1
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Reeder BJ, Svistunenko DA, Wilson MT. Hell's Gate Globin-I from Methylacidiphilum infernorum Displays a Unique Temperature-Independent pH Sensing Mechanism Utililized a Lipid-Induced Conformational Change. Int J Mol Sci 2024; 25:6794. [PMID: 38928500 PMCID: PMC11203436 DOI: 10.3390/ijms25126794] [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: 04/26/2024] [Revised: 06/05/2024] [Accepted: 06/14/2024] [Indexed: 06/28/2024] Open
Abstract
Hell's Gate globin-I (HGb-I) is a thermally stable globin from the aerobic methanotroph Methylacidiphilium infernorum. Here we report that HGb-I interacts with lipids stoichiometrically to induce structural changes in the heme pocket, changing the heme iron distal ligation coordination from hexacoordinate to pentacoordinate. Such changes in heme geometry have only been previously reported for cytochrome c and cytoglobin, linked to apoptosis regulation and enhanced lipid peroxidation activity, respectively. However, unlike cytoglobin and cytochrome c, the heme iron of HGb-I is altered by lipids in ferrous as well as ferric oxidation states. The apparent affinity for lipids in this thermally stable globin is highly pH-dependent but essentially temperature-independent within the range of 20-60 °C. We propose a mechanism to explain these observations, in which lipid binding and stability of the distal endogenous ligand are juxtaposed as a function of temperature. Additionally, we propose that these coupled equilibria may constitute a mechanism through which this acidophilic thermophile senses the pH of its environment.
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Affiliation(s)
- Brandon J. Reeder
- School of Biological Sciences, University of Essex, Wivenhoe Park Colchester, Essex CO4 3SQ, UK; (D.A.S.); (M.T.W.)
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2
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Shafaei Pishabad Z, Ledgerwood EC. The Y49H cytochrome c variant enhances megakaryocytic maturation of K-562 cells. Biochim Biophys Acta Mol Basis Dis 2024; 1870:167134. [PMID: 38531481 DOI: 10.1016/j.bbadis.2024.167134] [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: 10/31/2023] [Revised: 02/22/2024] [Accepted: 03/18/2024] [Indexed: 03/28/2024]
Abstract
Five pathogenic variants in the gene encoding cytochrome c (CYCS) associated with mild autosomal dominant thrombocytopenia have been reported. Previous studies of peripheral blood CD34+ or CD45+ cells from subjects with the G42S CYCS variant showed an acceleration in megakaryopoiesis compared to wild-type (WT) cells. To determine whether this result reflects a common feature of the CYCS variants, the c.145T>C mutation (Y49H variant) was introduced into the endogenous CYCS locus in K-562 cells, which undergo megakaryocytic maturation in response to treatment with a phorbol ester. The c.145T>C (Y49H) variant enhanced the megakaryocyte maturation of the K-562 cells, and this effect was seen when the cells were cultured at both 18 % and 5 % oxygen. Thus, alteration of megakaryopoiesis is common to both the G42S and Y49H CYCS variants and may contribute to the low platelet phenotype. The Y49H CYCS variant has previously been reported to impair mitochondrial respiratory chain function in vitro, however using extracellular flux analysis the c.145T>C (Y49H) variant does not alter mitochondrial bioenergetics of the K-562 cells, consistent with the lack of a phenotype characteristic of mitochondrial diseases in CYCS variant families. The Y49H variant has also been reported to enhance the ability of cytochrome c to trigger caspase activation in the intrinsic apoptosis pathway. However, as seen in peripheral blood cells from G42S CYCS variant carriers, the presence of Y49H cytochrome c in K-562 cells did not significantly change their response to an apoptotic stimulus.
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Affiliation(s)
- Zahra Shafaei Pishabad
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - Elizabeth C Ledgerwood
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, PO Box 56, Dunedin 9054, New Zealand.
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3
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Zhou Z, Arroum T, Luo X, Kang R, Lee YJ, Tang D, Hüttemann M, Song X. Diverse functions of cytochrome c in cell death and disease. Cell Death Differ 2024; 31:387-404. [PMID: 38521844 PMCID: PMC11043370 DOI: 10.1038/s41418-024-01284-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Revised: 03/13/2024] [Accepted: 03/18/2024] [Indexed: 03/25/2024] Open
Abstract
The redox-active protein cytochrome c is a highly positively charged hemoglobin that regulates cell fate decisions of life and death. Under normal physiological conditions, cytochrome c is localized in the mitochondrial intermembrane space, and its distribution can extend to the cytosol, nucleus, and extracellular space under specific pathological or stress-induced conditions. In the mitochondria, cytochrome c acts as an electron carrier in the electron transport chain, facilitating adenosine triphosphate synthesis, regulating cardiolipin peroxidation, and influencing reactive oxygen species dynamics. Upon cellular stress, it can be released into the cytosol, where it interacts with apoptotic peptidase activator 1 (APAF1) to form the apoptosome, initiating caspase-dependent apoptotic cell death. Additionally, following exposure to pro-apoptotic compounds, cytochrome c contributes to the survival of drug-tolerant persister cells. When translocated to the nucleus, it can induce chromatin condensation and disrupt nucleosome assembly. Upon its release into the extracellular space, cytochrome c may act as an immune mediator during cell death processes, highlighting its multifaceted role in cellular biology. In this review, we explore the diverse structural and functional aspects of cytochrome c in physiological and pathological responses. We summarize how posttranslational modifications of cytochrome c (e.g., phosphorylation, acetylation, tyrosine nitration, and oxidation), binding proteins (e.g., HIGD1A, CHCHD2, ITPR1, and nucleophosmin), and mutations (e.g., G41S, Y48H, and A51V) affect its function. Furthermore, we provide an overview of the latest advanced technologies utilized for detecting cytochrome c, along with potential therapeutic approaches related to this protein. These strategies hold tremendous promise in personalized health care, presenting opportunities for targeted interventions in a wide range of conditions, including neurodegenerative disorders, cardiovascular diseases, and cancer.
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Affiliation(s)
- Zhuan Zhou
- Department of Surgery, UT Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Tasnim Arroum
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, 48201, USA
| | - Xu Luo
- Eppley Institute for Research in Cancer and Allied Diseases, Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Rui Kang
- Department of Surgery, UT Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Yong J Lee
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, 8700 Beverly Blvd, Los Angeles, CA, 90048, USA
| | - Daolin Tang
- Department of Surgery, UT Southwestern Medical Center, Dallas, TX, 75390, USA.
| | - Maik Hüttemann
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, 48201, USA.
- Department of Biochemistry, Microbiology, and Immunology, Wayne State University, Detroit, MI, 48201, USA.
| | - Xinxin Song
- Department of Surgery, UT Southwestern Medical Center, Dallas, TX, 75390, USA.
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4
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Chin TC, Wilbanks SM, Ledgerwood EC. Altered conformational dynamics contribute to species-specific effects of cytochrome c mutations on caspase activation. J Biol Inorg Chem 2024; 29:169-176. [PMID: 38472487 PMCID: PMC11098916 DOI: 10.1007/s00775-024-02044-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 01/08/2024] [Indexed: 03/14/2024]
Abstract
Variants in the gene encoding human cytochrome c (CYCS) cause mild autosomal dominant thrombocytopenia. Despite high sequence conservation between mouse and human cytochrome c, this phenotype is not recapitulated in mice for the sole mutant (G41S) that has been investigated. The effect of the G41S mutation on the in vitro activities of cytochrome c is also not conserved between human and mouse. Peroxidase activity is increased in both mouse and human G41S variants, whereas apoptosome activation is increased for human G41S cytochrome c but decreased for mouse G41S cytochrome c. These apoptotic activities of cytochrome c are regulated at least in part by conformational dynamics of the main chain. Here we use computational and in vitro approaches to understand why the impact of the G41S mutation differs between mouse and human cytochromes c. The G41S mutation increases the inherent entropy and main chain mobility of human but not mouse cytochrome c. Exclusively in human G41S cytochrome c this is accompanied by a decrease in occupancy of H-bonds between protein and heme during simulations. These data demonstrate that binding of cytochrome c to Apaf-1 to trigger apoptosome formation, but not the peroxidase activity of cytochrome c, is enhanced by increased mobility of the native protein conformation.
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Affiliation(s)
- Thomas C Chin
- Biochemistry Department, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Sigurd M Wilbanks
- Biochemistry Department, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Elizabeth C Ledgerwood
- Biochemistry Department, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand.
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5
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Lučić M, Wilson MT, Pullin J, Hough MA, Svistunenko DA, Worrall JAR. New insights into controlling radical migration pathways in heme enzymes gained from the study of a dye-decolorising peroxidase. Chem Sci 2023; 14:12518-12534. [PMID: 38020392 PMCID: PMC10646903 DOI: 10.1039/d3sc04453j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 10/06/2023] [Indexed: 12/01/2023] Open
Abstract
In heme enzymes, such as members of the dye-decolorising peroxidase (DyP) family, the formation of the highly oxidising catalytic Fe(iv)-oxo intermediates following reaction with hydrogen peroxide can lead to free radical migration (hole hopping) from the heme to form cationic tyrosine and/or tryptophan radicals. These species are highly oxidising (∼1 V vs. NHE) and under certain circumstances can catalyse the oxidation of organic substrates. Factors that govern which specific tyrosine or tryptophan the free radical migrates to in heme enzymes are not well understood, although in the case of tyrosyl radical formation the nearby proximity of a proton acceptor is a recognised facilitating factor. By using an A-type member of the DyP family (DtpAa) as an exemplar, we combine protein engineering, X-ray crystallography, hole-hopping calculations, EPR spectroscopy and kinetic modelling to provide compelling new insights into the control of radical migration pathways following reaction of the heme with hydrogen peroxide. We demonstrate that the presence of a tryptophan/tyrosine dyad motif displaying a T-shaped orientation of aromatic rings on the proximal side of the heme dominates the radical migration landscape in wild-type DtpAa and continues to do so following the rational engineering into DtpAa of a previously identified radical migration pathway in an A-type homolog on the distal side of the heme. Only on disrupting the proximal dyad, through removal of an oxygen atom, does the radical migration pathway then switch to the engineered distal pathway to form the desired tyrosyl radical. Implications for protein design and biocatalysis are discussed.
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Affiliation(s)
- Marina Lučić
- School of Life Sciences, University of Essex Wivenhoe Park Colchester Essex CO4 3SQ UK
| | - Michael T Wilson
- School of Life Sciences, University of Essex Wivenhoe Park Colchester Essex CO4 3SQ UK
| | - Jacob Pullin
- School of Life Sciences, University of Essex Wivenhoe Park Colchester Essex CO4 3SQ UK
| | - Michael A Hough
- School of Life Sciences, University of Essex Wivenhoe Park Colchester Essex CO4 3SQ UK
- Diamond Light Source, Harwell Science and Innovation Campus Didcot Oxfordshire OX11 0DE UK
| | - Dimitri A Svistunenko
- School of Life Sciences, University of Essex Wivenhoe Park Colchester Essex CO4 3SQ UK
| | - Jonathan A R Worrall
- School of Life Sciences, University of Essex Wivenhoe Park Colchester Essex CO4 3SQ UK
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6
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Li YY, Long SS, Yu L, Liu AK, Gao SQ, Tan X, Lin YW. Effects of naturally occurring S47F/A mutations on the structure and function of human cytochrome c. J Inorg Biochem 2023; 246:112296. [PMID: 37356378 DOI: 10.1016/j.jinorgbio.2023.112296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 06/14/2023] [Accepted: 06/16/2023] [Indexed: 06/27/2023]
Abstract
The sequence and structure of human cytochrome c (hCyt c) exhibit evolutionary conservations, with only a limited number of naturally occurring mutations in humans. Herein, we investigated the effects of the naturally occurring S47F/A mutations on the structure and function of hCyt c in the oxidized form. Although the naturally occurring S47F/A mutations did not largely alter the protein structure, the S47F and S47A variants exhibited a small fraction of high-spin species. Kinetic studies showed that the peroxidase activity of the variants was enhanced by ∼2.5-fold under neutral pH conditions, as well as for the rate in reaction with H2O2, when compared to those of wild-type hCyt c. In addition, we evaluated the interaction between hCyt c and human neuroglobin (hNgb) by isothermal titration calorimetry (ITC) studies, which revealed that the binding constant was reduced by ∼8-fold as result of the mutation of the hydrophilic Ser to the hydrophobic Phe/Ala. These findings provide valuable insights into the role of Ser47 in Ω-loop C in sustaining the structure and function of hCyt c.
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Affiliation(s)
- Yan-Yan Li
- School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China
| | - Shuang-Shuang Long
- School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China.
| | - Lu Yu
- High Magnetic Field Laboratory, Chinese Academy of Sciences, Hefei, Anhui 230031, China
| | - Ao-Kun Liu
- High Magnetic Field Laboratory, Chinese Academy of Sciences, Hefei, Anhui 230031, China
| | - Shu-Qin Gao
- Key Lab of Protein Structure and Function of Universities in Hunan Province, University of South China, Hengyang 421001, China
| | - Xiangshi Tan
- Department of Chemistry & Institute of Biomedical Science, Fudan University, Shanghai 200433, China
| | - Ying-Wu Lin
- School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China; Key Lab of Protein Structure and Function of Universities in Hunan Province, University of South China, Hengyang 421001, China.
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7
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Nutho B, Samsri S, Pornsuwan S. Structural Dynamics of the Precatalytic State of Human Cytochrome c upon T28C, G34C, and A50C Mutations: A Molecular Dynamics Simulation Perspective. ACS OMEGA 2023; 8:15229-15238. [PMID: 37151554 PMCID: PMC10157674 DOI: 10.1021/acsomega.3c00220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 04/06/2023] [Indexed: 05/09/2023]
Abstract
The native structure of cytochrome c (cytc) contains hexacoordinate heme iron with His18 and Met80 residues ligated at the axial sites. Mutations of cytc at Ω-loops have been investigated in modulating the peroxidase activity and, hence, related to the initiation of the apoptotic pathway. Our previous experimental data reported on the peroxidase activity of the cysteine-directed mutants at different parts of the Ω-loop of human cytc (hCytc), that is, T28C, G34C, and A50C. In this work, we performed 1 μs molecular dynamics (MD) simulations to elucidate the detailed structural and dynamic changes upon these mutations, particularly at the proximal Ω-loop. The structures of hCytc were modeled in the hexacoordinated form, which was referred to as the "precatalytic state". The results showed that the structural features of the G34C mutant were more distinctive than those of other mutants. G34C mutation caused local destabilization and flexibility at the proximal Ω-loop (residues 12-28) and an extended distance between this Ω-loop region and heme iron. Besides, analysis of the orientation of the Arg38 side chain of the G34C mutant revealed the Arg38 conformer facing away from the heme iron. The obtained MD results also suggested structural diversity of the precatalytic states for the three hCytc mutants, specifically the effect of G34C mutation on the flexibility of the proximal Ω-loops. Therefore, our MD simulations combined with previous experimental data provide detailed insights into the structural basis of hCytc that could contribute to its pro-apoptotic function.
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Affiliation(s)
- Bodee Nutho
- Department
of Pharmacology, Faculty of Science, Mahidol
University, Bangkok 10400, Thailand
| | - Sasiprapa Samsri
- Department
of Chemistry and Center of Excellence for Innovation in Chemistry,
Faculty of Science, Mahidol University, Bangkok 10400, Thailand
| | - Soraya Pornsuwan
- Department
of Chemistry and Center of Excellence for Innovation in Chemistry,
Faculty of Science, Mahidol University, Bangkok 10400, Thailand
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8
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The oxidative nuclease activity of human cytochrome c with mutations in Ω-loop C/D. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2023; 1871:140897. [PMID: 36642204 DOI: 10.1016/j.bbapap.2023.140897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/06/2023] [Accepted: 01/09/2023] [Indexed: 01/15/2023]
Abstract
Natural and artificial nucleases have extensive applications in biotechnology and biomedicine. The exploration of protein with potential DNA cleavage activity also inspires the design of artificial nuclease and helps to understand the physiological process of DNA damage. In this study, we engineered four human cytochrome c (Cyt c) mutants (N52S, N52A, I81N, and I81D Cyt c), which showed enhanced DNA cleavage activity and degradation in comparison with WT Cyt c, especially under acidic conditions. The mechanism assays revealed that the superoxide (O2•-) plays an important role in the nuclease reaction. The kinetic assays showed that the peroxidase activity of the I81D Cyt c mutant enhanced up to 9-fold at pH 5. This study suggests that the mutations of Ile81 and Asn52 in Ω-loop C/D are critical for the nuclease activity of Cyt c, which may have physiological significance in DNA damage and potential applications in biomedicine.
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9
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Yang J, Yin GN, Kim DK, Han AR, Lee DS, Min KW, Fu Y, Yun J, Suh JK, Ryu JK, Kim HM. Crystal structure of LRG1 and the functional significance of LRG1 glycan for LPHN2 activation. Exp Mol Med 2023:10.1038/s12276-023-00992-4. [PMID: 37121976 DOI: 10.1038/s12276-023-00992-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Accepted: 02/21/2023] [Indexed: 05/02/2023] Open
Abstract
The serum glycoprotein leucine-rich ɑ-2-glycoprotein 1 (LRG1), primarily produced by hepatocytes and neutrophils, is a multifunctional protein that modulates various signaling cascades, mainly TGFβ signaling. Serum LRG1 and neutrophil-derived LRG1 have different molecular weights due to differences in glycosylation, but the impact of the differential glycan composition in LRG1 on its cellular function is largely unknown. We previously reported that LRG1 can promote both angiogenic and neurotrophic processes under hyperglycemic conditions by interacting with LPHN2. Here, we determined the crystal structure of LRG1, identifying the horseshoe-like solenoid structure of LRG1 and its four N-glycosylation sites. In addition, our biochemical and cell-biological analyses found that the deglycosylation of LRG1, particularly the removal of glycans on N325, is critical for the high-affinity binding of LRG1 to LPHN2 and thus promotes LRG1/LPHN2-mediated angiogenic and neurotrophic processes in mouse tissue explants, even under normal glucose conditions. Moreover, the intracavernous administration of deglycosylated LRG1 in a diabetic mouse model ameliorated vascular and neurological abnormalities and restored erectile function. Collectively, these data indicate a novel role of LRG1 glycans as molecular switches that can tune the range of LRG1's cellular functions, particularly the LRG1/LPHN2 signaling axis.
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Affiliation(s)
- Jimin Yang
- Center for Biomolecular and Cellular Structure, Institute for Basic Science (IBS), Daejeon, 34126, Republic of Korea
| | - Guo Nan Yin
- National Research Center for Sexual Medicine and Department of Urology, Inha University School of Medicine, Incheon, 22332, Republic of Korea
| | - Do-Kyun Kim
- Center for Biomolecular and Cellular Structure, Institute for Basic Science (IBS), Daejeon, 34126, Republic of Korea
- Korea Zoonosis Research Institute, Jeonbuk National University, Iksan, 54596, Republic of Korea
| | - Ah-Reum Han
- Center for Biomolecular and Cellular Structure, Institute for Basic Science (IBS), Daejeon, 34126, Republic of Korea
| | - Dong Sun Lee
- Center for Biomolecular and Cellular Structure, Institute for Basic Science (IBS), Daejeon, 34126, Republic of Korea
| | - Kwang Wook Min
- Center for Biomolecular and Cellular Structure, Institute for Basic Science (IBS), Daejeon, 34126, Republic of Korea
| | - Yaoyao Fu
- Center for Biomolecular and Cellular Structure, Institute for Basic Science (IBS), Daejeon, 34126, Republic of Korea
| | - Jeongwon Yun
- Graduate School of Medical Science & Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
| | - Jun-Kyu Suh
- National Research Center for Sexual Medicine and Department of Urology, Inha University School of Medicine, Incheon, 22332, Republic of Korea.
| | - Ji-Kan Ryu
- National Research Center for Sexual Medicine and Department of Urology, Inha University School of Medicine, Incheon, 22332, Republic of Korea.
| | - Ho Min Kim
- Center for Biomolecular and Cellular Structure, Institute for Basic Science (IBS), Daejeon, 34126, Republic of Korea.
- Graduate School of Medical Science & Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea.
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10
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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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11
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Jo Y, Woo JS, Lee AR, Lee SY, Shin Y, Lee LP, Cho ML, Kang T. Inner-Membrane-Bound Gold Nanoparticles as Efficient Electron Transfer Mediators for Enhanced Mitochondrial Electron Transport Chain Activity. NANO LETTERS 2022; 22:7927-7935. [PMID: 36137175 DOI: 10.1021/acs.nanolett.2c02957] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Electron transfer through the mitochondrial electron transport chain (ETC) can be critically blocked by the dysfunction of protein complexes. Redox-active molecules have been used to mediate the electron transfer in place of the dysfunctional complexes; however, they are limited to replacing complex I and are known to be toxic. Here we report artificial mitochondrial electron transfer pathways that enhance ETC activity by exploiting inner-membrane-bound gold nanoparticles (GNPs) as efficient electron transfer mediators. The hybridization of mitochondria with GNPs, driven by electrostatic interaction, is successfully visualized in real time at the level of a single mitochondrion. By observing quantized quenching dips via plasmon resonance energy transfer, we reveal that the hybridized GNPs are bound to the inner membrane of mitochondria irrespective of the presence of the outer membrane. The ETC activity of mitochondria with GNPs such as membrane potential, oxygen consumption, and ATP production is remarkably increased in vitro.
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Affiliation(s)
- Yuseung Jo
- Department of Chemical and Biomolecular Engineering, Sogang University, Seoul 04107, Korea
| | - Jin Seok Woo
- Rheumatism Research Center, College of Medicine, Catholic Research Institute of Medical Science, The Catholic University of Korea, Seoul 06591, Korea
| | - A Ram Lee
- Rheumatism Research Center, College of Medicine, Catholic Research Institute of Medical Science, The Catholic University of Korea, Seoul 06591, Korea
- Department of Biomedicine & Health Sciences, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea
| | - Seon-Yeong Lee
- Rheumatism Research Center, College of Medicine, Catholic Research Institute of Medical Science, The Catholic University of Korea, Seoul 06591, Korea
| | - Yonghee Shin
- Department of Chemical and Biomolecular Engineering, Sogang University, Seoul 04107, Korea
| | - Luke P Lee
- Harvard Medical School, Harvard University; Renal Division and Division of Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts 02115, United States
- Department of Bioengineering, and Department of Electrical Engineering and Computer Science, University of California, Berkeley, Berkeley, California 94720, United States
- Institute of Quantum Biophysics, Department of Biophysics, Sungkyunkwan University, Suwon 16419, Korea
| | - Mi-La Cho
- Department of Biomedicine & Health Sciences, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea
- Department of Medical Life Scieneces, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea
| | - Taewook Kang
- Department of Chemical and Biomolecular Engineering, Sogang University, Seoul 04107, Korea
- Institute of Integrated Biotechnology, Sogang University, Seoul 04107, Korea
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12
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Feng Y, Liu XC, Li L, Gao SQ, Wen GB, Lin YW. Naturally Occurring I81N Mutation in Human Cytochrome c Regulates Both Inherent Peroxidase Activity and Interactions with Neuroglobin. ACS OMEGA 2022; 7:11510-11518. [PMID: 35415373 PMCID: PMC8992277 DOI: 10.1021/acsomega.2c01256] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 03/14/2022] [Indexed: 05/24/2023]
Abstract
Human cytochrome c (hCyt c) is a crucial heme protein and plays an indispensable role in energy conversion and intrinsic apoptosis pathways. The sequence and structure of Cyt c were evolutionarily conserved and only a few naturally occurring mutants were detected in humans. Among those variable sites, position 81 was proposed to act as a peroxidase switch in the initiation stages of apoptosis. In this study, we show that Ile81 not only suppresses the intrinsic peroxidase activity but also is essential for Cyt c to interact with neuroglobin (Ngb), a potential protein partner. The kinetic assays showed that the peroxidase activity of the naturally occurring variant I81N was enhanced up to threefold under pH 5. The local stability of the Ω-loop D (residues 70-85) in the I81N variant was decreased. Moreover, the Alphafold2 program predicted that Ile81 forms stable contact with human Ngb. Meanwhile, the Ile81 to Asn81 missense mutation abolishes the interaction interface, resulting in a ∼40-fold decrease in binding affinity. These observations provide an insight into the structure-function relationship of the conserved Ile81 in vertebrate Cyt c.
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Affiliation(s)
- Yu Feng
- 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
| | - Lianzhi Li
- School
of Chemistry and Chemical Engineering, Liaocheng
University, Liaocheng 252059, China
| | - Shu-Qin Gao
- Key
Lab of Protein Structure and Function of Universities in Hunan Province, University of South China, Hengyang 421001, China
| | - Ge-Bo Wen
- Key
Lab of Protein Structure and Function of Universities in Hunan Province, University of South China, Hengyang 421001, China
| | - Ying-Wu Lin
- School
of Chemistry and Chemical Engineering, University
of South China, Hengyang 421001, China
- Key
Lab of Protein Structure and Function of Universities in Hunan Province, University of South China, Hengyang 421001, China
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13
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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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14
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Samsri S, Prasertsuk P, Nutho B, Pornsuwan S. Molecular insights on the conformational dynamics of a P76C mutant of human cytochrome c and the enhancement on its peroxidase activity. Arch Biochem Biophys 2021; 716:109112. [PMID: 34954215 DOI: 10.1016/j.abb.2021.109112] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 12/17/2021] [Accepted: 12/20/2021] [Indexed: 11/16/2022]
Abstract
In apoptotic pathway, the interaction of Cytochrome c (Cytc) with cardiolipin in vivo is a key process to induce peroxidase activity of Cytc and trigger the release of Cytc in the inner mitochondria into cytosol. The peroxidase active form of Cytc occurs due to local conformational changes that support the opening of the heme crevice and the loss of an axial ligand between Met80 and heme Fe. Structural adjustments at the Ω-loop segments of Cytc are required for such process. To study the role of the distal Ω-loop segments comprising residues 71-85 in human Cytc (hCytc), we investigated a cysteine mutation at Pro76, one of the highly conserved residues in this loop. The effect of P76C mutant was explored by the combination of experimental characterizations and molecular dynamics (MD) simulations. The peroxidase activity of the P76C mutant was found to be significantly increased by ∼13 folds relative to the wild type. Experimental data on global denaturation, alkaline transition, heme bleaching, and spin-labeling Electron Spin Resonance were in good agreement with the enhancement of peroxidase activity. The MD results of hCytc in the hexacoordinate form suggest the important changes in P76C mutant occurred due to the unfolding at the central Ω-loop (residues 40-57), and the weakening of H-bond between Tyr67 and Met80. Whereas the experimental data implied that the P76C mutant tend to be in equilibrium between the pentacoordinate and hexacoordinate forms, the MD and experimental information are complementary and were used to support the mechanisms of peroxidase active form of hCytc.
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Affiliation(s)
- Sasiprapa Samsri
- Department of Chemistry and Center of Excellence for Innovation in Chemistry, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand
| | - Possawee Prasertsuk
- Department of Chemistry and Center of Excellence for Innovation in Chemistry, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand
| | - Bodee Nutho
- Department of Pharmacology, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand.
| | - Soraya Pornsuwan
- Department of Chemistry and Center of Excellence for Innovation in Chemistry, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand.
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15
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Pessoa J. Prospective antibacterial inhibition of c-type cytochrome synthesis. Trends Mol Med 2021; 27:928-930. [PMID: 34303616 DOI: 10.1016/j.molmed.2021.07.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 07/08/2021] [Accepted: 07/12/2021] [Indexed: 11/13/2022]
Abstract
Sutherland et al. recently reported the in vitro inhibition of Helicobacter hepaticus cytochrome c (cyt c) synthase, which may inactivate c-type cytochromes in this and in other pathogenic bacteria. Here, I discuss the impact of this work, which identifies this conserved synthase as a potential antibacterial target.
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Affiliation(s)
- João Pessoa
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal.
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16
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Altered structure and dynamics of pathogenic cytochrome c variants correlate with increased apoptotic activity. Biochem J 2021; 478:669-684. [PMID: 33480393 DOI: 10.1042/bcj20200793] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Revised: 01/17/2021] [Accepted: 01/21/2021] [Indexed: 01/16/2023]
Abstract
Mutation of cytochrome c in humans causes mild autosomal dominant thrombocytopenia. The role of cytochrome c in platelet formation, and the molecular mechanism underlying the association of cytochrome c mutations with thrombocytopenia remains unknown, although a gain-of-function is most likely. Cytochrome c contributes to several cellular processes, with an exchange between conformational states proposed to regulate changes in function. Here, we use experimental and computational approaches to determine whether pathogenic variants share changes in structure and function, and to understand how these changes might occur. Three pathogenic variants (G41S, Y48H, A51V) cause an increase in apoptosome activation and peroxidase activity. Molecular dynamics simulations of these variants, and two non-naturally occurring variants (G41A, G41T), indicate that increased apoptosome activation correlates with the increased overall flexibility of cytochrome c, particularly movement of the Ω loops. Crystal structures of Y48H and G41T complement these studies which overall suggest that the binding of cytochrome c to apoptotic protease activating factor-1 (Apaf-1) may involve an 'induced fit' mechanism which is enhanced in the more conformationally mobile variants. In contrast, peroxidase activity did not significantly correlate with protein dynamics. Thus, the mechanism by which the variants increase peroxidase activity is not related to the conformational dynamics of the native hexacoordinate state of cytochrome c. Recent molecular dynamics data proposing conformational mobility of specific cytochrome c regions underpins changes in reduction potential and alkaline transition pK was not fully supported. These data highlight that conformational dynamics of cytochrome c drive some but not all of its properties and activities.
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17
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Kotrasová V, Keresztesová B, Ondrovičová G, Bauer JA, Havalová H, Pevala V, Kutejová E, Kunová N. Mitochondrial Kinases and the Role of Mitochondrial Protein Phosphorylation in Health and Disease. Life (Basel) 2021; 11:life11020082. [PMID: 33498615 PMCID: PMC7912454 DOI: 10.3390/life11020082] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 01/19/2021] [Accepted: 01/20/2021] [Indexed: 02/07/2023] Open
Abstract
The major role of mitochondria is to provide cells with energy, but no less important are their roles in responding to various stress factors and the metabolic changes and pathological processes that might occur inside and outside the cells. The post-translational modification of proteins is a fast and efficient way for cells to adapt to ever changing conditions. Phosphorylation is a post-translational modification that signals these changes and propagates these signals throughout the whole cell, but it also changes the structure, function and interaction of individual proteins. In this review, we summarize the influence of kinases, the proteins responsible for phosphorylation, on mitochondrial biogenesis under various cellular conditions. We focus on their role in keeping mitochondria fully functional in healthy cells and also on the changes in mitochondrial structure and function that occur in pathological processes arising from the phosphorylation of mitochondrial proteins.
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Affiliation(s)
- Veronika Kotrasová
- Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská Cesta 21, 845 51 Bratislava, Slovakia; (V.K.); (B.K.); (G.O.); (J.A.B.); (H.H.); (V.P.)
| | - Barbora Keresztesová
- Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská Cesta 21, 845 51 Bratislava, Slovakia; (V.K.); (B.K.); (G.O.); (J.A.B.); (H.H.); (V.P.)
- First Faculty of Medicine, Institute of Biology and Medical Genetics, Charles University, 128 00 Prague, Czech Republic
| | - Gabriela Ondrovičová
- Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská Cesta 21, 845 51 Bratislava, Slovakia; (V.K.); (B.K.); (G.O.); (J.A.B.); (H.H.); (V.P.)
| | - Jacob A. Bauer
- Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská Cesta 21, 845 51 Bratislava, Slovakia; (V.K.); (B.K.); (G.O.); (J.A.B.); (H.H.); (V.P.)
| | - Henrieta Havalová
- Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská Cesta 21, 845 51 Bratislava, Slovakia; (V.K.); (B.K.); (G.O.); (J.A.B.); (H.H.); (V.P.)
| | - Vladimír Pevala
- Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská Cesta 21, 845 51 Bratislava, Slovakia; (V.K.); (B.K.); (G.O.); (J.A.B.); (H.H.); (V.P.)
| | - Eva Kutejová
- Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská Cesta 21, 845 51 Bratislava, Slovakia; (V.K.); (B.K.); (G.O.); (J.A.B.); (H.H.); (V.P.)
- Correspondence: (E.K.); (N.K.)
| | - Nina Kunová
- Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská Cesta 21, 845 51 Bratislava, Slovakia; (V.K.); (B.K.); (G.O.); (J.A.B.); (H.H.); (V.P.)
- First Faculty of Medicine, Institute of Biology and Medical Genetics, Charles University, 128 00 Prague, Czech Republic
- Correspondence: (E.K.); (N.K.)
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18
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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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19
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Osmotic pressure effects identify dehydration upon cytochrome c-cytochrome c oxidase complex formation contributing to a specific electron pathway formation. Biochem J 2020; 477:1565-1578. [PMID: 32250438 DOI: 10.1042/bcj20200023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 03/27/2020] [Accepted: 04/06/2020] [Indexed: 01/18/2023]
Abstract
In the electron transfer (ET) reaction from cytochrome c (Cyt c) to cytochrome c oxidase (CcO), we determined the number and sites of the hydration water released from the protein surface upon the formation of the ET complex by evaluating the osmotic pressure dependence of kinetics for the ET from Cyt c to CcO. We identified that ∼20 water molecules were dehydrated in complex formation under turnover conditions, and systematic Cyt c mutations in the interaction site for CcO revealed that nearly half of the released hydration water during the complexation were located around Ile81, one of the hydrophobic amino acid residues near the exposed heme periphery of Cyt c. Such a dehydration dominantly compensates for the entropy decrease due to the association of Cyt c with CcO, resulting in the entropy-driven ET reaction. The energetic analysis of the interprotein interactions in the ET complex predicted by the docking simulation suggested the formation of hydrophobic interaction sites surrounding the exposed heme periphery of Cyt c in the Cyt c-CcO interface (a 'molecular breakwater'). Such sites would contribute to the formation of the hydrophobic ET pathway from Cyt c to CcO by blocking water access from the bulk water phase.
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20
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Cytochrome c modification and oligomerization induced by cardiolipin hydroperoxides in a membrane mimetic model. Arch Biochem Biophys 2020; 693:108568. [DOI: 10.1016/j.abb.2020.108568] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Revised: 08/10/2020] [Accepted: 08/27/2020] [Indexed: 12/31/2022]
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21
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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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22
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Steele HBB, Elmer-Dixon MM, Rogan JT, Ross JBA, Bowler BE. The Human Cytochrome c Domain-Swapped Dimer Facilitates Tight Regulation of Intrinsic Apoptosis. Biochemistry 2020; 59:2055-2068. [PMID: 32428404 PMCID: PMC7291863 DOI: 10.1021/acs.biochem.0c00326] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Oxidation of cardiolipin (CL) by cytochrome c (cytc) has been proposed to initiate the intrinsic pathway of apoptosis. Domain-swapped dimer (DSD) conformations of cytc have been reported both by our laboratory and by others. The DSD is an alternate conformer of cytc that could oxygenate CL early in apoptosis. We demonstrate here that the cytc DSD has a set of properties that would provide tighter regulation of the intrinsic pathway. We show that the human DSD is kinetically more stable than horse and yeast DSDs. Circular dichroism data indicate that the DSD has a less asymmetric heme environment, similar to that seen when the monomeric protein binds to CL vesicles at high lipid:protein ratios. The dimer undergoes the alkaline conformational transition near pH 7.0, 2.5 pH units lower than that of the monomer. Data from fluorescence correlation spectroscopy and fluorescence anisotropy suggest that the alkaline transition of the DSD may act as a switch from a high affinity for CL nanodiscs at pH 7.4 to a much lower affinity at pH 8.0. Additionally, the peroxidase activity of the human DSD increases 7-fold compared to that of the monomer at pH 7 and 8, but by 14-fold at pH 6 when mixed Met80/H2O ligation replaces the lysine ligation of the alkaline state. We also present data that indicate that cytc binding shows a cooperative effect as the concentration of cytc is increased. The DSD appears to have evolved into a pH-inducible switch that provides a means to control activation of apoptosis near pH 7.0.
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Affiliation(s)
- Harmen B. B. Steele
- Department of Chemistry & Biochemistry, University of Montana, Missoula, Montana 59812, United States
- Center for Biomolecular Structure & Dynamics, University of Montana, Missoula, Montana 59812, United States
| | - Margaret M. Elmer-Dixon
- Department of Chemistry & Biochemistry, University of Montana, Missoula, Montana 59812, United States
- Center for Biomolecular Structure & Dynamics, University of Montana, Missoula, Montana 59812, United States
| | - James T. Rogan
- Department of Chemistry & Biochemistry, University of Montana, Missoula, Montana 59812, United States
| | - J. B. Alexander Ross
- Department of Chemistry & Biochemistry, University of Montana, Missoula, Montana 59812, United States
- Center for Biomolecular Structure & Dynamics, University of Montana, Missoula, Montana 59812, United States
| | - Bruce E. Bowler
- Department of Chemistry & Biochemistry, University of Montana, Missoula, Montana 59812, United States
- Center for Biomolecular Structure & Dynamics, University of Montana, Missoula, Montana 59812, United States
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23
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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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24
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Comparison of the structural dynamic and mitochondrial electron-transfer properties of the proapoptotic human cytochrome c variants, G41S, Y48H and A51V. J Inorg Biochem 2020; 203:110924. [DOI: 10.1016/j.jinorgbio.2019.110924] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 11/08/2019] [Accepted: 11/12/2019] [Indexed: 01/02/2023]
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25
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Buhrke D, Hildebrandt P. Probing Structure and Reaction Dynamics of Proteins Using Time-Resolved Resonance Raman Spectroscopy. Chem Rev 2019; 120:3577-3630. [PMID: 31814387 DOI: 10.1021/acs.chemrev.9b00429] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The mechanistic understanding of protein functions requires insight into the structural and reaction dynamics. To elucidate these processes, a variety of experimental approaches are employed. Among them, time-resolved (TR) resonance Raman (RR) is a particularly versatile tool to probe processes of proteins harboring cofactors with electronic transitions in the visible range, such as retinal or heme proteins. TR RR spectroscopy offers the advantage of simultaneously providing molecular structure and kinetic information. The various TR RR spectroscopic methods can cover a wide dynamic range down to the femtosecond time regime and have been employed in monitoring photoinduced reaction cascades, ligand binding and dissociation, electron transfer, enzymatic reactions, and protein un- and refolding. In this account, we review the achievements of TR RR spectroscopy of nearly 50 years of research in this field, which also illustrates how the role of TR RR spectroscopy in molecular life science has changed from the beginning until now. We outline the various methodological approaches and developments and point out current limitations and potential perspectives.
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Affiliation(s)
- David Buhrke
- Technische Universität Berlin, Institut für Chemie, Sekr. PC14, Straße des 17, Juni 135, D-10623 Berlin, Germany
| | - Peter Hildebrandt
- Technische Universität Berlin, Institut für Chemie, Sekr. PC14, Straße des 17, Juni 135, D-10623 Berlin, Germany
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26
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Regulation of Respiration and Apoptosis by Cytochrome c Threonine 58 Phosphorylation. Sci Rep 2019; 9:15815. [PMID: 31676852 PMCID: PMC6825195 DOI: 10.1038/s41598-019-52101-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 10/02/2019] [Indexed: 12/16/2022] Open
Abstract
Cytochrome c (Cytc) is a multifunctional protein, acting as an electron carrier in the electron transport chain (ETC), where it shuttles electrons from bc1 complex to cytochrome c oxidase (COX), and as a trigger of type II apoptosis when released from the mitochondria. We previously showed that Cytc is regulated in a highly tissue-specific manner: Cytc isolated from heart, liver, and kidney is phosphorylated on Y97, Y48, and T28, respectively. Here, we have analyzed the effect of a new Cytc phosphorylation site, threonine 58, which we mapped in rat kidney Cytc by mass spectrometry. We generated and overexpressed wild-type, phosphomimetic T58E, and two controls, T58A and T58I Cytc; the latter replacement is found in human and testis-specific Cytc. In vitro, COX activity, caspase-3 activity, and heme degradation in the presence of H2O2 were decreased with phosphomimetic Cytc compared to wild-type. Cytc-knockout cells expressing T58E or T58I Cytc showed a reduction in intact cell respiration, mitochondrial membrane potential (∆Ψm), ROS production, and apoptotic activity compared to wild-type. We propose that, under physiological conditions, Cytc is phosphorylated, which controls mitochondrial respiration and apoptosis. Under conditions of stress Cytc phosphorylations are lost leading to maximal respiration rates, ∆Ψm hyperpolarization, ROS production, and apoptosis.
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27
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Lei H, Bowler BE. Naturally Occurring A51V Variant of Human Cytochrome c Destabilizes the Native State and Enhances Peroxidase Activity. J Phys Chem B 2019; 123:8939-8953. [PMID: 31557440 DOI: 10.1021/acs.jpcb.9b05869] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The A51V variant of human cytochrome c is linked to thrombocytopenia 4 (THC4), a condition that causes decreased blood platelet counts. A 1.82 Å structure of the A51V variant shows only minor changes in tertiary structure relative to the wild-type (WT) protein. Guanidine hydrochloride denaturation demonstrates that the global stability of the A51V variant is 1.3 kcal/mol less than that of the WT protein. The midpoint pH, pH1/2, of the alkaline transition of the A51V variant is 1 unit less than that of the WT protein. Stopped-flow pH jump experiments show that the A51V substitution affects the triggering ionization for one of two kinetically distinguishable alkaline conformers and enhances the accessibility of a high-spin heme transient. The pH1/2 for acid unfolding of the A51V variant is 0.7 units higher than for that of the WT protein. Consistent with the greater accessibility of non-native conformers for the A51V variant, the kcat values for its peroxidase activity increase by 6- to 15-fold in the pH range of 5-8 versus those of the WT protein. These data along with previously reported data for the other THC4-linked variants, G41S and Y48H, underscore the role of Ω-loop C (residues 40-57) in modulating the peroxidase activity of cytochrome c early in apoptosis.
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Affiliation(s)
- Haotian Lei
- Department of Chemistry and Biochemistry, Center for Bimolecular Structure and Dynamics , University of Montana , Missoula , Montana 59812 , United States
| | - Bruce E Bowler
- Department of Chemistry and Biochemistry, Center for Bimolecular Structure and Dynamics , University of Montana , Missoula , Montana 59812 , United States
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28
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Lamiable A, Bitard-Feildel T, Rebehmed J, Quintus F, Schoentgen F, Mornon JP, Callebaut I. A topology-based investigation of protein interaction sites using Hydrophobic Cluster Analysis. Biochimie 2019; 167:68-80. [PMID: 31525399 DOI: 10.1016/j.biochi.2019.09.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 09/11/2019] [Indexed: 01/20/2023]
Abstract
Hydrophobic clusters, as defined by Hydrophobic Cluster Analysis (HCA), are conditioned binary patterns, made of hydrophobic and non-hydrophobic positions, whose limits fit well those of regular secondary structures. They were proved to be useful for predicting secondary structures in proteins from the only information of a single amino acid sequence and have permitted to assess, in a comprehensive way, the leading role of binary patterns in secondary structure preference towards a particular state. Here, we considered the available experimental 3D structures of protein globular domains to enlarge our previously reported hydrophobic cluster database (HCDB), almost doubling the number of hydrophobic cluster species (each species being defined by a unique binary pattern) that represent the most frequent structural bricks encountered within protein globular domains. We then used this updated HCDB to show that the hydrophobic amino acids of discordant clusters, i.e. those less abundant clusters for which the observed secondary structure is in disagreement with the binary pattern preference of the species to which they belong, are more exposed to solvent and are more involved in protein interfaces than the hydrophobic amino acids of concordant clusters. As amino acid composition differs between concordant/discordant clusters, considering binary patterns may be used to gain novel insights into key features of protein globular domain cores and surfaces. It can also provide useful information on possible conformational plasticity, including disorder to order transitions.
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Affiliation(s)
- Alexis Lamiable
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, 75005, Paris, France
| | - Tristan Bitard-Feildel
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, 75005, Paris, France
| | - Joseph Rebehmed
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, 75005, Paris, France; Lebanese American University, Department of Computer Science and Mathematics, Beirut, Lebanon
| | - Flavien Quintus
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, 75005, Paris, France
| | - Françoise Schoentgen
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, 75005, Paris, France
| | - Jean-Paul Mornon
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, 75005, Paris, France
| | - Isabelle Callebaut
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, 75005, Paris, France.
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Lei H, Nold SM, Motta LJ, Bowler BE. Effect of V83G and I81A Substitutions to Human Cytochrome c on Acid Unfolding and Peroxidase Activity below a Neutral pH. Biochemistry 2019; 58:2921-2933. [DOI: 10.1021/acs.biochem.9b00295] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Haotian Lei
- Department of Chemistry and Biochemistry, University of Montana, Missoula, Montana 59812, United States
- Center for Biomolecular Structure and Dynamics, University of Montana, Missoula, Montana 59812, United States
| | - Shiloh M. Nold
- Department of Chemistry and Biochemistry, University of Montana, Missoula, Montana 59812, United States
| | - Luis Jung Motta
- Department of Chemistry and Biochemistry, University of Montana, Missoula, Montana 59812, United States
| | - Bruce E. Bowler
- Department of Chemistry and Biochemistry, University of Montana, Missoula, Montana 59812, United States
- Center for Biomolecular Structure and Dynamics, University of Montana, Missoula, Montana 59812, United States
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30
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Svistunenko DA, Manole A. Tyrosyl radical in haemoglobin and haptoglobin-haemoglobin complex: how does haptoglobin make haemoglobin less toxic? J Biomed Res 2019; 34:281-291. [PMID: 32475850 PMCID: PMC7386409 DOI: 10.7555/jbr.33.20180084] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
One of the difficulties in creating a blood substitute on the basis of human haemoglobin (Hb) is the toxic nature of Hb when it is outside the safe environment of the red blood cells. The plasma protein haptoglobin (Hp) takes care of the Hb physiologically leaked into the plasma – it binds Hb and makes it much less toxic while retaining the Hb's high oxygen transporting capacity. We used Electron Paramagnetic Resonance (EPR) spectroscopy to show that the protein bound radical induced by H2O2 in Hb and Hp-Hb complex is formed on the same tyrosine residue(s), but, in the complex, the radical is found in a more hydrophobic environment and decays slower than in unbound Hb, thus mitigating its oxidative capacity. The data obtained in this study might set new directions in engineering blood substitutes for transfusion that would have the oxygen transporting efficiency typical of Hb, but which would be non-toxic.
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Affiliation(s)
- Dimitri A Svistunenko
- Biomedical EPR Facility, School of Life Sciences, University of Essex, Colchester, Essex CO4 3SQ, UK
| | - Andreea Manole
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
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31
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Chaplin AK, Chicano TM, Hampshire BV, Wilson MT, Hough MA, Svistunenko DA, Worrall JAR. An Aromatic Dyad Motif in Dye Decolourising Peroxidases Has Implications for Free Radical Formation and Catalysis. Chemistry 2019; 25:6141-6153. [PMID: 30945782 DOI: 10.1002/chem.201806290] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Indexed: 01/27/2023]
Abstract
Dye decolouring peroxidases (DyPs) are the most recent class of heme peroxidase to be discovered. On reacting with H2 O2 , DyPs form a high-valent iron(IV)-oxo species and a porphyrin radical (Compound I) followed by stepwise oxidation of an organic substrate. In the absence of substrate, the ferryl species decays to form transient protein-bound radicals on redox active amino acids. Identification of radical sites in DyPs has implications for their oxidative mechanism with substrate. Using a DyP from Streptomyces lividans, referred to as DtpA, which displays low reactivity towards synthetic dyes, activation with H2 O2 was explored. A Compound I EPR spectrum was detected, which in the absence of substrate decays to a protein-bound radical EPR signal. Using a newly developed version of the Tyrosyl Radical Spectra Simulation Algorithm, the radical EPR signal was shown to arise from a pristine tyrosyl radical and not a mixed Trp/Tyr radical that has been widely reported in DyP members exhibiting high activity with synthetic dyes. The radical site was identified as Tyr374, with kinetic studies inferring that although Tyr374 is not on the electron-transfer pathway from the dye RB19, its replacement with a Phe does severely compromise activity with other organic substrates. These findings hint at the possibility that alternative electron-transfer pathways for substrate oxidation are operative within the DyP family. In this context, a role for a highly conserved aromatic dyad motif is discussed.
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Affiliation(s)
- Amanda K Chaplin
- Present address: Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Tadeo Moreno Chicano
- Present address: Department of Molecular Mechanisms, Max Planck Institute for Medical Research, Jahnstraße 29, 69120, Heidelberg, Germany
| | - Bethany V Hampshire
- Present address: Department of Physics, University of Warwick, Coventry, CV4 7AL, UK
| | - Michael T Wilson
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK
| | - Michael A Hough
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK
| | - Dimitri A Svistunenko
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK
| | - Jonathan A R Worrall
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK
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32
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Kalpage HA, Bazylianska V, Recanati MA, Fite A, Liu J, Wan J, Mantena N, Malek MH, Podgorski I, Heath EI, Vaishnav A, Edwards BF, Grossman LI, Sanderson TH, Lee I, Hüttemann M. Tissue-specific regulation of cytochrome c by post-translational modifications: respiration, the mitochondrial membrane potential, ROS, and apoptosis. FASEB J 2019; 33:1540-1553. [PMID: 30222078 PMCID: PMC6338631 DOI: 10.1096/fj.201801417r] [Citation(s) in RCA: 142] [Impact Index Per Article: 28.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 08/14/2018] [Indexed: 02/02/2023]
Abstract
Cytochrome c (Cyt c) plays a vital role in the mitochondrial electron transport chain (ETC). In addition, it is a key regulator of apoptosis. Cyt c has multiple other functions including ROS production and scavenging, cardiolipin peroxidation, and mitochondrial protein import. Cyt c is tightly regulated by allosteric mechanisms, tissue-specific isoforms, and post-translational modifications (PTMs). Distinct residues of Cyt c are modified by PTMs, primarily phosphorylations, in a highly tissue-specific manner. These modifications downregulate mitochondrial ETC flux and adjust the mitochondrial membrane potential (ΔΨm), to minimize reactive oxygen species (ROS) production under normal conditions. In pathologic and acute stress conditions, such as ischemia-reperfusion, phosphorylations are lost, leading to maximum ETC flux, ΔΨm hyperpolarization, excessive ROS generation, and the release of Cyt c. It is also the dephosphorylated form of the protein that leads to maximum caspase activation. We discuss the complex regulation of Cyt c and propose that it is a central regulatory step of the mammalian ETC that can be rate limiting in normal conditions. This regulation is important because it maintains optimal intermediate ΔΨm, limiting ROS generation. We examine the role of Cyt c PTMs, including phosphorylation, acetylation, methylation, nitration, nitrosylation, and sulfoxidation and consider their potential biological significance by evaluating their stoichiometry.-Kalpage, H. A., Bazylianska, V., Recanati, M. A., Fite, A., Liu, J., Wan, J., Mantena, N., Malek, M. H., Podgorski, I., Heath, E. I., Vaishnav, A., Edwards, B. F., Grossman, L. I., Sanderson, T. H., Lee, I., Hüttemann, M. Tissue-specific regulation of cytochrome c by post-translational modifications: respiration, the mitochondrial membrane potential, ROS, and apoptosis.
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Affiliation(s)
- Hasini A. Kalpage
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Wayne State University, Detroit, Michigan, USA
| | - Viktoriia Bazylianska
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Wayne State University, Detroit, Michigan, USA
- Department of Biochemistry, Microbiology, and Immunology, Wayne State University School of Medicine, Wayne State University, Detroit, Michigan, USA
| | - Maurice A. Recanati
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Wayne State University, Detroit, Michigan, USA
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Wayne State University, Detroit, Michigan, USA
| | - Alemu Fite
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Wayne State University, Detroit, Michigan, USA
| | - Jenney Liu
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Wayne State University, Detroit, Michigan, USA
| | - Junmei Wan
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Wayne State University, Detroit, Michigan, USA
- Department of Biochemistry, Microbiology, and Immunology, Wayne State University School of Medicine, Wayne State University, Detroit, Michigan, USA
| | - Nikhil Mantena
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Wayne State University, Detroit, Michigan, USA
| | - Moh H. Malek
- Department of Health Care Sciences, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, Detroit, Michigan, USA
- Cardiovascular Research Institute, Wayne State University School of Medicine, Wayne State University, Detroit, Michigan, USA
| | - Izabela Podgorski
- Department of Pharmacology, Wayne State University School of Medicine, Wayne State University, Detroit, Michigan, USA
| | - Elizabeth I. Heath
- Department of Oncology, Karmanos Cancer Institute, Wayne State University School of Medicine, Wayne State University, Detroit, Michigan, USA
| | - Asmita Vaishnav
- Department of Biochemistry, Microbiology, and Immunology, Wayne State University School of Medicine, Wayne State University, Detroit, Michigan, USA
| | - Brian F. Edwards
- Department of Biochemistry, Microbiology, and Immunology, Wayne State University School of Medicine, Wayne State University, Detroit, Michigan, USA
| | - Lawrence I. Grossman
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Wayne State University, Detroit, Michigan, USA
| | - Thomas H. Sanderson
- Cardiovascular Research Institute, Wayne State University School of Medicine, Wayne State University, Detroit, Michigan, USA
- Department of Emergency Medicine, University of Michigan Medical School, University of Michigan, Ann Arbor, Michigan, USA
- Department of Molecular and Integrative Physiology, University of Michigan Medical School, University of Michigan, Ann Arbor, Michigan, USA
| | - Icksoo Lee
- College of Medicine, Dankook University, Cheonan-si, Chungcheongnam-do, South Korea
| | - Maik Hüttemann
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Wayne State University, Detroit, Michigan, USA
- Department of Biochemistry, Microbiology, and Immunology, Wayne State University School of Medicine, Wayne State University, Detroit, Michigan, USA
- Cardiovascular Research Institute, Wayne State University School of Medicine, Wayne State University, Detroit, Michigan, USA
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33
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Ledgerwood EC, Dunstan-Harrison C, Ong L, Morison IM. CYCS gene variants associated with thrombocytopenia. Platelets 2018; 30:672-674. [PMID: 30452302 DOI: 10.1080/09537104.2018.1543866] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Elizabeth C Ledgerwood
- a Department of Biochemistry, School of Biomedical Sciences , University of Otago , Dunedin , New Zealand
| | - Caitlin Dunstan-Harrison
- a Department of Biochemistry, School of Biomedical Sciences , University of Otago , Dunedin , New Zealand
| | - Lily Ong
- a Department of Biochemistry, School of Biomedical Sciences , University of Otago , Dunedin , New Zealand
| | - Ian M Morison
- b Department of Pathology, Dunedin School of Medicine , University of Otago , Dunedin , New Zealand
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34
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Tomášková N, Varhač R, Lysáková V, Musatov A, Sedlák E. Peroxidase activity of cytochrome c in its compact state depends on dynamics of the heme region. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2018; 1866:1073-1083. [DOI: 10.1016/j.bbapap.2018.09.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 09/06/2018] [Accepted: 09/10/2018] [Indexed: 10/28/2022]
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35
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Uchiyama Y, Yanagisawa K, Kunishima S, Shiina M, Ogawa Y, Nakashima M, Hirato J, Imagawa E, Fujita A, Hamanaka K, Miyatake S, Mitsuhashi S, Takata A, Miyake N, Ogata K, Handa H, Matsumoto N, Mizuguchi T. A novel CYCS mutation in the α-helix of the CYCS C-terminal domain causes non-syndromic thrombocytopenia. Clin Genet 2018; 94:548-553. [PMID: 30051457 DOI: 10.1111/cge.13423] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 07/20/2018] [Accepted: 07/24/2018] [Indexed: 12/28/2022]
Abstract
We report a patient with thrombocytopenia from a Japanese family with hemophilia A spanning four generations. Various etiologies of thrombocytopenia, including genetic, immunological, and hematopoietic abnormalities, determine the prognosis for this disease. In this study, we identified a novel heterozygous mutation in a gene encoding cytochrome c, somatic (CYCS, MIM123970) using whole exome sequencing. This variant (c.301_303del:p.Lys101del) is located in the α-helix of the cytochrome c (CYCS) C-terminal domain. In silico structural analysis suggested that this mutation results in protein folding instability. CYCS is one of the key factors regulating the intrinsic apoptotic pathway and the mitochondrial respiratory chain. Using the yeast model system, we clearly demonstrated that this one amino acid deletion (in-frame) resulted in significantly reduced cytochrome c protein expression and functional defects in the mitochondrial respiratory chain, indicating that the loss of function of cytochrome c underlies thrombocytopenia. The clinical features of known CYCS variants have been reported to be confined to mild or asymptomatic thrombocytopenia, as was observed for the patient in our study. This study clearly demonstrates that thrombocytopenia can result from CYCS loss-of-function variants.
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Affiliation(s)
- Yuri Uchiyama
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan.,Department of Oncology, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Kunio Yanagisawa
- Department of Hematology, Gunma University Graduate School of Medicine, Maebashi, Japan
| | - Shinji Kunishima
- Department of Medical Technology, Gifu University of Medical Science, Seki, Japan
| | - Masaaki Shiina
- Department of Biochemistry, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Yoshiyuki Ogawa
- Department of Hematology, Gunma University Graduate School of Medicine, Maebashi, Japan
| | - Mitsuko Nakashima
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan.,Department of Biochemistry, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Junko Hirato
- Department of Pathology, Gunma University Hospital, Maebashi, Japan
| | - Eri Imagawa
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Atsushi Fujita
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Kohei Hamanaka
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Satoko Miyatake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan.,Clinical Genetics Department, Yokohama City University Hospital, Yokohama, Japan
| | - Satomi Mitsuhashi
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Atsushi Takata
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Noriko Miyake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Kazuhiro Ogata
- Department of Biochemistry, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Hiroshi Handa
- Department of Oncology, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Takeshi Mizuguchi
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
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36
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Deacon OM, Svistunenko DA, Moore GR, Wilson MT, Worrall JA. Naturally Occurring Disease-Related Mutations in the 40–57 Ω-Loop of Human Cytochrome c Control Triggering of the Alkaline Isomerization. Biochemistry 2018; 57:4276-4288. [DOI: 10.1021/acs.biochem.8b00520] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Oliver M. Deacon
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, U.K
| | - Dimitri A. Svistunenko
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, U.K
| | - Geoffrey R. Moore
- School of Chemistry, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, U.K
| | - Michael T. Wilson
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, U.K
| | - Jonathan A.R. Worrall
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, U.K
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37
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Mano CM, Guaratini T, Cardozo KHM, Colepicolo P, Bechara EJH, Barros MP. Astaxanthin Restrains Nitrative-Oxidative Peroxidation in Mitochondrial-Mimetic Liposomes: A Pre-Apoptosis Model. Mar Drugs 2018; 16:md16040126. [PMID: 29649159 PMCID: PMC5923413 DOI: 10.3390/md16040126] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Revised: 03/19/2018] [Accepted: 04/04/2018] [Indexed: 01/14/2023] Open
Abstract
Astaxanthin (ASTA) is a ketocarotenoid found in many marine organisms and that affords many benefits to human health. ASTA is particularly effective against radical-mediated lipid peroxidation, and recent findings hypothesize a “mitochondrial-targeted” action of ASTA in cells. Therefore, we examined the protective effects of ASTA against lipid peroxidation in zwitterionic phosphatidylcholine liposomes (PCLs) and anionic phosphatidylcholine: phosphatidylglycerol liposomes (PCPGLs), at different pHs (6.2 to 8.0), which were challenged by oxidizing/nitrating conditions that mimic the regular and preapoptotic redox environment of active mitochondria. Pre-apoptotic conditions were created by oxidized/nitr(osyl)ated cytochrome c and resulted in the highest levels of lipoperoxidation in both PCL and PCPGLs (pH 7.4). ASTA was less protective at acidic conditions, especially in anionic PCPGLs. Our data demonstrated the ability of ASTA to hamper oxidative and nitrative events that lead to cytochrome c-peroxidase apoptosis and lipid peroxidation, although its efficiency changes with pH and lipid composition of membranes.
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Affiliation(s)
- Camila M Mano
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo (IQUSP), 05508-000 São Paulo, SP, Brazil.
- Instituto de Ciências da Atividade Física e do Esporte (ICAFE), Universidade Cruzeiro do Sul, 01506-000 São Paulo, SP, Brazil.
- Superintendência da Polícia Técnico Científica, 05507-060 São Paulo, SP, Brazil.
| | - Thais Guaratini
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo (IQUSP), 05508-000 São Paulo, SP, Brazil.
- Lychnoflora Pesquisa e Desenvolvimento em Produtos Naturais LTDA, 14030-090 Ribeirão Preto, SP, Brazil.
| | - Karina H M Cardozo
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo (IQUSP), 05508-000 São Paulo, SP, Brazil.
- Grupo Fleury, 04344-070 São Paulo, SP, Brazil.
| | - Pio Colepicolo
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo (IQUSP), 05508-000 São Paulo, SP, Brazil.
| | - Etelvino J H Bechara
- Departamento de Ciências Exatas e da Terra, Universidade Federal de São Paulo, Diadema, UNIFESP, 09972-270 Diadema, SP, Brazil.
- Departamento de Química Fundamental, Instituto de Química, Universidade de São Paulo (IQUSP), 05508-000 São Paulo, SP, Brazil.
| | - Marcelo P Barros
- Instituto de Ciências da Atividade Física e do Esporte (ICAFE), Universidade Cruzeiro do Sul, 01506-000 São Paulo, SP, Brazil.
- Instituto de Agroquímica y Tecnología de Alimentos (IATA-CSIC), Departamento de Ciencia de los Alimentos, Calle Catedrático Agustín Escardino 7, 46980 Paterna, Spain.
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Abstract
Bovine heart cytochrome c (bCyt c) is an extensively studied hemoprotein of only 104 residues. Due to the existence of isoforms generated by non-enzymatic deaminidation, crystallization of bCyt c is difficult and involves extensive purification and the use of microseeding or the presence of an electric field. Taking advantage of the capacity of cytochrome c (cyt c) to bind anions on its protein surface, the commercially available bCyt c was crystallized without extra purifications, using ammonium sulfate as precipitant and nitrate ions as additives. The structure of the ferric bCyt c in a new crystal form is described and compared with that previously solved at low ionic strength and with those of human and horse cyt c. The overall structure of bCyt c is conserved, while the side chains of several residues that play a role in the interactions of cyt c with its partners have different rotamers in the two structures. The effect of the presence of nitrate ions on the structure of the protein is then evaluated and compared with that observed in the case of ferrous and ferric horse heart cyt c.
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39
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Lin YW. Structure and function of heme proteins regulated by diverse post-translational modifications. Arch Biochem Biophys 2018; 641:1-30. [DOI: 10.1016/j.abb.2018.01.009] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 01/10/2018] [Accepted: 01/13/2018] [Indexed: 01/08/2023]
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40
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Lei H, Bowler BE. Humanlike substitutions to Ω-loop D of yeast iso-1-cytochrome c only modestly affect dynamics and peroxidase activity. J Inorg Biochem 2018. [PMID: 29530594 DOI: 10.1016/j.jinorgbio.2018.02.022] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Structural studies of yeast iso-1-cytochrome c (L.J. McClelland, T.-C. Mou, M.E. Jeakins-Cooley, S.R. Sprang, B.E. Bowler, Proc. Natl. Acad. Sci. U.S.A. 111 (2014) 6648-6653) show that modest movement of Ω-loop D (residues 70-85, average RMSD versus the native structure: 0.81 Å) permits loss of Met80-heme ligation creating an available coordination site to catalyze the peroxidase activity mediated by cytochrome c early in apoptosis. However, Ala81 and Gly83 move significantly (RMSDs of 2.18 and 1.26 Å, respectively). Ala81 and Gly83 evolve to Ile and Val, respectively, in human cytochrome c and peroxidase activity decreases 25-fold relative to the yeast protein at pH 7. To test the hypothesis that these residues evolved to restrict the peroxidase activity of cytochrome c, A81I and G83V variants of yeast iso-1-cytochrome c were prepared. For both variants, the apparent pKa of the alkaline transition increases by 0.2 to 0.3 relative to the wild type (WT) protein and the rate of opening the heme crevice is slowed. The cooperativity of acid unfolding is decreased for the G83V variant. At pH 7 and 8, the catalytic rate constant, kcat, for the peroxidase activity of both variants decreases relative to WT, consistent with the effects on alkaline isomerization. Below pH 7, the loss in the cooperativity of acid unfolding causes kcat for peroxidase activity to increase for the G83V variant relative to WT. Neither variant decreases kcat to the level of the human protein, indicating that other residues also contribute to the low peroxidase activity of human cytochrome c.
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Affiliation(s)
- Haotian Lei
- Department of Chemistry and Biochemistry, University of Montana, Missoula, MT 59812, United States; Center for Biomolecular Structure and Dynamics, University of Montana, Missoula, MT 59812, United States
| | - Bruce E Bowler
- Department of Chemistry and Biochemistry, University of Montana, Missoula, MT 59812, United States; Center for Biomolecular Structure and Dynamics, University of Montana, Missoula, MT 59812, United States.
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41
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Deacon OM, Karsisiotis AI, Moreno-Chicano T, Hough MA, Macdonald C, Blumenschein TMA, Wilson MT, Moore GR, Worrall JAR. Heightened Dynamics of the Oxidized Y48H Variant of Human Cytochrome c Increases Its Peroxidatic Activity. Biochemistry 2017; 56:6111-6124. [PMID: 29083920 DOI: 10.1021/acs.biochem.7b00890] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Proteins performing multiple biochemical functions are called "moonlighting proteins" or extreme multifunctional (EMF) proteins. Mitochondrial cytochrome c is an EMF protein that binds multiple partner proteins to act as a signaling molecule, transfers electrons in the respiratory chain, and acts as a peroxidase in apoptosis. Mutations in the cytochrome c gene lead to the disease thrombocytopenia, which is accompanied by enhanced apoptotic activity. The Y48H variant arises from one such mutation and is found in the 40-57 Ω-loop, the lowest-unfolding free energy substructure of the cytochrome c fold. A 1.36 Å resolution X-ray structure of the Y48H variant reveals minimal structural changes compared to the wild-type structure, with the axial Met80 ligand coordinated to the heme iron. Despite this, the intrinsic peroxidase activity is enhanced, implying that a pentacoordinate heme state is more prevalent in the Y48H variant, corroborated through determination of a Met80 "off rate" of >125 s-1 compared to a rate of ∼6 s-1 for the wild-type protein. Heteronuclear nuclear magnetic resonance measurements with the oxidized Y48H variant reveal heightened dynamics in the 40-57 Ω-loop and the Met80-containing 71-85 Ω-loop relative to the wild-type protein, illustrating communication between these substructures. Placed into context with the G41S cytochrome c variant, also implicated in thrombocytopenia, a dynamic picture associated with this disease relative to cytochrome c is emerging whereby increasing dynamics in substructures of the cytochrome c fold serve to facilitate an increased population of the peroxidatic pentacoordinate heme state in the following order: wild type < G41S < Y48H.
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Affiliation(s)
- Oliver M Deacon
- School of Biological Sciences, University of Essex , Wivenhoe Park, Colchester CO4 3SQ, U.K
| | | | - Tadeo Moreno-Chicano
- School of Biological Sciences, University of Essex , Wivenhoe Park, Colchester CO4 3SQ, U.K
| | - Michael A Hough
- School of Biological Sciences, University of Essex , Wivenhoe Park, Colchester CO4 3SQ, U.K
| | - Colin Macdonald
- School of Chemistry, University of East Anglia , Norwich Research Park, Norwich NR4 7TJ, U.K
| | - Tharin M A Blumenschein
- School of Chemistry, University of East Anglia , Norwich Research Park, Norwich NR4 7TJ, U.K
| | - Michael T Wilson
- School of Biological Sciences, University of Essex , Wivenhoe Park, Colchester CO4 3SQ, U.K
| | - Geoffrey R Moore
- School of Chemistry, University of East Anglia , Norwich Research Park, Norwich NR4 7TJ, U.K
| | - Jonathan A R Worrall
- School of Biological Sciences, University of Essex , Wivenhoe Park, Colchester CO4 3SQ, U.K
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42
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Alvarez-Paggi D, Hannibal L, Castro MA, Oviedo-Rouco S, Demicheli V, Tórtora V, Tomasina F, Radi R, Murgida DH. Multifunctional Cytochrome c: Learning New Tricks from an Old Dog. Chem Rev 2017; 117:13382-13460. [DOI: 10.1021/acs.chemrev.7b00257] [Citation(s) in RCA: 135] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Damián Alvarez-Paggi
- Departamento
de Química Inorgánica, Analítica y Química
Física and INQUIMAE (CONICET-UBA), Facultad de Ciencias Exactas
y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. 2, piso 1, Buenos Aires C1428EHA, Argentina
| | - Luciana Hannibal
- Department
of Pediatrics, Universitätsklinikum Freiburg, Mathildenstrasse 1, Freiburg 79106, Germany
- Departamento
de Bioquímica and Center for Free Radical and Biomedical Research,
Facultad de Medicina, Universidad de la República, Av.
Gral. Flores 2125, Montevideo 11800, Uruguay
| | - María A. Castro
- Departamento
de Química Inorgánica, Analítica y Química
Física and INQUIMAE (CONICET-UBA), Facultad de Ciencias Exactas
y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. 2, piso 1, Buenos Aires C1428EHA, Argentina
| | - Santiago Oviedo-Rouco
- Departamento
de Química Inorgánica, Analítica y Química
Física and INQUIMAE (CONICET-UBA), Facultad de Ciencias Exactas
y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. 2, piso 1, Buenos Aires C1428EHA, Argentina
| | - Veronica Demicheli
- Departamento
de Bioquímica and Center for Free Radical and Biomedical Research,
Facultad de Medicina, Universidad de la República, Av.
Gral. Flores 2125, Montevideo 11800, Uruguay
| | - Veronica Tórtora
- Departamento
de Bioquímica and Center for Free Radical and Biomedical Research,
Facultad de Medicina, Universidad de la República, Av.
Gral. Flores 2125, Montevideo 11800, Uruguay
| | - Florencia Tomasina
- Departamento
de Bioquímica and Center for Free Radical and Biomedical Research,
Facultad de Medicina, Universidad de la República, Av.
Gral. Flores 2125, Montevideo 11800, Uruguay
| | - Rafael Radi
- Departamento
de Bioquímica and Center for Free Radical and Biomedical Research,
Facultad de Medicina, Universidad de la República, Av.
Gral. Flores 2125, Montevideo 11800, Uruguay
| | - Daniel H. Murgida
- Departamento
de Química Inorgánica, Analítica y Química
Física and INQUIMAE (CONICET-UBA), Facultad de Ciencias Exactas
y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. 2, piso 1, Buenos Aires C1428EHA, Argentina
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43
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Elmer-Dixon MM, Bowler BE. Site A-Mediated Partial Unfolding of Cytochrome c on Cardiolipin Vesicles Is Species-Dependent and Does Not Require Lys72. Biochemistry 2017; 56:4830-4839. [DOI: 10.1021/acs.biochem.7b00694] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Margaret M. Elmer-Dixon
- Department
of Chemistry and Biochemistry, University of Montana, Missoula, Montana 59812, United States
- Center
for Bimolecular Structure and Dynamics, University of Montana, Missoula, Montana 59812, United States
| | - Bruce E. Bowler
- Department
of Chemistry and Biochemistry, University of Montana, Missoula, Montana 59812, United States
- Center
for Bimolecular Structure and Dynamics, University of Montana, Missoula, Montana 59812, United States
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44
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Nold SM, Lei H, Mou TC, Bowler BE. Effect of a K72A Mutation on the Structure, Stability, Dynamics, and Peroxidase Activity of Human Cytochrome c. Biochemistry 2017; 56:3358-3368. [PMID: 28598148 PMCID: PMC5564420 DOI: 10.1021/acs.biochem.7b00342] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We test the hypothesis that Lys72 suppresses the intrinsic peroxidase activity of human cytochrome c, as observed previously for yeast iso-1-cytochrome c [McClelland, L. J., et al. (2014) Proc. Natl. Acad. Sci. U. S. A. 111, 6648-6653]. A 1.25 Å X-ray structure of K72A human cytochrome c shows that the mutation minimally affects structure. Guanidine hydrochloride denaturation demonstrates that the K72A mutation increases global stability by 0.5 kcal/mol. The K72A mutation also increases the apparent pKa of the alkaline transition, a measure of the stability of the heme crevice, by 0.5 unit. Consistent with the increase in the apparent pKa, the rate of formation of the dominant alkaline conformer decreases, and this conformer is no longer stabilized by proline isomerization. Peroxidase activity measurements show that the K72A mutation increases kcat by 1.6-4-fold at pH 7-10, an effect larger than that seen for the yeast protein. X-ray structures of wild type and K72A human cytochrome c indicate that direct interactions of Lys72 with the far side of Ω-loop D, which are seen in X-ray structures of horse and yeast cytochrome c and could suppress peroxidase activity, are lacking. Instead, we propose that the stronger effect of the K72A mutation on the peroxidase activity of human versus yeast cytochrome c results from relief of steric interactions between the side chains at positions 72 and 81 (Ile in human vs Ala in yeast), which suppress the dynamics of Ω-loop D necessary for the intrinsic peroxidase activity of cytochrome c.
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Affiliation(s)
- Shiloh M. Nold
- Department of Chemistry and Biochemistry, University of Montana, Missoula, Montana 59812
- Center for Bimolecular Structure and Dynamics, University of Montana, Missoula, Montana 59812
| | - Haotian Lei
- Department of Chemistry and Biochemistry, University of Montana, Missoula, Montana 59812
- Center for Bimolecular Structure and Dynamics, University of Montana, Missoula, Montana 59812
| | - Tung-Chung Mou
- Division of Biological Sciences, University of Montana, Missoula, Montana 59812
- Center for Bimolecular Structure and Dynamics, University of Montana, Missoula, Montana 59812
| | - Bruce E. Bowler
- Department of Chemistry and Biochemistry, University of Montana, Missoula, Montana 59812
- Center for Bimolecular Structure and Dynamics, University of Montana, Missoula, Montana 59812
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45
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Zhang M, Zheng J, Nussinov R, Ma B. Release of Cytochrome C from Bax Pores at the Mitochondrial Membrane. Sci Rep 2017; 7:2635. [PMID: 28572603 PMCID: PMC5453941 DOI: 10.1038/s41598-017-02825-7] [Citation(s) in RCA: 103] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 04/19/2017] [Indexed: 12/12/2022] Open
Abstract
How cytochrome C is released from the mitochondria to the cytosol via Bax oligomeric pores, a process which is required for apoptosis, is still a mystery. Based on experimentally measured residue-residue distances, we recently solved the first atomic model for Bax oligomeric pores at the membranes using computational approaches. Here, we investigate the mechanism at the microsecond time- and nanometer space- scale using MD simulations. Our free energy landscape depicts a low barrier for the permeation of cytochrome C into the Bax C-terminal mouth, with the pathway proceeding to the inner cavity and exiting via the N-terminal mouth. Release is guided by organized charged/hydrophilic surfaces. The hydrophilicity and negative charge of the pore surface gradually increase along the release pathway from the pore entry to the exit opening. Rather than inert passing of the cytochrome C through a rigid pore, the flexible pore may selectively aid the cytochrome C passage. Once the Bax pore is formed in the membrane, with a low energy barrier, the release of cytochrome C may be readily achieved through energy fluctuations. Collectively, our work provides mechanistic insight in atomic detail into the release of cytochrome C through Bax oligomeric pores.
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Affiliation(s)
- Mingzhen Zhang
- Department of Chemical & Biomolecular Engineering, the University of Akron, Akron, Ohio, 44325, USA
| | - Jie Zheng
- Department of Chemical & Biomolecular Engineering, the University of Akron, Akron, Ohio, 44325, USA
| | - Ruth Nussinov
- Basic Science Program, Leidos Biomedical Research, Inc. Cancer and Inflammation Program, National Cancer Institute, Frederick, MD, 21702, USA
- Sackler Inst. of Molecular Medicine, Department of Human Genetics and Molecular Medicine, Sackler School of Medicine, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Buyong Ma
- Basic Science Program, Leidos Biomedical Research, Inc. Cancer and Inflammation Program, National Cancer Institute, Frederick, MD, 21702, USA.
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46
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Structural basis of mitochondrial dysfunction in response to cytochrome c phosphorylation at tyrosine 48. Proc Natl Acad Sci U S A 2017; 114:E3041-E3050. [PMID: 28348229 DOI: 10.1073/pnas.1618008114] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Regulation of mitochondrial activity allows cells to adapt to changing conditions and to control oxidative stress, and its dysfunction can lead to hypoxia-dependent pathologies such as ischemia and cancer. Although cytochrome c phosphorylation-in particular, at tyrosine 48-is a key modulator of mitochondrial signaling, its action and molecular basis remain unknown. Here we mimic phosphorylation of cytochrome c by replacing tyrosine 48 with p-carboxy-methyl-l-phenylalanine (pCMF). The NMR structure of the resulting mutant reveals significant conformational shifts and enhanced dynamics around pCMF that could explain changes observed in its functionality: The phosphomimetic mutation impairs cytochrome c diffusion between respiratory complexes, enhances hemeprotein peroxidase and reactive oxygen species scavenging activities, and hinders caspase-dependent apoptosis. Our findings provide a framework to further investigate the modulation of mitochondrial activity by phosphorylated cytochrome c and to develop novel therapeutic approaches based on its prosurvival effects.
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47
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Engineered holocytochrome c synthases that biosynthesize new cytochromes c. Proc Natl Acad Sci U S A 2017; 114:2235-2240. [PMID: 28196881 DOI: 10.1073/pnas.1615929114] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Cytochrome c (cyt c), required for electron transport in mitochondria, possesses a covalently attached heme cofactor. Attachment is catalyzed by holocytochrome c synthase (HCCS), leading to two thioether bonds between heme and a conserved CXXCH motif of cyt c In cyt c, histidine (His19) of CXXCH acts as an axial ligand to heme iron and upon release of holocytochrome c from HCCS, folding leads to formation of a second axial interaction with methionine (Met81). We previously discovered mutations in human HCCS that facilitate increased biosynthesis of cyt c in recombinant Escherichia coli Focusing on HCCS E159A, novel cyt c variants in quantities that are sufficient for biophysical analysis are biosynthesized. Cyt c H19M, the first bis-Met liganded cyt c, is compared with other axial ligand variants (M81A, M81H) and single thioether cyt c variants. For variants with axial ligand substitutions, electronic absorption, near-UV circular dichroism, and electron paramagnetic resonance spectroscopy provide evidence that axial ligands are changed and the heme environment is altered. Circular dichroism spectra in far UV and thermal denaturation analyses demonstrate that axial ligand changes do not affect secondary structures and stability. Redox potentials span a 400-mV range (+349 mV vs. standard hydrogen electrode, H19M; +252 mV, WT; -19 mV, M81A; -69 mV, M81H). We discuss the results in the context of a four-step mechanism for HCCS, whereby HCCS mutants such as E159A are enhanced in release (step 4) of cyt c from the HCCS active site; thus, we term these "release mutants."
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48
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Kerkis I, de Brandão Prieto da Silva AR, Pompeia C, Tytgat J, de Sá Junior PL. Toxin bioportides: exploring toxin biological activity and multifunctionality. Cell Mol Life Sci 2017; 74:647-661. [PMID: 27554773 PMCID: PMC11107510 DOI: 10.1007/s00018-016-2343-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Revised: 07/27/2016] [Accepted: 08/15/2016] [Indexed: 10/21/2022]
Abstract
Toxins have been shown to have many biological functions and to constitute a rich source of drugs and biotechnological tools. We focus on toxins that not only have a specific activity, but also contain residues responsible for transmembrane penetration, which can be considered bioportides-a class of cell-penetrating peptides that are also intrinsically bioactive. Bioportides are potential tools in pharmacology and biotechnology as they help deliver substances and nanoparticles to intracellular targets. Bioportides characterized so far are peptides derived from human proteins, such as cytochrome c (CYCS), calcitonin receptor (camptide), and endothelial nitric oxide synthase (nosangiotide). However, toxins are usually disregarded as potential bioportides. In this review, we discuss the inclusion of some toxins and molecules derived thereof as a new class of bioportides based on structure activity relationship, minimization, and biological activity studies. The comparative analysis of the amino acid residue composition of toxin-derived bioportides and their short molecular variants is an innovative analytical strategy which allows us to understand natural toxin multifunctionality in vivo and plan novel pharmacological and biotechnological products. Furthermore, we discuss how many bioportide toxins have a rigid structure with amphiphilic properties important for both cell penetration and bioactivity.
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Affiliation(s)
- Irina Kerkis
- Laboratório de Genética, Instituto Butantan, Av. Vital Brasil 1500, São Paulo, SP, 05503-900, Brazil.
| | | | - Celine Pompeia
- Laboratório de Genética, Instituto Butantan, Av. Vital Brasil 1500, São Paulo, SP, 05503-900, Brazil
| | - Jan Tytgat
- Toxicology and Pharmacology, University of Leuven (KU Leuven), Louvain, Belgium
| | - Paulo L de Sá Junior
- Laboratório de Genética, Instituto Butantan, Av. Vital Brasil 1500, São Paulo, SP, 05503-900, Brazil.
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49
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Bradley JM, Svistunenko DA, Moore GR, Le Brun NE. Tyr25, Tyr58 and Trp133 ofEscherichia colibacterioferritin transfer electrons between iron in the central cavity and the ferroxidase centre. Metallomics 2017; 9:1421-1428. [DOI: 10.1039/c7mt00187h] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Tyr58 and Trp133 play key roles in the formation and decay of the Tyr25 radical species ofE. coliBFR.
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Affiliation(s)
- Justin M. Bradley
- Centre for Molecular and Structural Biochemistry
- School of Chemistry
- University of East Anglia
- Norwich Research Park
- Norwich
| | | | - Geoffrey R. Moore
- Centre for Molecular and Structural Biochemistry
- School of Chemistry
- University of East Anglia
- Norwich Research Park
- Norwich
| | - Nick E. Le Brun
- Centre for Molecular and Structural Biochemistry
- School of Chemistry
- University of East Anglia
- Norwich Research Park
- Norwich
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50
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Feifel SC, Stieger KR, Kapp A, Weber D, Allegrozzi M, Piccioli M, Turano P, Lisdat F. Insights into Interprotein Electron Transfer of Human Cytochrome c Variants Arranged in Multilayer Architectures by Means of an Artificial Silica Nanoparticle Matrix. ACS OMEGA 2016; 1:1058-1066. [PMID: 30023500 PMCID: PMC6044710 DOI: 10.1021/acsomega.6b00213] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Accepted: 11/04/2016] [Indexed: 06/08/2023]
Abstract
The redox behavior of proteins plays a crucial part in the design of bioelectronic systems. We have demonstrated several functional systems exploiting the electron exchange properties of the redox protein cytochrome c (cyt c) in combination with enzymes and photoactive proteins. The operation is based on an effective reaction at modified electrodes but also to a large extent on the capability of self-exchange between cyt c molecules in a surface-fixed state. In this context, different variants of human cyt c have been examined here with respect to an altered heterogeneous electron transfer (ET) rate in a monolayer on electrodes as well as an enhanced self-exchange rate while being incorporated in multilayer architectures. For this purpose, mutants of the wild-type (WT) protein have been prepared to change the chemical nature of the surface contact area near the heme edge. The structural integrity of the variants has been verified by NMR and UV-vis measurements. It is shown that the single-point mutations can significantly influence the heterogeneous ET rate at thiol-modified gold electrodes and that electroactive protein/silica nanoparticle multilayers can be constructed with all forms of human cyt c prepared. The kinetic behavior of electron exchange for the mutant proteins in comparison with that of the WT has been found altered in some multilayer arrangements. Higher self-exchange rates have been found for K79A. The results demonstrate that the position of the introduced change in the charge situation of cyt c has a profound influence on the exchange behavior. In addition, the behavior of the cyt c variants in assembled multilayers is found to be rather similar to the situation of cyt c self-exchange in solution verified by NMR.
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Affiliation(s)
- Sven Christian Feifel
- Institute
of Applied Life Sciences, Biosystems Technology, Technical University of Applied Sciences Wildau, Hochschulring 1, 15745 Wildau, Germany
| | - Kai Ralf Stieger
- Institute
of Applied Life Sciences, Biosystems Technology, Technical University of Applied Sciences Wildau, Hochschulring 1, 15745 Wildau, Germany
| | - Andreas Kapp
- Institute
of Applied Life Sciences, Biosystems Technology, Technical University of Applied Sciences Wildau, Hochschulring 1, 15745 Wildau, Germany
| | - Dennis Weber
- Institute
of Applied Life Sciences, Biosystems Technology, Technical University of Applied Sciences Wildau, Hochschulring 1, 15745 Wildau, Germany
| | - Marco Allegrozzi
- Department
of Chemistry and Magnetic Resonance Center, University of Florence, Via Luigi Sacconi 2, 50019 Sesto Fiorentino, Florence, Italy
| | - Mario Piccioli
- Department
of Chemistry and Magnetic Resonance Center, University of Florence, Via Luigi Sacconi 2, 50019 Sesto Fiorentino, Florence, Italy
| | - Paola Turano
- Department
of Chemistry and Magnetic Resonance Center, University of Florence, Via Luigi Sacconi 2, 50019 Sesto Fiorentino, Florence, Italy
| | - Fred Lisdat
- Institute
of Applied Life Sciences, Biosystems Technology, Technical University of Applied Sciences Wildau, Hochschulring 1, 15745 Wildau, Germany
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