1
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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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2
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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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3
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Che F, Zhao J, Zhao Y, Wang Z, Zhang L, Yang Y. A Novel Heterozygous Pathogenic Variation in CYCS Gene Cause Autosomal Dominant Non-Syndromic Thrombocytopenia 4 in a Large Chinese Family. Front Genet 2022; 12:783455. [PMID: 35126455 PMCID: PMC8811603 DOI: 10.3389/fgene.2021.783455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Accepted: 12/06/2021] [Indexed: 11/23/2022] Open
Abstract
Aim: To determine the etiology of a Chinese family with thrombocytopenia by analyzing the clinical features and genetic variation. Methods: Clinical profiles and genomic DNA extracts of the family members were collected for the study. Whole exome sequencing and Sanger sequencing was used to detect the associated genetic variation and verify the family co-segregation respectively. Bioinformatics analysis assessed the pathogenicity of missense mutations. Results: The study reported a 3-generation pedigree including eight family members with thrombocytopenia. The platelet counts of the patients were varied, ranging from 38 to 110 × 109/L (reference range: 150–450 x 109/L). The mean volumes and morphology of the sampled platelet were both normal. The bleeding abnormality and mitochondriopathy were not observed in all the patients. Clinical signs of thrombocytopenia were mild. A novel heterozygous missense variant c.79C > T (p.His27Tyr) was identified in CYCS gene associated with autosomal dominant thrombocytopenia. Conclusion: We report the first large family with autosomal dominant non-syndromic thrombocytopenia 4 in a Chinese family, a novel heterozygous missense variant c.79C > T (p.His27Tyr) was identified. The whole exome sequencing is an efficient tool for screening the variants specifically associated with the disease. The finding enriches the mutation spectrum of CYCS gene and laid a foundation for future studies on the correlation between genotype and phenotype.
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Affiliation(s)
- Fengyu Che
- Shaanxi Institute for Pediatric Diseases, Xi’an Children’s Hospital, Xi’an, China
| | - Jiangang Zhao
- Department of Neonatology, Xi’an Children’s Hospital, Xi’an, China
| | - Yujuan Zhao
- Department of Neonatology, Xi’an Children’s Hospital, Xi’an, China
| | - Zhi Wang
- Department of Neonatology, Xi’an Children’s Hospital, Xi’an, China
| | - Liyu Zhang
- Shaanxi Institute for Pediatric Diseases, Xi’an Children’s Hospital, Xi’an, China
| | - Ying Yang
- Shaanxi Institute for Pediatric Diseases, Xi’an Children’s Hospital, Xi’an, China
- *Correspondence: Ying Yang,
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4
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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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5
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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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6
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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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7
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Josefsson EC, Vainchenker W, James C. Regulation of Platelet Production and Life Span: Role of Bcl-xL and Potential Implications for Human Platelet Diseases. Int J Mol Sci 2020; 21:ijms21207591. [PMID: 33066573 PMCID: PMC7589436 DOI: 10.3390/ijms21207591] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 10/09/2020] [Accepted: 10/10/2020] [Indexed: 01/14/2023] Open
Abstract
Blood platelets have important roles in haemostasis, where they quickly stop bleeding in response to vascular damage. They have also recognised functions in thrombosis, immunity, antimicrobal defense, cancer growth and metastasis, tumour angiogenesis, lymphangiogenesis, inflammatory diseases, wound healing, liver regeneration and neurodegeneration. Their brief life span in circulation is strictly controlled by intrinsic apoptosis, where the prosurvival Bcl-2 family protein, Bcl-xL, has a major role. Blood platelets are produced by large polyploid precursor cells, megakaryocytes, residing mainly in the bone marrow. Together with Mcl-1, Bcl-xL regulates megakaryocyte survival. This review describes megakaryocyte maturation and survival, platelet production, platelet life span and diseases of abnormal platelet number with a focus on the role of Bcl-xL during these processes.
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Affiliation(s)
- Emma C Josefsson
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC 3052, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, VIC 3052, Australia
| | - William Vainchenker
- University Paris-Saclay, INSERM UMR 1270, Gustave Roussy, 94800 Villejuif, France
| | - Chloe James
- University of Bordeaux, INSERM U1034, Biology of Cardiovascular Diseases, 33600 Pessac, France
- Laboratory of Hematology, Bordeaux University Hospital Center, Haut-Leveque Hospital, 33604 Pessac, France
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8
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Lalli D, Rosa C, Allegrozzi M, Turano P. Distal Unfolding of Ferricytochrome c Induced by the F82K Mutation. Int J Mol Sci 2020; 21:ijms21062134. [PMID: 32244917 PMCID: PMC7139943 DOI: 10.3390/ijms21062134] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 03/17/2020] [Accepted: 03/18/2020] [Indexed: 01/03/2023] Open
Abstract
It is well known that axial coordination of heme iron in mitochondrial cytochrome c has redox-dependent stability. The Met80 heme iron axial ligand in the ferric form of the protein is relatively labile and can be easily replaced by alternative amino acid side chains under non-native conditions induced by alkaline pH, high temperature, or denaturing agents. Here, we showed a redox-dependent destabilization induced in human cytochrome c by substituting Phe82-conserved amino acid and a key actor in cytochrome c intermolecular interactions-with a Lys residue. Introducing a positive charge at position 82 did not significantly affect the structure of ferrous cytochrome c but caused localized unfolding of the distal site in the ferric state. As revealed by 1H NMR fingerprint, the ferric form of the F82K variant had axial coordination resembling the renowned alkaline species, where the detachment of the native Met80 ligand favored the formation of multiple conformations involving distal Lys residues binding to iron, but with more limited overall structural destabilization.
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Affiliation(s)
- Daniela Lalli
- Magnetic Resonance Center (CERM) and Department of Chemistry, University of Florence, 50019 Sesto Fiorentino, Florence, Italy; (D.L.); (C.R.); (M.A.)
- Present Address: Dipartimento di Scienze e Innovazione Tecnologica, Università del Piemonte Orientale “A. Avogadro”, Viale T. Michel 11, 15121 Alessandria, Italy
| | - Camilla Rosa
- Magnetic Resonance Center (CERM) and Department of Chemistry, University of Florence, 50019 Sesto Fiorentino, Florence, Italy; (D.L.); (C.R.); (M.A.)
| | - Marco Allegrozzi
- Magnetic Resonance Center (CERM) and Department of Chemistry, University of Florence, 50019 Sesto Fiorentino, Florence, Italy; (D.L.); (C.R.); (M.A.)
| | - Paola Turano
- Magnetic Resonance Center (CERM) and Department of Chemistry, University of Florence, 50019 Sesto Fiorentino, Florence, Italy; (D.L.); (C.R.); (M.A.)
- Correspondence: ; Tel.: +39-055-457-4266
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9
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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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10
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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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11
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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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12
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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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13
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Ciambellotti S, Turano P. Structural Biology of Iron‐Binding Proteins by NMR Spectroscopy. Eur J Inorg Chem 2019. [DOI: 10.1002/ejic.201801261] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Silvia Ciambellotti
- Resonance Magnetic Center (CERM) University of Florence via Luigi Sacconi 6 50019 Sesto Fiorentino Italy
- Department of Chemistry University of Florence via della Lastruccia 3 50019 Sesto Fiorentino, Italy
| | - Paola Turano
- Resonance Magnetic Center (CERM) University of Florence via Luigi Sacconi 6 50019 Sesto Fiorentino Italy
- Department of Chemistry University of Florence via della Lastruccia 3 50019 Sesto Fiorentino, Italy
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14
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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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15
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About the use of 13C- 13C NOESY in bioinorganic chemistry. J Inorg Biochem 2018; 192:25-32. [PMID: 30562672 DOI: 10.1016/j.jinorgbio.2018.12.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Revised: 12/07/2018] [Accepted: 12/08/2018] [Indexed: 10/27/2022]
Abstract
Herein we present examples of the application of the 13C-13C Nuclear Overhauser Effect Spectroscopy (NOESY) experiment to the study of metalloproteins and we critically discuss the advantages and drawbacks of the method as a function of the molecular size of the investigated systems. The contribution is focused on a few case studies among the systems analyzed in the group of the corresponding author. The 13C-13C NOESY experiment represents the gold standard for the observation of NMR signals in the 480 kDa ferritin nanocage and for monitoring its interaction with iron. By decreasing the protein size, the experiment progressively loses its importance as a tool for the detection of the complete spin pattern of the amino acid side chains, as exemplified by nickel-dependent regulatory protein, NikR (molecular mass of the homo-tetramer ~80 kDa). In very small proteins, such as mitochondrial cytochrome c (12.3 kDa), we are only able to detect cross peaks between adjacent 13C nuclei; this feature turned out to be useful for the assignment of the 13C core resonances of the porphyrin in a uniformly enriched heme.
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16
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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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17
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Parakra RD, Kleffmann T, Jameson GNL, Ledgerwood EC. The proportion of Met80-sulfoxide dictates peroxidase activity of human cytochrome c. Dalton Trans 2018; 47:9128-9135. [PMID: 29944150 DOI: 10.1039/c8dt02185f] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The peroxidase activity of cytochrome c is proposed to contribute to apoptosis by peroxidation of cardiolipin in the mitochondrial inner membrane. However, cytochrome c heme is hexa-coordinate with a methionine (Met80) on the distal side, stopping it from acting as an efficient peroxidase. The first naturally occurring variant of cytochrome c discovered, G41S, has higher peroxidase activity than wild-type. To understand the basis for this increase and gain insight into the peroxidase activity of wild-type, we have studied wild-type, G41S and the unnatural variant G41T. Through a combined kinetic and mass spectrometric analysis, we have shown that hydrogen peroxide specifically oxidizes Met80 to the sulfoxide. In the absence of substrate this can be further oxidized to the sulfone, leading to a decrease in peroxidase activity. Peroxidase activity can be correlated with the proportion of sulfoxide present and if fully in that form, all variants have the same activity without a lag phase caused by activation of the protein.
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Affiliation(s)
- Rinky D Parakra
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, PO Box 56, Dunedin 9054, New Zealand.
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18
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Deng Y, Zhong F, Alden SL, Hoke KR, Pletneva EV. The K79G Mutation Reshapes the Heme Crevice and Alters Redox Properties of Cytochrome c. Biochemistry 2018; 57:5827-5840. [PMID: 30142276 DOI: 10.1021/acs.biochem.8b00650] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The two roles of cytochrome c (cyt c), in oxidative phosphorylation and apoptosis, critically depend on redox properties of its heme iron center. The K79G mutant has served as a parent protein for a series of mutants of yeast iso-1 cyt c. The mutation preserves the Met80 coordination to the heme iron, as found in WT* (K72A/C102S), and many spectroscopic properties of K79G and WT* are indistinguishable. The K79G mutation does not alter the global stability, fold, rate of Met80 dissociation, or thermodynamics of the alkaline transition (p Ka) of the protein. However, the reduction potential of the heme iron decreases; further, the p KH of the trigger group and the rate of the Met-to-Lys ligand exchange associated with the alkaline transition decrease, suggesting changes in the environment of the heme. The rates of electron self-exchange and bimolecular electron transfer (ET) with positively charged inorganic complexes increase, as does the intrinsic peroxidase activity. Analysis of the reaction rates suggests that there is increased accessibility of the heme edge in K79G and supports the importance of the Lys79 site for bimolecular ET reactions of cyt c, including those with some of its native redox partners. Structural modeling rationalizes the observed effects to arise from changes in the volume of the heme pocket and solvent accessibility of the heme group. Kinetic and structural analyses of WT* characterize the properties of the heme crevice of this commonly employed reference variant. This study highlights the important role of Lys79 for defining functional redox properties of cyt c.
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Affiliation(s)
- Yunling Deng
- Department of Chemistry , Dartmouth College , Hanover , New Hampshire 03755 , United States
| | - 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
| | - 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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19
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Carbene capture in a myoglobin mutant. Nat Catal 2018. [DOI: 10.1038/s41929-018-0129-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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20
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Taguchi AT, Miyajima-Nakano Y, Fukazawa R, Lin MT, Baldansuren A, Gennis RB, Hasegawa K, Kumasaka T, Dikanov SA, Iwasaki T. Unpaired Electron Spin Density Distribution across Reduced [2Fe-2S] Cluster Ligands by 13Cβ-Cysteine Labeling. Inorg Chem 2017; 57:741-746. [DOI: 10.1021/acs.inorgchem.7b02676] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Alexander T. Taguchi
- Department of Biochemistry and Molecular Biology, Nippon Medical School, Sendagi, Tokyo 113-8602, Japan
| | - Yoshiharu Miyajima-Nakano
- Department of Biochemistry and Molecular Biology, Nippon Medical School, Sendagi, Tokyo 113-8602, Japan
| | - Risako Fukazawa
- Department of Biochemistry and Molecular Biology, Nippon Medical School, Sendagi, Tokyo 113-8602, Japan
| | | | - Amgalanbaatar Baldansuren
- Department of Veterinary
Clinical Medicine, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Robert B. Gennis
- Department of Biochemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Kazuya Hasegawa
- Japan Synchrotron Radiation Research Institute (SPring-8/JASRI), Sayo, Hyogo 679-5198, Japan
| | - Takashi Kumasaka
- Japan Synchrotron Radiation Research Institute (SPring-8/JASRI), Sayo, Hyogo 679-5198, Japan
| | - Sergei A. Dikanov
- Department of Veterinary
Clinical Medicine, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Toshio Iwasaki
- Department of Biochemistry and Molecular Biology, Nippon Medical School, Sendagi, Tokyo 113-8602, Japan
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21
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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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22
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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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23
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Investigation of structural dynamics of Thrombocytopenia Cargeeg mutants of human apoptotic cytochrome c: A molecular dynamics simulation approach. Biophys Chem 2017; 230:117-126. [PMID: 28958449 DOI: 10.1016/j.bpc.2017.09.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2017] [Revised: 09/04/2017] [Accepted: 09/21/2017] [Indexed: 11/24/2022]
Abstract
Naturally occurring mutations to cytochrome c (cyt-c) have been identified recently in patients with mild autosomal dominant thrombocytopenia (low platelet levels), which yield cyt-c mutants with enhanced apoptotic activity. However, the molecular mechanism underlying this low platelet production and enhanced apoptosis remain unclear. Therefore, an attempt is made herein for the first time to investigate the effects of mutations of glycine 41 by serine (G41S) and tyrosine 48 by histidine (Y48H) on the conformational and dynamic changes of apoptotic (Fe3+) cyt-c using all atom molecular dynamics (MD) simulations in explicit water solvent. Our 30ns MD simulations demonstrate considerable structural differences in G41S and Y48H compared to wild type (WT) cyt-c, such as increasing distances between the critical electron transfer residues results in open conformation at the heme active site, large fluctuations in β-turns and α-helices. Additionally, although the β-sheets remain mostly unaffected in all the three cyt-c simulations, the α-helices undergo conformational switch to β-turns in both the mutant simulations. Importantly, this conformational switch of α-helix to β-turn around heme active site should attributes to the loss of intraprotein H-bonds in the mutant simulations especially between NE2 (His26) and O (Pro44) in agreement with the experimental report. Further, essential dynamics analysis reveals that overall motions of WT cyt-c is mainly involved only in the first eigenvector, but in G41S and Y48H the overall motions are mainly in three and two eigenvectors respectively. Overall, the detailed atomistic level information provide a unifying description for the molecular mechanism of structural destabilization, disregulation of platelet formation and enhanced peroxidase activity of the mutant cyt-c's in the pathology of intrinsic apoptosis.
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24
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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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25
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Gu J, Shin DW, Pletneva EV. Remote Perturbations in Tertiary Contacts Trigger Ligation of Lysine to the Heme Iron in Cytochrome c. Biochemistry 2017; 56:2950-2966. [PMID: 28474881 DOI: 10.1021/acs.biochem.6b01187] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Perturbations in protein structure define the mechanism of allosteric regulation and biological information transfer. In cytochrome c (cyt c), ligation of Met80 to the heme iron is critical for the protein's electron-transfer (ET) function in oxidative phosphorylation and for suppressing its peroxidase activity in apoptosis. The hard base Lys is a better match for the hard ferric iron than the soft base Met is, suggesting the key role of the protein scaffold in favoring Met ligation. To probe the role of the protein structure in the maintenance of Met ligation, mutations T49V and Y67R/M80A were designed to disrupt hydrogen bonding and packing of the heme coordination loop, respectively. Electronic absorption, nuclear magnetic resonance, and electron paramagnetic resonance spectra reveal that ferric forms of both variants are Lys-ligated at neutral pH. A minor change in the tertiary contacts in T49V, away from the heme coordination loop, appears to be sufficient to execute a change in ligation, suggesting a cross-talk between the different regions of the protein structure and a possibility of built-in conformational switches in cyt c. Analyses of thermodynamic stability, kinetics of Lys binding and dissociation, and the pH-dependent changes in ligation provide a detailed characterization of the Lys coordination in these variants and relate these properties to the extent of structural perturbations. The findings emphasize the importance of the hydrogen-bonding network in controlling ligation of the native Met80 to the heme iron.
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Affiliation(s)
- Jie Gu
- Department of Chemistry, Dartmouth College , Hanover, New Hampshire 03755, United States
| | - Dong-Woo Shin
- 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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26
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Ong L, Morison IM, Ledgerwood EC. Megakaryocytes fromCYCSmutation-associated thrombocytopenia release platelets by both proplatelet-dependent and -independent processes. Br J Haematol 2016; 176:268-279. [DOI: 10.1111/bjh.14421] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Accepted: 08/31/2016] [Indexed: 12/30/2022]
Affiliation(s)
- Lily Ong
- Department of Biochemistry; Otago School of Medical Sciences; University of Otago; Dunedin New Zealand
| | - Ian M. Morison
- Department of Pathology; Dunedin School of Medicine; University of Otago; Dunedin New Zealand
| | - Elizabeth C. Ledgerwood
- Department of Biochemistry; Otago School of Medical Sciences; University of Otago; Dunedin New Zealand
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27
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Bren KL. Going with the Electron Flow: Heme Electronic Structure and Electron Transfer in Cytochrome
c. Isr J Chem 2016. [DOI: 10.1002/ijch.201600021] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Kara L. Bren
- Department of Chemistry University of Rochester Rochester NY 14627-0216 USA
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28
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Karsisiotis AI, Deacon OM, Wilson MT, Macdonald C, Blumenschein TMA, Moore GR, Worrall JAR. Increased dynamics in the 40-57 Ω-loop of the G41S variant of human cytochrome c promote its pro-apoptotic conformation. Sci Rep 2016; 6:30447. [PMID: 27461282 PMCID: PMC4962053 DOI: 10.1038/srep30447] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Accepted: 07/05/2016] [Indexed: 12/26/2022] Open
Abstract
Thrombocytopenia 4 is an inherited autosomal dominant thrombocytopenia, which occurs due to mutations in the human gene for cytochrome c that results in enhanced mitochondrial apoptotic activity. The Gly41Ser mutation was the first to be reported. Here we report stopped-flow kinetic studies of azide binding to human ferricytochrome c and its Gly41Ser variant, together with backbone amide H/D exchange and 15N-relaxation dynamics using NMR spectroscopy, to show that alternative conformations are kinetically and thermodynamically more readily accessible for the Gly41Ser variant than for the wild-type protein. Our work reveals a direct conformational link between the 40–57 Ω-loop in which residue 41 resides and the dynamical properties of the axial ligand to the heme iron, Met80, such that the replacement of glycine by serine promotes the dissociation of the Met80 ligand, thereby increasing the population of a peroxidase active state, which is a key non-native conformational state in apoptosis.
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Affiliation(s)
| | - Oliver M Deacon
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK
| | - Michael T Wilson
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK
| | - Colin Macdonald
- School of Chemistry, University of East Anglia, Norwich Research Park, NR4 7TJ, UK
| | | | - Geoffrey R Moore
- School of Chemistry, University of East Anglia, Norwich Research Park, NR4 7TJ, UK
| | - Jonathan A R Worrall
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK
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29
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Senge MO, MacGowan SA, O'Brien JM. Conformational control of cofactors in nature - the influence of protein-induced macrocycle distortion on the biological function of tetrapyrroles. Chem Commun (Camb) 2016; 51:17031-63. [PMID: 26482230 DOI: 10.1039/c5cc06254c] [Citation(s) in RCA: 135] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Tetrapyrrole-containing proteins are one of the most fundamental classes of enzymes in nature and it remains an open question to give a chemical rationale for the multitude of biological reactions that can be catalyzed by these pigment-protein complexes. There are many fundamental processes where the same (i.e., chemically identical) porphyrin cofactor is involved in chemically quite distinct reactions. For example, heme is the active cofactor for oxygen transport and storage (hemoglobin, myoglobin) and for the incorporation of molecular oxygen in organic substrates (cytochrome P450). It is involved in the terminal oxidation (cytochrome c oxidase) and the metabolism of H2O2 (catalases and peroxidases) and catalyzes various electron transfer reactions in cytochromes. Likewise, in photosynthesis the same chlorophyll cofactor may function as a reaction center pigment (charge separation) or as an accessory pigment (exciton transfer) in light harvesting complexes (e.g., chlorophyll a). Whilst differences in the apoprotein sequences alone cannot explain the often drastic differences in physicochemical properties encountered for the same cofactor in diverse protein complexes, a critical factor for all biological functions must be the close structural interplay between bound cofactors and the respective apoprotein in addition to factors such as hydrogen bonding or electronic effects. Here, we explore how nature can use the same chemical molecule as a cofactor for chemically distinct reactions using the concept of conformational flexibility of tetrapyrroles. The multifaceted roles of tetrapyrroles are discussed in the context of the current knowledge on distorted porphyrins. Contemporary analytical methods now allow a more quantitative look at cofactors in protein complexes and the development of the field is illustrated by case studies on hemeproteins and photosynthetic complexes. Specific tetrapyrrole conformations are now used to prepare bioengineered designer proteins with specific catalytic or photochemical properties.
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Affiliation(s)
- Mathias O Senge
- School of Chemistry, SFI Tetrapyrrole Laboratory, Trinity Biomedical Sciences Institute, Trinity College Dublin, The University of Dublin, 152-160 Pearse Street, Dublin 2, Ireland and Medicinal Chemistry, Institute of Molecular Medicine, Trinity Centre for Health Sciences, Trinity College Dublin, St. James's Hospital, Dublin 8, Ireland.
| | - Stuart A MacGowan
- School of Chemistry, SFI Tetrapyrrole Laboratory, Trinity Biomedical Sciences Institute, Trinity College Dublin, The University of Dublin, 152-160 Pearse Street, Dublin 2, Ireland
| | - Jessica M O'Brien
- Medicinal Chemistry, Institute of Molecular Medicine, Trinity Centre for Health Sciences, Trinity College Dublin, St. James's Hospital, Dublin 8, Ireland.
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30
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Structural and functional characterization of phosphomimetic mutants of cytochrome c at threonine 28 and serine 47. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2016; 1857:387-95. [PMID: 26806033 DOI: 10.1016/j.bbabio.2016.01.011] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2015] [Revised: 01/15/2016] [Accepted: 01/20/2016] [Indexed: 12/31/2022]
Abstract
Protein function is frequently modulated by post-translational modifications of specific residues. Cytochrome c, in particular, is phosphorylated in vivo at threonine 28 and serine 47. However, the effect of such modifications on the physiological functions of cytochrome c - namely, the transfer of electrons in the respiratory electron transport chain and the triggering of programmed cell death - is still unknown. Here we replace each of these two residues by aspartate, in order to mimic phosphorylation, and report the structural and functional changes in the resulting cytochrome c variants. We find that the T28D mutant causes a 30-mV decrease on the midpoint redox potential and lowers the affinity for the distal site of Arabidopsis thaliana cytochrome c1 in complex III. Both the T28D and S47D variants display a higher efficiency as electron donors for the cytochrome c oxidase activity of complex IV. In both protein mutants, the peroxidase activity is significantly higher, which is related to the ability of cytochrome c to leave the mitochondria and reach the cytoplasm. We also find that both mutations at serine 47 (S47D and S47A) impair the ability of cytoplasmic cytochrome c to activate the caspases cascade, which is essential for triggering programmed cell death.
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31
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Hannibal L, Tomasina F, Capdevila DA, Demicheli V, Tórtora V, Alvarez-Paggi D, Jemmerson R, Murgida DH, Radi R. Alternative Conformations of Cytochrome c: Structure, Function, and Detection. Biochemistry 2016; 55:407-28. [DOI: 10.1021/acs.biochem.5b01385] [Citation(s) in RCA: 89] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Luciana Hannibal
- Departamento
de Bioquímica, Facultad de Medicina, Universidad de la República, Avda. General Flores 2125, 11800 Montevideo, Uruguay
- Centro
de Investigaciones Biomédicas (CEINBIO), Facultad de Medicina, Universidad de la República, Avda. General Flores 2125, 11800 Montevideo, Uruguay
- Center
for Pediatrics and Adolescent Medicine, Medical Center, University of Freiburg, Mathildenstrasse 1, Freiburg D-79106, Germany
| | - Florencia Tomasina
- Departamento
de Bioquímica, Facultad de Medicina, Universidad de la República, Avda. General Flores 2125, 11800 Montevideo, Uruguay
- Centro
de Investigaciones Biomédicas (CEINBIO), Facultad de Medicina, Universidad de la República, Avda. General Flores 2125, 11800 Montevideo, Uruguay
| | - Daiana A. Capdevila
- Departamento
de Química Inorgánica, Analítica y Química
Física/INQUIMAE, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Pabellón 2, Ciudad Universitaria, C1428EHA Buenos Aires, Argentina
| | - Verónica Demicheli
- Departamento
de Bioquímica, Facultad de Medicina, Universidad de la República, Avda. General Flores 2125, 11800 Montevideo, Uruguay
- Centro
de Investigaciones Biomédicas (CEINBIO), Facultad de Medicina, Universidad de la República, Avda. General Flores 2125, 11800 Montevideo, Uruguay
| | - Verónica Tórtora
- Departamento
de Bioquímica, Facultad de Medicina, Universidad de la República, Avda. General Flores 2125, 11800 Montevideo, Uruguay
- Centro
de Investigaciones Biomédicas (CEINBIO), Facultad de Medicina, Universidad de la República, Avda. General Flores 2125, 11800 Montevideo, Uruguay
| | - Damián Alvarez-Paggi
- Departamento
de Química Inorgánica, Analítica y Química
Física/INQUIMAE, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Pabellón 2, Ciudad Universitaria, C1428EHA Buenos Aires, Argentina
| | - Ronald Jemmerson
- Department
of Microbiology and Immunology, University of Minnesota, MMC 196,
420 Delaware Street, Southeast, Minneapolis, Minnesota 55455, United States
| | - Daniel H. Murgida
- Departamento
de Química Inorgánica, Analítica y Química
Física/INQUIMAE, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Pabellón 2, Ciudad Universitaria, C1428EHA Buenos Aires, Argentina
| | - Rafael Radi
- Departamento
de Bioquímica, Facultad de Medicina, Universidad de la República, Avda. General Flores 2125, 11800 Montevideo, Uruguay
- Centro
de Investigaciones Biomédicas (CEINBIO), Facultad de Medicina, Universidad de la República, Avda. General Flores 2125, 11800 Montevideo, Uruguay
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32
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Kleingardner JG, Bren KL. Biological significance and applications of heme c proteins and peptides. Acc Chem Res 2015; 48:1845-52. [PMID: 26083801 DOI: 10.1021/acs.accounts.5b00106] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Hemes are ubiquitous in biology and carry out a wide range of functions. The heme group is largely invariant across proteins with different functions, although there are a few variations seen in nature. The most common variant is heme c, which is formed by a post-translational modification in which heme is covalently linked to two Cys residues on the polypeptide via thioether bonds. In this Account, the influence of this covalent attachment on heme c properties and function is discussed, and examples of how covalent attachment has been used in selected applications are presented. Proteins that bind heme c are among the most well-characterized proteins in biochemistry. Most of these proteins are cytochromes c (cyts c) that serve as electron carriers in photosynthesis and respiration. Despite the intense study of cyts c, the functional significance of heme covalent attachment has remained elusive. One observation is that heme c reaches a lower reduction potential in nature than its noncovalently linked counterpart, heme b, when comparing proteins with the same axial ligands. Furthermore, covalent attachment is known to enhance protein stability and allow the heme to be relatively solvent exposed. However, an inorganic chemistry perspective on the effects of covalent attachment has been lacking. Spectroscopic measurements and computations on cyts c and model systems reveal a number of effects of covalent attachment on heme electronic structure and reactivity. One is that the predominant nonplanar ruffling distortion seen in heme c lowers heme reduction potential. Another is that covalent attachment influences the interaction of the heme iron with the proximal His ligand. Heme ruffling also has been shown to influence electronic coupling to redox partners and, therefore, electron transfer rates by altering the distribution of the orbital hole on the porphyrin in oxidized cyt c. Another consequence of heme covalent attachment is the strong vibrational coupling seen between the iron and the protein surface as revealed by nuclear resonance vibrational spectroscopy studies. Finally, heme covalent attachment is proposed to be an important feature supporting multiple roles of cyt c in programmed cell death (apoptosis). Heme covalent attachment is not only vital for the biological functions of cyt c but also provides a useful handle in a number of applications. For one, the engineering of heme c onto an exposed portion of a protein of interest has been shown to provide a visible affinity purification tag. In addition, peptides with covalently attached heme, known as microperoxidases, have been studied as model compounds and oxidation catalysts and, more recently, in applications for energy conversion and storage. The wealth of insight gained about heme c through fundamental studies of cyts c forms a basis for future efforts toward engineering natural and artificial cytochromes for a variety of applications.
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Affiliation(s)
- Jesse G. Kleingardner
- Department
of Chemistry, Ithaca College, Ithaca, New York 14850, United States
- Department
of Chemistry, University of Rochester, Rochester, New York 14618, United States
| | - Kara L. Bren
- Department
of Chemistry, University of Rochester, Rochester, New York 14618, United States
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33
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Josephs TM, Hibbs ME, Ong L, Morison IM, Ledgerwood EC. Interspecies Variation in the Functional Consequences of Mutation of Cytochrome c. PLoS One 2015; 10:e0130292. [PMID: 26086723 PMCID: PMC4472513 DOI: 10.1371/journal.pone.0130292] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Accepted: 05/19/2015] [Indexed: 01/08/2023] Open
Abstract
The naturally occurring human cytochrome c variant (G41S) is associated with a mild autosomal dominant thrombocytopenia (Thrombocytopenia Cargeeg) caused by dysregulation of platelet production. The molecular basis of the platelet production defect is unknown. Despite high conservation of cytochrome c between human and mouse (91.4% identity), introducing the G41S mutation into mouse cytochrome c in a knockin mouse (CycsG41S/G41S) did not recapitulate the low platelet phenotype of Thrombocytopenia Cargeeg. While investigating the cause of this disparity we found a lack of conservation of the functional impact of cytochrome c mutations on caspase activation across species. Mutation of cytochrome c at residue 41 has distinct effects on the ability of cytochrome c to activate caspases depending on the species of both the cytochrome c and its binding partner Apaf-1. In contrast to our previous results showing the G41S mutation increases the ability of human cytochrome c to activate caspases, here we find this activity is decreased in mouse G41S cytochrome c. Additionally unlike wildtype human cytochrome c, G41S cytochrome c is unable to activate caspases in Xenopus embryo extracts. Taken together these results demonstrate a previously unreported species-specific component to the interaction of cytochrome c with Apaf-1. This suggests that the electrostatic interaction between cytochrome c and Apaf-1 is not the sole determinant of binding, with additional factors controlling binding specificity and affinity. These results have important implications for studies of the effects of cytochrome c mutations on the intrinsic apoptosis pathway.
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Affiliation(s)
- Tracy M. Josephs
- Department of Biochemistry, Otago School of Medical Sciences, University of Otago, Dunedin, New Zealand
| | - Moira E. Hibbs
- Department of Biochemistry, Otago School of Medical Sciences, University of Otago, Dunedin, New Zealand
| | - Lily Ong
- Department of Biochemistry, Otago School of Medical Sciences, University of Otago, Dunedin, New Zealand
| | - Ian M. Morison
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Elizabeth C. Ledgerwood
- Department of Biochemistry, Otago School of Medical Sciences, University of Otago, Dunedin, New Zealand
- * E-mail:
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34
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The hydrogen-peroxide-induced radical behaviour in human cytochrome c-phospholipid complexes: implications for the enhanced pro-apoptotic activity of the G41S mutant. Biochem J 2015; 456:441-52. [PMID: 24099549 DOI: 10.1042/bj20130758] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
We have investigated whether the pro-apoptotic properties of the G41S mutant of human cytochrome c can be explained by a higher than wild-type peroxidase activity triggered by phospholipid binding. A key complex in mitochondrial apoptosis involves cytochrome c and the phospholipid cardiolipin. In this complex cytochrome c has its native axial Met(80) ligand dissociated from the haem-iron, considerably augmenting the peroxidase capability of the haem group upon H2O2 binding. By EPR spectroscopy we reveal that the magnitude of changes in the paramagnetic haem states, as well as the yield of protein-bound free radical, is dependent on the phospholipid used and is considerably greater in the G41S mutant. A high-resolution X-ray crystal structure of human cytochrome c was determined and, in combination with the radical EPR signal analysis, two tyrosine residues, Tyr(46) and Tyr(48), have been rationalized to be putative radical sites. Subsequent single and double tyrosine-to-phenylalanine mutations revealed that the EPR signal of the radical, found to be similar in all variants, including G41S and wild-type, originates not from a single tyrosine residue, but is instead a superimposition of multiple EPR signals from different radical sites. We propose a mechanism of multiple radical formations in the cytochrome c-phospholipid complexes under H2O2 treatment, consistent with the stabilization of the radical in the G41S mutant, which elicits a greater peroxidase activity from cytochrome c and thus has implications in mitochondrial apoptosis.
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35
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The selective interaction between silica nanoparticles and enzymes from molecular dynamics simulations. PLoS One 2014; 9:e107696. [PMID: 25243748 PMCID: PMC4171504 DOI: 10.1371/journal.pone.0107696] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2014] [Accepted: 08/14/2014] [Indexed: 11/19/2022] Open
Abstract
Nanoscale particles have become promising materials in many fields, such as cancer therapeutics, diagnosis, imaging, drug delivery, catalysis, as well as biosensors. In order to stimulate and facilitate these applications, there is an urgent need for the understanding of the interaction mode between the nano-particles and proteins. In this study, we investigate the orientation and adsorption between several enzymes (cytochrome c, RNase A, lysozyme) and 4 nm/11 nm silica nanoparticles (SNPs) by using molecular dynamics (MD) simulation. Our results show that three enzymes are adsorbed onto the surfaces of both 4 nm and 11 nm SNPs during our MD simulations and the small SNPs induce greater structural stabilization. The active site of cytochrome c is far away from the surface of 4 nm SNPs, while it is adsorbed onto the surface of 11 nm SNPs. We also explore the influences of different groups (-OH, -COOH, -NH2 and CH3) coated onto silica nanoparticles, which show significantly different impacts. Our molecular dynamics results indicate the selective interaction between silicon nanoparticles and enzymes, which is consistent with experimental results. Our study provides useful guides for designing/modifying nanomaterials to interact with proteins for their bio-applications.
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36
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Enhancing the peroxidase activity of cytochrome c by mutation of residue 41: implications for the peroxidase mechanism and cytochrome c release. Biochem J 2014; 458:259-65. [DOI: 10.1042/bj20131386] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Enzymatic and mitochondrial release analyses of residue 41 variants of native and cardiolipin-bound mammalian cytochromes c implicate mobility of the 40–57 Ω loop in induction of peroxidase activity, but show that loss of axial Fe co-ordination is not essential.
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37
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Gu J, Yang S, Rajic AJ, Kurnikov IV, Prytkova TR, Pletneva EV. Control of cytochrome c redox reactivity through off-pathway modifications in the protein hydrogen-bonding network. Chem Commun (Camb) 2014; 50:5355-7. [DOI: 10.1039/c3cc47943a] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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38
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De Rocco D, Cerqua C, Goffrini P, Russo G, Pastore A, Meloni F, Nicchia E, Moraes CT, Pecci A, Salviati L, Savoia A. Mutations of cytochrome c identified in patients with thrombocytopenia THC4 affect both apoptosis and cellular bioenergetics. Biochim Biophys Acta Mol Basis Dis 2013; 1842:269-74. [PMID: 24326104 DOI: 10.1016/j.bbadis.2013.12.002] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2013] [Revised: 11/26/2013] [Accepted: 12/02/2013] [Indexed: 10/25/2022]
Abstract
Inherited thrombocytopenias are heterogeneous diseases caused by at least 20 genes playing different role in the processes of megakaryopoiesis and platelet production. Some forms, such as thrombocytopenia 4 (THC4), are very rare and not well characterized. THC4 is an autosomal dominant mild thrombocytopenia described in only one large family from New Zealand and due to a mutation (G41S) of the somatic isoform of the cytochrome c (CYCS) gene. We report a novel CYCS mutation (Y48H) in patients from an Italian family. Similar to individuals carrying G41S, they have platelets of normal size and morphology, which are only partially reduced in number, but no prolonged bleeding episodes. In order to determine the pathogenetic consequences of Y48H, we studied the effects of the two CYCS mutations in yeast and mouse cellular models. In both cases, we found reduction of respiratory level and increased apoptotic rate, supporting the pathogenetic role of CYCS in thrombocytopenia.
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Affiliation(s)
- Daniela De Rocco
- Department of Medical Sciences, University of Trieste, Trieste, Italy
| | - Cristina Cerqua
- Clinical Genetics Unit, Dept. of Woman and Child Health, University of Padova, IRP Città della Speranza, Padova, Italy
| | - Paola Goffrini
- Department of Life Sciences, University of Parma, Parma, Italy
| | - Giovanna Russo
- Division of Pediatric Hematology/Oncology, University of Catania, Catania, Italy
| | | | | | - Elena Nicchia
- Department of Medical Sciences, University of Trieste, Trieste, Italy
| | - Carlos T Moraes
- Department of Neurology, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Alessandro Pecci
- Department of Internal Medicine, University of Pavia-IRCCS Policlinico San Matteo Foundation, Pavia, Italy
| | - Leonardo Salviati
- Clinical Genetics Unit, Dept. of Woman and Child Health, University of Padova, IRP Città della Speranza, Padova, Italy
| | - Anna Savoia
- Department of Medical Sciences, University of Trieste, Trieste, Italy; Institute for Maternal and Child Health-IRCCS Burlo Garofolo, Trieste, Italy.
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39
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GUIDOLIN DIEGO, AGNATI LUIGIF, TORTORELLA CINZIA, MARCOLI MANUELA, MAURA GUIDO, ALBERTIN GIOVANNA, FUXE KJELL. Neuroglobin as a regulator of mitochondrial-dependent apoptosis: A bioinformatics analysis. Int J Mol Med 2013; 33:111-6. [DOI: 10.3892/ijmm.2013.1564] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2013] [Accepted: 11/01/2013] [Indexed: 11/05/2022] Open
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40
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Parui PP, Deshpande MS, Nagao S, Kamikubo H, Komori H, Higuchi Y, Kataoka M, Hirota S. Formation of Oligomeric Cytochrome c during Folding by Intermolecular Hydrophobic Interaction between N- and C-Terminal α-Helices. Biochemistry 2013; 52:8732-44. [DOI: 10.1021/bi400986g] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Partha Pratim Parui
- Graduate
School of Materials Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
- Department
of Chemistry, Jadavpur University, Kolkata 700032, India
| | - Megha Subhash Deshpande
- Graduate
School of Materials Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Satoshi Nagao
- Graduate
School of Materials Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Hironari Kamikubo
- Graduate
School of Materials Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Hirofumi Komori
- Department
of Life Science, Graduate School of Life Science, University of Hyogo, 3-2-1 Koto, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan
- RIKEN SPring-8 Center, 1-1-1
Koto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Yoshiki Higuchi
- Department
of Life Science, Graduate School of Life Science, University of Hyogo, 3-2-1 Koto, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan
- RIKEN SPring-8 Center, 1-1-1
Koto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Mikio Kataoka
- Graduate
School of Materials Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Shun Hirota
- Graduate
School of Materials Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
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41
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Can M, Krucinska J, Zoppellaro G, Andersen NH, Wedekind JE, Hersleth HP, Andersson KK, Bren KL. Structural characterization of nitrosomonas europaea cytochrome c-552 variants with marked differences in electronic structure. Chembiochem 2013; 14:1828-38. [PMID: 23908017 DOI: 10.1002/cbic.201300118] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Indexed: 11/09/2022]
Abstract
Nitrosomonas europaea cytochrome c-552 (Ne c-552) variants with the same His/Met axial ligand set but with different EPR spectra have been characterized structurally, to aid understanding of how molecular structure determines heme electronic structure. Visible light absorption, Raman, and resonance Raman spectroscopy of the protein crystals was performed along with structure determination. The structures solved are those of Ne c-552, which displays a "HALS" (or highly anisotropic low-spin) EPR spectrum, and of the deletion mutant Ne N64Δ, which has a rhombic EPR spectrum. Two X-ray crystal structures of wild-type Ne c-552 are reported; one is of the protein isolated from N. europaea cells (Ne c-552n, 2.35 Å resolution), and the other is of recombinant protein expressed in Escherichia coli (Ne c-552r, 1.63 Å resolution). Ne N64Δ crystallized in two different space groups, and two structures are reported [monoclinic (2.1 Å resolution) and hexagonal (2.3 Å resolution)]. Comparison of the structures of the wild-type and mutant proteins reveals that heme ruffling is increased in the mutant; increased ruffling is predicted to yield a more rhombic EPR spectrum. The 2.35 Å Ne c-552n structure shows 18 molecules in the asymmetric unit; analysis of the structure is consistent with population of more than one axial Met configuration, as seen previously by NMR. Finally, the mutation was shown to yield a more hydrophobic heme pocket and to expel water molecules from near the axial Met. These structures reveal that heme pocket residue 64 plays multiple roles in regulating the axial ligand orientation and the interaction of water with the heme. These results support the hypothesis that more ruffled hemes lead to more rhombic EPR signals in cytochromes c with His/Met axial ligation.
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Affiliation(s)
- Mehmet Can
- Department of Chemistry, University of Rochester, Rochester, NY 14627 (USA)
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42
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Cacciatore S, Piccioli M, Turano P. Electron self-exchange of cytochrome c measured via13C detected protonless NMR. J PORPHYR PHTHALOCYA 2013. [DOI: 10.1142/s1088424612501404] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The use of protonless 13C′–13C′ EXSY (COCO-EXSY) is proposed here to measure electron self-exchange rates. The experiment is compared to the commonly employed 1H and 15N EXSY experiments using as a reference system human cytochrome c. In COCO-EXSY, the exchange peaks are stronger than in the other experiments with respect to the self peaks and their intensity is less dependent on the choice of the EXSY mixing time. The use of 13C directed detection may be essential for all those cases where T2 relaxation is detrimental, as in the case of proteins containing highly paramagnetic metal centers, or rotating slowly in solution, or where the amide signals are difficult to detect due to chemical or conformational exchange. The proposed experiment has a general applicability and can be used to monitor exchange phenomena different from electron self-exchange.
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Affiliation(s)
- Stefano Cacciatore
- Magnetic Resonance Center (CERM) and Department of Chemistry, University of Florence, Via L. Sacconi 6, Sesto, Fiorentino 50019, Italy
| | - Mario Piccioli
- Magnetic Resonance Center (CERM) and Department of Chemistry, University of Florence, Via L. Sacconi 6, Sesto, Fiorentino 50019, Italy
| | - Paola Turano
- Magnetic Resonance Center (CERM) and Department of Chemistry, University of Florence, Via L. Sacconi 6, Sesto, Fiorentino 50019, Italy
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43
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Conformational change and human cytochrome c function: mutation of residue 41 modulates caspase activation and destabilizes Met-80 coordination. J Biol Inorg Chem 2013; 18:289-97. [PMID: 23334161 DOI: 10.1007/s00775-012-0973-1] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2012] [Accepted: 12/26/2012] [Indexed: 01/22/2023]
Abstract
Cytochrome c is a highly conserved protein, with 20 residues identical in all eukaryotic cytochromes c. Gly-41 is one of these invariant residues, and is the position of the only reported naturally occurring mutation in cytochrome c (human G41S). The basis, if any, for the conservation of Gly-41 is unknown. The mutation of Gly-41 to Ser enhances the apoptotic activity of cytochrome c without altering its role in mitochondrial electron transport. Here we have studied additional residue 41 variants and determined their effects on cytochrome c functions and conformation. A G41T mutation decreased the ability of cytochrome c to induce caspase activation and decreased the redox potential, whereas a G41A mutation had no impact on caspase induction but the redox potential increased. All residue 41 variants decreased the pK (a) of a structural transition of oxidized cytochrome c to the alkaline conformation, and this correlated with a destabilization of the interaction of Met-80 with the heme iron(III) at physiological pH. In reduced cytochrome c the G41T and G41S mutations had distinct effects on a network of hydrogen bonds involving Met-80, and in G41T the conformational mobility of two Ω-loops was altered. These results suggest the impact of residue 41 on the conformation of cytochrome c influences its ability to act in both of its physiological roles, electron transport and caspase activation.
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44
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Kulikov AV, Shilov ES, Mufazalov IA, Gogvadze V, Nedospasov SA, Zhivotovsky B. Cytochrome c: the Achilles' heel in apoptosis. Cell Mol Life Sci 2012; 69:1787-97. [PMID: 22179840 PMCID: PMC11114681 DOI: 10.1007/s00018-011-0895-z] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2011] [Revised: 10/30/2011] [Accepted: 11/22/2011] [Indexed: 10/14/2022]
Abstract
Cytochrome c is a well-known mitochondrial protein that fulfills life-supporting functions by transferring electrons to the respiratory chain to maintain ATP production. However, during the activation of apoptotic machinery, it is released from mitochondria and, being in the cytosol, it either triggers the activation of the caspase cascade in intrinsic apoptotic pathway, or it is involved in the amplification of extrinsic apoptotic signaling. Accumulating evidence suggests that only unmodified holocytochrome c is efficient in the stimulation of apoptosis. Considering the importance of cytochrome c in both life and death, it was of significant interest to investigate the complete or partial cytochrome c deficiency in vivo. Here, we discuss the importance of distinct amino acid residues for various functions of cytochrome c in cells and mice with targeted cytochrome c mutations.
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Affiliation(s)
- A V Kulikov
- Faculty of Fundamental Medicine, Lomonosov Moscow State University, Moscow, Russia
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45
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Ly HK, Utesch T, Díaz-Moreno I, García-Heredia JM, De La Rosa MÁ, Hildebrandt P. Perturbation of the Redox Site Structure of Cytochrome c Variants upon Tyrosine Nitration. J Phys Chem B 2012; 116:5694-702. [DOI: 10.1021/jp302301m] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- H. Khoa Ly
- Institut für Chemie, Technische Universität Berlin, Sekr. PC14, Straße
des 17 Juni 135, D-10623 Berlin, Germany
| | - Tillmann Utesch
- Institut für Chemie, Technische Universität Berlin, Sekr. PC14, Straße
des 17 Juni 135, D-10623 Berlin, Germany
| | - Irene Díaz-Moreno
- Instituto de Bioquímica
Vegetal y Fotosíntesis, cicCartuja, Universidad de Sevialla-CSIC, Avda Americo Vespucio 49, Sevilla
41092, Spain
| | - José M. García-Heredia
- Instituto de Bioquímica
Vegetal y Fotosíntesis, cicCartuja, Universidad de Sevialla-CSIC, Avda Americo Vespucio 49, Sevilla
41092, Spain
| | - Miguel Ángel De La Rosa
- Instituto de Bioquímica
Vegetal y Fotosíntesis, cicCartuja, Universidad de Sevialla-CSIC, Avda Americo Vespucio 49, Sevilla
41092, Spain
| | - Peter Hildebrandt
- Institut für Chemie, Technische Universität Berlin, Sekr. PC14, Straße
des 17 Juni 135, D-10623 Berlin, Germany
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