1
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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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2
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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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3
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Tang J, Zhu J, Xie H, Song L, Xu G, Li W, Cai L, Han XX. Mitochondria-Specific Molecular Crosstalk between Ferroptosis and Apoptosis Revealed by In Situ Raman Spectroscopy. NANO LETTERS 2024; 24:2384-2391. [PMID: 38341873 DOI: 10.1021/acs.nanolett.3c05039] [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: 02/13/2024]
Abstract
Ferroptosis and apoptosis are two types of regulated cell death that are closely associated with the pathophysiological processes of many diseases. The significance of ferroptosis-apoptosis crosstalk in cell fate determination has been reported, but the underlying molecular mechanisms are poorly understood. Herein mitochondria-mediated molecular crosstalk is explored. Based on a comprehensive spectroscopic investigation and mass spectrometry, cytochrome c-involved Fenton-like reactions and lipid peroxidation are revealed. More importantly, cytochrome c is found to induce ROS-independent and cardiolipin-specific lipid peroxidation depending on its redox state. In situ Raman spectroscopy unveiled that erastin can interrupt membrane permeability, specifically through cardiolipin, facilitating cytochrome c release from the mitochondria. Details of the erastin-cardiolipin interaction are determined using molecular dynamics simulations. This study provides novel insights into how molecular crosstalk occurs around mitochondrial membranes to trigger ferroptosis and apoptosis, with significant implications for the rational design of mitochondria-targeted cell death reducers in cancer therapy.
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Affiliation(s)
- Jinping Tang
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, P. R. China
| | - Jinyu Zhu
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, P. R. China
| | - Han Xie
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, P. R. China
| | - Li Song
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, P. R. China
| | - Guangyang Xu
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, P. R. China
| | - Wei Li
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, P. R. China
| | - Linjun Cai
- National Engineering Laboratory for AIDS Vaccine, School of Life Science, Jilin University, Changchun 130012, P. R. China
| | - Xiao Xia Han
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, P. R. China
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Bharadwaj P, Shet SM, Bisht M, Sarkar DK, Franklin G, Sanna Kotrappanavar N, Mondal D. Suitability of Adenosine Derivatives in Improving the Activity and Stability of Cytochrome c under Stress: Insights into the Effect of Phosphate Groups. J Phys Chem B 2024; 128:86-95. [PMID: 38127495 PMCID: PMC10788901 DOI: 10.1021/acs.jpcb.3c05996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 11/16/2023] [Accepted: 12/04/2023] [Indexed: 12/23/2023]
Abstract
It is well known that adenosine and its phosphate derivatives play a crucial role in biological phenomena such as apoptosis and cell signaling and act as the energy currency of the cell. Although their interactions with various proteins and enzymes have been described, the focus of this work is to demonstrate the effect of the phosphate group on the activity and stability of the native heme metalloprotein cytochrome c (Cyt c), which is important from both biological and industrial aspects. In situ and in silico characterizations are used to correlate the relationship between the binding affinity of adenosine and its phosphate groups with unfolding behavior, corresponding peroxidase activities, and stability factors. Interaction of adenosine (ADN), adenosine monophosphate (AMP), adenosine 5'-diphosphate (ADP), and adenosine 5'-triphosphate (ATP) with Cyt c increases peroxidase-like activity by up to 1.8-6.5-fold compared to native Cyt c. This activity is significantly maintained even after multiple stress conditions such as oxidative stress and the presence of a chaotropic agent such as guanidine hydrochloride (GuHCl). With binding affinities on the order of ADN < AMP < ADP < ATP, adenosine derivatives were found to stabilize Cyt c by varying the secondary structural features of the protein. Thus, in addition to being a fundamental study, the current work also proposes a way of stabilizing protein systems to be used for real-time biocatalytic applications.
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Affiliation(s)
- Pranav Bharadwaj
- Centre
for Nano and Material Sciences, Jain University, Bangalore 562112, India
- Institute
of Plant Genetics (IPG), Polish Academy
of Sciences, Strzeszyńska 34, 60-479 Poznań, Poland
| | - Sachin M. Shet
- Centre
for Nano and Material Sciences, Jain University, Bangalore 562112, India
| | - Meena Bisht
- Institute
of Plant Genetics (IPG), Polish Academy
of Sciences, Strzeszyńska 34, 60-479 Poznań, Poland
| | - Dheeraj Kumar Sarkar
- Laboratory
of Biomolecular Interactions and Transport, Department of Gene Expression,
Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, 61-614 Poznan, Poland
- International
Institute of Molecular and Cell Biology in Warsaw, Ks Trojdena 4, 02-109 Warsaw, Poland
| | - Gregory Franklin
- Institute
of Plant Genetics (IPG), Polish Academy
of Sciences, Strzeszyńska 34, 60-479 Poznań, Poland
| | - Nataraj Sanna Kotrappanavar
- Centre
for Nano and Material Sciences, Jain University, Bangalore 562112, India
- School of
Polymer Science and Engineering, Chonnam
National University, 77 Yongbong-ro, Buk-gu, Gwangju 61186, South Korea
| | - Dibyendu Mondal
- Centre
for Nano and Material Sciences, Jain University, Bangalore 562112, India
- Institute
of Plant Genetics (IPG), Polish Academy
of Sciences, Strzeszyńska 34, 60-479 Poznań, Poland
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5
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Abramczyk H, Surmacki J. Effect of COVID-19 mRNA Vaccine on Human Lung Carcinoma Cells In Vitro by Means of Raman Spectroscopy and Imaging. ACS OMEGA 2023; 8:42555-42564. [PMID: 38024689 PMCID: PMC10653051 DOI: 10.1021/acsomega.3c05287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 10/06/2023] [Accepted: 10/11/2023] [Indexed: 12/01/2023]
Abstract
The effect of COVID-19 mRNA vaccine on human lung epithelial carcinoma cells (A549) in vitro as a convenient preclinical model was studied by means of Raman spectroscopy and imaging. The article focuses on Raman imaging as a tool to explore apoptosis and oxidative phosphorylation in mitochondrial dysfunctions. The Raman results demonstrate alterations in the oxidation-reduction pathways associated with cytochrome c. We found that the COVID-19 mRNA vaccine downregulates the concentration of cytochrome c upon incubation with tumorous lung cells. The concentration of the oxidized form of cytochrome c in the mitochondria of lung cells decreases upon incubation with the COVID-19 mRNA vaccine. A lower concentration of oxidized cytochrome c in mitochondria illustrates lower effectiveness of oxidative phosphorylation (respiration), reduced apoptosis, and lessened ATP production. Moreover, mRNA vaccine significantly increases de novo lipids synthesis in lipid droplets up to 96 h and alterations in biochemical composition. It seems that the lipid composition of cells returns to the normal level for a longer incubation time (14 days). In the cell nucleus, the mRNA vaccine does not produce statistically significant changes.
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Affiliation(s)
- Halina Abramczyk
- Department of Chemistry,
Institute of Applied Radiation Chemistry, Laboratory of Laser Molecular
Spectroscopy, Lodz University of Technology, Wróblewskiego 15, 93-590 Łódź, Poland
| | - Jakub Surmacki
- Department of Chemistry,
Institute of Applied Radiation Chemistry, Laboratory of Laser Molecular
Spectroscopy, Lodz University of Technology, Wróblewskiego 15, 93-590 Łódź, Poland
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6
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Sethi O, Singh M, Sood AK, Kang TS. Water Induced Alterations in Self-Assembly of a Bio-Surfactant in Deep Eutectic Solvent for Enhanced Enzyme Activity. Chemphyschem 2023; 24:e202300293. [PMID: 37431953 DOI: 10.1002/cphc.202300293] [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: 04/24/2023] [Revised: 07/08/2023] [Accepted: 07/11/2023] [Indexed: 07/12/2023]
Abstract
Deep eutectic solvents (DESs) meet important requirements for green solvent technology, including non-toxicity, biodegradability, sustainability, and affordability. Despite possessing low cohesive energy density than water, DESs have been found to support the self-assembly of amphiphiles. It is very much pertinent to examine the effect of water on self-assembly of surfactants in DESs as the presence of water alters the inherent structure of DES, which is expected to affect the characteristic properties of self-assembly. Following this, we have investigated the self-assembly of amino-acid based surfactant, Sodium N-lauroyl sarcosinate (SLS), in DES-water mixtures (10, 30 and 50 w/w% of water) and explored the catalytic activity of Cytochrome-c (Cyt-c) in the formed colloidal systems. Investigations using surface tension, fluorescence, dynamic light scattering (DLS), and isothermal titration calorimetry (ITC) have shown that DES-water mixtures promote the aggregation of SLS, resulting in the lower critical aggregation concentration (cac ∼1.5-6-fold) of the surfactant as compared to water. The nanoclustering of DES at low water content and it's complete de-structuring at high water content affects the self-assembly in a contrasting manner governed by different set of interactions. Further, Cyt-c dispersed in DES-water colloidal solutions demonstrated 5-fold higher peroxidase activity than that observed in phosphate buffer.
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Affiliation(s)
- Omish Sethi
- Department of Chemistry, UGC Centre for Advance Studies-II, Guru Nanak Dev University, Amritsar, 143005, Punjab, India
| | - Manpreet Singh
- Department of Chemistry, UGC Centre for Advance Studies-II, Guru Nanak Dev University, Amritsar, 143005, Punjab, India
| | - Ashwani Kumar Sood
- Department of Chemistry, UGC Centre for Advance Studies-II, Guru Nanak Dev University, Amritsar, 143005, Punjab, India
| | - Tejwant Singh Kang
- Department of Chemistry, UGC Centre for Advance Studies-II, Guru Nanak Dev University, Amritsar, 143005, Punjab, India
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7
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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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8
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Tang J, Song L, Xie H, Zhu J, Li W, Xu G, Cai L, Han XX. In Situ and Real-Time Monitoring of Mitochondria-Endoplasmic Reticulum Crosstalk in Apoptosis via Surface-Enhanced Resonance Raman Spectroscopy. NANO LETTERS 2023; 23:8363-8369. [PMID: 37610372 DOI: 10.1021/acs.nanolett.3c02764] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
The crosstalk between mitochondria and endoplasmic reticula plays a crucial role in apoptotic pathways in which reactive oxygen species (ROS) produced by microsomal monooxygenase (MMO) are believed to accelerate cytochrome c release. Herein, we successfully demonstrate the potential of surface-enhanced resonance Raman spectroscopy (SERRS) for monitoring MMO-derived ROS formation and ROS-mediated cytochrome c release. Silver nanoparticles coated with nickel shells are used as both Raman signal enhancers and electron donors for cytochrome c. SERRS of cytochrome c is found to be sensitive to ROS, allowing for in situ probing of ROS formation with a cell death inducer. Label-free evaluation of ROS-induced apoptosis is achieved by SERRS-based monitoring of cytochrome c release in living cells. This study verifies the capability of SERRS for label-free, in situ, and real-time monitoring of the mitochondria-endoplasmic reticulum crosstalk in apoptosis and provides a novel strategy for the rational design and screening of ROS-inducing drugs for cancer treatment.
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Affiliation(s)
- Jinping Tang
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, P. R. China
| | - Li Song
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, P. R. China
| | - Han Xie
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, P. R. China
| | - Jinyu Zhu
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, P. R. China
| | - Wei Li
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, P. R. China
| | - Guangyang Xu
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, P. R. China
| | - Linjun Cai
- National Engineering Laboratory for AIDS Vaccine, School of Life Science, Jilin University, Changchun 130012, P. R. China
| | - Xiao Xia Han
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, P. R. China
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9
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Liu W, Berge-Lefranc D, Chaspoul F, Slaveykova VI. Cytochrome c - silver nanoparticle interactions: Spectroscopy, thermodynamic and enzymatic activity studies. Chem Biol Interact 2023; 382:110647. [PMID: 37499996 DOI: 10.1016/j.cbi.2023.110647] [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: 06/21/2023] [Revised: 07/19/2023] [Accepted: 07/24/2023] [Indexed: 07/29/2023]
Abstract
Cytochrome c, an iron containing metalloprotein in the mitochondria of the cells with an oxide/redox property, plays key role in the cell apoptotic pathway. In this study, the interaction of silver nanoparticles (AgNPs) with cytochrome c (Cyt c) was investigated by using a combination of spectroscopic, imaging and thermodynamic techniques, including dynamic light scattering (DLS), ultraviolet-visible (UV-vis) spectroscopy, transmission electron microscopy (TEM), fluorescence spectroscopy, near and far circular dichroism (CD) spectroscopy, and isothermal titration calorimetry (ITC). DLS and UV-vis analysis evidenced the formation of surface complexes of Cyt c on AgNPs. The saturation of surface coverage of AgNPs was observed at 4.36 Cyt c molecules per nm2 of AgNPs. The surface complexation resulted in a promotion of the Ag dissolution overtime. The negative sign of enthalpic (ΔH) contribution suggested that electrostatic forces are indicative forces in the interaction between protein and AgNPs. Moreover, the fluorescence spectra revealed that the conformation of protein was altered around tryptophan (Trp) and tyrosine (Tyr) residues indicating the alteration of the tertiary structure of Cyt c. CD analysis evidenced that the secondary structure of Cyt c was modified under AgNPs-Cyt c interactions and the binding of Cyt c onto AgNPs resulted in remarkable structural perturbation around the active site heme, which in turn alter the protein enzymatic activity. The results of the present study contributed to a deeper insight on the mechanisms of interaction between NPs and biomacromolecules and could help establish the in vivo fate of AgNPs on cellular redox homeostasis.
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Affiliation(s)
- Wei Liu
- University of Geneva, Faculty of Sciences, Department F.-A. Forel for Environmental and Aquatic Sciences, Switzerland.
| | - David Berge-Lefranc
- ICR UMR Aix Marseille Université - CNRS 7273, IMBE UMR Aix Marseille Université - CNRS - IRD - AUPV 7263, France
| | - Florence Chaspoul
- ICR UMR Aix Marseille Université - CNRS 7273, IMBE UMR Aix Marseille Université - CNRS - IRD - AUPV 7263, France
| | - Vera I Slaveykova
- University of Geneva, Faculty of Sciences, Department F.-A. Forel for Environmental and Aquatic Sciences, Switzerland
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10
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Li J, Tan W, Li X, Zhang P, Jin P, Fan J, Li K. Silver Ion-Facilitated Singular Poulos-Kraut Mechanism of O-O Heterolysis to Enhance the Light Activation of H 2O 2 over Peroxidase-Mimicking Photonanozymes. Anal Chem 2023; 95:12435-12442. [PMID: 37566745 DOI: 10.1021/acs.analchem.3c02095] [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: 08/13/2023]
Abstract
The Poulos-Kraut heterolytic O-O cleavage mechanism is essential for natural peroxidases to activate H2O2. Current existing peroxidase-mimicking nanozymes, including photonanozymes (PNZs), however, are generally believed to prefer the Fenton-type mechanism of O-O homolysis, which produces •OH radicals. Here, Ag+ ions are introduced into TiO2 PNZs to boost the hot hole-driven O-O heterolysis for the expedited H2O2 activation in the peroxidase-like photonanozymatic reaction while inhibiting the Fenton-type O-O homolysis. The Ag+-facilitated Poulos-Kraut heterolytic O-O cleavage mechanism for H2O2 activation is explicated in terms of the speedy capture and exhaustion of photogenerated electrons by Ag+ and the dissociation of the peroxo-oxygen bridge in Ti-O-OH promoted by accumulated hot holes. Moreover, the enhanced photonanozymatic activity of TiO2 PNZs enables the construction of a rapid colorimetric sensing platform for Ag+ determination. This work provides valuable insights into the mechanism of H2O2 activation and exemplifies a novel photoregulation strategy for controlling reaction pathways in nanozymes.
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Affiliation(s)
- Jinzhao Li
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha 410082, P. R. China
| | - Wenlong Tan
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha 410082, P. R. China
| | - Xu Li
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha 410082, P. R. China
| | - Pei Zhang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha 410082, P. R. China
| | - Peng Jin
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha 410082, P. R. China
| | - Jinsong Fan
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha 410082, P. R. China
| | - Kun Li
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha 410082, P. R. China
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11
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Bollmeyer MM, Coleman RE, Majer SH, Ferrao SD, Lancaster KM. Cytochrome P460 Cofactor Maturation Proceeds via Peroxide-Dependent Post-translational Modification. J Am Chem Soc 2023; 145:14404-14416. [PMID: 37338957 PMCID: PMC10431212 DOI: 10.1021/jacs.3c03608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/21/2023]
Abstract
Cytochrome P460s are heme enzymes that oxidize hydroxylamine to nitrous oxide. They bear specialized "heme P460" cofactors that are cross-linked to their host polypeptides by a post-translationally modified lysine residue. Wild-type N. europaea cytochrome P460 may be isolated as a cross-link-deficient proenzyme following anaerobic overexpression in E. coli. When treated with peroxide, this proenzyme undergoes maturation to active enzyme with spectroscopic and catalytic properties that match wild-type cyt P460. This maturation reactivity requires no chaperones─it is intrinsic to the protein. This behavior extends to the broader cytochrome c'β superfamily. Accumulated data reveal key contributions from the secondary coordination sphere that enable selective, complete maturation. Spectroscopic data support the intermediacy of a ferryl species along the maturation pathway.
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Affiliation(s)
- Melissa M. Bollmeyer
- Department of Chemistry and Chemical Biology Cornell University, Baker Laboratory, 162 Sciences Drive, Ithaca, NY 14853, USA
| | - Rachael E. Coleman
- Department of Chemistry and Chemical Biology Cornell University, Baker Laboratory, 162 Sciences Drive, Ithaca, NY 14853, USA
| | - Sean H. Majer
- Department of Chemistry and Chemical Biology Cornell University, Baker Laboratory, 162 Sciences Drive, Ithaca, NY 14853, USA
| | - Silas D. Ferrao
- Department of Chemistry and Chemical Biology Cornell University, Baker Laboratory, 162 Sciences Drive, Ithaca, NY 14853, USA
| | - Kyle M. Lancaster
- Department of Chemistry and Chemical Biology Cornell University, Baker Laboratory, 162 Sciences Drive, Ithaca, NY 14853, USA
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12
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Du Z, Nam E, Lin Y, Hong M, Molnár T, Kondo I, Ishimori K, Baik MH, Lee YH, Lim MH. Unveiling the impact of oxidation-driven endogenous protein interactions on the dynamics of amyloid-β aggregation and toxicity. Chem Sci 2023; 14:5340-5349. [PMID: 37234895 PMCID: PMC10208028 DOI: 10.1039/d3sc00881a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 04/24/2023] [Indexed: 05/28/2023] Open
Abstract
Cytochrome c (Cyt c), a multifunctional protein with a crucial role in controlling cell fate, has been implicated in the amyloid pathology associated with Alzheimer's disease (AD); however, the interaction between Cyt c and amyloid-β (Aβ) with the consequent impact on the aggregation and toxicity of Aβ is not known. Here we report that Cyt c can directly bind to Aβ and alter the aggregation and toxicity profiles of Aβ in a manner that is dependent on the presence of a peroxide. When combined with hydrogen peroxide (H2O2), Cyt c redirects Aβ peptides into less toxic, off-pathway amorphous aggregates, whereas without H2O2, it promotes Aβ fibrillization. The mechanisms behind these effects may involve a combination of the complexation between Cyt c and Aβ, the oxidation of Aβ by Cyt c and H2O2, and the modification of Cyt c by H2O2. Our findings demonstrate a new function of Cyt c as a modulator against Aβ amyloidogenesis.
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Affiliation(s)
- Zhi Du
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST) Daejeon 34141 Republic of Korea
- Department of Biomedical Engineering, College of Biomedical Engineering, Taiyuan University of Technology Taiyuan 030024 PR China
| | - Eunju Nam
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST) Daejeon 34141 Republic of Korea
| | - Yuxi Lin
- Research Center for Bioconvergence Analysis, Korea Basic Science Institute (KBSI) Ochang Chungbuk 28119 Republic of Korea
| | - Mannkyu Hong
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST) Daejeon 34141 Republic of Korea
- Center for Catalytic Hydrocarbon Functionalizations, Institute for Basic Science (IBS) Daejeon 34141 Republic of Korea
| | - Tamás Molnár
- Department of Biochemistry, Institute of Biology, Eötvös Loránd University H-1117 Budapest Hungary
| | - Ikufumi Kondo
- Graduate School of Chemical Sciences and Engineering, Hokkaido University Kita 13, Nishi 8, Kita-ku Sapporo 060-8628 Japan
| | - Koichiro Ishimori
- Graduate School of Chemical Sciences and Engineering, Hokkaido University Kita 13, Nishi 8, Kita-ku Sapporo 060-8628 Japan
- Department of Chemistry, Faculty of Science, Hokkaido University Kita 10, Nishi 8, Kita-ku Sapporo 060-0810 Japan
| | - Mu-Hyun Baik
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST) Daejeon 34141 Republic of Korea
- Center for Catalytic Hydrocarbon Functionalizations, Institute for Basic Science (IBS) Daejeon 34141 Republic of Korea
| | - Young-Ho Lee
- Research Center for Bioconvergence Analysis, Korea Basic Science Institute (KBSI) Ochang Chungbuk 28119 Republic of Korea
- Bio-Analytical Science, University of Science and Technology (UST) Daejeon 34113 Republic of Korea
- Graduate School of Analytical Science and Technology, Chungnam National University Daejeon 34134 Republic of Korea
- Research Headquarters, Korea Brain Research Institute (KBRI) Daegu 41068 Republic of Korea
| | - Mi Hee Lim
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST) Daejeon 34141 Republic of Korea
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13
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Zhong C, Li G, Tian W, Ouyang D, Ji Y, Cai Z, Lin Z. Construction of Covalent Organic Framework Capsule-Based Nanoreactor for Sensitive Glucose Detection. ACS APPLIED MATERIALS & INTERFACES 2023; 15:10158-10165. [PMID: 36786379 DOI: 10.1021/acsami.2c19408] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Enzyme immobilization is critical to boosting its application in various areas. Covalent organic frameworks (COFs) are ideal hosts for enzyme immobilization due to their porous and predesignable structures. Nevertheless, the construction of COFs-based enzyme immobilization systems with high activity via existing immobilization methods (including covalent linkages and channel entrapment) remains a considerable challenge. Herein, a versatile approach was introduced to encapsulate enzymes within hollow COF capsule (named enzyme@COF) using metal-organic frameworks (including ZPF-1(C8H11N4O4.5Zn), ZIF-8(C8H10N4Zn), and ZIF-90(C8H6N4O2Zn)) as sacrificial templates. The obtained porous COF capsule could not only facilitate the efficient mass transfer of enzymatic reactions but also protect enzymes against the incompatible conditions, resulting in enhanced activity and stability of the encapsulated enzymes. Moreover, this approach offered an opportunity to spatially organize multienzymes in COF capsule to construct enzyme cascade system. For instance, glucose oxidase (GOx) and cytochrome c (Cyt c) were coencapsulated within COF capsule to construct GOx-Cyt c cascade. The integration of GOx and Cyt c within COF capsule achieved ∼1.6-fold improvement in catalytic activity than that of free enzymes and the resultant GOx-Cyt c@COF was successfully adopted as a nanoreactor for the sensitive determination of glucose in serum. This work provided a new insight into the design of COFs-based enzyme immobilization systems.
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Affiliation(s)
- Chao Zhong
- Ministry of Education Key Laboratory of Analytical Science for Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, Fujian 350108 China
| | - Guorong Li
- Ministry of Education Key Laboratory of Analytical Science for Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, Fujian 350108 China
| | - Wenchang Tian
- Ministry of Education Key Laboratory of Analytical Science for Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, Fujian 350108 China
| | - Dan Ouyang
- Ministry of Education Key Laboratory of Analytical Science for Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, Fujian 350108 China
| | - Yin Ji
- Ministry of Education Key Laboratory of Analytical Science for Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, Fujian 350108 China
| | - Zongwei Cai
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, 224 Waterloo Road, Kowloon Tong, Hong Kong SAR, P.R. China
| | - Zian Lin
- Ministry of Education Key Laboratory of Analytical Science for Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, Fujian 350108 China
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14
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Hashemnia S, Karmand Z, Mokhtari Z. Chemical Modification of Acidic Residues of Cytochrome c with Safranin: pH Effect on Structure and Function of the Modified Protein. ChemistrySelect 2023. [DOI: 10.1002/slct.202203637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Sedigheh Hashemnia
- Department of Chemistry Faculty of Nano and Bio Science and Technology Persian Gulf University Bushehr 75169 Iran
| | - Zahra Karmand
- Department of Chemistry Faculty of Nano and Bio Science and Technology Persian Gulf University Bushehr 75169 Iran
| | - Zaynab Mokhtari
- Department of Chemistry Faculty of Nano and Bio Science and Technology Persian Gulf University Bushehr 75169 Iran
- Department of Chemical Industry Technical and Vocational University (TVU) Bushehr Iran
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15
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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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16
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Shukla AK, Abidi SMS, Sharma C, Chand Saini T, Acharya A. Single-walled carbon nanotube conjugated cytochrome c as exogenous nano catalytic medicine to combat intracellular oxidative stress. Free Radic Biol Med 2022; 193:238-252. [PMID: 36257485 DOI: 10.1016/j.freeradbiomed.2022.10.276] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 10/04/2022] [Accepted: 10/12/2022] [Indexed: 10/31/2022]
Abstract
Mitochondrial dysfunction has been reported to be one of the main causes of many diseases including cancer, type2 diabetes, neurodegenerative disorders, cardiac ischemia, sepsis, muscular dystrophy, etc. Under in vitro conditions, Cytochrome C (Cyt C) maintains mitochondrial homeostasis and stimulates apoptosis, along with being a key participant in the life-supporting function of ATP synthesis. Hence, the medicinal importance of Cyt C as catalytic defense is immensely important in various mitochondrial disorders. Here, we have developed a nanomaterial via electrostatically conjugating oxidized single-wall carbon nanotube with Cyt C (Cyt C@cSWCNT) for the exogenous delivery of Cyt C. The chemical and morphological characterization of the developed Cyt C@cSWCNT was done using UV-vis, FTIR, XPS, powder XRD, TGA/DSC, TEM, etc. The developed Cyt C@cSWCNT exhibited bifunctional catalase and peroxidase activity with Km (∼ 642.7 μM and 351.6 μM) and Vmax (∼0.33 μM/s and 2.62 μM/s) values, respectively. Also, through this conjugation Cyt C was found to retain its catalytic activity even at 60 °C, excellent catalytic recyclability (at least up to 3 times), and wider pH activity (pH = 3 to 9). Cyt C@cSWCNT was found to promote intracellular ROS quenching and maintain mitochondrial membrane potential and cellular membrane integrity via Na+/K+ ion homeostasis during the H2O2 stress. Overall the present strategy provides an alternative approach for the exogenous delivery of Cyt C which can be used as nano catalytic medicine.
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Affiliation(s)
- Ashish K Shukla
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur (H.P.), 176061, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
| | - Syed M S Abidi
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur (H.P.), 176061, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
| | - Chandni Sharma
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur (H.P.), 176061, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
| | - Trilok Chand Saini
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur (H.P.), 176061, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
| | - Amitabha Acharya
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur (H.P.), 176061, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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17
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Dou M, Wu Y, Du J. Luminescent gold nanoclusters as a signal reporter for cytochrome c assay with a double signal amplification strategy. J CHIN CHEM SOC-TAIP 2022. [DOI: 10.1002/jccs.202200263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Min‐Na Dou
- Normal Department Xianyang Vocational Technical College Xianyang China
| | - Yifan Wu
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering Shaanxi Normal University Xi′an China
| | - Jianxiu Du
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering Shaanxi Normal University Xi′an China
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18
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Van Stappen C, Deng Y, Liu Y, Heidari H, Wang JX, Zhou Y, Ledray AP, Lu Y. Designing Artificial Metalloenzymes by Tuning of the Environment beyond the Primary Coordination Sphere. Chem Rev 2022; 122:11974-12045. [PMID: 35816578 DOI: 10.1021/acs.chemrev.2c00106] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Metalloenzymes catalyze a variety of reactions using a limited number of natural amino acids and metallocofactors. Therefore, the environment beyond the primary coordination sphere must play an important role in both conferring and tuning their phenomenal catalytic properties, enabling active sites with otherwise similar primary coordination environments to perform a diverse array of biological functions. However, since the interactions beyond the primary coordination sphere are numerous and weak, it has been difficult to pinpoint structural features responsible for the tuning of activities of native enzymes. Designing artificial metalloenzymes (ArMs) offers an excellent basis to elucidate the roles of these interactions and to further develop practical biological catalysts. In this review, we highlight how the secondary coordination spheres of ArMs influence metal binding and catalysis, with particular focus on the use of native protein scaffolds as templates for the design of ArMs by either rational design aided by computational modeling, directed evolution, or a combination of both approaches. In describing successes in designing heme, nonheme Fe, and Cu metalloenzymes, heteronuclear metalloenzymes containing heme, and those ArMs containing other metal centers (including those with non-native metal ions and metallocofactors), we have summarized insights gained on how careful controls of the interactions in the secondary coordination sphere, including hydrophobic and hydrogen bonding interactions, allow the generation and tuning of these respective systems to approach, rival, and, in a few cases, exceed those of native enzymes. We have also provided an outlook on the remaining challenges in the field and future directions that will allow for a deeper understanding of the secondary coordination sphere a deeper understanding of the secondary coordintion sphere to be gained, and in turn to guide the design of a broader and more efficient variety of ArMs.
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Affiliation(s)
- Casey Van Stappen
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States
| | - Yunling Deng
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States
| | - Yiwei Liu
- Department of Chemistry, University of Illinois, Urbana-Champaign, 505 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Hirbod Heidari
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States
| | - Jing-Xiang Wang
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States
| | - Yu Zhou
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States
| | - Aaron P Ledray
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States
| | - Yi Lu
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States.,Department of Chemistry, University of Illinois, Urbana-Champaign, 505 South Mathews Avenue, Urbana, Illinois 61801, United States
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19
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Xie H, Song L, Katz S, Zhu J, Liu Y, Tang J, Cai L, Hildebrandt P, Han XX. Electron transfer between cytochrome c and microsomal monooxygenase generates reactive oxygen species that accelerates apoptosis. Redox Biol 2022; 53:102340. [PMID: 35609401 PMCID: PMC9130584 DOI: 10.1016/j.redox.2022.102340] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 05/13/2022] [Accepted: 05/13/2022] [Indexed: 11/20/2022] Open
Abstract
Generation of reactive oxygen species (ROS) are possibly induced by the crosstalk between mitochondria and endoplasmic reticula, which is physiologically important in apoptosis. Cytochrome c (Cyt c) is believed to play a crucial role in such signaling pathway by interrupting the coupling within microsomal monooxygenase (MMO). In this study, the correlation of ROS production with the electron transfer between Cyt c and the MMO system is investigated by resonance Raman (RR) spectroscopy. Binding of Cyt c to MMO is found to induce the production of ROS, which is quantitatively determined by the in-situ RR spectroscopy reflecting the interactions of Cyt c with generated ROS. The amount of ROS that is produced from isolated endoplasmic reticulum depends on the redox state of the Cyt c, indicating the important role of oxidized Cyt c in accelerating apoptosis. The role of electron transfer from MMO to Cyt c in the apoptotic mitochondria-endoplasmic reticulum pathway is accordingly proposed. This study is of significance for a deeper understanding of how Cyt c regulates apoptotic pathways through the endoplasmic reticulum, and thus may provide a rational basis for the design of antitumor drugs for cancer therapy.
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Affiliation(s)
- Han Xie
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun, 130012, PR China
| | - Li Song
- National Engineering Laboratory for AIDS Vaccine, School of Life Science, Jilin University, Changchun, 130012, PR China
| | - Sagie Katz
- Department of Chemistry, Technische Universität Berlin, 10623, Berlin, Germany
| | - Jinyu Zhu
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun, 130012, PR China
| | - Yawen Liu
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun, 130012, PR China
| | - Jinping Tang
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun, 130012, PR China
| | - Linjun Cai
- National Engineering Laboratory for AIDS Vaccine, School of Life Science, Jilin University, Changchun, 130012, PR China
| | - Peter Hildebrandt
- Department of Chemistry, Technische Universität Berlin, 10623, Berlin, Germany.
| | - Xiao Xia Han
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun, 130012, PR China.
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20
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Devassy AM, Kamalakshan A, Jamuna NA, Ansilda R, Mandal S. Enhanced Catalytic Activity of a New Nanobiocatalytic System Formed by the Adsorption of Cytochrome c on Pluronic Triblock Copolymer Stabilized MoS 2 Nanosheets. ACS OMEGA 2022; 7:16593-16604. [PMID: 35601299 PMCID: PMC9118411 DOI: 10.1021/acsomega.2c00839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 04/15/2022] [Indexed: 06/15/2023]
Abstract
The formation of nanobiohybrids through the immobilization of enzymes on functional nanomaterials has opened up exciting research opportunities at the nanobiointerfaces. These systems hold great promise for a wide range of applications in biosensing, biocatalytic, and biomedical fields. Here, we report the formation of a hybrid nanobiocatalytic system through the adsorption of cytochrome c (Cyt c) on pluronic triblock copolymer, P123 (PEO-b-PPO-b-PEO), stabilized MoS2 nanosheets. The use of pluronic polymer has helped not only to greatly stabilize the exfoliated MoS2 nanosheets but also to allow easy adsorption of Cyt c on the nanosheets without major structural changes due to its excellent biocompatibility and soft protein-binding property. By comparing the catalytic activity of the Cyt c-MoS2 nanobiohybrid with that of the free Cyt c and as-prepared MoS2 nanosheets, we have demonstrated the active role of the nanobiointeractions in enhancing the catalytic activity of the hybrid. Slight structural perturbation at the active site of the Cyt c upon adsorption on MoS2 has primarily facilitated the peroxidase activity of the Cyt c. As the MoS2 nanosheets and the native Cyt c individually exhibit weaker intrinsic peroxidase activities, their mutual modulation at the nanobiointerface has made the Cyt c-MoS2 a novel nanobiocatalyst with superior activity.
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Affiliation(s)
| | - Adithya Kamalakshan
- Department of Chemistry, National Institute of Technology, Tiruchirappalli, Tamil Nadu 620015, India
| | - Nidhi Anilkumar Jamuna
- Department of Chemistry, National Institute of Technology, Tiruchirappalli, Tamil Nadu 620015, India
| | - Roselin Ansilda
- Department of Chemistry, National Institute of Technology, Tiruchirappalli, Tamil Nadu 620015, India
| | - Sarthak Mandal
- Department of Chemistry, National Institute of Technology, Tiruchirappalli, Tamil Nadu 620015, India
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21
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Structural and functional roles of non-bilayer lipid phases of chloroplast thylakoid membranes and mitochondrial inner membranes. Prog Lipid Res 2022; 86:101163. [DOI: 10.1016/j.plipres.2022.101163] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Revised: 03/23/2022] [Accepted: 03/23/2022] [Indexed: 12/11/2022]
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22
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Effect on intrinsic peroxidase activity of substituting coevolved residues from Ω-loop C of human cytochrome c into yeast Iso-1-cytochrome c. J Inorg Biochem 2022; 232:111819. [DOI: 10.1016/j.jinorgbio.2022.111819] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 03/25/2022] [Accepted: 04/02/2022] [Indexed: 11/15/2022]
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23
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Jiang Z, Pan Y, Wang J, Li J, Yang H, Guo Q, Liang S, Chen S, Hu Y, Wang L. Bone-Targeted ICG/Cyt c@ZZF-8 Nanoparticles Based on the Zeolitic Imidazolate Framework-8: A New Synergistic Photodynamic and Protein Therapy for Bone Metastasis. Biomater Sci 2022; 10:2345-2357. [PMID: 35383343 DOI: 10.1039/d2bm00185c] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Bone metastasis (BM) is a solid tumor confined to narrow bone marrow cavities with a relatively poor blood supply and hypoxic environment, making conventional anticancer treatments difficult. In our study,...
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Affiliation(s)
- Zichao Jiang
- Department of Orthopedics, Xiangya Hospital, Central South University, China.
- University Hunan Engineering Research Center of Biomedical Metal and Ceramic Implants, Xiangya Hospital, Central South University, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Yixiao Pan
- Department of Orthopedics, Xiangya Hospital, Central South University, China.
- University Hunan Engineering Research Center of Biomedical Metal and Ceramic Implants, Xiangya Hospital, Central South University, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Jiahao Wang
- Department of Orthopedics, Xiangya Hospital, Central South University, China.
- University Hunan Engineering Research Center of Biomedical Metal and Ceramic Implants, Xiangya Hospital, Central South University, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Jingyi Li
- Department of Orthopedics, Xiangya Hospital, Central South University, China.
- University Hunan Engineering Research Center of Biomedical Metal and Ceramic Implants, Xiangya Hospital, Central South University, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Haoze Yang
- Department of Cardiology, Second Xiangya Hospital, Central South University, China
| | - Qi Guo
- Department of Orthopedics, Xiangya Hospital, Central South University, China.
- University Hunan Engineering Research Center of Biomedical Metal and Ceramic Implants, Xiangya Hospital, Central South University, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Shuailong Liang
- Department of Orthopedics, Xiangya Hospital, Central South University, China.
- University Hunan Engineering Research Center of Biomedical Metal and Ceramic Implants, Xiangya Hospital, Central South University, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Sijie Chen
- Department of Ultrasound Diagnosis, Second Xiangya Hospital, Central South University, China
| | - Yihe Hu
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
- Department of Orthopedics, First Affiliated Hospital, School of Medicine, Zhejiang, China.
| | - Long Wang
- Department of Orthopedics, Xiangya Hospital, Central South University, China.
- University Hunan Engineering Research Center of Biomedical Metal and Ceramic Implants, Xiangya Hospital, Central South University, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
- Hunan key laboratary of aging biology, Xiangya Hospital, Central South University, Changsha, China
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24
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Luo P, Liu Z, Zhang T, Wang X, Liu J, Liu Y, Zhou X, Chen Y, Dong W, Xiao C, Jin Y, Yang X, Wang F. Chloride-Mediated Peroxide-Free Photochemical Oxidation of Proteins (PPOP) in Mass Spectrometry-Based Structural Analysis. Anal Chem 2021; 94:1135-1142. [PMID: 34965100 DOI: 10.1021/acs.analchem.1c04209] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Ultraviolet (UV) laser photolysis of hydrogen peroxide (H2O2) for the in situ generation of hydroxyl radicals (•OH) is a widely utilized strategy in the oxidation footprinting of native proteins and mass spectrometry (MS)-based structural analysis. However, it remains challenging to realize peroxide-free photochemical oxidation footprinting. Herein, we describe the footprinting of native proteins by chloride-mediated peroxide-free photochemical oxidation of proteins (PPOP). The protein samples are prepared within biocompatible phosphate-buffered saline (PBS) containing 10 mM Gln as radical scavengers and oxidized in a capillary flow reactor directly under a single-pulse (10 ns) irradiation of a 193 nm ArF UV laser. The main oxidized protein residues are CMYWFHLI. We demonstrate that the PPOP-MS strategy is highly sensitive to the protein high-order structures and can be applied to monitor the protein-drug interfaces, which provides a promising footprinting alternative for protein structure-function explorations.
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Affiliation(s)
- Pan Luo
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zheyi Liu
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Tingting Zhang
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaolei Wang
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.,State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Jing Liu
- College of Pharmacy, Dalian Medical University, Dalian 116044, China
| | - Yiqiang Liu
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaohu Zhou
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yang Chen
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wenrui Dong
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Chunlei Xiao
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Yan Jin
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Xueming Yang
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Fangjun Wang
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.,University of Chinese Academy of Sciences, Beijing 100049, China
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25
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Kan J, Hu Y, Ge Y, Zhang W, Lu S, Zhao C, Zhang R, Liu Y. Declined expressions of vast mitochondria-related genes represented by CYCS and transcription factor ESRRA in skeletal muscle aging. Bioengineered 2021; 12:3485-3502. [PMID: 34229541 PMCID: PMC8806411 DOI: 10.1080/21655979.2021.1948951] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 06/22/2021] [Accepted: 06/23/2021] [Indexed: 11/23/2022] Open
Abstract
Age-related skeletal muscle deterioration (sarcopenia) has a significant effect on the elderly's health and quality of life, but the molecular and gene regulatory mechanisms remain largely unknown. It is necessary to identify the candidate genes related to skeletal muscle aging and prospective therapeutic targets for effective treatments. The age-line-related genes (ALRGs) and age-line-related transcripts (ALRTs) were investigated using the gene expression profiles of GSE47881 and GSE118825 from the Gene Expression Omnibus (GEO) database. The protein-protein interaction (PPI) networks were performed to identify the key molecules with Cytoscape, and Gene Set Enrichment Analysis (GSEA) was used to clarify the potential molecular functions. Two hub molecules were finally obtained and verified with quantitative real-time PCR (qRT-PCR). The results showed that the expression of mitochondria genes involved in mitochondrial electron transport, complex assembly of the respiratory chain, tricarboxylic acid cycle, oxidative phosphorylation, and ATP synthesis were down-regulated in skeletal muscle with aging. We further identified a primary hub gene of CYCS (Cytochrome C) and a key transcription factor of ESRRA (Estrogen-related Receptor Alpha) to be associated closely with skeletal muscle aging. PCR analysis confirmed the expressions of CYCS and ESRRA in gastrocnemius muscles of mice of different ages were significantly different, and decreased gradually with age. In conclusion, the main cause of skeletal muscle aging may be the systematically reduced expression of mitochondrial functional genes. The CYCS and ESRRA may play significant roles in the progression of skeletal muscle aging and serve as potential biomarkers for future diagnosis and treatment.
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Affiliation(s)
- Jingbao Kan
- Department of Geriatrics, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yifang Hu
- Department of Geriatrics, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yaoqi Ge
- Department of Geriatrics, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - WenSong Zhang
- Department of Geriatrics, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Shan Lu
- Department of Geriatrics, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Cuiping Zhao
- Department of Geriatrics, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Rihua Zhang
- Department of Geriatrics, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yun Liu
- Department of Geriatrics, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
- Department of Medical Informatics, School of Biomedical Engineering and Informatics, Nanjing Medical University, Nanjing, China
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26
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Scrosati PM, Yin V, Konermann L. Hydrogen/Deuterium Exchange Measurements May Provide an Incomplete View of Protein Dynamics: a Case Study on Cytochrome c. Anal Chem 2021; 93:14121-14129. [PMID: 34644496 DOI: 10.1021/acs.analchem.1c02471] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Many aspects of protein function rely on conformational fluctuations. Hydrogen/deuterium exchange (HDX) mass spectrometry (MS) provides a window into these dynamics. Despite the widespread use of HDX-MS, it remains unclear whether this technique provides a truly comprehensive view of protein dynamics. HDX is mediated by H-bond-opening/closing events, implying that HDX methods provide an H-bond-centric view. This raises the question if there could be fluctuations that leave the H-bond network unaffected, thereby rendering them undetectable by HDX-MS. We explore this issue in experiments on cytochrome c (cyt c). Compared to the Fe(II) protein, Fe(III) cyt c shows enhanced deuteration on both the distal and proximal sides of the heme. Previous studies have attributed the enhanced dynamics of Fe(III) cyt c to the facile and reversible rupture of the distal M80-Fe(III) bond. Using molecular dynamics (MD) simulations, we conducted a detailed analysis of various cyt c conformers. Our MD data confirm that rupture of the M80-Fe(III) contact triggers major reorientation of the distal Ω loop. Surprisingly, this event takes place with only miniscule H-bonding alterations. In other words, the distal loop dynamics are almost "HDX-silent". Moreover, distal loop movements cannot account for enhanced dynamics on the opposite (proximal) side of the heme. Instead, enhanced deuteration of Fe(III) cyt c is attributed to sparsely populated conformers where both the distal (M80) and proximal (H18) coordination bonds have been ruptured, along with opening of numerous H-bonds on both sides of the heme. We conclude that there can be major structural fluctuations that are only weakly coupled to changes in H-bonding, making them virtually impossible to track by HDX-MS. In such cases, HDX-MS may provide an incomplete view of protein dynamics.
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Affiliation(s)
- Pablo M Scrosati
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Victor Yin
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Lars Konermann
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
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27
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NMR Reveals the Conformational Changes of Cytochrome C upon Interaction with Cardiolipin. Life (Basel) 2021; 11:life11101031. [PMID: 34685404 PMCID: PMC8540660 DOI: 10.3390/life11101031] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 09/22/2021] [Accepted: 09/27/2021] [Indexed: 01/06/2023] Open
Abstract
Conformational change of cytochrome c (cyt c) caused by interaction with cardiolipin (CL) is an important step during apoptosis, but the underlying mechanism is controversial. To comprehensively clarify the structural transformations of cyt c upon interaction with CL and avoid the unpredictable alias that might come from protein labeling or mutations, the conformation of purified yeast iso–1 cyt c with natural isotopic abundance in different contents of CL was measured by using NMR spectroscopy, in which the trimethylated group of the protein was used as a natural probe. The data demonstrate that cyt c has two partially unfolded conformations when interacted with CL: one with Fe–His33 coordination and the other with a penta–coordination heme. The Fe–His33 coordination conformation can be converted into a penta–coordination heme conformation in high content of CL. The structure of cyt c becomes partially unfolded with more exposed heme upon interaction with CL, suggesting that cyt c prefers a high peroxidase activity state in the mitochondria, which, in turn, makes CL easy to be oxidized, and causes the release of cyt c into the cytoplasm as a trigger in apoptosis.
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28
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Decreased proteasomal cleavage at nitrotyrosine sites in proteins and peptides. Redox Biol 2021; 46:102106. [PMID: 34455147 PMCID: PMC8403764 DOI: 10.1016/j.redox.2021.102106] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 08/05/2021] [Accepted: 08/15/2021] [Indexed: 11/22/2022] Open
Abstract
Removal of moderately oxidized proteins is mainly carried out by the proteasome, while highly modified proteins are no longer degradable. However, in the case of proteins modified by nitration of tyrosine residues to 3-nitrotyrosine (NO2Y), the role of the proteasome remains to be established. For this purpose, degradation assays and mass spectrometry analyses were performed using isolated proteasome and purified fractions of native cytochrome c (Cyt c) and tyrosine nitrated proteoforms (NO2Y74-Cyt c and NO2Y97-Cyt c). While Cyt c treated under mild conditions with hydrogen peroxide was preferentially degraded by the proteasome, NO2Y74- and NO2Y97-Cyt c species did not show an increased degradation rate with respect to native Cyt c. Peptide mapping analysis confirmed a decreased chymotrypsin-like cleavage at C-terminal of NO2Y sites within the protein, with respect to unmodified Y residues. Additionally, studies with the proteasome substrate suc-LLVY-AMC (Y-AMC) and its NO2Y-containing analog, suc-LLVNO2Y-AMC (NO2Y-AMC) were performed, both using isolated 20S-proteasome and astrocytoma cell lysates as the proteasomal source. Comparisons of both substrates showed a significantly decreased proteasome activity towards NO2Y-AMC. Moreover, NO2Y-AMC, but not Y-AMC degradation rates, were largely diminished by increasing the reaction pH, suggesting an inhibitory influence of the additional negative charge contained in NO2Y-AMC secondary to nitration. The mechanism of slowing of proteasome activity in NO2Y-contaning peptides was further substantiated in studies using the phenylalanine and nitro-phenylalanine peptide analog substrates. Finally, degradation rates of Y-AMC and NO2Y-AMC with proteinase K were the same, demonstrating the selective inability of the proteasome to readily cleave at nitrotyrosine sites. Altogether, data indicate that the proteasome has a decreased capability to cleave at C-terminal of NO2Y residues in proteins with respect to the unmodified residues, making this a possible factor that decreases the turnover of oxidized proteins, if they are not unfolded, and facilitating the accumulation of nitrated proteins.
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29
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How to Turn an Electron Transfer Protein into a Redox Enzyme for Biosensing. Molecules 2021; 26:molecules26164950. [PMID: 34443538 PMCID: PMC8398203 DOI: 10.3390/molecules26164950] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 08/10/2021] [Accepted: 08/13/2021] [Indexed: 01/10/2023] Open
Abstract
Cytochrome c is a small globular protein whose main physiological role is to shuttle electrons within the mitochondrial electron transport chain. This protein has been widely investigated, especially as a paradigmatic system for understanding the fundamental aspects of biological electron transfer and protein folding. Nevertheless, cytochrome c can also be endowed with a non-native catalytic activity and be immobilized on an electrode surface for the development of third generation biosensors. Here, an overview is offered of the most significant examples of such a functional transformation, carried out by either point mutation(s) or controlled unfolding. The latter can be induced chemically or upon protein immobilization on hydrophobic self-assembled monolayers. We critically discuss the potential held by these systems as core constituents of amperometric biosensors, along with the issues that need to be addressed to optimize their applicability and response.
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30
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Kocabey S, Ekim Kocabey A, Schneiter R, Rüegg C. Membrane-Interacting DNA Nanotubes Induce Cancer Cell Death. NANOMATERIALS 2021; 11:nano11082003. [PMID: 34443832 PMCID: PMC8397952 DOI: 10.3390/nano11082003] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 07/25/2021] [Accepted: 07/30/2021] [Indexed: 12/31/2022]
Abstract
DNA nanotechnology offers to build nanoscale structures with defined chemistries to precisely position biomolecules or drugs for selective cell targeting and drug delivery. Owing to the negatively charged nature of DNA, for delivery purposes, DNA is frequently conjugated with hydrophobic moieties, positively charged polymers/peptides and cell surface receptor-recognizing molecules or antibodies. Here, we designed and assembled cholesterol-modified DNA nanotubes to interact with cancer cells and conjugated them with cytochrome c to induce cancer cell apoptosis. By flow cytometry and confocal microscopy, we observed that DNA nanotubes efficiently bound to the plasma membrane as a function of the number of conjugated cholesterol moieties. The complex was taken up by the cells and localized to the endosomal compartment. Cholesterol-modified DNA nanotubes, but not unmodified ones, increased membrane permeability, caspase activation and cell death. Irreversible inhibition of caspase activity with a caspase inhibitor, however, only partially prevented cell death. Cytochrome c-conjugated DNA nanotubes were also efficiently taken up but did not increase the rate of cell death. These results demonstrate that cholesterol-modified DNA nanotubes induce cancer cell death associated with increased cell membrane permeability and are only partially dependent on caspase activity, consistent with a combined form of apoptotic and necrotic cell death. DNA nanotubes may be further developed as primary cytotoxic agents, or drug delivery vehicles, through cholesterol-mediated cellular membrane interactions and uptake.
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Affiliation(s)
- Samet Kocabey
- Department of Oncology, Microbiology and Immunology, Faculty of Science and Medicine, University of Fribourg, Chemin du Musée 18, PER17, 1700 Fribourg, Switzerland
- Correspondence: (S.K.); (C.R.)
| | - Aslihan Ekim Kocabey
- Department of Biology, Faculty of Science and Medicine, University of Fribourg, Chemin du Musée 10, PER05, 1700 Fribourg, Switzerland; (A.E.K.); (R.S.)
| | - Roger Schneiter
- Department of Biology, Faculty of Science and Medicine, University of Fribourg, Chemin du Musée 10, PER05, 1700 Fribourg, Switzerland; (A.E.K.); (R.S.)
| | - Curzio Rüegg
- Department of Oncology, Microbiology and Immunology, Faculty of Science and Medicine, University of Fribourg, Chemin du Musée 18, PER17, 1700 Fribourg, Switzerland
- Correspondence: (S.K.); (C.R.)
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31
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Xie H, Zhu H, Lei L, Yang X, Hua Y, Ye R, Bai G, Xu S. Fabrication of large size individual octahedral tungsten oxide hydrate and Au NPs as SERS platforms for sensitive detection of cytochrome C. Anal Chim Acta 2021; 1174:338711. [PMID: 34247742 DOI: 10.1016/j.aca.2021.338711] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Revised: 05/06/2021] [Accepted: 05/27/2021] [Indexed: 02/01/2023]
Abstract
Surface-enhanced Raman scattering (SERS) has attracted much attention with its powerful trace detection and analysis capabilities, especially biological and environmental molecules. However, building a protein SERS detection platform based on semiconductor devices is a huge challenge. Herein, through the synergy of NH3 and nickel foam, a large-sized semiconductor tungsten oxide hydrate platform (WOHP) was synthesized. The crystal plane of a single WOHP particle is larger than the excitation spot. As a SERS substrate, WOHP can make full use of the excitation light without destroying the structure during the protein molecules detection process. Through the synergy of WOHP and Au NPs, the enhancement factor is 1.5 × 104. Raman peaks of WOHP can be used as references for the detection of typical protein cytochrome C (Cyt C). As the Cyt C concentration decreases, the ICyt C/IWOHP ratio decreases, and the signal can still be obtained when the concentration is as low as 5 × 10-9 mol L-1. More importantly, the method does not affect the catalytic activity of Cyt C and can be applied to the detection of Cyt C concentration in serum.
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Affiliation(s)
- Hangqing Xie
- Institute of Optoelectronic Materials and Devices, China Jiliang University, Hangzhou, 310018, People's Republic of China
| | - Haogang Zhu
- National Laboratory of Solid State Microstructures and School of Physics, Nanjing University, Nanjing, 210093, People's Republic of China
| | - Lei Lei
- Institute of Optoelectronic Materials and Devices, China Jiliang University, Hangzhou, 310018, People's Republic of China
| | - Xiaolei Yang
- Institute of Optoelectronic Materials and Devices, China Jiliang University, Hangzhou, 310018, People's Republic of China
| | - Youjie Hua
- Institute of Optoelectronic Materials and Devices, China Jiliang University, Hangzhou, 310018, People's Republic of China
| | - Renguang Ye
- College of Optical and Electronic Technology, China Jiliang University, 310018, Hangzhou, China
| | - Gongxun Bai
- College of Optical and Electronic Technology, China Jiliang University, 310018, Hangzhou, China.
| | - Shiqing Xu
- Institute of Optoelectronic Materials and Devices, China Jiliang University, Hangzhou, 310018, People's Republic of China.
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32
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Tanaka M, Chock PB. Oxidative Modifications of RNA and Its Potential Roles in Biosystem. Front Mol Biosci 2021; 8:685331. [PMID: 34055897 PMCID: PMC8149912 DOI: 10.3389/fmolb.2021.685331] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 04/27/2021] [Indexed: 12/12/2022] Open
Abstract
Elevated level of oxidized RNA was detected in vulnerable neurons in Alzheimer patients. Subsequently, several diseases and pathological conditions were reported to be associated with RNA oxidation. In addition to several oxidized derivatives, cross-linking and unique strand breaks are generated by RNA oxidation. With a premise that dysfunctional RNA mediated by oxidation is the pathogenetic molecular mechanism, intensive investigations have revealed the mechanism for translation errors, including premature termination, which gives rise to aberrant polypeptides. To this end, we and others revealed that mRNA oxidation could compromise its translational activity and fidelity. Under certain conditions, oxidized RNA can also induce several signaling pathways, to mediate inflammatory response and induce apoptosis. In this review, we focus on the oxidative modification of RNA and its resulting effect on protein synthesis as well as cell signaling. In addition, we will also discuss the potential roles of enzymatic oxidative modification of RNA in mediating cellular effects.
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Affiliation(s)
- Mikiei Tanaka
- Biochemistry and Biophysics Center, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, United States
| | - P Boon Chock
- Biochemistry and Biophysics Center, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, United States
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33
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34
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Tomášková N, Novák P, Kožár T, Petrenčáková M, Jancura D, Yassaghi G, Man P, Sedlák E. Early modification of cytochrome c by hydrogen peroxide triggers its fast degradation. Int J Biol Macromol 2021; 174:413-423. [PMID: 33529629 DOI: 10.1016/j.ijbiomac.2021.01.189] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 01/26/2021] [Accepted: 01/28/2021] [Indexed: 12/16/2022]
Abstract
Cytochrome c (cyt c), in addition to its function as an electron shuttle in respiratory chain, is able to perform as a pseudo-peroxidase with a critical role during apoptosis. Incubation of cyt c with an excess of hydrogen peroxide leads to a suicide inactivation of the protein, which is accompanied by heme destruction and covalent modification of numerous amino acid residues. Although steady-state reactions of cyt c with an excess of hydrogen peroxide represent non-physiological conditions, they might be used for analysis of the first-modified amino acid in in vivo. Here, we observed oxidation of tyrosine residues 67 and 74 and heme as the first modifications found upon incubation with hydrogen peroxide. The positions of the oxidized tyrosines suggest a possible migration pathway of hydrogen peroxide-induced radicals from the site of heme localization to the protein surface. Analysis of a size of folded fraction of cyt c upon limited incubation with hydrogen peroxide indicates that the early oxidation of amino acids triggers an accelerated destruction of cyt c. Position of channels from molecular dynamics simulation structures of cyt c points to a location of amino acid residues exposed to reactive oxidants that are thus more prone to covalent modification.
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Affiliation(s)
- Nataša Tomášková
- Department of Biochemistry, Faculty of Science, P.J. Šafárik University, Moyzesova 11, 041 54 Košice, Slovakia
| | - Petr Novák
- Institute of Microbiology - BioCeV, Vídeňská 1083, 142 20 Prague 4, Czech Republic
| | - Tibor Kožár
- Center for Interdisciplinary Biosciences, Technology and Innovation Park, P.J. Šafárik University, Jesenná 5, 041 54 Košice, Slovakia
| | - Martina Petrenčáková
- Center for Interdisciplinary Biosciences, Technology and Innovation Park, P.J. Šafárik University, Jesenná 5, 041 54 Košice, Slovakia
| | - Daniel Jancura
- Department of Biophysics, Faculty of Science, P.J. Šafárik University, Jesenná 5, 041 54 Košice, Slovakia
| | - Ghazaleh Yassaghi
- Institute of Microbiology - BioCeV, Vídeňská 1083, 142 20 Prague 4, Czech Republic
| | - Petr Man
- Institute of Microbiology - BioCeV, Vídeňská 1083, 142 20 Prague 4, Czech Republic.
| | - Erik Sedlák
- Department of Biochemistry, Faculty of Science, P.J. Šafárik University, Moyzesova 11, 041 54 Košice, Slovakia; Center for Interdisciplinary Biosciences, Technology and Innovation Park, P.J. Šafárik University, Jesenná 5, 041 54 Košice, Slovakia.
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35
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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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36
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Yin V, Konermann L. Probing the Effects of Heterogeneous Oxidative Modifications on the Stability of Cytochrome c in Solution and in the Gas Phase. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:73-83. [PMID: 32401029 DOI: 10.1021/jasms.0c00089] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Covalent modifications by reactive oxygen species can modulate the function and stability of proteins. Thermal unfolding experiments in solution are a standard tool for probing oxidation-induced stability changes. Complementary to such solution investigations, the stability of electrosprayed protein ions can be assessed in the gas phase by collision-induced unfolding (CIU) and ion-mobility spectrometry. A question that remains to be explored is whether oxidation-induced stability alterations in solution are mirrored by the CIU behavior of gaseous protein ions. Here, we address this question using chloramine-T-oxidized cytochrome c (CT-cyt c) as a model system. CT-cyt c comprises various proteoforms that have undergone MetO formation (+16 Da) and Lys carbonylation (LysCH2-NH2 → LysCHO, -1 Da). We found that CT-cyt c in solution was destabilized, with a ∼5 °C reduced melting temperature compared to unmodified controls. Surprisingly, CIU experiments revealed the opposite trend, i.e., a stabilization of CT-cyt c in the gas phase. To pinpoint the source of this effect, we performed proteoform-resolved CIU on CT-cyt c fractions that had been separated by cation exchange chromatography. In this way, it was possible to identify MetO formation at residue 80 as the key modification responsible for stabilization in the gas phase. Possibly, this effect is caused by newly formed contacts of the sulfoxide with aromatic residues in the protein core. Overall, our results demonstrate that oxidative modifications can affect protein stability in solution and in the gas phase very differently.
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Affiliation(s)
- Victor Yin
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Lars Konermann
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
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Lou D, Liu XC, Wang XJ, Gao SQ, Wen GB, Lin YW. The importance of Asn52 in the structure-function relationship of human cytochrome c. RSC Adv 2020; 10:44768-44772. [PMID: 35516242 PMCID: PMC9058552 DOI: 10.1039/d0ra09961a] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 12/07/2020] [Indexed: 01/30/2023] Open
Abstract
The function of the highly conserved residue Asn52 in human cytochrome c (H-Cyt c) is not fully understood. Herein, we show that the naturally occurring variant N52S H-Cyt c has a perturbed secondary structure, with a small fraction of high-spin species. Remarkably, it exhibits an enhanced peroxidase activity by 3-8-fold at neutral pH, as well as self-oxidation in reaction with H2O2. This study suggests that the H-bond network mediated by Asn52 is essential to suppress the apoptotic activity of H-Cyt c under physiological conditions.
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Affiliation(s)
- Dan Lou
- School of Chemistry and Chemical Engineering, University of South China Hengyang 421001 China
| | - Xi-Chun Liu
- School of Chemistry and Chemical Engineering, University of South China Hengyang 421001 China
| | - Xiao-Juan Wang
- School of Chemistry and Chemical Engineering, University of South China Hengyang 421001 China
| | - Shu-Qin Gao
- Laboratory of Protein Structure and Function, University of South China Medical School Hengyang 421001 China
| | - Ge-Bo Wen
- Laboratory of Protein Structure and Function, University of South China Medical School Hengyang 421001 China
| | - Ying-Wu Lin
- School of Chemistry and Chemical Engineering, University of South China Hengyang 421001 China .,Laboratory of Protein Structure and Function, University of South China Medical School Hengyang 421001 China
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Guerra-Castellano A, Márquez I, Pérez-Mejías G, Díaz-Quintana A, De la Rosa MA, Díaz-Moreno I. Post-Translational Modifications of Cytochrome c in Cell Life and Disease. Int J Mol Sci 2020; 21:E8483. [PMID: 33187249 PMCID: PMC7697256 DOI: 10.3390/ijms21228483] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 11/05/2020] [Accepted: 11/07/2020] [Indexed: 02/07/2023] Open
Abstract
Mitochondria are the powerhouses of the cell, whilst their malfunction is related to several human pathologies, including neurodegenerative diseases, cardiovascular diseases, and various types of cancer. In mitochondrial metabolism, cytochrome c is a small soluble heme protein that acts as an essential redox carrier in the respiratory electron transport chain. However, cytochrome c is likewise an essential protein in the cytoplasm acting as an activator of programmed cell death. Such a dual role of cytochrome c in cell life and death is indeed fine-regulated by a wide variety of protein post-translational modifications. In this work, we show how these modifications can alter cytochrome c structure and functionality, thus emerging as a control mechanism of cell metabolism but also as a key element in development and prevention of pathologies.
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Affiliation(s)
| | | | | | | | | | - Irene Díaz-Moreno
- Instituto de Investigaciones Químicas (IIQ), Centro de Investigaciones Científicas Isla de la Cartuja (cicCartuja), Universidad de Sevilla, Consejo Superior de Investigaciones Científicas (CSIC), Avda. Américo Vespucio 49, 41092 Sevilla, Spain; (A.G.-C.); (I.M.); (G.P.-M.); (A.D.-Q.); (M.A.D.l.R.)
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Yin V, Holzscherer D, Konermann L. Delineating Heme-Mediated versus Direct Protein Oxidation in Peroxidase-Activated Cytochrome c by Top-Down Mass Spectrometry. Biochemistry 2020; 59:4108-4117. [PMID: 32991149 DOI: 10.1021/acs.biochem.0c00609] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Oxidation of key residues in cytochrome c (cyt c) by chloramine T (CT) converts the protein from an electron transporter to a peroxidase. This peroxidase-activated state represents an important model system for exploring the early steps of apoptosis. CT-induced transformations include oxidation of the distal heme ligand Met80 (MetO, +16 Da) and carbonylation (LysCHO, -1 Da) in the range of Lys53/55/72/73. Remarkably, the 15 remaining Lys residues in cyt c are not susceptible to carbonylation. The cause of this unusual selectivity is unknown. Here we applied top-down mass spectrometry (MS) to examine whether CT-induced oxidation is catalyzed by heme. To this end, we compared the behavior of cyt c with (holo-cyt c) and without heme (apoSS-cyt c). CT caused MetO formation at Met80 for both holo- and apoSS-cyt c, implying that this transformation can proceed independently of heme. The aldehyde-specific label Girard's reagent T (GRT) reacted with oxidized holo-cyt c, consistent with the presence of several LysCHO. In contrast, oxidized apo-cyt c did not react with GRT, revealing that LysCHO forms only in the presence of heme. The heme dependence of LysCHO formation was further confirmed using microperoxidase-11 (MP11). CT exposure of apoSS-cyt c in the presence of MP11 caused extensive nonselective LysCHO formation. Our results imply that the selectivity of LysCHO formation at Lys53/55/72/73 in holo-cyt c is caused by the spatial proximity of these sites to the reactive (distal) heme face. Overall, this work highlights the utility of top-down MS for unravelling complex oxidative modifications.
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Affiliation(s)
- Victor Yin
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Derek Holzscherer
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Lars Konermann
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
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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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Guo J, Yang L, Gao Z, Zhao C, Mei Y, Song YY. Insight of MOF Environment-Dependent Enzyme Activity via MOFs-in-Nanochannels Configuration. ACS Catal 2020. [DOI: 10.1021/acscatal.0c00591] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Junli Guo
- College of Sciences, Northeastern University, Shenyang 110004, China
| | - Lingling Yang
- College of Sciences, Northeastern University, Shenyang 110004, China
| | - Zhida Gao
- College of Sciences, Northeastern University, Shenyang 110004, China
| | - Chenxi Zhao
- College of Sciences, Northeastern University, Shenyang 110004, China
| | - Ye Mei
- State Key Laboratory of Precision Spectroscopy, School of Physics and Electronic Science, East China Normal University, Shanghai 200062, China
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China
- Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan, Shanxi 030006, China
| | - Yan-Yan Song
- College of Sciences, Northeastern University, Shenyang 110004, China
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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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Wu X, Xiong J, Liu S, Chen B, Liang S, Lou W, Zong M. Peroxidase Encapsulated in Peroxidase Mimics via in situAssembly with Enhanced Catalytic Performance. ChemCatChem 2020. [DOI: 10.1002/cctc.201902055] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Xiaoling Wu
- Lab of Applied Biocatalysis School of Food Science and EngineeringSouth China University of Technology Guangzhou 510640 P.R. China
| | - Jun Xiong
- Lab of Applied Biocatalysis School of Food Science and EngineeringSouth China University of Technology Guangzhou 510640 P.R. China
| | - Shuli Liu
- Lab of Applied Biocatalysis School of Food Science and EngineeringSouth China University of Technology Guangzhou 510640 P.R. China
| | - Bin Chen
- Lab of Applied Biocatalysis School of Food Science and EngineeringSouth China University of Technology Guangzhou 510640 P.R. China
| | - Shan Liang
- Lab of Applied Biocatalysis School of Food Science and EngineeringSouth China University of Technology Guangzhou 510640 P.R. China
| | - Wenyong Lou
- Lab of Applied Biocatalysis School of Food Science and EngineeringSouth China University of Technology Guangzhou 510640 P.R. China
- Innovation Center of Bioactive Molecule Development and ApplicationSouth China Institute of Collaborative Innovation Dongguan 221116 P.R. China
| | - Minhua Zong
- Lab of Applied Biocatalysis School of Food Science and EngineeringSouth China University of Technology Guangzhou 510640 P.R. China
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Hara T, Shibata Y, Amagai R, Okado-Matsumoto A. Use of in-gel peroxidase assay for cytochrome c to visualize mitochondrial complexes III and IV. Biol Open 2020; 9:bio.047936. [PMID: 31852667 PMCID: PMC6955206 DOI: 10.1242/bio.047936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The in-gel activity assay (IGA) is a powerful technique that uses enzymatic activity and compares intensities of detected bands in mitochondrial respiratory chain supercomplexes, and it is applicable to eukaryotic organisms. However, no IGA has been established for complex III because of the difficulty of access by ubiquinol, a substrate for complex III. Herein, we demonstrate that cytochrome c (Cyt c) showed peroxidase activity on IGA as a component of complexes III and IV. We used pre-incubation with sodium dodecyl sulfate (SDS) before IGA to loosen complexes in the gel after high-resolution clear native polyacrylamide gel electrophoresis (hrCN-PAGE), a refinement of blue native PAGE. The signals of IGA based on peroxidase activity were obtained using enhanced chemiluminescence solution. Then, the gel was directly used in western blotting or hrCN/SDS two-dimensional PAGE. Our findings indicate that IGA for Cyt c reflected the indirect activity of complexes III and IV. Summary: An improved in-gel activity assay visualized respiratory chain complexes III, IV and supercomplexes through cytochrome c. Pre-incubation of detergents enhanced the in-gel activity assay.
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Affiliation(s)
- Tsukasa Hara
- Department of Biology, Faculty of Science, Toho University, Miyama 2-2-1, Funabashi, Chiba 274-8510, Japan
| | - Yuma Shibata
- Department of Biology, Faculty of Science, Toho University, Miyama 2-2-1, Funabashi, Chiba 274-8510, Japan
| | - Ryosuke Amagai
- Department of Biology, Faculty of Science, Toho University, Miyama 2-2-1, Funabashi, Chiba 274-8510, Japan
| | - Ayako Okado-Matsumoto
- Department of Biology, Faculty of Science, Toho University, Miyama 2-2-1, Funabashi, Chiba 274-8510, Japan
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Chea EE, Deredge DJ, Jones LM. Insights on the Conformational Ensemble of Cyt C Reveal a Compact State during Peroxidase Activity. Biophys J 2019; 118:128-137. [PMID: 31810655 DOI: 10.1016/j.bpj.2019.11.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 10/29/2019] [Accepted: 11/11/2019] [Indexed: 12/19/2022] Open
Abstract
Cytochrome c (cyt c) is known for its role in the electron transport chain but transitions to a peroxidase-active state upon exposure to oxidative species. The peroxidase activity ultimately results in the release of cyt c into the cytosol for the engagement of apoptosis. The accumulation of oxidative modifications that accompany the onset of the peroxidase function are well-characterized. However, the concurrent structural and conformational transitions of cyt c remain undercharacterized. Fast photochemical oxidation of proteins (FPOP) coupled with mass spectrometry is a protein footprinting technique used to structurally characterize proteins. FPOP coupled with native ion mobility separation shows that exposure to H2O2 results in the accumulation of a compact state of cyt c. Subsequent top-down fragmentation to localize FPOP modifications reveals changes in heme coordination between conformers. A time-resolved functional assay suggests that this compact conformer is peroxidase active. Altogether, combining FPOP, ion mobility separation, and top-down and bottom-up mass spectrometry allows us to discern individual conformations in solution and obtain a better understanding of the conformational ensemble and structural transitions of cyt c as it transitions from a respiratory role to a proapoptotic role.
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Affiliation(s)
- Emily E Chea
- Department of Pharmaceutical Sciences, University of Maryland Baltimore, Baltimore, Maryland
| | - Daniel J Deredge
- Department of Pharmaceutical Sciences, University of Maryland Baltimore, Baltimore, Maryland
| | - Lisa M Jones
- Department of Pharmaceutical Sciences, University of Maryland Baltimore, Baltimore, Maryland.
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Cytochrome c: An extreme multifunctional protein with a key role in cell fate. Int J Biol Macromol 2019; 136:1237-1246. [DOI: 10.1016/j.ijbiomac.2019.06.180] [Citation(s) in RCA: 88] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 06/24/2019] [Accepted: 06/24/2019] [Indexed: 01/25/2023]
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47
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Szymkowicz L, Lento C, Wilson DJ. Impact of Cardiolipin and Phosphatidylcholine Interactions on the Conformational Ensemble of Cytochrome c. Biochemistry 2019; 58:3617-3626. [DOI: 10.1021/acs.biochem.9b00495] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Lisa Szymkowicz
- Department of Chemistry, York University, Toronto, Ontario, Canada M3J 1P3
| | - Cristina Lento
- Department of Chemistry, York University, Toronto, Ontario, Canada M3J 1P3
| | - Derek J. Wilson
- Department of Chemistry, York University, Toronto, Ontario, Canada M3J 1P3
- Centre for Research in Mass Spectrometry, York University, Toronto, Ontario, Canada M3J 1P3
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Spectroscopic approach for the interaction of carbon nanoparticles with cytochrome c and BY-2 cells: Protein structure and mitochondrial function. Int J Biol Macromol 2019; 138:29-36. [PMID: 31302123 DOI: 10.1016/j.ijbiomac.2019.07.076] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 07/10/2019] [Accepted: 07/10/2019] [Indexed: 12/24/2022]
Abstract
In this study, we employed multiple spectroscopic methods to analyze the effects of carbon nanoparticles (CNPs) on structure of cytochrome c (Cyt c) and mitochondrial function in plant cells. The tertiary structures of aromatic amino acid in Cyt c were not changed after addition of CNPs. Cyt c was found to be absorbed on the surfaces of CNPs in a non-linear manner and only bound Cyt c can be reduced. In addition, the binding of Cyt c was found to increase the diameter of CNPs at lower concentrations. The redox potential of Cyt c was almost not affected after treatment with CNPs. There were no obvious differences in cellular ATP after exposure to CNPs, and the mitochondrial membrane potential (MMP) was significantly decreased once the CNPs concentration exceeded 31.25 μg/mL. The levels of reactive oxygen species (ROS) also were increased in BY-2 cells. Taken together, these findings provide basis for the interactions between CNPs and Cyt c, as well as the effect of CNPs treatment on the mitochondria function in plant cells.
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Dual species transcript profiling during the interaction between banana (Musa acuminata) and the fungal pathogen Fusarium oxysporum f. sp. cubense. BMC Genomics 2019; 20:519. [PMID: 31234790 PMCID: PMC6591919 DOI: 10.1186/s12864-019-5902-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Accepted: 06/12/2019] [Indexed: 12/15/2022] Open
Abstract
Background Banana wilt disease, caused by Fusarium oxysporum f. sp. cubense Tropical Race 4 (Foc TR4), is one of the most devastating diseases in banana (Musa spp.). Foc is a soil borne pathogen that causes rot of the roots or wilt of leaves by colonizing the xylem vessels. The dual RNA sequencing is used to simultaneously assess the transcriptomes of pathogen and host. This method greatly helps to understand the responses of pathogen and host to each other and discover the potential pathogenic mechanism. Results Plantlets of two economically important banana cultivars, Foc TR4 less susceptible cultivar NK and susceptible cultivar BX, were used to research the Foc-banana interaction mechanism. Notably, the infected NK had more significantly up-regulated genes on the respiration machinery including TCA cycle, glyoxylate, glycerol, and glycolysis compared to BX at 27 h post inoculation (hpi). In addition, genes involved in plant-pathogen interaction, starch, sucrose, linolenic acid and sphingolipid metabolisms were uniquely more greatly induced in BX than those in NK during the whole infection. Genes related to the biosynthesis and metabolism of SA and JA were greatly induced in the infected NK; while auxin and abscisic acid metabolisms related genes were strongly stimulated in the infected BX at 27 hpi. Furthermore, most of fungal genes were more highly expressed in the roots of BX than in those of NK. The fungal genes related to pathogenicity, pectin and chitin metabolism, reactive oxygen scavenging played the important roles during the infection of Foc. CCP1 (cytochrome c peroxidase 1) was verified to involve in cellulose utilization, oxidative stress response and pathogenicity of fungus. Conclusion The transcriptome indicated that NK had much faster defense response against Foc TR4 than BX and the expression levels of fungal genes were higher in BX than those in NK. The metabolisms of carbon, nitrogen, and signal transduction molecular were differentially involved in pathogen infection in BX and NK. Additionally, the putative virulence associated fungal genes involved in colonization, nutrition acquirement and transport provided more insights into the infection process of Foc TR4 in banana roots. Electronic supplementary material The online version of this article (10.1186/s12864-019-5902-z) contains supplementary material, which is available to authorized users.
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Tarpani L, Bellezza F, Sassi P, Gambucci M, Cipiciani A, Latterini L. New Insights into the Effects of Surface Functionalization on the Peroxidase Activity of Cytochrome c Adsorbed on Silica Nanoparticles. J Phys Chem B 2019; 123:2567-2575. [DOI: 10.1021/acs.jpcb.8b11762] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Luigi Tarpani
- Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, via Elce di Sotto, 8, 06123 Perugia, Italy
| | - Francesca Bellezza
- Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, via Elce di Sotto, 8, 06123 Perugia, Italy
| | - Paola Sassi
- Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, via Elce di Sotto, 8, 06123 Perugia, Italy
| | - Marta Gambucci
- Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, via Elce di Sotto, 8, 06123 Perugia, Italy
| | - Antonio Cipiciani
- Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, via Elce di Sotto, 8, 06123 Perugia, Italy
| | - Loredana Latterini
- Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, via Elce di Sotto, 8, 06123 Perugia, Italy
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