuoka 819-0395, Japan
| | - Ryosuke Minami
- Department of Chemistry, Faculty of Science, Kyushu University, Fukuoka 819-0395, Japan
| | - Koshiro Ota
- Department of Chemistry, Faculty of Science, Kyushu University, Fukuoka 819-0395, Japan
| | - Junya Adachi
- Department of Chemistry, Faculty of Science, Kyushu University, Fukuoka 819-0395, Japan
| | - Yuichiro Hori
- Department of Chemistry, Faculty of Science, Kyushu University, Fukuoka 819-0395, Japan
| | - Ryo Ohtani
- Department of Chemistry, Faculty of Science, Kyushu University, Fukuoka 819-0395, Japan
| | - Benjamin Le Ouay
- Department of Chemistry, Faculty of Science, Kyushu University, Fukuoka 819-0395, Japan
| | - Masaaki Ohba
- Department of Chemistry, Faculty of Science, Kyushu University, Fukuoka 819-0395, Japan
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3
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Schweitzer-Stenner R. Probing the versatility of cytochrome c by spectroscopic means: A Laudatio on resonance Raman spectroscopy. J Inorg Biochem 2024; 259:112641. [PMID: 38901065 DOI: 10.1016/j.jinorgbio.2024.112641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Revised: 06/03/2024] [Accepted: 06/12/2024] [Indexed: 06/22/2024]
Abstract
Over the last 50 years resonance Raman spectroscopy has become an invaluable tool for the exploration of chromophores in biological macromolecules. Among them, heme proteins and metal complexes have attracted considerable attention. This interest results from the fact that resonance Raman spectroscopy probes the vibrational dynamics of these chromophores without direct interference from the surrounding. However, the indirect influence via through-bond and through-space chromophore-protein interactions can be conveniently probed and analyzed. This review article illustrates this point by focusing on class 1 cytochrome c, a comparatively simple heme protein generally known as electron carrier in mitochondria. The article demonstrates how through selective excitation of resonance Raman active modes information about the ligation, the redox state and the spin state of the heme iron can be obtained from band positions in the Raman spectra. The investigation of intensities and depolarization ratios emerged as tools for the analysis of in-plane and out-of-plane deformations of the heme macrocycle. The article further shows how resonance Raman spectroscopy was used to characterize partially unfolded states of oxidized cytochrome c. Finally, it describes its use for exploring structural changes due to the protein's binding to anionic surfaces like cardiolipin containing membranes.
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4
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De Simone G, di Masi A, Sbardella D, Ascenzi P, Coletta M. Nitric Oxide Binding Geometry in Heme-Proteins: Relevance for Signal Transduction. Antioxidants (Basel) 2024; 13:666. [PMID: 38929104 PMCID: PMC11201058 DOI: 10.3390/antiox13060666] [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: 04/12/2024] [Revised: 05/22/2024] [Accepted: 05/23/2024] [Indexed: 06/28/2024] Open
Abstract
Nitric oxide (NO) synthesis, signaling, and scavenging is associated to relevant physiological and pathological events. In all tissues and organs, NO levels and related functions are regulated at different levels, with heme proteins playing pivotal roles. Here, we focus on the structural changes related to the different binding modes of NO to heme-Fe(II), as well as the modulatory effects of this diatomic messenger on heme-protein functions. Specifically, the ability of heme proteins to bind NO at either the distal or proximal side of the heme and the transient interchanging of the binding site is reported. This sheds light on the regulation of O2 supply to tissues with high metabolic activity, such as the retina, where a precise regulation of blood flow is necessary to meet the demand of nutrients.
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Affiliation(s)
- Giovanna De Simone
- Dipartimento di Scienze, Università degli Studi Roma Tre, 00146 Rome, Italy; (G.D.S.); (A.d.M.)
| | - Alessandra di Masi
- Dipartimento di Scienze, Università degli Studi Roma Tre, 00146 Rome, Italy; (G.D.S.); (A.d.M.)
- Centro Linceo Interdisciplinare “Beniamino Segre”, Accademia dei Lincei, 00165 Rome, Italy
| | | | - Paolo Ascenzi
- Dipartimento di Scienze, Università degli Studi Roma Tre, 00146 Rome, Italy; (G.D.S.); (A.d.M.)
- Accademia Nazionale dei Lincei, 00165 Rome, Italy
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5
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Kopeć M, Borek-Dorosz A, Jarczewska K, Barańska M, Abramczyk H. The role of cardiolipin and cytochrome c in mitochondrial metabolism of cancer cells determined by Raman imaging: in vitro study on the brain glioblastoma U-87 MG cell line. Analyst 2024; 149:2697-2708. [PMID: 38506099 DOI: 10.1039/d4an00015c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2024]
Abstract
In this paper, we present Raman imaging as a non-invasive approach for studying changes in mitochondrial metabolism caused by cardiolipin-cytochrome c interactions. We investigated the effect of mitochondrial dysregulation on cardiolipin (CL) and cytochrome c (Cyt c) interactions for a brain cancer cell line (U-87 MG). Mitochondrial metabolism was monitored by checking the intensities of the Raman bands at 750 cm-1, 1126 cm-1, 1310 cm-1, 1337 cm-1, 1444 cm-1 and 1584 cm-1. The presented results indicate that under pathological conditions, the content and redox status of Cyt c in mitochondria can be used as a Raman marker to characterize changes in cellular metabolism. This work provides evidence that cardiolipin-cytochrome c interactions are crucial for mitochondrial energy homeostasis by controlling the redox status of Cyt c in the electron transport chain, switching from disabling Cyt c reduction and enabling peroxidase activity. This paper provides experimental support for the hypothesis of how cardiolipin-cytochrome c interactions regulate electron transfer in the respiratory chain, apoptosis and mROS production in mitochondria.
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Affiliation(s)
- Monika Kopeć
- Lodz University of Technology, Institute of Applied Radiation Chemistry, Laboratory of Laser Molecular Spectroscopy, Wroblewskiego 15, 93-590 Lodz, Poland.
- Jagiellonian University, Faculty of Chemistry, Gronostajowa 2, 30-387 Krakow, Poland
| | | | - Karolina Jarczewska
- Lodz University of Technology, Institute of Applied Radiation Chemistry, Laboratory of Laser Molecular Spectroscopy, Wroblewskiego 15, 93-590 Lodz, Poland.
| | - Małgorzata Barańska
- Jagiellonian University, Faculty of Chemistry, Gronostajowa 2, 30-387 Krakow, Poland
| | - Halina Abramczyk
- Lodz University of Technology, Institute of Applied Radiation Chemistry, Laboratory of Laser Molecular Spectroscopy, Wroblewskiego 15, 93-590 Lodz, Poland.
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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: 38067638 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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7
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Paradisi A, Bellei M, Bortolotti CA, Di Rocco G, Ranieri A, Borsari M, Sola M, Battistuzzi G. Effects of removal of the axial methionine heme ligand on the binding of S. cerevisiae iso-1 cytochrome c to cardiolipin. J Inorg Biochem 2024; 252:112455. [PMID: 38141433 DOI: 10.1016/j.jinorgbio.2023.112455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Revised: 12/05/2023] [Accepted: 12/13/2023] [Indexed: 12/25/2023]
Abstract
The cleavage of the axial S(Met) - Fe bond in cytochrome c (cytc) upon binding to cardiolipin (CL), a glycerophospholipid of the inner mitochondrial membrane, is one of the key molecular changes that impart cytc with (lipo)peroxidase activity essential to its pro-apoptotic function. In this work, UV - VIS, CD, MCD and fluorescence spectroscopies were used to address the role of the Fe - M80 bond in controlling the cytc-CL interaction, by studying the binding of the Met80Ala (M80A) variant of S. cerevisiae iso-1 cytc (ycc) to CL liposomes in comparison with the wt protein [Paradisi et al. J. Biol. Inorg. Chem. 25 (2020) 467-487]. The results show that the integrity of the six-coordinate heme center along with the distal heme site containing the Met80 ligand is a not requisite for cytc binding to CL. Indeed, deletion of the Fe - S(Met80) bond has a little impact on the mechanism of ycc-CL interaction, although it results in an increased heme accessibility to solvent and a reduced structural stability of the protein. In particular, M80A features a slightly tighter binding to CL at low CL/cytc ratios compared to wt ycc, possibly due to the lift of some constraints to the insertion of the CL acyl chains into the protein hydrophobic core. M80A binding to CL maintains the dependence on the CL-to-cytc mixing scheme displayed by the wt species.
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Affiliation(s)
- Alessandro Paradisi
- Department of Life Sciences, University of Modena and Reggio Emilia, via Campi 103, 41126 Modena, Italy
| | - Marzia Bellei
- Department of Life Sciences, University of Modena and Reggio Emilia, via Campi 103, 41126 Modena, Italy
| | - Carlo Augusto Bortolotti
- Department of Life Sciences, University of Modena and Reggio Emilia, via Campi 103, 41126 Modena, Italy
| | - Giulia Di Rocco
- Department of Life Sciences, University of Modena and Reggio Emilia, via Campi 103, 41126 Modena, Italy
| | - Antonio Ranieri
- Department of Life Sciences, University of Modena and Reggio Emilia, via Campi 103, 41126 Modena, Italy
| | - Marco Borsari
- Department of Chemistry and Geology, University of Modena and Reggio Emilia, via Campi 103, 41126 Modena, Italy
| | - Marco Sola
- Department of Life Sciences, University of Modena and Reggio Emilia, via Campi 103, 41126 Modena, Italy
| | - Gianantonio Battistuzzi
- Department of Chemistry and Geology, University of Modena and Reggio Emilia, via Campi 103, 41126 Modena, Italy.
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8
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Zhan J, Zeng D, Xiao X, Fang Z, Huang T, Zhao B, Zhu Q, Liu C, Jiang B, Zhou X, Li C, He L, Yang D, Liu M, Zhang X. Real-Time Observation of Conformational Changes and Translocation of Endogenous Cytochrome c within Intact Mitochondria. J Am Chem Soc 2024; 146:4455-4466. [PMID: 38335066 DOI: 10.1021/jacs.3c10216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2024]
Abstract
Cytochrome c (cyt c) is a multifunctional protein with varying conformations. However, the conformation of cyt c in its native environment, mitochondria, is still unclear. Here, we applied NMR spectroscopy to investigate the conformation and location of endogenous cyt c within intact mitochondria at natural isotopic abundance, mainly using widespread methyl groups as probes. By monitoring time-dependent chemical shift perturbations, we observed that most cyt c is located in the inner mitochondrial membrane and partially unfolded, which is distinct from its native conformation in solution. When suffering oxidative stress, cyt c underwent oxidative modifications due to increasing reactive oxygen species (ROS), weakening electrostatic interactions with the membrane, and gradually translocating into the inner membrane spaces of mitochondria. Meanwhile, the lethality of oxidatively modified cyt c to cells was reduced compared with normal cyt c. Our findings significantly improve the understanding of the molecular mechanisms underlying the regulation of ROS by cyt c in mitochondria. Moreover, it highlights the potential of NMR to monitor high-concentration molecules at a natural isotopic abundance within intact cells or organelles.
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Affiliation(s)
- Jianhua Zhan
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement of Science and Technology, Chinese Academy of Sciences, Wuhan 430071, People's Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Danyun Zeng
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement of Science and Technology, Chinese Academy of Sciences, Wuhan 430071, People's Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Xiong Xiao
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement of Science and Technology, Chinese Academy of Sciences, Wuhan 430071, People's Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Zhongpei Fang
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement of Science and Technology, Chinese Academy of Sciences, Wuhan 430071, People's Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Tao Huang
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement of Science and Technology, Chinese Academy of Sciences, Wuhan 430071, People's Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Beibei Zhao
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement of Science and Technology, Chinese Academy of Sciences, Wuhan 430071, People's Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Qinjun Zhu
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement of Science and Technology, Chinese Academy of Sciences, Wuhan 430071, People's Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Caixiang Liu
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement of Science and Technology, Chinese Academy of Sciences, Wuhan 430071, People's Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Bin Jiang
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement of Science and Technology, Chinese Academy of Sciences, Wuhan 430071, People's Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
- Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430071, People's Republic of China
- Optics Valley Laboratory, Wuhan 430074, People's Republic of China
| | - Xin Zhou
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement of Science and Technology, Chinese Academy of Sciences, Wuhan 430071, People's Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
- Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430071, People's Republic of China
- Optics Valley Laboratory, Wuhan 430074, People's Republic of China
| | - Conggang Li
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement of Science and Technology, Chinese Academy of Sciences, Wuhan 430071, People's Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
- Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430071, People's Republic of China
| | - Lichun He
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement of Science and Technology, Chinese Academy of Sciences, Wuhan 430071, People's Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Daiwen Yang
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543, Singapore
| | - Maili Liu
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement of Science and Technology, Chinese Academy of Sciences, Wuhan 430071, People's Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
- Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430071, People's Republic of China
- Optics Valley Laboratory, Wuhan 430074, People's Republic of China
| | - Xu Zhang
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement of Science and Technology, Chinese Academy of Sciences, Wuhan 430071, People's Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
- Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430071, People's Republic of China
- Optics Valley Laboratory, Wuhan 430074, People's Republic of China
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9
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López-Sánchez C, Lagoa R, Poejo J, García-López V, García-Martínez V, Gutierrez-Merino C. An Update of Kaempferol Protection against Brain Damage Induced by Ischemia-Reperfusion and by 3-Nitropropionic Acid. Molecules 2024; 29:776. [PMID: 38398528 PMCID: PMC10893315 DOI: 10.3390/molecules29040776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 02/01/2024] [Accepted: 02/02/2024] [Indexed: 02/25/2024] Open
Abstract
Kaempferol, a flavonoid present in many food products, has chemical and cellular antioxidant properties that are beneficial for protection against the oxidative stress caused by reactive oxygen and nitrogen species. Kaempferol administration to model experimental animals can provide extensive protection against brain damage of the striatum and proximal cortical areas induced by transient brain cerebral ischemic stroke and by 3-nitropropionic acid. This article is an updated review of the molecular and cellular mechanisms of protection by kaempferol administration against brain damage induced by these insults, integrated with an overview of the contributions of the work performed in our laboratories during the past years. Kaempferol administration at doses that prevent neurological dysfunctions inhibit the critical molecular events that underlie the initial and delayed brain damage induced by ischemic stroke and by 3-nitropropionic acid. It is highlighted that the protection afforded by kaempferol against the initial mitochondrial dysfunction can largely account for its protection against the reported delayed spreading of brain damage, which can develop from many hours to several days. This allows us to conclude that kaempferol administration can be beneficial not only in preventive treatments, but also in post-insult therapeutic treatments.
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Affiliation(s)
- Carmen López-Sánchez
- Institute of Molecular Pathology Biomarkers, University of Extremadura, 06006 Badajoz, Spain; (J.P.); (V.G.-L.); (V.G.-M.)
- Department of Human Anatomy and Embryology, Faculty of Medicine and Health Sciences, University of Extremadura, 06006 Badajoz, 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), Polytechnic Institute of Leiria, 2411-901 Leiria, Portugal
| | - Joana Poejo
- Institute of Molecular Pathology Biomarkers, University of Extremadura, 06006 Badajoz, Spain; (J.P.); (V.G.-L.); (V.G.-M.)
| | - Virginio García-López
- Institute of Molecular Pathology Biomarkers, University of Extremadura, 06006 Badajoz, Spain; (J.P.); (V.G.-L.); (V.G.-M.)
- Department of Medical and Surgical Therapeutics, Pharmacology Area, Faculty of Medicine and Health Sciences, University of Extremadura, 06006 Badajoz, Spain
| | - Virginio García-Martínez
- Institute of Molecular Pathology Biomarkers, University of Extremadura, 06006 Badajoz, Spain; (J.P.); (V.G.-L.); (V.G.-M.)
- Department of Human Anatomy and Embryology, Faculty of Medicine and Health Sciences, University of Extremadura, 06006 Badajoz, Spain
| | - Carlos Gutierrez-Merino
- Institute of Molecular Pathology Biomarkers, University of Extremadura, 06006 Badajoz, Spain; (J.P.); (V.G.-L.); (V.G.-M.)
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10
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Genceroglu MY, Cavdar C, Manioglu S, Bayraktar H. Genetically Encoded Fluorescent Probe for Detection of Heme-Induced Conformational Changes in Cytochrome c. BIOSENSORS 2023; 13:890. [PMID: 37754124 PMCID: PMC10526477 DOI: 10.3390/bios13090890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 09/11/2023] [Accepted: 09/14/2023] [Indexed: 09/28/2023]
Abstract
Cytochrome c (Cytc) is a key redox protein for energy metabolism and apoptosis in cells. The activation of Cytc is composed of several steps, including its transfer to the mitochondrial membrane, binding to cytochrome c heme lyase (CCHL) and covalent attachment to heme. The spectroscopic methods are often applied to study the structural changes of Cytc. However, they require the isolation of Cytc from cells and have limited availability under physiological conditions. Despite recent studies to elucidate the tightly regulated folding mechanism of Cytc, the role of these events and their association with different conformational states remain elusive. Here, we provide a genetically encoded fluorescence method that allows monitoring of the conformational changes of Cytc upon binding to heme and CCHL. Cerulean and Venus fluorescent proteins attached at the N and C terminals of Cytc can be used to determine its unfolded, intermediate, and native states by measuring FRET amplitude. We found that the noncovalent interaction of heme in the absence of CCHL induced a shift in the FRET signal, indicating the formation of a partially folded state. The higher concentration of heme and coexpression of CCHL gave rise to the recovery of Cytc native structure. We also found that Cytc was weakly associated with CCHL in the absence of heme. As a result, a FRET-based fluorescence approach was demonstrated to elucidate the mechanism of heme-induced Cytc conformational changes with spatiotemporal resolution and can be applied to study its interaction with small molecules and other protein partners in living cells.
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Affiliation(s)
- Mehmet Yunus Genceroglu
- Department of Molecular Biology and Genetics, Istanbul Technical University, Istanbul 34467, Turkey
| | - Cansu Cavdar
- Department of Molecular Biology and Genetics, Istanbul Technical University, Istanbul 34467, Turkey
| | - Selen Manioglu
- Biomedical Science and Engineering Program, Koç University, Istanbul 34450, Turkey
| | - Halil Bayraktar
- Department of Molecular Biology and Genetics, Istanbul Technical University, Istanbul 34467, Turkey
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11
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Priyadarshi A, Devi HM, Swaminathan R. Disruption of Spatial Proximities among Charged Groups in Equilibrium-Denatured States of Proteins Tracked Using Protein Charge Transfer Spectra. Biochemistry 2023. [PMID: 37162303 DOI: 10.1021/acs.biochem.3c00006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
The absorption and luminescence originating from protein charge transfer spectra (ProCharTS) depend on the proximity between multiple charged groups in a protein. This makes ProCharTS absorbance/luminescence intensity a sensitive probe for detecting changes in the protein structure, which alter the proximity among charged groups in the protein. In this work, ProCharTS absorbance of charge-rich proteins like human serum albumin (HSA), α3C, and α3W was used to monitor structural changes upon chemical denaturant-induced protein unfolding under equilibrium conditions. The denaturation midpoints were estimated using nonlinear regression analysis. For HSA, absorbance at 325 and 340 nm estimated the GdnHCl-induced denaturation midpoints to be 0.80 and 0.61 M, respectively. A similar analysis of α3C and α3W ProCharTS absorbance yielded denaturation midpoints of 0.88 and 0.86 M at 325 nm and 0.96 and 0.66 M at 340 nm, respectively. A previously reported molten globule-like state in the GdnHCl-induced HSA unfolding pathway was detected by the increase in HSA ProCharTS absorbance at 0.5 M GdnHCl. To validate the above results, protein unfolding was additionally monitored using conventional methods like circular dichroism (CD), Trp, and dansyl fluorescence. Our results suggest that disruption of charged amino acid sidechain contacts as revealed by ProCharTS occurs at lower denaturant concentrations compared to the loss of secondary/folded structure monitored by CD and fluorescence. Further, HSA ProCharTS absorbance at 315-340 nm revealed that tertiary contacts among charged residues were disrupted at lower GdnHCl concentrations compared to sequence adjacent contacts. Our data underscore the utility of ProCharTS as a novel label-free tool to track unfolding in charge-rich proteins.
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Affiliation(s)
- Anurag Priyadarshi
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781 039, Assam, India
| | - Himanshi Maniram Devi
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781 039, Assam, India
| | - Rajaram Swaminathan
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781 039, Assam, India
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12
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Wang WJ, Tan CP, Mao ZW. Metals and inorganic molecules in regulating protein and nucleic acid phase separation. Curr Opin Chem Biol 2023; 74:102308. [PMID: 37088005 DOI: 10.1016/j.cbpa.2023.102308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 03/20/2023] [Accepted: 03/22/2023] [Indexed: 04/25/2023]
Abstract
The realization that liquid-liquid phase separation (LLPS) underlies the formation of membraneless compartments in cells has motivated efforts to modulate the condensation process of biomolecules. Increasing evidence shows that metals and inorganic molecules abundantly distributed in cells play important roles in the regulation of biomolecular condensation. Herein, we briefly reviewed the background of biomacromolecular phase separation and summarized the recent research progress on the roles of metals and inorganic molecules in regulating protein and nucleic acid phase separation in vitro and in cells.
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Affiliation(s)
- Wen-Jin Wang
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou, 510006, PR China
| | - Cai-Ping Tan
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou, 510006, PR China.
| | - Zong-Wan Mao
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou, 510006, PR China.
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13
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Yeo WS, Dyzenhaus S, Torres VJ, Brinsmade SR, Bae T. Regulation of Bacterial Two-Component Systems by Cardiolipin. Infect Immun 2023; 91:e0004623. [PMID: 36975788 PMCID: PMC10112254 DOI: 10.1128/iai.00046-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 03/09/2023] [Indexed: 03/29/2023] Open
Abstract
The regulation of membrane protein activity for cellular functions is critically dependent on the composition of phospholipid membranes. Cardiolipin, a unique phospholipid found in bacterial membranes and mitochondrial membranes of eukaryotes, plays a crucial role in stabilizing membrane proteins and maintaining their function. In the human pathogen Staphylococcus aureus, the SaeRS two-component system (TCS) controls the expression of key virulence factors essential for the bacterium's virulence. The SaeS sensor kinase activates the SaeR response regulator via phosphoryl transfer to bind its gene target promoters. In this study, we report that cardiolipin is critical for sustaining the full activity of SaeRS and other TCSs in S. aureus. The sensor kinase protein SaeS binds directly to cardiolipin and phosphatidylglycerol, enabling SaeS activity. Elimination of cardiolipin from the membrane reduces SaeS kinase activity, indicating that bacterial cardiolipin is necessary for modulating the kinase activities of SaeS and other sensor kinases during infection. Moreover, the deletion of cardiolipin synthase genes cls1 and cls2 leads to reduced cytotoxicity to human neutrophils and lower virulence in a mouse model of infection. These findings suggest a model where cardiolipin modulates the kinase activity of SaeS and other sensor kinases after infection to adapt to the hostile environment of the host and expand our knowledge of how phospholipids contribute to membrane protein function.
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Affiliation(s)
- Won-Sik Yeo
- Department of Microbiology and Immunology, Indiana University School of Medicine-Northwest, Gary, Indiana, USA
| | - Sophie Dyzenhaus
- Department of Microbiology, New York University School of Medicine, New York, New York, USA
| | - Victor J. Torres
- Department of Microbiology, New York University School of Medicine, New York, New York, USA
| | | | - Taeok Bae
- Department of Microbiology and Immunology, Indiana University School of Medicine-Northwest, Gary, Indiana, USA
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14
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Zhang M, Tai H, Yanagisawa S, Yamanaka M, Ogura T, Hirota S. Resonance Raman Studies on Heme Ligand Stretching Modes in Methionine80-Depleted Cytochrome c: Fe-His, Fe-O 2, and O-O Stretching Modes. J Phys Chem B 2023; 127:2441-2449. [PMID: 36919258 PMCID: PMC10041640 DOI: 10.1021/acs.jpcb.3c00514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
Abstract
The peroxidase activity of cytochrome (cyt) c increases when Met80 dissociates from the heme iron, which is related to the initial cyt c membrane permeation step of apoptosis. Met80-dissociated cyt c can form an oxygenated species. Herein, resonance Raman spectra of Met80-depleted horse cyt c (M80A cyt c) were analyzed to elucidate the heme ligand properties of Met80-dissociated cyt c. The Fe-His stretching (νFe-His) mode of ferrous M80A cyt c was observed at 236 cm-1, and this frequency decreased by 1.5 cm-1 for the 15N-labeled protein. The higher νFe-His frequency of M80A cyt c than of other His-ligated heme proteins indicates strong heme coordination and the imidazolate character of His18. Peaks attributed to the Fe-O2 stretching (νFe-O2) and O-O stretching (νO-O) modes of the oxygenated species of M80A cyt c were observed at 576 and 1148 cm-1, respectively, under an 16O2 atmosphere, whereas the frequencies decreased to 544 and 1077 cm-1, respectively, under an 18O2 atmosphere. The νFe-O2 mode of Hydrogenobacter thermophilus (HT) M59A cyt c552 was observed at 580 cm-1 under an 16O2 atmosphere, whereas the frequency decreased to 553 cm-1 under an 18O2 atmosphere, indicating that relatively high νFe-O2 frequencies are characteristic of c-type cyt proteins. By comparison of the simultaneously observed νFe-O2 and νO-O frequencies of oxygenated cyt c and other oxygenated His-ligated heme proteins, the frequencies tend to have a positive linear relationship; the νFe-O2 frequency increases when the νO-O frequency increases. The imidazolate character of the heme-coordinated His and strong Fe-O and O-O bonds are characteristic of cyt c and apparently related to the peroxidase activity when Met80 dissociates from the heme iron.
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Affiliation(s)
- Mohan Zhang
- Division of Materials Science, Graduate School of Science and Technology, Nara Institute of Science and Technology (NAIST), 8916-5, Takayama, Ikoma, Nara 630-0192, Japan
| | - Hulin Tai
- Division of Materials Science, Graduate School of Science and Technology, Nara Institute of Science and Technology (NAIST), 8916-5, Takayama, Ikoma, Nara 630-0192, Japan
| | - Sachiko Yanagisawa
- Graduate School of Life Science, University of Hyogo, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan
| | - Masaru Yamanaka
- Division of Materials Science, Graduate School of Science and Technology, Nara Institute of Science and Technology (NAIST), 8916-5, Takayama, Ikoma, Nara 630-0192, Japan
| | - Takashi Ogura
- Graduate School of Life Science, University of Hyogo, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan
| | - Shun Hirota
- Division of Materials Science, Graduate School of Science and Technology, Nara Institute of Science and Technology (NAIST), 8916-5, Takayama, Ikoma, Nara 630-0192, Japan
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15
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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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16
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Yurchenko AA, Korotkova PD, Timofeev VI, Shumm AB, Vladimirov YA. Modeling of the Interaction of Cytochrome c with Cardiolipin. CRYSTALLOGR REP+ 2022. [DOI: 10.1134/s1063774522030257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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17
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Lei H, Kelly AD, Bowler BE. Alkaline State of the Domain-Swapped Dimer of Human Cytochrome c: A Conformational Switch for Apoptotic Peroxidase Activity. J Am Chem Soc 2022; 144:21184-21195. [PMID: 36346995 PMCID: PMC9743720 DOI: 10.1021/jacs.2c08325] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
A 2.08 Å structure of an alkaline conformer of the domain-swapped dimer of K72A human cytochrome c (Cytc) crystallized at pH 9.9 is presented. In the structure, Lys79 is ligated to the heme. All other domain-swapped dimer structures of Cytc have water bound to this coordination site. Part of Ω-loop D (residues 70-85) forms a flexible linker between the subunits in other Cytc domain-swapped dimer structures but instead converts to a helix in the alkaline conformer of the dimer combining with the C-terminal helix to form two 26-residue helices that bracket both sides of the dimer. The alkaline transition of the K72A human dimer monitored at both 625 nm (high spin heme) and 695 nm (Met80 ligation) yields midpoint pH values of 6.6 and 7.6, respectively, showing that the Met80 → Lys79 and high spin to low spin transitions are distinct. The dimer peroxidase activity increases rapidly below pH 7, suggesting that population of the high spin form of the heme is what promotes peroxidase activity. Comparison of the structures of the alkaline dimer and the neutral pH dimer shows that the neutral pH conformer has a better electrostatic surface for binding to a cardiolipin-containing membrane and provides better access for small molecules to the heme iron. Given that the pH of mitochondrial cristae ranges from 6.9 to 7.2, the alkaline transition of the Cytc dimer could provide a conformational switch to tune the peroxidase activity of Cytc that oxygenates cardiolipin in the early stages of apoptosis.
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Affiliation(s)
| | - Allison D. Kelly
- Department of Chemistry and Biochemistry and Center for Biomolecular Structure and Dynamics, University of Montana, Missoula, Montana 59812, USA
| | - Bruce E. Bowler
- Department of Chemistry and Biochemistry and Center for Biomolecular Structure and Dynamics, University of Montana, Missoula, Montana 59812, USA
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18
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Tomasina F, Martínez J, Zeida A, Chiribao ML, Demicheli V, Correa A, Quijano C, Castro L, Carnahan RH, Vinson P, Goff M, Cooper T, McDonald WH, Castellana N, Hannibal L, Morse PT, Wan J, Hüttemann M, Jemmerson R, Piacenza L, Radi R. De novo sequencing and construction of a unique antibody for the recognition of alternative conformations of cytochrome c in cells. Proc Natl Acad Sci U S A 2022; 119:e2213432119. [PMID: 36378644 PMCID: PMC9704708 DOI: 10.1073/pnas.2213432119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 10/13/2022] [Indexed: 11/16/2022] Open
Abstract
Cytochrome c (cyt c) can undergo reversible conformational changes under biologically relevant conditions. Revealing these alternative cyt c conformers at the cell and tissue level is challenging. A monoclonal antibody (mAb) identifying a key conformational change in cyt c was previously reported, but the hybridoma was rendered nonviable. To resurrect the mAb in a recombinant form, the amino-acid sequences of the heavy and light chains were determined by peptide mapping-mass spectrometry-bioinformatic analysis and used to construct plasmids encoding the full-length chains. The recombinant mAb (R1D3) was shown to perform similarly to the original mAb in antigen-binding assays. The mAb bound to a variety of oxidatively modified cyt c species (e.g., nitrated at Tyr74 or oxidized at Met80), which lose the sixth heme ligation (Fe-Met80); it did not bind to several cyt c phospho- and acetyl-mimetics. Peptide competition assays together with molecular dynamic studies support that R1D3 binds a neoepitope within the loop 40-57. R1D3 was employed to identify alternative conformations of cyt c in cells under oxidant- or senescence-induced challenge as confirmed by immunocytochemistry and immunoaffinity studies. Alternative conformers translocated to the nuclei without causing apoptosis, an observation that was further confirmed after pinocytic loading of oxidatively modified cyt c to B16-F1 cells. Thus, alternative cyt c conformers, known to gain peroxidatic function, may represent redox messengers at the cell nuclei. The availability and properties of R1D3 open avenues of interrogation regarding the presence and biological functions of alternative conformations of cyt c in mammalian cells and tissues.
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Affiliation(s)
- Florencia Tomasina
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Montevideo 11800, Uruguay
- Centro de Investigaciones Biomédicas, Facultad de Medicina, Universidad de la República, Montevideo 11800, Uruguay
| | - Jennyfer Martínez
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Montevideo 11800, Uruguay
- Centro de Investigaciones Biomédicas, Facultad de Medicina, Universidad de la República, Montevideo 11800, Uruguay
| | - Ari Zeida
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Montevideo 11800, Uruguay
- Centro de Investigaciones Biomédicas, Facultad de Medicina, Universidad de la República, Montevideo 11800, Uruguay
| | - María Laura Chiribao
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Montevideo 11800, Uruguay
- Centro de Investigaciones Biomédicas, Facultad de Medicina, Universidad de la República, Montevideo 11800, Uruguay
- Unidad de Biología Molecular, Laboratorio de Interacción Hospedero Patógeno, Institut Pasteur de Montevideo, Montevideo 11400, Uruguay
| | - Verónica Demicheli
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Montevideo 11800, Uruguay
- Centro de Investigaciones Biomédicas, Facultad de Medicina, Universidad de la República, Montevideo 11800, Uruguay
| | - Agustín Correa
- Recombinant Protein Unit, Institut Pasteur de Montevideo, Montevideo 11400, Uruguay
| | - Celia Quijano
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Montevideo 11800, Uruguay
- Centro de Investigaciones Biomédicas, Facultad de Medicina, Universidad de la República, Montevideo 11800, Uruguay
| | - Laura Castro
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Montevideo 11800, Uruguay
- Centro de Investigaciones Biomédicas, Facultad de Medicina, Universidad de la República, Montevideo 11800, Uruguay
| | - Robert H. Carnahan
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN 37232
| | | | - Matt Goff
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232
| | - Tracy Cooper
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232
| | - W. Hayes McDonald
- Department of Biochemistry and the Proteomics Core of the Mass Spectrometry Research Center, Vanderbilt University School of Medicine, Nashville, TN 37240
| | | | - Luciana Hannibal
- Centro de Investigaciones Biomédicas, Facultad de Medicina, Universidad de la República, Montevideo 11800, Uruguay
- Laboratory of Clinical Biochemistry and Metabolism, Department of General Pediatrics, Adolescent Medicine and Neonatology, Faculty of Medicine, Medical Center-University of Freiburg, 79106 Freiburg, Germany
| | - Paul T. Morse
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI 48201
| | - Junmei Wan
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI 48201
| | - Maik Hüttemann
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI 48201
- Department of Biochemistry, Microbiology, and Immunology, Wayne State University, Detroit, MI 48201
| | - Ronald Jemmerson
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN 55455
| | - Lucía Piacenza
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Montevideo 11800, Uruguay
- Centro de Investigaciones Biomédicas, Facultad de Medicina, Universidad de la República, Montevideo 11800, Uruguay
| | - Rafael Radi
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Montevideo 11800, Uruguay
- Centro de Investigaciones Biomédicas, Facultad de Medicina, Universidad de la República, Montevideo 11800, Uruguay
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19
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Korotkova PD, Yurchenko AA, Timofeev VI, Podshivalov DD, Gusel’nikova AR, Shumm AB, Vladimirov YA. Modeling of the Interaction of Cytochrome c with the Lipid Bilayer. CRYSTALLOGR REP+ 2022. [DOI: 10.1134/s1063774522030117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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20
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Liu X, Du H, Sun Y, Shao L. Role of abnormal energy metabolism in the progression of chronic kidney disease and drug intervention. Ren Fail 2022; 44:790-805. [PMID: 35535500 PMCID: PMC9103584 DOI: 10.1080/0886022x.2022.2072743] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Chronic kidney disease (CKD) is a severe clinical syndrome with significant socioeconomic impact worldwide. Orderly energy metabolism is essential for normal kidney function and energy metabolism disorders are increasingly recognized as an important player in CKD. Energy metabolism disorders are characterized by ATP deficits and reactive oxygen species increase. Oxygen and mitochondria are essential for ATP production, hypoxia and mitochondrial dysfunction both affect the energy production process. Renin-angiotensin and adenine signaling pathway also play important regulatory roles in energy metabolism. In addition, disturbance of energy metabolism is a key factor in the development of hereditary nephropathy such as autosomal dominant polycystic kidney disease. Currently, drugs with clinically clear renal function protection, such as Angiotensin II Type 1 receptor blockers and fenofibrate, have been proven to improve energy metabolism disorders. The sodium-glucose co-transporter inhibitors 2 that can mediate glucose metabolism disorders not only delay the progress of diabetic nephropathy, but also have significant protective effects in non-diabetic nephropathy. Hypoxia-inducible factor enhances ATP production to the kidney by improving renal oxygen supply and increasing glycolysis, and the mitochondria targeted peptides (SS-31) plays a protective role by stabilizing the mitochondrial inner membrane. Moreover, several drugs are being studied and are predicted to have potential renal protective properties. We propose that the regulation of energy metabolism represents a promising strategy to delay the progression of CKD.
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Affiliation(s)
- Xuyan Liu
- Department of Nephrology, The Affiliated Qingdao Municipal Hospital of Qingdao University, Qingdao, China
| | - Huasheng Du
- Department of Nephrology, The Affiliated Qingdao Municipal Hospital of Qingdao University, Qingdao, China
| | - Yan Sun
- Department of Nephrology, The Affiliated Qingdao Municipal Hospital of Qingdao University, Qingdao, China
| | - Leping Shao
- Department of Nephrology, The Affiliated Qingdao Municipal Hospital of Qingdao University, Qingdao, China
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21
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Chertkova RV, Firsov AM, Brazhe NA, Nikelshparg EI, Bochkova ZV, Bryantseva TV, Semenova MA, Baizhumanov AA, Kotova EA, Kirpichnikov MP, Maksimov GV, Antonenko YN, Dolgikh DA. Multiple Mutations in the Non-Ordered Red Ω-Loop Enhance the Membrane-Permeabilizing and Peroxidase-like Activity of Cytochrome c. Biomolecules 2022; 12:665. [PMID: 35625593 PMCID: PMC9138828 DOI: 10.3390/biom12050665] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Revised: 04/27/2022] [Accepted: 04/30/2022] [Indexed: 02/04/2023] Open
Abstract
A key event in the cytochrome c-dependent apoptotic pathway is the permeabilization of the outer mitochondrial membrane, resulting in the release of various apoptogenic factors, including cytochrome c, into the cytosol. It is believed that the permeabilization of the outer mitochondrial membrane can be induced by the peroxidase activity of cytochrome c in a complex with cardiolipin. Using a number of mutant variants of cytochrome c, we showed that both substitutions of Lys residues from the universal binding site for oppositely charged Glu residues and mutations leading to a decrease in the conformational mobility of the red Ω-loop in almost all cases did not affect the ability of cytochrome c to bind to cardiolipin. At the same time, the peroxidase activity of all mutant variants in a complex with cardiolipin was three to five times higher than that of the wild type. A pronounced increase in the ability to permeabilize the lipid membrane in the presence of hydrogen peroxide, as measured by calcein leakage from liposomes, was observed only in the case of four substitutions in the red Ω-loop (M4 mutant). According to resonance and surface-enhanced Raman spectroscopy, the mutations caused significant changes in the heme of oxidized cytochrome c molecules resulting in an increased probability of the plane heme conformation and the enhancement of the rigidity of the protein surrounding the heme. The binding of wild-type and mutant forms of oxidized cytochrome c to cardiolipin-containing liposomes caused the disordering of the acyl lipid chains that was more pronounced for the M4 mutant. Our findings indicate that the Ω-loop is important for the pore formation in cardiolipin-containing membranes.
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Affiliation(s)
- Rita V. Chertkova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (Z.V.B.); (T.V.B.); (M.A.S.); (M.P.K.); (D.A.D.)
| | - Alexander M. Firsov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia; (A.M.F.); (E.A.K.); (Y.N.A.)
| | - Nadezda A. Brazhe
- Biophysics Department, Biological Faculty, Lomonosov Moscow State University, 119234 Moscow, Russia; (E.I.N.); (A.A.B.); (G.V.M.)
| | - Evelina I. Nikelshparg
- Biophysics Department, Biological Faculty, Lomonosov Moscow State University, 119234 Moscow, Russia; (E.I.N.); (A.A.B.); (G.V.M.)
| | - Zhanna V. Bochkova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (Z.V.B.); (T.V.B.); (M.A.S.); (M.P.K.); (D.A.D.)
- Biophysics Department, Biological Faculty, Lomonosov Moscow State University, 119234 Moscow, Russia; (E.I.N.); (A.A.B.); (G.V.M.)
| | - Tatyana V. Bryantseva
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (Z.V.B.); (T.V.B.); (M.A.S.); (M.P.K.); (D.A.D.)
- Biology Department, Lomonosov Moscow State University, 119899 Moscow, Russia
| | - Marina A. Semenova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (Z.V.B.); (T.V.B.); (M.A.S.); (M.P.K.); (D.A.D.)
| | - Adil A. Baizhumanov
- Biophysics Department, Biological Faculty, Lomonosov Moscow State University, 119234 Moscow, Russia; (E.I.N.); (A.A.B.); (G.V.M.)
| | - Elena A. Kotova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia; (A.M.F.); (E.A.K.); (Y.N.A.)
| | - Mikhail P. Kirpichnikov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (Z.V.B.); (T.V.B.); (M.A.S.); (M.P.K.); (D.A.D.)
- Biology Department, Lomonosov Moscow State University, 119899 Moscow, Russia
| | - Georgy V. Maksimov
- Biophysics Department, Biological Faculty, Lomonosov Moscow State University, 119234 Moscow, Russia; (E.I.N.); (A.A.B.); (G.V.M.)
- Federal State Autonomous Educational Institution of Higher Education “National Research Technological University “MISiS””, 119049 Moscow, Russia
| | - Yuriy N. Antonenko
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia; (A.M.F.); (E.A.K.); (Y.N.A.)
| | - Dmitry A. Dolgikh
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (Z.V.B.); (T.V.B.); (M.A.S.); (M.P.K.); (D.A.D.)
- Biology Department, Lomonosov Moscow State University, 119899 Moscow, Russia
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22
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Modeling the molecular dynamics of cytochrome C in aqueous and water–methanol environment. MENDELEEV COMMUNICATIONS 2022. [DOI: 10.1016/j.mencom.2022.05.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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23
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The effects of cardiolipin on the structural dynamics of the mitochondrial ADP/ATP carrier in its cytosol-open state. J Lipid Res 2022; 63:100227. [PMID: 35569528 PMCID: PMC9189224 DOI: 10.1016/j.jlr.2022.100227] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 05/09/2022] [Accepted: 05/10/2022] [Indexed: 11/21/2022] Open
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24
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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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25
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Samsri S, Prasertsuk P, Nutho B, Pornsuwan S. Molecular insights on the conformational dynamics of a P76C mutant of human cytochrome c and the enhancement on its peroxidase activity. Arch Biochem Biophys 2021; 716:109112. [PMID: 34954215 DOI: 10.1016/j.abb.2021.109112] [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: 11/09/2021] [Revised: 12/17/2021] [Accepted: 12/20/2021] [Indexed: 11/16/2022]
Abstract
In apoptotic pathway, the interaction of Cytochrome c (Cytc) with cardiolipin in vivo is a key process to induce peroxidase activity of Cytc and trigger the release of Cytc in the inner mitochondria into cytosol. The peroxidase active form of Cytc occurs due to local conformational changes that support the opening of the heme crevice and the loss of an axial ligand between Met80 and heme Fe. Structural adjustments at the Ω-loop segments of Cytc are required for such process. To study the role of the distal Ω-loop segments comprising residues 71-85 in human Cytc (hCytc), we investigated a cysteine mutation at Pro76, one of the highly conserved residues in this loop. The effect of P76C mutant was explored by the combination of experimental characterizations and molecular dynamics (MD) simulations. The peroxidase activity of the P76C mutant was found to be significantly increased by ∼13 folds relative to the wild type. Experimental data on global denaturation, alkaline transition, heme bleaching, and spin-labeling Electron Spin Resonance were in good agreement with the enhancement of peroxidase activity. The MD results of hCytc in the hexacoordinate form suggest the important changes in P76C mutant occurred due to the unfolding at the central Ω-loop (residues 40-57), and the weakening of H-bond between Tyr67 and Met80. Whereas the experimental data implied that the P76C mutant tend to be in equilibrium between the pentacoordinate and hexacoordinate forms, the MD and experimental information are complementary and were used to support the mechanisms of peroxidase active form of hCytc.
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Affiliation(s)
- Sasiprapa Samsri
- Department of Chemistry and Center of Excellence for Innovation in Chemistry, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand
| | - Possawee Prasertsuk
- Department of Chemistry and Center of Excellence for Innovation in Chemistry, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand
| | - Bodee Nutho
- Department of Pharmacology, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand.
| | - Soraya Pornsuwan
- Department of Chemistry and Center of Excellence for Innovation in Chemistry, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand.
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26
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Fox CA, Lethcoe K, Ryan RO. Calcium-induced release of cytochrome c from cardiolipin nanodisks: Implications for apoptosis. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2021; 1863:183722. [PMID: 34400138 PMCID: PMC8464532 DOI: 10.1016/j.bbamem.2021.183722] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 07/19/2021] [Accepted: 07/29/2021] [Indexed: 06/13/2023]
Abstract
Miniature bilayer membranes comprised of phospholipid and an apolipoprotein scaffold, termed nanodisks (ND), have been used in binding studies. When ND formulated with cardiolipin (CL), but not phosphatidylcholine, were incubated with cytochrome c, FPLC gel filtration chromatography provided evidence of a stable binding interaction. Incubation of CL ND with CaCl2 resulted in a concentration-dependent increase in sample turbidity caused by ND particle disruption. Prior incubation of CL ND with cytochrome c increased CL ND sensitivity to CaCl2-induced effects. Centrifugation of CaCl2-treated CL ND samples yielded pellet and supernatant fractions. Whereas the ND scaffold protein, apolipophorin III, was recovered in the pellet fraction along with CL, the majority of the cytochrome c pool was in the supernatant fraction. Moreover, when cytochrome c CL ND were incubated with CaCl2 at concentrations below the threshold to induce ND particle disruption, FPLC analysis showed that cytochrome c was released. Pre-incubation of CL ND with CaCl2 under conditions that do not disrupt ND particle integrity prevented cytochrome c binding to CL ND. Thus, competition between Ca2+ and cytochrome c for a common binding site on CL modulates cytochrome c binding and likely plays a role in its dissociation from CL-rich cristae membranes in response to apoptotic stimuli.
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Affiliation(s)
- Colin A Fox
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, Reno, NV 89557, United States of America
| | - Kyle Lethcoe
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, Reno, NV 89557, United States of America
| | - Robert O Ryan
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, Reno, NV 89557, United States of America.
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27
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Gamero-Quijano A, Bhattacharya S, Cazade PA, Molina-Osorio AF, Beecher C, Djeghader A, Soulimane T, Dossot M, Thompson D, Herzog G, Scanlon MD. Modulating the pro-apoptotic activity of cytochrome c at a biomimetic electrified interface. SCIENCE ADVANCES 2021; 7:eabg4119. [PMID: 34739310 PMCID: PMC8570605 DOI: 10.1126/sciadv.abg4119] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 09/17/2021] [Indexed: 06/13/2023]
Abstract
Programmed cell death via apoptosis is a natural defence against excessive cell division, crucial for fetal development to maintenance of homeostasis and elimination of precancerous and senescent cells. Here, we demonstrate an electrified liquid biointerface that replicates the molecular machinery of the inner mitochondrial membrane at the onset of apoptosis. By mimicking in vivo cytochrome c (Cyt c) interactions with cell membranes, our platform allows us to modulate the conformational plasticity of the protein by simply varying the electrochemical environment at an aqueous-organic interface. We observe interfacial electron transfer between an organic electron donor decamethylferrocene and O2, electrocatalyzed by Cyt c. This interfacial reaction requires partial Cyt c unfolding, mimicking Cyt c in vivo peroxidase activity. As proof of concept, we use our electrified liquid biointerface to identify drug molecules, such as bifonazole, that can potentially down-regulate Cyt c and protect against uncontrolled neuronal cell death in neurodegenerative disorders.
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Affiliation(s)
- Alonso Gamero-Quijano
- The Bernal Institute, University of Limerick (UL), Limerick V94 T9PX, Ireland
- Department of Chemical Sciences, School of Natural Sciences, University of Limerick (UL), Limerick V94 T9PX, Ireland
| | - Shayon Bhattacharya
- The Bernal Institute, University of Limerick (UL), Limerick V94 T9PX, Ireland
- Department of Physics, School of Natural Sciences, University of Limerick (UL), Limerick V94 T9PX, Ireland
| | - Pierre-André Cazade
- The Bernal Institute, University of Limerick (UL), Limerick V94 T9PX, Ireland
- Department of Physics, School of Natural Sciences, University of Limerick (UL), Limerick V94 T9PX, Ireland
| | - Andrés F. Molina-Osorio
- The Bernal Institute, University of Limerick (UL), Limerick V94 T9PX, Ireland
- Department of Chemical Sciences, School of Natural Sciences, University of Limerick (UL), Limerick V94 T9PX, Ireland
| | - Cillian Beecher
- The Bernal Institute, University of Limerick (UL), Limerick V94 T9PX, Ireland
- Department of Chemical Sciences, School of Natural Sciences, University of Limerick (UL), Limerick V94 T9PX, Ireland
| | - Ahmed Djeghader
- Department of Chemical Sciences, School of Natural Sciences, University of Limerick (UL), Limerick V94 T9PX, Ireland
| | - Tewfik Soulimane
- Department of Chemical Sciences, School of Natural Sciences, University of Limerick (UL), Limerick V94 T9PX, Ireland
| | - Manuel Dossot
- Laboratoire de Chimie Physique et Microbiologie pour les Matériaux et l’Environnement, Université de Lorraine, CNRS, LCPME, F-54000 Nancy, France
| | - Damien Thompson
- The Bernal Institute, University of Limerick (UL), Limerick V94 T9PX, Ireland
- Department of Physics, School of Natural Sciences, University of Limerick (UL), Limerick V94 T9PX, Ireland
| | - Grégoire Herzog
- Laboratoire de Chimie Physique et Microbiologie pour les Matériaux et l’Environnement, Université de Lorraine, CNRS, LCPME, F-54000 Nancy, France
| | - Micheál D. Scanlon
- The Bernal Institute, University of Limerick (UL), Limerick V94 T9PX, Ireland
- Department of Chemical Sciences, School of Natural Sciences, University of Limerick (UL), Limerick V94 T9PX, Ireland
- Advanced Materials and Bioengineering Research (AMBER) Centre, Dublin, Ireland
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28
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Zhong F, Alden SL, Hughes RP, Pletneva EV. Comparing Properties of Common Bioinorganic Ligands with Switchable Variants of Cytochrome c. Inorg Chem 2021; 61:1207-1227. [PMID: 34699724 DOI: 10.1021/acs.inorgchem.1c02322] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Ligand substitution at the metal center is common in catalysis and signal transduction of metalloproteins. Understanding the effects of particular ligands, as well as the polypeptide surrounding, is critical for uncovering mechanisms of these biological processes and exploiting them in the design of bioinspired catalysts and molecular devices. A series of switchable K79G/M80X/F82C (X = Met, His, or Lys) variants of cytochrome (cyt) c was employed to directly compare the stability of differently ligated proteins and activation barriers for Met, His, and Lys replacement at the ferric heme iron. Studies of these variants and their nonswitchable counterparts K79G/M80X have revealed stability trends Met < Lys < His and Lys < His < Met for the protein FeIII-X and FeII-X species, respectively. The differences in the hydrogen-bonding interactions in folded proteins and in solvation of unbound X in the unfolded proteins explain these trends. Calculations of free energy of ligand dissociation in small heme model complexes reveal that the ease of the FeIII-X bond breaking increases in the series amine < imidazole < thioether, mirroring trends in hardness of these ligands. Experimental rate constants for X dissociation in differently ligated cyt c variants are consistent with this sequence, but the differences between Met and His dissociation rates are attenuated because the former process is limited by the heme crevice opening. Analyses of activation parameters and comparisons to those for the Lys-to-Met ligand switch in the alkaline transition suggest that ligand dissociation is entropically driven in all the variants and accompanied by Lys protonation at neutral pH. The described thiolate redox-linked switches have offered a wealth of new information about interactions of different protein-derived ligands with the heme iron in cyt c model proteins, and we anticipate that the strategy of employing these switches could benefit studies of other redox metalloproteins and model complexes.
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Affiliation(s)
- 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
| | - Russell P Hughes
- Department of Chemistry, Dartmouth College, Hanover, New Hampshire 03755, United States
| | - Ekaterina V Pletneva
- Department of Chemistry, Dartmouth College, Hanover, New Hampshire 03755, United States
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29
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Sharma GS, Bhattacharya R, Singh LR. Functional inhibition of redox regulated heme proteins: A novel mechanism towards oxidative stress induced by homocysteine. Redox Biol 2021; 46:102080. [PMID: 34325357 PMCID: PMC8334742 DOI: 10.1016/j.redox.2021.102080] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 07/22/2021] [Indexed: 11/19/2022] Open
Abstract
Homocysteine (Hcy) is a sulfur containing non-protein toxic amino acid synthesized from methionine. Elevated level of Hcy is associated with cardiovascular complications and neurodegeneration. Hcy is believed to induce organ damage and apoptosis via oxidative stress. The pro-oxidant nature of Hcy is considered to originate from the metal-induced oxidation of thiol group-containing molecules forming disulfides (Hcy-Hcy, Hcy-cysteine, Hcy-glutathione, etc) or with free cysteine residues of proteins (a process called protein S-homocysteinylation). Formation of such disulfides indeed results in the generation of reactive oxygen species (ROS) which eventually leads to loss of cellular integrity. In the present manuscript, we performed systematic investigation of the effect of Hcy on iron containing proteins. We discover a novel mechanism of Hcy toxicity wherein Hcy oxidation is linked with the functional loss of the protein with iron as cofactors. Our results indicate that redox regulated heme proteins might be primarily involved in the Hcy toxicity and associated oxidative stress.
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Affiliation(s)
- Gurumayum Suraj Sharma
- Department of Botany, Bhaskaracharya College of Applied Sciences, University of Delhi, Delhi, 110075, India
| | - Reshmee Bhattacharya
- Dr. B. R. Ambedkar Center for Biomedical Research, University of Delhi, Delhi, 110007, India
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30
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Donia T, Khamis A. Management of oxidative stress and inflammation in cardiovascular diseases: mechanisms and challenges. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:34121-34153. [PMID: 33963999 DOI: 10.1007/s11356-021-14109-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 04/21/2021] [Indexed: 06/12/2023]
Abstract
Cardiovascular diseases (CVDs) have diverse physiopathological mechanisms with interconnected oxidative stress and inflammation as one of the common etiologies which result in the onset and development of atherosclerotic plaques. In this review, we illustrate this strong crosstalk between oxidative stress, inflammation, and CVD. Also, mitochondrial functions underlying this crosstalk, and various approaches for the prevention of redox/inflammatory biological impacts will be illustrated. In part, we focus on the laboratory biomarkers and physiological tests for the evaluation of oxidative stress status and inflammatory processes. The impact of a healthy lifestyle on CVD onset and development is displayed as well. Furthermore, the differences in oxidative stress and inflammation are related to genetic susceptibility to cardiovascular diseases and the variability in the assessment of CVDs risk between individuals; Omics technologies for measuring oxidative stress and inflammation will be explored. Finally, we display the oxidative stress-related microRNA and the functions of the redox basis of epigenetic modifications.
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Affiliation(s)
- Thoria Donia
- Biochemistry Division, Chemistry Department, Faculty of Science, Tanta University, Tanta, Egypt
| | - Abeer Khamis
- Biochemistry Division, Chemistry Department, Faculty of Science, Tanta University, Tanta, Egypt.
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31
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Pani I, K M FN, Sharma M, Pal SK. Probing Nanoscale Lipid-Protein Interactions at the Interface of Liquid Crystal Droplets. NANO LETTERS 2021; 21:4546-4553. [PMID: 34048245 DOI: 10.1021/acs.nanolett.0c05139] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Aqueous interfaces of liquid crystals (LCs) are widely explored in the design of functional interfaces to recapitulate the key aspects of biomolecular interactions in cellular milieu. Herein, using aqueous LC dispersions, we explore the interactions between mitochondrial cardiolipin and membrane-associated cytochrome c which play a pivotal role in the apoptotic signaling cascade. Conventional techniques used to decipher LC ordering at the droplet interface fail to give information about the interactions at a molecular level. Besides, owing to the complexity of LC systems and multiple determinants driving the LC reorientation, accurate analysis of the underlying mechanism responsible for the LC ordering transition remains challenging. Using a combination of atomistic simulations and microscopic and spectroscopic readouts, for the first time, we unveil the lipid-protein interactions that drive the reorientation at the LC droplet interface. The insights from our work are fundamental to the design of these interfaces for a spectrum of interfacial applications.
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32
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Li M, Sun W, Tyurin VA, DeLucia M, Ahn J, Kagan VE, van der Wel PCA. Activation of Cytochrome C Peroxidase Function Through Coordinated Foldon Loop Dynamics upon Interaction with Anionic Lipids. J Mol Biol 2021; 433:167057. [PMID: 34033821 DOI: 10.1016/j.jmb.2021.167057] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 05/07/2021] [Accepted: 05/13/2021] [Indexed: 02/06/2023]
Abstract
Cardiolipin (CL) is a mitochondrial anionic lipid that plays important roles in the regulation and signaling of mitochondrial apoptosis. CL peroxidation catalyzed by the assembly of CL-cytochrome c (cyt c) complexes at the inner mitochondrial membrane is a critical checkpoint. The structural changes in the protein, associated with peroxidase activation by CL and different anionic lipids, are not known at a molecular level. To better understand these peripheral protein-lipid interactions, we compare how phosphatidylglycerol (PG) and CL lipids trigger cyt c peroxidase activation, and correlate functional differences to structural and motional changes in membrane-associated cyt c. Structural and motional studies of the bound protein are enabled by magic angle spinning solid state NMR spectroscopy, while lipid peroxidase activity is assayed by mass spectrometry. PG binding results in a surface-bound state that preserves a nativelike fold, which nonetheless allows for significant peroxidase activity, though at a lower level than binding its native substrate CL. Lipid-specific differences in peroxidase activation are found to correlate to corresponding differences in lipid-induced protein mobility, affecting specific protein segments. The dynamics of omega loops C and D are upregulated by CL binding, in a way that is remarkably controlled by the protein:lipid stoichiometry. In contrast to complete chemical denaturation, membrane-induced protein destabilization reflects a destabilization of select cyt c foldons, while the energetically most stable helices are preserved. Our studies illuminate the interplay of protein and lipid dynamics in the creation of lipid peroxidase-active proteolipid complexes implicated in early stages of mitochondrial apoptosis.
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Affiliation(s)
- Mingyue Li
- Department of Structural Biology, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Wanyang Sun
- Department of Environmental and Occupational Health, University of Pittsburgh, Pittsburgh, PA 15213, USA; Center for Free Radical and Antioxidant Health, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Vladimir A Tyurin
- Department of Environmental and Occupational Health, University of Pittsburgh, Pittsburgh, PA 15213, USA; Center for Free Radical and Antioxidant 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; Center for Free Radical and Antioxidant 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; Institute for Regenerative Medicine, 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, Groningen, the Netherlands.
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33
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Electrical unfolding of cytochrome c during translocation through a nanopore constriction. Proc Natl Acad Sci U S A 2021; 118:2016262118. [PMID: 33883276 DOI: 10.1073/pnas.2016262118] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Many small proteins move across cellular compartments through narrow pores. In order to thread a protein through a constriction, free energy must be overcome to either deform or completely unfold the protein. In principle, the diameter of the pore, along with the effective driving force for unfolding the protein, as well as its barrier to translocation, should be critical factors that govern whether the process proceeds via squeezing, unfolding/threading, or both. To probe this for a well-established protein system, we studied the electric-field-driven translocation behavior of cytochrome c (cyt c) through ultrathin silicon nitride (SiNx) solid-state nanopores of diameters ranging from 1.5 to 5.5 nm. For a 2.5-nm-diameter pore, we find that, in a threshold electric-field regime of ∼30 to 100 MV/m, cyt c is able to squeeze through the pore. As electric fields inside the pore are increased, the unfolded state of cyt c is thermodynamically stabilized, facilitating its translocation. In contrast, for 1.5- and 2.0-nm-diameter pores, translocation occurs only by threading of the fully unfolded protein after it transitions through a higher energy unfolding intermediate state at the mouth of the pore. The relative energies between the metastable, intermediate, and unfolded protein states are extracted using a simple thermodynamic model that is dictated by the relatively slow (∼ms) protein translocation times for passing through the nanopore. These experiments map the various modes of protein translocation through a constriction, which opens avenues for exploring protein folding structures, internal contacts, and electric-field-induced deformability.
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34
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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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35
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Lysine 72 substitutions differently affect lipid membrane permeabilizing and proapoptotic activities of horse heart cytochrome c. Biochem Biophys Res Commun 2021; 548:74-77. [PMID: 33631678 DOI: 10.1016/j.bbrc.2021.02.023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 02/05/2021] [Indexed: 12/25/2022]
Abstract
Peroxidase activity of cytochrome c (cyt c)/cardiolipin (CL) complex is supposed to be involved in the initiation of apoptosis via peroxidative induction of mitochondrial membrane permeabilization. As cyt c binding to CL-containing membranes is at least partially associated with electrostatic protein/lipid interaction, we screened single-point mutants of horse heart cyt c with various substitutions of lysine at position 72, considered to play a significant role in both the binding and peroxidase activity of the protein. Contrary to expectations, K72A, K72R and K72L substitutions exerted slight effects on both the cyt c binding to CL-containing liposomal membranes and the cyt c/H2O2-induced calcein leakage from liposomes, used here as a membrane permeabilization assay. Both the binding and permeabilization were decreased to various extents, but not significantly, in the case of K72E and K72N mutants. A drastic difference was found between the sequence of the permeabilizing activities of the cyt c variants and the previously described order of their proapoptotic activities (Chertkova et al., 2008).
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Hirota S, Nagao S. New Aspects of Cytochromec: 3D Domain Swapping, Membrane Interaction, Peroxidase Activity, and Met80 Sulfoxide Modification. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2021. [DOI: 10.1246/bcsj.20200272] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Shun Hirota
- Division of Materials Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma, Nara 630-0192, Japan
| | - Satoshi Nagao
- Graduate School of Life Science, University of Hyogo, 3-2-1 Koto, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan
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Sun SC, Huang HW, Lo YT, Chuang MC, Hsu YHH. Unraveling cardiolipin-induced conformational change of cytochrome c through H/D exchange mass spectrometry and quartz crystal microbalance. Sci Rep 2021; 11:1090. [PMID: 33441668 PMCID: PMC7806790 DOI: 10.1038/s41598-020-79905-8] [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: 07/16/2020] [Accepted: 12/04/2020] [Indexed: 11/21/2022] Open
Abstract
Cardiolipin (CL), a crucial component in inner mitochondrial membranes, interacts with cytochrome c (cyt c) to form a peroxidase complex for the catalysis of CL oxidation. Such interaction is pivotal to the mitochondrial regulation of apoptosis and is affected by the redox state of cyt c. In the present study, the redox-dependent interaction of cyt c with CL was investigated through amide hydrogen/deuterium exchange coupled with mass spectrometry (HDXMS) and quartz crystal microbalance with dissipation monitoring (QCM-D). Ferrous cyt c exhibited a more compact conformation compared with its ferric form, which was supported by the lower number of deuterons accumulated and the greater amplitude reduction on dissipation. Upon association with CL, ferrous cyt c resulted in a moderate increase in deuteration, whereas the ferric form caused a drastic increase of deuteration, which indicated that CL-bound ferric cyt c formed an extended conformation. These results were consistent with those of the frequency (f) − dissipation (D) experiments, which revealed that ferric cyt c yielded greater values of |ΔD/Δf| within the first minute. Further fragmentation analysis based on HDXMS indicated that the effect of CL binding was considerably different on ferric and ferrous cyt c in the C-helix and the Loop 9–24. In ferric cyt c, CL binding affected Met80 and destabilized His18 interaction with heme, which was not observed with ferrous cyt c. An interaction model was proposed to explain the aforementioned results.
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Affiliation(s)
- Sin-Cih Sun
- Department of Chemistry, Tunghai University, Taichung, Taiwan
| | - Hung-Wei Huang
- Department of Chemistry, Tunghai University, Taichung, Taiwan
| | - Yi-Ting Lo
- Department of Chemistry, Tunghai University, Taichung, Taiwan
| | - Min-Chieh Chuang
- Department of Chemistry, Tunghai University, Taichung, Taiwan. .,Department of Environmental Science and Engineering, Taichung, Taiwan.
| | - Yuan-Hao Howard Hsu
- Department of Chemistry, Tunghai University, Taichung, Taiwan. .,Biological Science Center, Tunghai University, Taichung, Taiwan.
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Gusev ID, Firsov AM, Chertkova RV, Kotova EA, Dolgikh DA, Kirpichnikov MP, Antonenko YN. Study of Interaction of Fluorescent Cytochrome C with Liposomes, Mitochondria, and Mitoplasts by Fluorescence Correlation Spectroscopy. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2020. [DOI: 10.1134/s1068162020060084] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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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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Gai Z, Gui T, Kullak-Ublick GA, Li Y, Visentin M. The Role of Mitochondria in Drug-Induced Kidney Injury. Front Physiol 2020; 11:1079. [PMID: 33013462 PMCID: PMC7500167 DOI: 10.3389/fphys.2020.01079] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 08/05/2020] [Indexed: 12/11/2022] Open
Abstract
The kidneys utilize roughly 10% of the body’s oxygen supply to produce the energy required for accomplishing their primary function: the regulation of body fluid composition through secreting, filtering, and reabsorbing metabolites and nutrients. To ensure an adequate ATP supply, the kidneys are particularly enriched in mitochondria, having the second highest mitochondrial content and thus oxygen consumption of our body. The bulk of the ATP generated in the kidneys is consumed to move solutes toward (reabsorption) or from (secretion) the peritubular capillaries through the concerted action of an array of ATP-binding cassette (ABC) pumps and transporters. ABC pumps function upon direct ATP hydrolysis. Transporters are driven by the ion electrochemical gradients and the membrane potential generated by the asymmetric transport of ions across the plasma membrane mediated by the ATPase pumps. Some of these transporters, namely the polyspecific organic anion transporters (OATs), the organic anion transporting polypeptides (OATPs), and the organic cation transporters (OCTs) are highly expressed on the proximal tubular cell membranes and happen to also transport drugs whose levels in the proximal tubular cells can rapidly rise, thereby damaging the mitochondria and resulting in cell death and kidney injury. Drug-induced kidney injury (DIKI) is a growing public health concern and a major cause of drug attrition in drug development and post-marketing approval. As part of the article collection “Mitochondria in Renal Health and Disease,” here, we provide a critical overview of the main molecular mechanisms underlying the mitochondrial damage caused by drugs inducing nephrotoxicity.
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Affiliation(s)
- Zhibo Gai
- Experimental Center, Shandong University of Traditional Chinese Medicine, Jinan, China.,Department of Clinical Pharmacology and Toxicology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Ting Gui
- Experimental Center, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Gerd A Kullak-Ublick
- Department of Clinical Pharmacology and Toxicology, University Hospital Zurich, University of Zurich, Zurich, Switzerland.,Mechanistic Safety, CMO & Patient Safety, Global Drug Development, Novartis Pharma, Basel, Switzerland
| | - Yunlun Li
- Innovation Research Institute of Traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan, China.,The Third Department of Cardiovascular Diseases, Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Michele Visentin
- Department of Clinical Pharmacology and Toxicology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
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Nie J, Yang J, Wei Y, Wei X. The role of oxidized phospholipids in the development of disease. Mol Aspects Med 2020; 76:100909. [PMID: 33023753 DOI: 10.1016/j.mam.2020.100909] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 08/29/2020] [Accepted: 09/21/2020] [Indexed: 02/05/2023]
Abstract
Oxidized phospholipids (OxPLs), complex mixtures of phospholipid oxidation products generated during normal or pathological processes, are increasingly recognized to show bioactive effects on many cellular signalling pathways. There is a growing body of evidence showing that OxPLs play an important role in many diseases, so it is essential to define the specific role of OxPLs in different diseases for the design of disease therapies. In vastly diverse pathological processes, OxPLs act as pro-inflammatory agents and contribute to the progression of many diseases; in addition, they play a role in anti-inflammatory processes, promoting the dissipation of inflammation and inhibiting the progression of some diseases. In addition to participating in the regulation of inflammatory responses, OxPLs affect the occurrence and development of diseases through other pathways, such as apoptosis promotion. In this review, the different and even opposite effects of different OxPL molecular species are discussed. Furthermore, the specific effects of OxPLs in various diseases, as well as the receptor and cellular mechanisms involved, are summarized.
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Affiliation(s)
- Ji Nie
- Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, China; Department of Respiration, First People's Hospital of Yunnan Province, Yunnan, 650032, China; The Affiliated Hospital of Kunming University of Science and Technology, Kunming, Yunnan, 650032, China
| | - Jing Yang
- Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, China; Melanoma and Sarcoma Medical Oncology Unit, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, 651 Dongfeng Road East, Guangzhou, 510060, China; State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
| | - Yuquan Wei
- Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Xiawei Wei
- Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, China.
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42
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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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43
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Adsorbing surface strongly influences the pseudoperoxidase and nitrite reductase activity of electrode-bound yeast cytochrome c. The effect of hydrophobic immobilization. Bioelectrochemistry 2020; 136:107628. [PMID: 32795942 DOI: 10.1016/j.bioelechem.2020.107628] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Revised: 07/31/2020] [Accepted: 07/31/2020] [Indexed: 02/02/2023]
Abstract
The Met80Ala and Met80Ala/Tyr67Ala variants of S. cerevisiae iso-1 cytochrome c (ycc) and their adducts with cardiolipin immobilized onto a gold electrode coated with a hydrophobic self-assembled monolayer (SAM) of decane-1-thiol were studied through cyclic voltammetry and surface-enhanced resonance Raman spectroscopy (SERRS). The electroactive species - containing a six-coordinate His/His axially ligated heme and a five-coordinate His/- heme stable in the oxidized and reduced state, respectively - and the pseudoperoxidase activity match those found previously for the wt species and are only slightly affected by CL binding. Most importantly, the reduced His/- ligated form of these variants is able to catalytically reduce the nitrite ion, while electrode-immobilized wt ycc and other His/Met heme ligated variants under a variety of conditions are not. Besides the pseudoperoxidase and nitrite reductase functions, which are the most physiologically relevant abilities of these constructs, also axial heme ligation and the equilibria between conformers are strongly affected by the nature - hydrophobic vs. electrostatic - of the non-covalent interactions determining protein immobilization. Also affected are the catalytic activity changes induced by a given mutation as well as those due to partial unfolding due to CL binding. It follows that under the same solution conditions the structural and functional properties of immobilized ycc are surface-specific and therefore cannot be transferred from an immobilized system to another involving different interfacial protein-SAM interactions.
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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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Négrerie M. Iron transitions during activation of allosteric heme proteins in cell signaling. Metallomics 2020; 11:868-893. [PMID: 30957812 DOI: 10.1039/c8mt00337h] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Allosteric heme proteins can fulfill a very large number of different functions thanks to the remarkable chemical versatility of heme through the entire living kingdom. Their efficacy resides in the ability of heme to transmit both iron coordination changes and iron redox state changes to the protein structure. Besides the properties of iron, proteins may impose a particular heme geometry leading to distortion, which allows selection or modulation of the electronic properties of heme. This review focusses on the mechanisms of allosteric protein activation triggered by heme coordination changes following diatomic binding to proteins as diverse as the human NO-receptor, cytochromes, NO-transporters and sensors, and a heme-activated potassium channel. It describes at the molecular level the chemical capabilities of heme to achieve very different tasks and emphasizes how the properties of heme are determined by the protein structure. Particularly, this reviews aims at giving an overview of the exquisite adaptability of heme, from bacteria to mammals.
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Affiliation(s)
- Michel Négrerie
- Laboratoire d'Optique et Biosciences, INSERM, CNRS, Ecole Polytechnique, 91120 Palaiseau, France.
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46
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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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47
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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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Govind C, Paul M, Karunakaran V. Ultrafast Heme Relaxation Dynamics Probing the Unfolded States of Cytochrome c Induced by Liposomes: Effect of Charge of Phospholipids. J Phys Chem B 2020; 124:2769-2777. [DOI: 10.1021/acs.jpcb.9b11957] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Chinju Govind
- Photosciences and Photonics Section, Chemical Sciences and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Thiruvananthapuram 695 019, Kerala, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Megha Paul
- Photosciences and Photonics Section, Chemical Sciences and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Thiruvananthapuram 695 019, Kerala, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Venugopal Karunakaran
- Photosciences and Photonics Section, Chemical Sciences and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Thiruvananthapuram 695 019, Kerala, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
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Comparison of the structural dynamic and mitochondrial electron-transfer properties of the proapoptotic human cytochrome c variants, G41S, Y48H and A51V. J Inorg Biochem 2020; 203:110924. [DOI: 10.1016/j.jinorgbio.2019.110924] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 11/08/2019] [Accepted: 11/12/2019] [Indexed: 01/02/2023]
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50
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Kagan VE, Tyurina YY, Sun WY, Vlasova II, Dar H, Tyurin VA, Amoscato AA, Mallampalli R, van der Wel PCA, He RR, Shvedova AA, Gabrilovich DI, Bayir H. Redox phospholipidomics of enzymatically generated oxygenated phospholipids as specific signals of programmed cell death. Free Radic Biol Med 2020; 147:231-241. [PMID: 31883467 PMCID: PMC7037592 DOI: 10.1016/j.freeradbiomed.2019.12.028] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 12/17/2019] [Accepted: 12/20/2019] [Indexed: 01/16/2023]
Abstract
High fidelity and effective adaptive changes of the cell and tissue metabolism to changing environments require strict coordination of numerous biological processes. Multicellular organisms developed sophisticated signaling systems of monitoring and responding to these different contexts. Among these systems, oxygenated lipids play a significant role realized via a variety of re-programming mechanisms. Some of them are enacted as a part of pro-survival pathways that eliminate harmful or unnecessary molecules or organelles by a variety of degradation/hydrolytic reactions or specialized autophageal processes. When these "partial" intracellular measures are insufficient, the programs of cells death are triggered with the aim to remove irreparably damaged members of the multicellular community. These regulated cell death mechanisms are believed to heavily rely on signaling by a highly diversified group of molecules, oxygenated phospholipids (PLox). Out of thousands of detectable individual PLox species, redox phospholipidomics deciphered several specific molecules that seem to be diagnostic of specialized death programs. Oxygenated cardiolipins (CLs) and phosphatidylethanolamines (PEs) have been identified as predictive biomarkers of apoptosis and ferroptosis, respectively. This has led to decoding of the enzymatic mechanisms of their formation involving mitochondrial oxidation of CLs by cytochrome c and endoplasmic reticulum-associated oxidation of PE by lipoxygenases. Understanding of the specific biochemical radical-mediated mechanisms of these oxidative reactions opens new avenues for the design and search of highly specific regulators of cell death programs. This review emphasizes the usefulness of such selective lipid peroxidation mechanisms in contrast to the concept of random poorly controlled free radical reactions as instruments of non-specific damage of cells and their membranes. Detailed analysis of two specific examples of phospholipid oxidative signaling in apoptosis and ferroptosis along with their molecular mechanisms and roles in reprogramming has been presented.
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Affiliation(s)
- V E Kagan
- Center for Free Radical and Antioxidant Heath, USA; Department of Environmental and Occupational Health, University of Pittsburgh, USA; Department of Chemistry, University of Pittsburgh, USA; Department of Pharmacology and Chemical Biology, University of Pittsburgh, USA; Department of Radiation Oncology, University of Pittsburgh, USA; Laboratory of Navigational Redox Lipidomics, IM Sechenov Moscow State Medical University, Moscow, Russian Federation.
| | - Y Y Tyurina
- Center for Free Radical and Antioxidant Heath, USA; Department of Environmental and Occupational Health, University of Pittsburgh, USA
| | - W Y Sun
- Center for Free Radical and Antioxidant Heath, USA; Department of Environmental and Occupational Health, University of Pittsburgh, USA; International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Chinese Ministry of Education (MOE), College of Pharmacy, Jinan University, Guangzhou, Guangdong, China
| | - I I Vlasova
- Laboratory of Navigational Redox Lipidomics, IM Sechenov Moscow State Medical University, Moscow, Russian Federation
| | - H Dar
- Center for Free Radical and Antioxidant Heath, USA; Department of Environmental and Occupational Health, University of Pittsburgh, USA
| | - V A Tyurin
- Center for Free Radical and Antioxidant Heath, USA; Department of Environmental and Occupational Health, University of Pittsburgh, USA
| | - A A Amoscato
- Center for Free Radical and Antioxidant Heath, USA; Department of Environmental and Occupational Health, University of Pittsburgh, USA
| | | | - P C A van der Wel
- Zernike Institute for Advanced Materials, University of Groningen, Groningen, the Netherlands
| | - R R He
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Chinese Ministry of Education (MOE), College of Pharmacy, Jinan University, Guangzhou, Guangdong, China
| | - A A Shvedova
- Exposure Assessment Branch, NIOSH/CDC, Morgantown, WV, USA
| | | | - H Bayir
- Center for Free Radical and Antioxidant Heath, USA; Department of Critical Care Medicine, University of Pittsburgh, USA.
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