1
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Marzollo A, Zampieri S, Barozzi S, Yousaf MA, Quartararo J, De Rocco D, Faleschini M, Marconi C, Berti CC, Bozzi V, Russo G, Giordano P, Goffrini P, Bresolin S, Pastore A, Savoia A, Pecci A. Thrombocytopenia 4 (THC4): Six novel families with mutations of the cytochrome c gene. Br J Haematol 2024. [PMID: 38815995 DOI: 10.1111/bjh.19567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Accepted: 05/15/2024] [Indexed: 06/01/2024]
Abstract
Thrombocytopenia 4 (THC4) is an autosomal-dominant thrombocytopenia caused by mutations in CYCS, the gene encoding cytochrome c (CYCS), a small haeme protein essential for electron transport in mitochondria and cell apoptosis. THC4 is considered an extremely rare condition since only a few patients have been reported so far. These subjects presented mild thrombocytopenia and no or mild bleeding tendency. In this study, we describe six Italian families with five different heterozygous missense CYCS variants: p.Gly42Ser and p.Tyr49His previously associated with THC4, and three novel variants (p.Ala52Thr, p.Arg92Gly, and p.Leu99Val), which have been classified as pathogenic by bioinformatics and segregation analyses. Moreover, we supported functional effects of p.Ala52Thr and p.Arg92Gly on oxidative growth and respiratory activity in a yeast model. The clinical characterization of the 22 affected individuals, the largest series of THC4 patients ever reported, showed that this disorder is characterized by mild-to-moderate thrombocytopenia, normal platelet size, and function, low risk of bleeding, and no additional clinical phenotypes associated with reduced platelet count. Finally, we describe a significant correlation between the region of CYCS affected by mutations and the extent of thrombocytopenia, which could reflect different degrees of impairment of CYCS functions caused by different pathogenetic variants.
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Affiliation(s)
- Antonio Marzollo
- Pediatric Hematology, Oncology and Stem Cell Transplant Division, Padua University Hospital, Padua, Italy
| | - Stefania Zampieri
- Institute for Maternal and Child Health, IRCCS Burlo Garofolo, Trieste, Italy
| | - Serena Barozzi
- Medicina Generale 1, IRCCS Policlinico San Matteo Foundation, Pavia, Italy
| | - Muhammad Abrar Yousaf
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, Verona, Italy
| | - Jade Quartararo
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Daniela De Rocco
- Institute for Maternal and Child Health, IRCCS Burlo Garofolo, Trieste, Italy
| | - Michela Faleschini
- Institute for Maternal and Child Health, IRCCS Burlo Garofolo, Trieste, Italy
| | - Caterina Marconi
- Departement of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
| | - Camilla Ceccatelli Berti
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Valeria Bozzi
- Medicina Generale 1, IRCCS Policlinico San Matteo Foundation, Pavia, Italy
| | - Giovanna Russo
- Pediatric Hematology Oncology, Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
| | - Paola Giordano
- Interdisciplinary Department of Medicine, Pediatric Section, University of Bari "Aldo Moro", Bari, Italy
| | - Paola Goffrini
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Silvia Bresolin
- Maternal and Child Health Department, Padua University, Padua, Italy
- Pediatric Hematology, Oncology, and Hematopoietic Cell and Gene Therapy, Pediatric Research Institute "Città Della Speranza", Padua, Italy
| | - Annalisa Pastore
- Department of Clinical Neuroscience, King's College London, Denmark Hill Campus, London, UK
- European Synchrotron Radiation Facility 71, Grenoble, France
| | - Anna Savoia
- Department of Engineering for Innovation Medicine, University of Verona, Verona, Italy
| | - Alessandro Pecci
- Medicina Generale 1, IRCCS Policlinico San Matteo Foundation, Pavia, Italy
- Department of Internal Medicine, University of Pavia, Pavia, Italy
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2
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Bartocci A, Dumont E. Situating the phosphonated calixarene-cytochrome C association by molecular dynamics simulations. J Chem Phys 2024; 160:105101. [PMID: 38465686 DOI: 10.1063/5.0198522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 02/20/2024] [Indexed: 03/12/2024] Open
Abstract
Protein-calixarenes binding plays an increasingly central role in many applications, spanning from molecular recognition to drug delivery strategies and protein inhibition. These ligands obey a specific bio-supramolecular chemistry, which can be revealed by computational approaches, such as molecular dynamics simulations. In this paper, we rely on all-atom, explicit-solvent molecular dynamics simulations to capture the electrostatically driven association of a phosphonated calix-[4]-arene with cytochome-C, which critically relies on surface-exposed paired lysines. Beyond two binding sites identified in direct agreement with the x-ray structure, the association has a larger structural impact on the protein dynamics. Then, our simulations allow a direct comparison to analogous calixarenes, namely, sulfonato, similarly reported as "molecular glue." Our work can contribute to a robust in silico predictive tool to assess binding sites for any given protein of interest for crystallization, with the specificity of a macromolecular cage whose endo/exo orientation plays a role in the binding.
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Affiliation(s)
- Alessio Bartocci
- Department of Physics, University of Trento, Via Sommarive 14, I-38123 Trento, Italy
- INFN-TIFPA, Trento Institute for Fundamental Physics and Applications, Via Sommarive 14, I-38123 Trento, Italy
- Institut de Chimie de Strasbourg, UMR 7177, CNRS, Université de Strasbourg, Strasbourg Cedex 67083, France
| | - Elise Dumont
- Université Côte d'Azur, CNRS, Institut de Chimie de Nice, UMR 7272, 06108 Nice, France
- Institut Universitaire de France, 5 rue Descartes, 75005 Paris, France
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3
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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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4
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Martin WJ, McClelland LJ, Nold SM, Boshae KL, Bowler BE. Effect of proline content and histidine ligation on the dynamics of Ω-loop D and the peroxidase activity of iso-1-cytochrome c. J Inorg Biochem 2024; 252:112474. [PMID: 38176365 DOI: 10.1016/j.jinorgbio.2023.112474] [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: 10/16/2023] [Revised: 12/20/2023] [Accepted: 12/20/2023] [Indexed: 01/06/2024]
Abstract
To study how proline residues affect the dynamics of Ω-loop D (residues 70 to 85) of cytochrome c, we prepared G83P and G83A variants of yeast iso-1-cytochrome c (iso-1-Cytc) in the presence and absence of a K73H mutation. Ω-loop D is important in controlling both the electron transfer function of Cytc and the peroxidase activity of Cytc used in apoptosis because it provides the Met80 heme ligand. The G83P and G83A mutations have no effect on the global stability of iso-1-Cytc in presence or absence of the K73H mutation. However, both mutations destabilize the His73-mediated alkaline conformer relative to the native state. pH jump stopped-flow experiments show that the dynamics of the His73-mediated alkaline transition are significantly enhanced by the G83P mutation. Gated electron transfer studies show that the enhanced dynamics result from an increased rate of return to the native state, whereas the rate of loss of Met80 ligation is unchanged by the G83P mutation. Thus, the G83P substitution does not stiffen the conformation of the native state. Because bis-His heme ligation occurs when Cytc binds to cardiolipin-containing membranes, we studied the effect of His73 ligation on the peroxidase activity of Cytc, which acts as an early signal in apoptosis by causing oxygenation of cardiolipin. We find that the His73 alkaline conformer suppresses the peroxidase activity of Cytc. Thus, the bis-His ligated state of Cytc formed upon binding to cardiolipin is a negative effector for the peroxidase activity of Cytc early in apoptosis.
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Affiliation(s)
- William J Martin
- Department of Chemistry & Biochemistry, University of Montana, Missoula, MT 59812, United States
| | - Levi J McClelland
- Department of Chemistry & Biochemistry, University of Montana, Missoula, MT 59812, United States; Division of Biological Sciences, University of Montana, Missoula, MT 59812, United States; Center for Biomolecular Structure & Dynamics, University of Montana, Missoula, MT 59812, United States
| | - Shiloh M Nold
- Department of Chemistry & Biochemistry, University of Montana, Missoula, MT 59812, United States
| | - Kassandra L Boshae
- Department of Chemistry & Biochemistry, University of Montana, Missoula, MT 59812, United States
| | - Bruce E Bowler
- Department of Chemistry & Biochemistry, University of Montana, Missoula, MT 59812, United States; Center for Biomolecular Structure & Dynamics, University of Montana, Missoula, MT 59812, United States.
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5
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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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6
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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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7
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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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8
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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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9
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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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10
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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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11
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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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12
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Zhong F, Alden SL, Hughes RP, Pletneva EV. Comparing Properties of Common Bioinorganic Ligands with Switchable Variants of Cytochrome c. Inorg Chem 2021; 61:1207-1227. [PMID: 34699724 DOI: 10.1021/acs.inorgchem.1c02322] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Ligand substitution at the metal center is common in catalysis and signal transduction of metalloproteins. Understanding the effects of particular ligands, as well as the polypeptide surrounding, is critical for uncovering mechanisms of these biological processes and exploiting them in the design of bioinspired catalysts and molecular devices. A series of switchable K79G/M80X/F82C (X = Met, His, or Lys) variants of cytochrome (cyt) c was employed to directly compare the stability of differently ligated proteins and activation barriers for Met, His, and Lys replacement at the ferric heme iron. Studies of these variants and their nonswitchable counterparts K79G/M80X have revealed stability trends Met < Lys < His and Lys < His < Met for the protein FeIII-X and FeII-X species, respectively. The differences in the hydrogen-bonding interactions in folded proteins and in solvation of unbound X in the unfolded proteins explain these trends. Calculations of free energy of ligand dissociation in small heme model complexes reveal that the ease of the FeIII-X bond breaking increases in the series amine < imidazole < thioether, mirroring trends in hardness of these ligands. Experimental rate constants for X dissociation in differently ligated cyt c variants are consistent with this sequence, but the differences between Met and His dissociation rates are attenuated because the former process is limited by the heme crevice opening. Analyses of activation parameters and comparisons to those for the Lys-to-Met ligand switch in the alkaline transition suggest that ligand dissociation is entropically driven in all the variants and accompanied by Lys protonation at neutral pH. The described thiolate redox-linked switches have offered a wealth of new information about interactions of different protein-derived ligands with the heme iron in cyt c model proteins, and we anticipate that the strategy of employing these switches could benefit studies of other redox metalloproteins and model complexes.
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Affiliation(s)
- Fangfang Zhong
- Department of Chemistry, Dartmouth College, Hanover, New Hampshire 03755, United States
| | - Stephanie L Alden
- Department of Chemistry, Dartmouth College, Hanover, New Hampshire 03755, United States
| | - Russell P Hughes
- Department of Chemistry, Dartmouth College, Hanover, New Hampshire 03755, United States
| | - Ekaterina V Pletneva
- Department of Chemistry, Dartmouth College, Hanover, New Hampshire 03755, United States
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13
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Correlated electric field modulation of electron transfer parameters and the access to alternative conformations of multifunctional cytochrome c. Bioelectrochemistry 2021; 143:107956. [PMID: 34624727 DOI: 10.1016/j.bioelechem.2021.107956] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 09/10/2021] [Accepted: 09/22/2021] [Indexed: 11/21/2022]
Abstract
Cytochrome c (Cytc) is a multifunctional protein that, in its native conformation, shuttles electrons in the mitochondrial respiratory chain. Conformational transitions that involve replacement of the heme distal ligand lead to the gain of alternative peroxidase activity, which is crucial for membrane permeabilization during apoptosis. Using a time-resolved SERR spectroelectrochemical approach, we found that the key physicochemical parameters that characterize the electron transfer (ET) canonic function and those that determine the transition to alternative conformations are strongly correlated and are modulated by local electric fields (LEF) of biologically meaningful magnitude. The electron shuttling function is optimized at moderate LEFs of around 1 V nm-1. A decrease of the LEF is detrimental for ET as it rises the reorganization energy. Moreover, LEF values below and above the optimal for ET favor alternative conformations with peroxidase activity and downshifted reduction potentials. The underlying proposed mechanism is the LEF modulation of the flexibility of crucial protein segments, which produces a differential effect on the kinetic ET and conformational parameters of Cytc. These findings might be related to variations in the mitochondrial membrane potential during apoptosis, as the basis for the switch between canonic and alternative functions of Cytc. Moreover, they highlight the possible role of variable LEFs in determining the function of other moonlighting proteins through modulation of the protein dynamics.
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14
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How to Turn an Electron Transfer Protein into a Redox Enzyme for Biosensing. Molecules 2021; 26:molecules26164950. [PMID: 34443538 PMCID: PMC8398203 DOI: 10.3390/molecules26164950] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 08/10/2021] [Accepted: 08/13/2021] [Indexed: 01/10/2023] Open
Abstract
Cytochrome c is a small globular protein whose main physiological role is to shuttle electrons within the mitochondrial electron transport chain. This protein has been widely investigated, especially as a paradigmatic system for understanding the fundamental aspects of biological electron transfer and protein folding. Nevertheless, cytochrome c can also be endowed with a non-native catalytic activity and be immobilized on an electrode surface for the development of third generation biosensors. Here, an overview is offered of the most significant examples of such a functional transformation, carried out by either point mutation(s) or controlled unfolding. The latter can be induced chemically or upon protein immobilization on hydrophobic self-assembled monolayers. We critically discuss the potential held by these systems as core constituents of amperometric biosensors, along with the issues that need to be addressed to optimize their applicability and response.
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15
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Samsri S, Pornsuwan S. Influence of cysteine-directed mutations at the Ω-loops on peroxidase activity of human cytochrome c. Arch Biochem Biophys 2021; 709:108980. [PMID: 34224685 DOI: 10.1016/j.abb.2021.108980] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 06/08/2021] [Accepted: 06/22/2021] [Indexed: 11/19/2022]
Abstract
Cytochrome c (Cytc) is a multifunctional protein associated with electron shuttling in the inner membrane of mitochondria and also involving in the apoptotic pathway. It has been identified that mutations located in the flexible central 40-57 Ω-loop including the naturally occurring G41S, Y48H, and A51V mutants, which are found in patients with thrombocytopenia 4, a platelet disorder, alter the structural properties of human Cytc (hCytc) that associated to enhanced peroxidase activity. In this work we compared the cysteine-directed mutants of hCytc located in three different parts of Ω-loops, i.e., T28C and G34C (proximal Ω-loop), and A50C (central Ω-loop), with respect to the wild-type (WT) hCytc. The mutants and WT hCytc were structurally characterized by circular dichroism, heating and chemical denaturations, and fluorescence spectroscopy. The flexibility at the cysteine mutated sites was directly determined by site-directed spin-labeling Electron Spin Resonance. Alkaline transitions were determined by pH titration and the alkaline conformers were related to peroxidase activity of all hCytc proteins. Structural and dynamic characterizations were rationally correlated to the modulation of peroxidase activity in these mutants in comparison to the WT hCytc. We found that the cysteine mutations at residues T28 and G34, both located in the same region of Ω-loop, developed different conformations and dynamical properties that lead to different effects on the rates of peroxidase activity (G34C was ~2.6 folds higher), whereas the rate of G34C was closer to that of A50C mutant. The results implied that the flexibility and local structures of the proximal Ω-loop could also play an important role in modulating the peroxidase activity which can be associated to apoptosis.
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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, Thailand
| | - Soraya Pornsuwan
- Department of Chemistry and Center of Excellence for Innovation in Chemistry, Faculty of Science, Mahidol University, Bangkok, Thailand.
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16
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Sedlák E, Žár T, Varhač R, Musatov A, Tomášková N. Anion-Specific Effects on the Alkaline State of Cytochrome c. BIOCHEMISTRY (MOSCOW) 2021; 86:59-73. [PMID: 33705282 DOI: 10.1134/s0006297921010065] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Specific effects of anions on the structure, thermal stability, and peroxidase activity of native (state III) and alkaline (state IV) cytochrome c (cyt c) have been studied by the UV-VIS absorbance spectroscopy, intrinsic tryptophan fluorescence, and circular dichroism. Thermal and isothermal denaturation monitored by the tryptophan fluorescence and circular dichroism, respectively, implied lower stability of cyt c state IV in comparison with the state III. The pKa value of alkaline isomerization of cyt c depended on the present salts, i.e., kosmotropic anions increased and chaotropic anions decreased pKa (Hofmeister effect on protein stability). The peroxidase activity of cyt c in the state III, measured by oxidation of guaiacol, showed clear dependence on the salt position in the Hofmeister series, while cyt c in the alkaline state lacked the peroxidase activity regardless of the type of anions present in the solution. The alkaline isomerization of cyt c in the presence of 8 M urea, measured by Trp59 fluorescence, implied an existence of a high-affinity non-native ligand for the heme iron even in a partially denatured protein conformation. The conformation of the cyt c alkaline state in 8 M urea was considerably modulated by the specific effect of anions. Based on the Trp59 fluorescence quenching upon titration to alkaline pH in 8 M urea and molecular dynamics simulation, we hypothesize that the Lys79 conformer is most likely the predominant alkaline conformer of cyt c. The high affinity of the sixth ligand for the heme iron is likely a reason of the lack of peroxidase activity of cyt c in the alkaline state.
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Affiliation(s)
- Erik Sedlák
- Department of Biochemistry, Faculty of Science, P. J. Šafárik University in Košice, Košice, 04154, Slovakia. .,Centre for Interdisciplinary Biosciences, P. J. Šafárik University in Košice, Košice, 04154, Slovakia
| | - Tibor Žár
- Centre for Interdisciplinary Biosciences, P. J. Šafárik University in Košice, Košice, 04154, Slovakia.
| | - Rastislav Varhač
- Department of Biochemistry, Faculty of Science, P. J. Šafárik University in Košice, Košice, 04154, Slovakia.
| | - Andrej Musatov
- Department of Biophysics, Institute of Experimental Physics, Slovak Academy of Sciences, Košice, 040 01, Slovakia.
| | - Nataša Tomášková
- Department of Biochemistry, Faculty of Science, P. J. Šafárik University in Košice, Košice, 04154, Slovakia.
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17
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Yin V, Holzscherer D, Konermann L. Delineating Heme-Mediated versus Direct Protein Oxidation in Peroxidase-Activated Cytochrome c by Top-Down Mass Spectrometry. Biochemistry 2020; 59:4108-4117. [PMID: 32991149 DOI: 10.1021/acs.biochem.0c00609] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Oxidation of key residues in cytochrome c (cyt c) by chloramine T (CT) converts the protein from an electron transporter to a peroxidase. This peroxidase-activated state represents an important model system for exploring the early steps of apoptosis. CT-induced transformations include oxidation of the distal heme ligand Met80 (MetO, +16 Da) and carbonylation (LysCHO, -1 Da) in the range of Lys53/55/72/73. Remarkably, the 15 remaining Lys residues in cyt c are not susceptible to carbonylation. The cause of this unusual selectivity is unknown. Here we applied top-down mass spectrometry (MS) to examine whether CT-induced oxidation is catalyzed by heme. To this end, we compared the behavior of cyt c with (holo-cyt c) and without heme (apoSS-cyt c). CT caused MetO formation at Met80 for both holo- and apoSS-cyt c, implying that this transformation can proceed independently of heme. The aldehyde-specific label Girard's reagent T (GRT) reacted with oxidized holo-cyt c, consistent with the presence of several LysCHO. In contrast, oxidized apo-cyt c did not react with GRT, revealing that LysCHO forms only in the presence of heme. The heme dependence of LysCHO formation was further confirmed using microperoxidase-11 (MP11). CT exposure of apoSS-cyt c in the presence of MP11 caused extensive nonselective LysCHO formation. Our results imply that the selectivity of LysCHO formation at Lys53/55/72/73 in holo-cyt c is caused by the spatial proximity of these sites to the reactive (distal) heme face. Overall, this work highlights the utility of top-down MS for unravelling complex oxidative modifications.
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Affiliation(s)
- Victor Yin
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Derek Holzscherer
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Lars Konermann
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
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18
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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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19
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Oviedo-Rouco S, Perez-Bertoldi JM, Spedalieri C, Castro MA, Tomasina F, Tortora V, Radi R, Murgida DH. Electron transfer and conformational transitions of cytochrome c are modulated by the same dynamical features. Arch Biochem Biophys 2020; 680:108243. [DOI: 10.1016/j.abb.2019.108243] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2019] [Revised: 12/11/2019] [Accepted: 12/29/2019] [Indexed: 01/17/2023]
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20
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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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21
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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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22
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Deng Y, Weaver ML, Hoke KR, Pletneva EV. A Heme Propionate Staples the Structure of Cytochrome c for Methionine Ligation to the Heme Iron. Inorg Chem 2019; 58:14085-14106. [PMID: 31589413 DOI: 10.1021/acs.inorgchem.9b02111] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Ligand-switch reactions at the heme iron are common in biological systems, but their mechanisms and the features of the polypeptide fold that support dual ligation are not well understood. In cytochrome c (cyt c), two low-stability loops (Ω-loop C and Ω-loop D) are connected by the heme propionate HP6. At alkaline pH, the native Met80 ligand from Ω-loop D switches to a Lys residue from the same loop. Deprotonation of an as yet unknown group triggers the alkaline transition. We have created the two cyt c variants T49V/K79G and T78V/K79G with altered connections of these two loops to HP6. Electronic absorption, NMR, and EPR studies demonstrate that at pH 7.4 ferric forms of these variants are Lys-ligated, whereas ferrous forms maintain the native Met80 ligation. Measurements of protein stability, cyclic voltammetry, pH-jump and gated electron-transfer kinetics have revealed that these Thr to Val substitutions greatly affect the alkaline transition in both ferric and ferrous proteins. The substitutions modify the stability of the Met-ligated species and reduction potentials of the heme iron. The kinetics of ligand-switch processes are also altered, and analyses of these effects implicate redox-dependent differences in metal-ligand interactions and the role of the protein dynamics, including cross-talk between the two Ω-loops. With the two destabilized variants, it is possible to map energy levels for the Met- and Lys-ligated species in both ferric and ferrous proteins and assess the role of the protein scaffold in redox-dependent preferences for these two ligands. The estimated shift in the heme iron reduction potential upon deprotonation of the "trigger" group is consistent with those associated with deprotonation of an HP, suggesting that HP6, on its own or as a part of a hydrogen-bonded cluster, is a likely "trigger" for the Met to Lys ligand switch.
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Affiliation(s)
- Yunling Deng
- Department of Chemistry , Dartmouth College , Hanover , New Hampshire 03755 , United States
| | - Madeline L Weaver
- Department of Chemistry and Biochemistry , Berry College , Mount Berry , Georgia 30149 , United States
| | - Kevin R Hoke
- Department of Chemistry and Biochemistry , Berry College , Mount Berry , Georgia 30149 , United States
| | - Ekaterina V Pletneva
- Department of Chemistry , Dartmouth College , Hanover , New Hampshire 03755 , United States
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23
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Kalpage HA, Vaishnav A, Liu J, Varughese A, Wan J, Turner AA, Ji Q, Zurek MP, Kapralov AA, Kagan VE, Brunzelle JS, Recanati MA, Grossman LI, Sanderson TH, Lee I, Salomon AR, Edwards BFP, Hüttemann M. Serine-47 phosphorylation of cytochrome c in the mammalian brain regulates cytochrome c oxidase and caspase-3 activity. FASEB J 2019; 33:13503-13514. [PMID: 31570002 DOI: 10.1096/fj.201901120r] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Cytochrome c (Cytc) is a multifunctional protein that operates as an electron carrier in the mitochondrial electron transport chain and plays a key role in apoptosis. We have previously shown that tissue-specific phosphorylations of Cytc in the heart, liver, and kidney play an important role in the regulation of cellular respiration and cell death. Here, we report that Cytc purified from mammalian brain is phosphorylated on S47 and that this phosphorylation is lost during ischemia. We have characterized the functional effects in vitro using phosphorylated Cytc purified from pig brain tissue and a recombinant phosphomimetic mutant (S47E). We crystallized S47E phosphomimetic Cytc at 1.55 Å and suggest that it spatially matches S47-phosphorylated Cytc, making it a good model system. Both S47-phosphorylated and phosphomimetic Cytc showed a lower oxygen consumption rate in reaction with isolated Cytc oxidase, which we propose maintains intermediate mitochondrial membrane potentials under physiologic conditions, thus minimizing production of reactive oxygen species. S47-phosphorylated and phosphomimetic Cytc showed lower caspase-3 activity. Furthermore, phosphomimetic Cytc had decreased cardiolipin peroxidase activity and is more stable in the presence of H2O2. Our data suggest that S47 phosphorylation of Cytc is tissue protective and promotes cell survival in the brain.-Kalpage, H. A., Vaishnav, A., Liu, J., Varughese, A., Wan, J., Turner, A. A., Ji, Q., Zurek, M. P., Kapralov, A. A., Kagan, V. E., Brunzelle, J. S., Recanati, M.-A., Grossman, L. I., Sanderson, T. H., Lee, I., Salomon, A. R., Edwards, B. F. P, Hüttemann, M. Serine-47 phosphorylation of cytochrome c in the mammalian brain regulates cytochrome c oxidase and caspase-3 activity.
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Affiliation(s)
- Hasini A Kalpage
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan, USA
| | - Asmita Vaishnav
- Department of Biochemistry, Microbiology, and Immunology, Wayne State University, Detroit, Michigan, USA
| | - Jenney Liu
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan, USA
| | - Ashwathy Varughese
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan, USA.,Department of Biochemistry, Microbiology, and Immunology, Wayne State University, Detroit, Michigan, USA
| | - Junmei Wan
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan, USA.,Department of Biochemistry, Microbiology, and Immunology, Wayne State University, Detroit, Michigan, USA
| | - Alice A Turner
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan, USA.,Department of Biochemistry, Microbiology, and Immunology, Wayne State University, Detroit, Michigan, USA
| | - Qinqin Ji
- Department of Chemistry, Brown University, Providence, Rhode Island, USA
| | - Matthew P Zurek
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan, USA
| | - Alexandr A Kapralov
- Department of Environmental and Occupational Health, Center for Free Radical and Antioxidant Health, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Valerian E Kagan
- Department of Environmental and Occupational Health, Center for Free Radical and Antioxidant Health, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.,Laboratory of Navigational Redox Lipidomics, I. M. Sechenov Moscow Medical State University, Moscow, Russia
| | - Joseph S Brunzelle
- Center for Synchrotron Research, Northwestern University, Argonne, Illinois, USA
| | - Maurice-Andre Recanati
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan, USA.,Department of Obstetrics and Gynecology, Wayne State University, Detroit, Michigan, USA
| | - Lawrence I Grossman
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan, USA
| | - Thomas H Sanderson
- Department of Emergency Medicine, University of Michigan Medical School, Ann Arbor, Michigan, USA.,Department of Molecular and Integrative Physiology, University of Michigan Medical School, Ann Arbor, Michigan, USA.,Cardiovascular Research Institute, Wayne State University School of Medicine, Detroit, Michigan, USA
| | - Icksoo Lee
- College of Medicine, Dankook University, Cheonan-si, South Korea
| | - Arthur R Salomon
- Department of Chemistry, Brown University, Providence, Rhode Island, USA
| | - Brian F P Edwards
- Department of Biochemistry, Microbiology, and Immunology, Wayne State University, Detroit, Michigan, USA
| | - Maik Hüttemann
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan, USA.,Department of Biochemistry, Microbiology, and Immunology, Wayne State University, Detroit, Michigan, USA.,Cardiovascular Research Institute, Wayne State University School of Medicine, Detroit, Michigan, USA
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24
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Cytochrome c: An extreme multifunctional protein with a key role in cell fate. Int J Biol Macromol 2019; 136:1237-1246. [DOI: 10.1016/j.ijbiomac.2019.06.180] [Citation(s) in RCA: 88] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 06/24/2019] [Accepted: 06/24/2019] [Indexed: 01/25/2023]
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25
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Engilberge S, Rennie ML, Crowley PB. Calixarene capture of partially unfolded cytochrome c. FEBS Lett 2019; 593:2112-2117. [PMID: 31254353 DOI: 10.1002/1873-3468.13512] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 06/20/2019] [Accepted: 06/20/2019] [Indexed: 12/18/2022]
Abstract
Supramolecular receptors such as water-soluble calixarenes are in development as 'molecular glues' for protein assembly. Here, we obtained cocrystals of sulfonato-calix[6]arene (sclx6 ) and yeast cytochrome c (cytc) in the presence of imidazole. A crystal structure at 2.65 Å resolution reveals major structural rearrangement and disorder in imidazole-bound cytc. The largest protein-calixarene interface involves 440 Å2 of the protein surface with key contacts at Arg13, Lys73, and Lys79. These lysines participate in alkaline transitions of cytc and are part of Ω-loop D, which is substantially restructured in the complex with sclx6 . The structural modification also includes Ω-loop C, which is disordered (residues 41-55 inclusive). These results suggest the possibility of using supramolecular scaffolds to trap partially disordered proteins.
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Affiliation(s)
- Sylvain Engilberge
- School of Chemistry, National University of Ireland Galway, Galway, Ireland
| | - Martin L Rennie
- School of Chemistry, National University of Ireland Galway, Galway, Ireland
| | - Peter B Crowley
- School of Chemistry, National University of Ireland Galway, Galway, Ireland
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26
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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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27
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Oviedo-Rouco S, Castro MA, Alvarez-Paggi D, Spedalieri C, Tortora V, Tomasina F, Radi R, Murgida DH. The alkaline transition of cytochrome c revisited: Effects of electrostatic interactions and tyrosine nitration on the reaction dynamics. Arch Biochem Biophys 2019; 665:96-106. [DOI: 10.1016/j.abb.2019.02.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 02/18/2019] [Accepted: 02/19/2019] [Indexed: 12/19/2022]
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28
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Yin V, Mian SH, Konermann L. Lysine carbonylation is a previously unrecognized contributor to peroxidase activation of cytochrome c by chloramine-T. Chem Sci 2019; 10:2349-2359. [PMID: 30881663 PMCID: PMC6385661 DOI: 10.1039/c8sc03624a] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 12/30/2018] [Indexed: 12/31/2022] Open
Abstract
The peroxidase activity of cytochrome c (cyt c) plays a key role during apoptosis. Peroxidase catalysis requires a vacant Fe coordination site, i.e., cyt c must undergo an activation process involving structural changes that rupture the native Met80-Fe contact. A common strategy for dissociating this bond is the conversion of Met80 to sulfoxide (MetO). It is widely believed that this MetO formation in itself is sufficient for cyt c activation. This notion originates from studies on chloramine-T-treated cyt c (CT-cyt c) which represents a standard model for the peroxidase activated state. CT-cyt c is considered to be a "clean" species that has undergone selective MetO formation, without any other modifications. Using optical, chromatographic, and mass spectrometry techniques, the current work demonstrates that CT-induced activation of cyt c is more complicated than previously thought. MetO formation alone results in only marginal peroxidase activity, because dissociation of the Met80-Fe bond triggers alternative ligation scenarios where Lys residues interfere with access to the heme. We found that CT causes not only MetO formation, but also carbonylation of several Lys residues. Carbonylation is associated with -1 Da mass shifts that have gone undetected in the CT-cyt c literature. Proteoforms possessing both MetO and Lys carbonylation exhibit almost fourfold higher peroxidase activity than those with MetO alone. Carbonylation abrogates the capability of Lys to coordinate the heme, thereby freeing up the distal site as required for an active peroxidase. Previous studies on CT-cyt c may have inadvertently examined carbonylated proteoforms, potentially misattributing effects of carbonylation to solely MetO formation.
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Affiliation(s)
- Victor Yin
- Department of Chemistry and Department of Biochemistry , The University of Western Ontario , London , Ontario N6A 5B7 , Canada .
| | - Safee H Mian
- Department of Chemistry and Department of Biochemistry , The University of Western Ontario , London , Ontario N6A 5B7 , Canada .
| | - Lars Konermann
- Department of Chemistry and Department of Biochemistry , The University of Western Ontario , London , Ontario N6A 5B7 , Canada .
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