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Chkadua G, Nozadze E, Tsakadze L, Shioshvili L, Arutinova N, Leladze M, Dzneladze S, Javakhishvili M, Jariashvili T, Petriashvili E. The effect of cytochrome c on Na,K-ATPase. J Bioenerg Biomembr 2024; 56:221-234. [PMID: 38517564 DOI: 10.1007/s10863-024-10012-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 03/09/2024] [Indexed: 03/24/2024]
Abstract
Na,K-ATPase is a crucial enzyme responsible for maintaining Na+, K+-gradients across the cell membrane, which is essential for numerous physiological processes within various organs and tissues. Due to its significance in cellular physiology, inhibiting Na,K-ATPase can have profound physiological consequences. This characteristic makes it a target for various pharmacological applications, and drugs that modulate the pump's activity are thus used in the treatment of several medical conditions. Cytochrome c (Cytc) is a protein with dual functions in the cell. In the mitochondria, it is essential for ATP synthesis and energy production. However, in response to apoptotic stimuli, it is released into the cytosol, where it triggers programmed cell death through the intrinsic apoptosis pathway. Aside from its role in canonical intrinsic apoptosis, Cytc also plays additional roles. For instance, Cytc participates in certain non-apoptotic functions -those which are less well-understood in comparison to its role in apoptosis. Within this in vitro study, we have shown the impact of Cytc on Na,K-ATPase for the first time. Cytc has a biphasic action on Na,K-ATPase, with activation at low concentrations (0.06 ng/ml; 6 ng/ml) and inhibition at high concentration (120 ng/ml). Cytc moreover displays isoform/subunit specificity and regulates the Na+ form of the enzyme, while having no effect on the activity or kinetic parameters of the K+-dependent form of the enzyme. Changing the affinity of p-chloromercuribenzoic acid (PCMB) by Cytc is therefore both a required and sufficient condition for confirming that PCMB and Cytc share the same target, namely the thiol groups of cysteine in Na,K-ATPase.
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Affiliation(s)
- Gvantsa Chkadua
- Ivane Beritashvili Center of Experimental Biomedicine, 14 Gotua Str, 0160, Tbilisi, Georgia.
| | - Eka Nozadze
- Ivane Beritashvili Center of Experimental Biomedicine, 14 Gotua Str, 0160, Tbilisi, Georgia
| | - Leila Tsakadze
- Ivane Beritashvili Center of Experimental Biomedicine, 14 Gotua Str, 0160, Tbilisi, Georgia
| | - Lia Shioshvili
- Ivane Beritashvili Center of Experimental Biomedicine, 14 Gotua Str, 0160, Tbilisi, Georgia
| | - Nana Arutinova
- Ivane Beritashvili Center of Experimental Biomedicine, 14 Gotua Str, 0160, Tbilisi, Georgia
| | - Marine Leladze
- Ivane Beritashvili Center of Experimental Biomedicine, 14 Gotua Str, 0160, Tbilisi, Georgia
| | - Sopio Dzneladze
- Ivane Beritashvili Center of Experimental Biomedicine, 14 Gotua Str, 0160, Tbilisi, Georgia
| | - Maia Javakhishvili
- Ivane Beritashvili Center of Experimental Biomedicine, 14 Gotua Str, 0160, Tbilisi, Georgia
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Polák M, Černý J, Novák P. Isotopic Depletion Increases the Spatial Resolution of FPOP Top-Down Mass Spectrometry Analysis. Anal Chem 2024; 96:1478-1487. [PMID: 38226459 PMCID: PMC10831798 DOI: 10.1021/acs.analchem.3c03759] [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: 08/22/2023] [Revised: 11/08/2023] [Accepted: 12/15/2023] [Indexed: 01/17/2024]
Abstract
Protein radical labeling, like fast photochemical oxidation of proteins (FPOP), coupled to a top-down mass spectrometry (MS) analysis offers an alternative analytical method for probing protein structure or protein interaction with other biomolecules, for instance, proteins and DNA. However, with the increasing mass of studied analytes, the MS/MS spectra become complex and exhibit a low signal-to-noise ratio. Nevertheless, these difficulties may be overcome by protein isotope depletion. Thus, we aimed to use protein isotope depletion to analyze FPOP-oxidized samples by top-down MS analysis. For this purpose, we prepared isotopically natural (IN) and depleted (ID) forms of the FOXO4 DNA binding domain (FOXO4-DBD) and studied the protein-DNA interaction interface with double-stranded DNA, the insulin response element (IRE), after exposing the complex to hydroxyl radicals. As shown by comparing tandem mass spectra of natural and depleted proteins, the ID form increased the signal-to-noise ratio of useful fragment ions, thereby enhancing the sequence coverage by more than 19%. This improvement in the detection of fragment ions enabled us to detect 22 more oxidized residues in the ID samples than in the IN sample. Moreover, less common modifications were detected in the ID sample, including the formation of ketones and lysine carbonylation. Given the higher quality of ID top-down MSMS data set, these results provide more detailed information on the complex formation between transcription factors and DNA-response elements. Therefore, our study highlights the benefits of isotopic depletion for quantitative top-down proteomics. Data are available via ProteomeXchange with the identifier PXD044447.
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Affiliation(s)
- Marek Polák
- Institute
of Microbiology of the Czech Academy of Sciences, 14220 Prague, Czech Republic
- Department
of Biochemistry, Faculty of Science, Charles
University, 12843 Prague, Czech Republic
| | - Jiří Černý
- Laboratory
of Structural Bioinformatics of Proteins, Institute of Biotechnology of the Czech Academy of Sciences, 14220 Prague, Czech Republic
| | - Petr Novák
- Institute
of Microbiology of the Czech Academy of Sciences, 14220 Prague, Czech Republic
- Department
of Biochemistry, Faculty of Science, Charles
University, 12843 Prague, Czech Republic
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3
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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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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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Hovan A, Berta M, Sedláková D, Miskovsky P, Bánó G, Sedlák E. Heme is responsible for enhanced singlet oxygen deactivation in cytochrome c. Phys Chem Chem Phys 2021; 23:15557-15563. [PMID: 34259248 DOI: 10.1039/d1cp01517f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The deactivation of singlet oxygen, the lowest electronic excited state of molecular oxygen, by proteins is usually described through the interaction of singlet oxygen with certain amino acids. Changes in accessibility of these amino acids influence the quenching rate and the phosphorescence kinetics of singlet oxygen. In the cellular environment, however, numerous proteins with covalently bound or encapsulated cofactors are present. These cofactors could also influence the deactivation of singlet oxygen, and these have received little attention. To confront this issue, we used cytochrome c (cyt c) and apocytochrome c (apocyt c) to illustrate how the heme prosthetic group influences the rate constant of singlet oxygen deactivation upon acidic pH-induced conformational change of cyt c. Photo-excited flavin mononucleotide (FMN) was used to produce singlet oxygen. Our data show that the heme group has a significant and measurable effect on singlet oxygen quenching when the heme is exposed to solvents and is therefore more accessible to singlet oxygen. The effect of amino acids and heme accessibility on the FMN triplet state deactivation was also investigated.
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Affiliation(s)
- Andrej Hovan
- Department of Biophysics, Faculty of Science, P. J. Šafárik University in Košice, Jesenná 5, 041 54 Košice, Slovakia.
| | - Martin Berta
- Department of Biophysics, Faculty of Science, P. J. Šafárik University in Košice, Jesenná 5, 041 54 Košice, Slovakia.
| | - Dagmar Sedláková
- Department of Biophysics, Institute of Experimental Physics, Slovak Academy of Sciences, Watsonova 47, 040 01 Košice, Slovakia
| | - Pavol Miskovsky
- Center for Interdisciplinary Biosciences, Technology and Innovation Park, P. J. Šafárik University in Košice, Jesenná 5, 041 54 Košice, Slovakia. and SAFTRA Photonics Ltd., Moldavská cesta 51, 040 11 Košice, Slovakia
| | - Gregor Bánó
- Department of Biophysics, Faculty of Science, P. J. Šafárik University in Košice, Jesenná 5, 041 54 Košice, Slovakia.
| | - Erik Sedlák
- Center for Interdisciplinary Biosciences, Technology and Innovation Park, P. J. Šafárik University in Košice, Jesenná 5, 041 54 Košice, Slovakia.
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