1
|
Martin WJ, McClelland LJ, Nold SM, Boshae KL, Bowler BE. Effect of proline content and histidine ligation on the dynamics of Ω-loop D and the peroxidase activity of iso-1-cytochrome c. J Inorg Biochem 2024; 252:112474. [PMID: 38176365 DOI: 10.1016/j.jinorgbio.2023.112474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 12/20/2023] [Accepted: 12/20/2023] [Indexed: 01/06/2024]
Abstract
To study how proline residues affect the dynamics of Ω-loop D (residues 70 to 85) of cytochrome c, we prepared G83P and G83A variants of yeast iso-1-cytochrome c (iso-1-Cytc) in the presence and absence of a K73H mutation. Ω-loop D is important in controlling both the electron transfer function of Cytc and the peroxidase activity of Cytc used in apoptosis because it provides the Met80 heme ligand. The G83P and G83A mutations have no effect on the global stability of iso-1-Cytc in presence or absence of the K73H mutation. However, both mutations destabilize the His73-mediated alkaline conformer relative to the native state. pH jump stopped-flow experiments show that the dynamics of the His73-mediated alkaline transition are significantly enhanced by the G83P mutation. Gated electron transfer studies show that the enhanced dynamics result from an increased rate of return to the native state, whereas the rate of loss of Met80 ligation is unchanged by the G83P mutation. Thus, the G83P substitution does not stiffen the conformation of the native state. Because bis-His heme ligation occurs when Cytc binds to cardiolipin-containing membranes, we studied the effect of His73 ligation on the peroxidase activity of Cytc, which acts as an early signal in apoptosis by causing oxygenation of cardiolipin. We find that the His73 alkaline conformer suppresses the peroxidase activity of Cytc. Thus, the bis-His ligated state of Cytc formed upon binding to cardiolipin is a negative effector for the peroxidase activity of Cytc early in apoptosis.
Collapse
Affiliation(s)
- William J Martin
- Department of Chemistry & Biochemistry, University of Montana, Missoula, MT 59812, United States
| | - Levi J McClelland
- Department of Chemistry & Biochemistry, University of Montana, Missoula, MT 59812, United States; Division of Biological Sciences, University of Montana, Missoula, MT 59812, United States; Center for Biomolecular Structure & Dynamics, University of Montana, Missoula, MT 59812, United States
| | - Shiloh M Nold
- Department of Chemistry & Biochemistry, University of Montana, Missoula, MT 59812, United States
| | - Kassandra L Boshae
- Department of Chemistry & Biochemistry, University of Montana, Missoula, MT 59812, United States
| | - Bruce E Bowler
- Department of Chemistry & Biochemistry, University of Montana, Missoula, MT 59812, United States; Center for Biomolecular Structure & Dynamics, University of Montana, Missoula, MT 59812, United States.
| |
Collapse
|
2
|
Espino-Sanchez T, Wienkers H, Marvin R, Nalder SA, García-Guerrero A, VanNatta P, Jami-Alahmadi Y, Mixon Blackwell A, Whitby F, Wohlschlegel J, Kieber-Emmons M, Hill C, A. Sigala P. Direct tests of cytochrome c and c1 functions in the electron transport chain of malaria parasites. Proc Natl Acad Sci U S A 2023; 120:e2301047120. [PMID: 37126705 PMCID: PMC10175771 DOI: 10.1073/pnas.2301047120] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 03/30/2023] [Indexed: 05/03/2023] Open
Abstract
The mitochondrial electron transport chain (ETC) of Plasmodium malaria parasites is a major antimalarial drug target, but critical cytochrome (cyt) functions remain unstudied and enigmatic. Parasites express two distinct cyt c homologs (c and c-2) with unusually sparse sequence identity and uncertain fitness contributions. P. falciparum cyt c-2 is the most divergent eukaryotic cyt c homolog currently known and has sequence features predicted to be incompatible with canonical ETC function. We tagged both cyt c homologs and the related cyt c1 for inducible knockdown. Translational repression of cyt c and cyt c1 was lethal to parasites, which died from ETC dysfunction and impaired ubiquinone recycling. In contrast, cyt c-2 knockdown or knockout had little impact on blood-stage growth, indicating that parasites rely fully on the more conserved cyt c for ETC function. Biochemical and structural studies revealed that both cyt c and c-2 are hemylated by holocytochrome c synthase, but UV-vis absorbance and EPR spectra strongly suggest that cyt c-2 has an unusually open active site in which heme is stably coordinated by only a single axial amino acid ligand and can bind exogenous small molecules. These studies provide a direct dissection of cytochrome functions in the ETC of malaria parasites and identify a highly divergent Plasmodium cytochrome c with molecular adaptations that defy a conserved role in eukaryotic evolution.
Collapse
Affiliation(s)
| | - Henry Wienkers
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT84112
| | - Rebecca G. Marvin
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT84112
| | - Shai-anne Nalder
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT84112
| | | | - Peter E. VanNatta
- Department of Chemistry, University of Utah, Salt Lake City, UT84112
| | | | - Amanda Mixon Blackwell
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT84112
| | - Frank G. Whitby
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT84112
| | | | | | - Christopher P. Hill
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT84112
| | - Paul A. Sigala
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT84112
| |
Collapse
|
3
|
Espino-Sanchez TJ, Wienkers H, Marvin RG, Nalder SA, García-Guerrero AE, VanNatta PE, Jami-Alahmadi Y, Blackwell AM, Whitby FG, Wohlschlegel JA, Kieber-Emmons MT, Hill CP, Sigala PA. Direct Tests of Cytochrome Function in the Electron Transport Chain of Malaria Parasites. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.23.525242. [PMID: 36747727 PMCID: PMC9900762 DOI: 10.1101/2023.01.23.525242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The mitochondrial electron transport chain (ETC) of Plasmodium malaria parasites is a major antimalarial drug target, but critical cytochrome functions remain unstudied and enigmatic. Parasites express two distinct cyt c homologs ( c and c -2) with unusually sparse sequence identity and uncertain fitness contributions. P. falciparum cyt c -2 is the most divergent eukaryotic cyt c homolog currently known and has sequence features predicted to be incompatible with canonical ETC function. We tagged both cyt c homologs and the related cyt c 1 for inducible knockdown. Translational repression of cyt c and cyt c 1 was lethal to parasites, which died from ETC dysfunction and impaired ubiquinone recycling. In contrast, cyt c -2 knockdown or knock-out had little impact on blood-stage growth, indicating that parasites rely fully on the more conserved cyt c for ETC function. Biochemical and structural studies revealed that both cyt c and c -2 are hemylated by holocytochrome c synthase, but UV-vis absorbance and EPR spectra strongly suggest that cyt c -2 has an unusually open active site in which heme is stably coordinated by only a single axial amino-acid ligand and can bind exogenous small molecules. These studies provide a direct dissection of cytochrome functions in the ETC of malaria parasites and identify a highly divergent Plasmodium cytochrome c with molecular adaptations that defy a conserved role in eukaryotic evolution. SIGNIFICANCE STATEMENT Mitochondria are critical organelles in eukaryotic cells that drive oxidative metabolism. The mitochondrion of Plasmodium malaria parasites is a major drug target that has many differences from human cells and remains poorly studied. One key difference from humans is that malaria parasites express two cytochrome c proteins that differ significantly from each other and play untested and uncertain roles in the mitochondrial electron transport chain (ETC). Our study revealed that one cyt c is essential for ETC function and parasite viability while the second, more divergent protein has unusual structural and biochemical properties and is not required for growth of blood-stage parasites. This work elucidates key biochemical properties and evolutionary differences in the mitochondrial ETC of malaria parasites.
Collapse
Affiliation(s)
- Tanya J. Espino-Sanchez
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, United States
| | - Henry Wienkers
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, United States
| | - Rebecca G. Marvin
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, United States
| | - Shai-anne Nalder
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, United States
| | - Aldo E. García-Guerrero
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, United States
| | - Peter E. VanNatta
- Department of Chemistry, University of Utah, Salt Lake City, UT, United States
| | - Yasaman Jami-Alahmadi
- Department of Biological Chemistry, University of California, Los Angeles, CA, United States
| | - Amanda Mixon Blackwell
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, United States
| | - Frank G. Whitby
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, United States
| | - James A. Wohlschlegel
- Department of Biological Chemistry, University of California, Los Angeles, CA, United States
| | | | - Christopher P. Hill
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, United States
| | - Paul A. Sigala
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, United States,Corresponding author: Paul Sigala
| |
Collapse
|
4
|
Zhong F, Albert T, Moënne-Loccoz P, Pletneva EV. Influence of the Interdomain Interface on Structural and Redox Properties of Multiheme Proteins. Inorg Chem 2022; 61:20949-20963. [PMID: 36493379 PMCID: PMC11034829 DOI: 10.1021/acs.inorgchem.2c03427] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Multiheme proteins are important in energy conversion and biogeochemical cycles of nitrogen and sulfur. A diheme cytochrome c4 (c4) was used as a model to elucidate roles of the interdomain interface on properties of iron centers in its hemes A and B. Isolated monoheme domains c4-A and c4-B, together with the full-length diheme c4 and its Met-to-His ligand variants, were characterized by a variety of spectroscopic and stability measurements. In both isolated domains, the heme iron is Met/His-ligated at pH 5.0, as in the full-length c4, but becomes His/His-ligated in c4-B at higher pH. Intradomain contacts in c4-A are minimally affected by the separation of c4-A and c4-B domains, and isolated c4-A is folded. In contrast, the isolated c4-B is partially unfolded, and the interface with c4-A guides folding of this domain. The c4-A and c4-B domains have the propensity to interact even without the polypeptide linker. Thermodynamic cycles have revealed properties of monomeric folded isolated domains, suggesting that ferrous (FeII), but not ferric (FeIII) c4-A and c4-B, is stabilized by the interface. This study illustrates the effects of the interface on tuning structural and redox properties of multiheme proteins and enriches our understanding of redox-dependent complexation.
Collapse
Affiliation(s)
- Fangfang Zhong
- Department of Chemistry, Dartmouth College, Hanover, NH 03755, United States
| | - Therese Albert
- Department of Chemical Physiology and Biochemistry, School of Medicine, Oregon Health & Science University, Portland, OR 97239, United States
| | - Pierre Moënne-Loccoz
- Department of Chemical Physiology and Biochemistry, School of Medicine, Oregon Health & Science University, Portland, OR 97239, United States
| | | |
Collapse
|
5
|
Frederick AK, Thompson SL, Vakharia ZM, Cherney MM, Lei H, Evenson G, Bowler BE. Effect on intrinsic peroxidase activity of substituting coevolved residues from Ω-loop C of human cytochrome c into yeast iso-1-cytochrome c. J Inorg Biochem 2022; 232:111819. [PMID: 35428021 PMCID: PMC9162143 DOI: 10.1016/j.jinorgbio.2022.111819] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 03/25/2022] [Accepted: 04/02/2022] [Indexed: 11/15/2022]
Abstract
Naturally-occurring variants of human cytochrome c (Cytc) that induce thrombocytopenia IV occur within Ω-loop C (residues 40-57). These variants enhance the peroxidase activity of human Cytc apparently by facilitating access to the heme by destabilizing Ω-loops C and D (residues 70-85). Given the importance of peroxidase activity in the early stages of apoptosis, we identified three sites with the EVmutation algorithm in or near Ω-loop C that coevolve and differ between yeast iso-1-Cytc and human Cytc. We prepared iso-1-Cytc variants with all possible combinations of the S40T, V57I and N63T substitutions to determine if these residues decrease the peroxidase activity of iso-1-Cytc to that of human Cytc producing an effective off state for a peroxidase signaling switch. At pH 6 and above, all variants significantly decreased peroxidase activity. However, the correlation of peroxidase activity with local and global stability, expected if cooperative unfolding of Ω-loops C and D is required for peroxidase activity, was generally poor. The m-values derived from the guanidine hydrochloride dependence of the kinetics of imidazole binding to horse Cytc, which is well-characterized by native-state hydrogen exchange methods, and K72A/K73A/K79A iso-1-Cytc show that local structural fluctuations and not subglobal cooperative unfolding of Ω-loops C and D are sufficient to permit binding of a small molecule like peroxide to the heme. A 2.46 Å structure of N63T iso-1-Cytc identifies a change to a hydrogen bond network linking Ω-loops C and D that could modulate the local fluctuations needed for the intrinsic peroxidase activity of Cytc.
Collapse
Affiliation(s)
- Ariel K Frederick
- Department of Chemistry & Biochemistry, University of Montana, Missoula, MT 59812, United States; Center for Biomolecular Structure & Dynamics, University of Montana, Missoula, MT 59812, United States
| | - Sidney L Thompson
- Department of Chemistry & Biochemistry, University of Montana, Missoula, MT 59812, United States
| | - Zahra M Vakharia
- Department of Chemistry & Biochemistry, University of Montana, Missoula, MT 59812, United States
| | - Melisa M Cherney
- Department of Chemistry & Biochemistry, University of Montana, Missoula, MT 59812, United States
| | - Haotian Lei
- Department of Chemistry & Biochemistry, University of Montana, Missoula, MT 59812, United States; Center for Biomolecular Structure & Dynamics, University of Montana, Missoula, MT 59812, United States
| | - Garrett Evenson
- Department of Chemistry & Biochemistry, University of Montana, Missoula, MT 59812, United States
| | - Bruce E Bowler
- Department of Chemistry & Biochemistry, University of Montana, Missoula, MT 59812, United States; Center for Biomolecular Structure & Dynamics, University of Montana, Missoula, MT 59812, United States.
| |
Collapse
|
6
|
Fine Sampling of Sequence Space for Membrane Protein Structural Biology. J Mol Biol 2021; 433:167055. [PMID: 34022208 DOI: 10.1016/j.jmb.2021.167055] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 05/12/2021] [Accepted: 05/12/2021] [Indexed: 11/22/2022]
Abstract
We describe an enhancement of traditional genomics-based approaches to improve the success of structure determination of membrane proteins. Following a broad screen of sequence space to identify initial expression-positive targets, we employ a second step to select orthologs with closely related sequences to these hits. We demonstrate that a greater percentage of these latter targets express well and are stable in detergent, increasing the likelihood of identifying candidates that will ultimately yield structural information.
Collapse
|
7
|
Demicheli V, Tomasina F, Sastre S, Zeida A, Tórtora V, Lima A, Batthyány C, Radi R. Cardiolipin interactions with cytochrome c increase tyrosine nitration yields and site-specificity. Arch Biochem Biophys 2021; 703:108824. [PMID: 33675813 DOI: 10.1016/j.abb.2021.108824] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 02/19/2021] [Accepted: 02/25/2021] [Indexed: 12/13/2022]
Abstract
The interaction between cytochrome c and cardiolipin is a relevant process in the mitochondrial redox homeostasis, playing roles in the mechanism of electron transfer to cytochrome c oxidase and also modulating cytochrome c conformation, reactivity and function. Peroxynitrite is a widespread nitrating agent formed in mitochondria under oxidative stress conditions, and can result in the formation of tyrosine nitrated cytochrome c. Some of the nitro-cytochrome c species undergo conformational changes at physiological pH and increase its peroxidase activity. In this work we evaluated the influence of cardiolipin on peroxynitrite-mediated cytochrome c nitration yields and site-specificity. Our results show that cardiolipin enhances cytochrome c nitration by peroxynitrite and targets it to heme-adjacent Tyr67. Cytochrome c nitration also modifies the affinity of protein with cardiolipin. Using a combination of experimental techniques and computer modeling, it is concluded that structural modifications in the Tyr67 region are responsible for the observed changes in protein-derived radical and tyrosine nitration levels, distribution of nitrated proteoforms and affinity to cardiolipin. Increased nitration of cytochrome c in presence of cardiolipin within mitochondria and the gain of peroxidatic activity could then impact events such as the onset of apoptosis and other processes related to the disruption of mitochondrial redox homeostasis.
Collapse
Affiliation(s)
- Verónica Demicheli
- Departamento de Bioquímica, Facultad de Medicina, Universidad de La República, Montevideo, Uruguay; Centro de Investigaciones Biomédicas (CEINBIO), Universidad de la República, Montevideo, Uruguay
| | - Florencia Tomasina
- Departamento de Bioquímica, Facultad de Medicina, Universidad de La República, Montevideo, Uruguay; Centro de Investigaciones Biomédicas (CEINBIO), Universidad de la República, Montevideo, Uruguay
| | - Santiago Sastre
- Centro de Investigaciones Biomédicas (CEINBIO), Universidad de la República, Montevideo, Uruguay
| | - Ari Zeida
- Departamento de Bioquímica, Facultad de Medicina, Universidad de La República, Montevideo, Uruguay; Centro de Investigaciones Biomédicas (CEINBIO), Universidad de la República, Montevideo, Uruguay
| | - Verónica Tórtora
- Centro de Investigaciones Biomédicas (CEINBIO), Universidad de la República, Montevideo, Uruguay
| | - Analía Lima
- Institut Pasteur de Montevideo, Uruguay; Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - Carlos Batthyány
- Institut Pasteur de Montevideo, Uruguay; Centro de Investigaciones Biomédicas (CEINBIO), Universidad de la República, Montevideo, Uruguay
| | - Rafael Radi
- Departamento de Bioquímica, Facultad de Medicina, Universidad de La República, Montevideo, Uruguay; Centro de Investigaciones Biomédicas (CEINBIO), Universidad de la República, Montevideo, Uruguay.
| |
Collapse
|
8
|
Li M, Mandal A, Tyurin VA, DeLucia M, Ahn J, Kagan VE, van der Wel PCA. Surface-Binding to Cardiolipin Nanodomains Triggers Cytochrome c Pro-apoptotic Peroxidase Activity via Localized Dynamics. Structure 2019; 27:806-815.e4. [PMID: 30879887 DOI: 10.1016/j.str.2019.02.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 01/16/2019] [Accepted: 02/15/2019] [Indexed: 02/06/2023]
Abstract
The peroxidation of cardiolipins by reactive oxygen species, which is regulated and enhanced by cytochrome c (cyt c), is a critical signaling event in mitochondrial apoptosis. We probe the molecular underpinnings of this mitochondrial death signal through structural and functional studies of horse heart cyt c binding to mixed-lipid membranes containing cardiolipin with mono- and polyunsaturated acyl chains. Lipidomics reveal the selective oxidation of polyunsaturated fatty acid (PUFA) cardiolipin (CL), while multidimensional solid-state NMR probes the structure and dynamics of the membrane and the peripherally bound protein. The hydrophilic milieu at the membrane interface stabilizes a native-like fold, but also leads to localized flexibility at the membrane-interacting protein face. PUFA CL acts as both a preferred substrate and a dynamic regulator by affecting the dynamics of the cyt c N70-I85 Ω loop, which covers the heme cavity.
Collapse
Affiliation(s)
- Mingyue Li
- Department of Structural Biology, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Abhishek Mandal
- Department of Structural Biology, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Vladimir A Tyurin
- Department of Environmental and Occupational Health, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Maria DeLucia
- Department of Structural Biology, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Jinwoo Ahn
- Department of Structural Biology, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Valerian E Kagan
- Department of Environmental and Occupational Health, University of Pittsburgh, Pittsburgh, PA 15213, USA; Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15213, USA; Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA 15213, USA; Department of Radiation Oncology, University of Pittsburgh, Pittsburgh, PA 15213, USA; Center for Free Radical and Antioxidant Health, University of Pittsburgh, Pittsburgh, PA 15213, USA; Laboratory of Navigational Redox Lipidomics, IM Sechenov Moscow State Medical University, Moscow 119146, Russian Federation
| | - Patrick C A van der Wel
- Department of Structural Biology, University of Pittsburgh, Pittsburgh, PA 15213, USA; Zernike Institute for Advanced Materials, University of Groningen, 9747 AG Groningen, The Netherlands.
| |
Collapse
|
9
|
Mohammadyani D, Yanamala N, Samhan-Arias AK, Kapralov AA, Stepanov G, Nuar N, Planas-Iglesias J, Sanghera N, Kagan VE, Klein-Seetharaman J. Structural characterization of cardiolipin-driven activation of cytochrome c into a peroxidase and membrane perturbation. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2018; 1860:1057-1068. [PMID: 29227865 DOI: 10.1016/j.bbamem.2018.01.009] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Revised: 12/14/2017] [Accepted: 01/04/2018] [Indexed: 01/25/2023]
Abstract
The interaction between cardiolipin (CL) and cytochrome c (cyt-c) results in a gain of function of peroxidase activity by cyt-c. Despite intensive research, disagreements on nature and molecular details of this interaction remain. In particular, it is still not known how the interaction triggers the onset of apoptosis. Enzymatic characterization of peroxidase activity has highlighted the need for a critical threshold concentration of CL, a finding of profound physiological relevance in vivo. Using solution NMR, fluorescence spectroscopy, and in silico modeling approaches we here confirm that full binding of cyt-c to the membrane requires a CL:cyt-c threshold ratio of 5:1. Among three binding sites, the simultaneous binding of two sites, at two opposing sides of the heme, provides a mechanism to open the heme crevice to substrates. This results in "productive binding" in which cyt-c then sequesters CL, inducing curvature in the membrane. Membrane perturbation along with lipid peroxidation, due to interactions of heme/CL acyl chains, initiates the next step in the apoptotic pathway of making the membrane leaky. The third CL binding site while allowing interaction with the membrane, does not cluster CL or induce subsequent events, making this interaction "unproductive".
Collapse
Affiliation(s)
- Dariush Mohammadyani
- Department of Environmental and Occupational Health, University of Pittsburgh, PA 15219, USA; Thomas C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Naveena Yanamala
- National Institute for Occupational Safety and Health/Centers for Disease Control and Prevention, Morgantown, WV 26505, USA
| | - Alejandro K Samhan-Arias
- LAQV, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Alexander A Kapralov
- Department of Environmental and Occupational Health, University of Pittsburgh, PA 15219, USA
| | - German Stepanov
- Department of General and Medical Biophysics, Pirogov Russian National Research Medical University, Moscow 117997, Russia
| | - Nick Nuar
- Department of Bioengineering, University of Pittsburgh, PA 15213, USA
| | - Joan Planas-Iglesias
- Division of Metabolic and Vascular Health, Medical School, University of Warwick, Coventry CV4 7AL, UK
| | - Narinder Sanghera
- Division of Metabolic and Vascular Health, Medical School, University of Warwick, Coventry CV4 7AL, UK
| | - Valerian E Kagan
- Department of Environmental and Occupational Health, University of Pittsburgh, PA 15219, USA
| | - Judith Klein-Seetharaman
- Division of Metabolic and Vascular Health, Medical School, University of Warwick, Coventry CV4 7AL, UK.
| |
Collapse
|
10
|
Lagoa R, Samhan-Arias AK, Gutierrez-Merino C. Correlation between the potency of flavonoids for cytochrome c reduction and inhibition of cardiolipin-induced peroxidase activity. Biofactors 2017; 43:451-468. [PMID: 25850901 DOI: 10.1002/biof.1357] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/20/2016] [Revised: 01/16/2017] [Accepted: 02/07/2017] [Indexed: 12/23/2022]
Abstract
There are large differences between flavonoids to protect against apoptosis, a process in which cytochrome c (Cyt c) plays a key role. In this work, we show that 7 of 13 flavonoids studied have a capacity to reduce Cyt c similar or higher than ascorbate, the flavonols quercetin, kaempferol and myricetin, flavanol epigallocatechin-gallate, anthocyanidins cyanidin and malvidin, and the flavone luteolin. In contrast, the kaempferol 3(O)- and 3,4'(O)-methylated forms, the flavanone naringenin, and also apigenin and chrysin, had a negligible reducing capacity. Equilibrium dialysis and quenching of 1,6-diphenyl-1,3,5-hexatriene fluorescence experiments showed that flavonoids did not interfere with Cyt c binding to cardiolipin (CL)/phosphatidylcholine (PC) vesicles. However, the CL-induced loss of Cyt c Soret band intensity was largely attenuated by flavonoids, pointing out a stabilizing action against Cyt c unfolding in the complex. Moreover, flavonoids that behave as Cyt c reductants also inhibited the pro-apoptotic CL-induced peroxidase activity of Cyt c, indicating that modulation of Cyt c signaling are probable mechanisms behind the protective biological activities of flavonoids. © 2016 BioFactors, 43(3):451-468, 2017.
Collapse
Affiliation(s)
- Ricardo Lagoa
- ESTG, Polytechnic Institute of Leiria, Morro do Lena, Alto do Vieiro, Leiria, 2411-901, Portugal
- Department of Biochemistry and Molecular Biology, Faculty of Sciences, University of Extremadura, Avenida de Elvas s/n, Badajoz, 06006, Spain
| | - Alejandro K Samhan-Arias
- Department of Biochemistry and Molecular Biology, Faculty of Sciences, University of Extremadura, Avenida de Elvas s/n, Badajoz, 06006, Spain
| | - Carlos Gutierrez-Merino
- Department of Biochemistry and Molecular Biology, Faculty of Sciences, University of Extremadura, Avenida de Elvas s/n, Badajoz, 06006, Spain
| |
Collapse
|
11
|
Structural Changes and Proapoptotic Peroxidase Activity of Cardiolipin-Bound Mitochondrial Cytochrome c. Biophys J 2016; 109:1873-84. [PMID: 26536264 DOI: 10.1016/j.bpj.2015.09.016] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Revised: 08/11/2015] [Accepted: 09/18/2015] [Indexed: 01/19/2023] Open
Abstract
The cellular process of intrinsic apoptosis relies on the peroxidation of mitochondrial lipids as a critical molecular signal. Lipid peroxidation is connected to increases in mitochondrial reactive oxygen species, but there is also a required role for mitochondrial cytochrome c (cyt-c). In apoptotic mitochondria, cyt-c gains a new function as a lipid peroxidase that catalyzes the reactive oxygen species-mediated chemical modification of the mitochondrial lipid cardiolipin (CL). This peroxidase activity is caused by a conformational change in the protein, resulting from interactions between cyt-c and CL. The nature of the conformational change and how it causes this gain-of-function remain uncertain. Via a combination of functional, structural, and biophysical experiments we investigate the structure and peroxidase activity of cyt-c in its membrane-bound state. We reconstituted cyt-c with CL-containing lipid vesicles, and determined the increase in peroxidase activity resulting from membrane binding. We combined these assays of CL-induced proapoptotic activity with structural and dynamic studies of the membrane-bound protein via solid-state NMR and optical spectroscopy. Multidimensional magic angle spinning (MAS) solid-state NMR of uniformly (13)C,(15)N-labeled protein was used to detect site-specific conformational changes in oxidized and reduced horse heart cyt-c bound to CL-containing lipid bilayers. MAS NMR and Fourier transform infrared measurements show that the peripherally membrane-bound cyt-c experiences significant dynamics, but also retains most or all of its secondary structure. Moreover, in two-dimensional and three-dimensional MAS NMR spectra the CL-bound cyt-c displays a spectral resolution, and thus structural homogeneity, that is inconsistent with extensive membrane-induced unfolding. Cyt-c is found to interact primarily with the membrane interface, without significantly disrupting the lipid bilayer. Thus, membrane binding results in cyt-c gaining the increased peroxidase activity that represents its pivotal proapoptotic function, but we do not observe evidence for large-scale unfolding or penetration into the membrane core.
Collapse
|
12
|
O'Brien ES, Nucci NV, Fuglestad B, Tommos C, Wand AJ. Defining the Apoptotic Trigger: THE INTERACTION OF CYTOCHROME c AND CARDIOLIPIN. J Biol Chem 2015; 290:30879-87. [PMID: 26487716 PMCID: PMC4692216 DOI: 10.1074/jbc.m115.689406] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Revised: 10/14/2015] [Indexed: 11/06/2022] Open
Abstract
The interaction between cytochrome c and the anionic lipid cardiolipin has been proposed as a primary event in the apoptotic signaling cascade. Numerous studies that have examined the interaction of cytochrome c with cardiolipin embedded in a variety of model phospholipid membranes have suggested that partial unfolding of the protein is a precursor to the apoptotic response. However, these studies lacked site resolution and used model systems with negligible or a positive membrane curvature, which is distinct from the large negative curvature of the invaginations of the inner mitochondrial membrane where cytochrome c resides. We have used reverse micelle encapsulation to mimic the potential effects of confinement on the interaction of cytochrome c with cardiolipin. Encapsulation of oxidized horse cytochrome c in 1-decanoyl-rac-glycerol/lauryldimethylamine-N-oxide/hexanol reverse micelles prepared in pentane yields NMR spectra essentially identical to the protein in free aqueous solution. The structure of encapsulated ferricytochrome c was determined to high precision (bb ∼ 0.23 Å) using NMR-based methods and is closely similar to the cryogenic crystal structure (bb ∼ 1.2 Å). Incorporation of cardiolipin into the reverse micelle surfactant shell causes localized chemical shift perturbations of the encapsulated protein, providing the first view of the cardiolipin/cytochrome c interaction interface at atomic resolution. Three distinct sites of interaction are detected: the so-called A- and L-sites, plus a previously undocumented interaction centered on residues Phe-36, Gly-37, Thr-58, Trp-59, and Lys-60. Importantly, in distinct contrast to earlier studies of this interaction, the protein is not significantly disturbed by the binding of cardiolipin in the context of the reverse micelle.
Collapse
Affiliation(s)
- Evan S O'Brien
- From the Johnson Research Foundation and Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6059
| | - Nathaniel V Nucci
- From the Johnson Research Foundation and Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6059
| | - Brian Fuglestad
- From the Johnson Research Foundation and Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6059
| | - Cecilia Tommos
- From the Johnson Research Foundation and Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6059
| | - A Joshua Wand
- From the Johnson Research Foundation and Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6059
| |
Collapse
|
13
|
Capdevila DA, Oviedo Rouco S, Tomasina F, Tortora V, Demicheli V, Radi R, Murgida DH. Active Site Structure and Peroxidase Activity of Oxidatively Modified Cytochrome c Species in Complexes with Cardiolipin. Biochemistry 2015; 54:7491-504. [PMID: 26620444 DOI: 10.1021/acs.biochem.5b00922] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We report a resonance Raman and UV-vis characterization of the active site structure of oxidatively modified forms of cytochrome c (Cyt-c) free in solution and in complexes with cardiolipin (CL). The studied post-translational modifications of Cyt-c include methionine sulfoxidation and tyrosine nitration, which lead to altered heme axial ligation and increased peroxidase activity with respect to those of the wild-type protein. In spite of the structural and activity differences between the protein variants free in solution, binding to CL liposomes induces in all cases the formation of a spectroscopically identical bis-His axial coordination conformer that more efficiently promotes lipid peroxidation. The spectroscopic results indicate that the bis-His form is in equilibrium with small amounts of high-spin species, thus suggesting a labile distal His ligand as the basis for the CL-induced increase in enzymatic activity observed for all protein variants. For Cyt-c nitrated at Tyr74 and sulfoxidized at Met80, the measured apparent binding affinities for CL are ∼4 times larger than for wild-type Cyt-c. On the basis of these results, we propose that these post-translational modifications may amplify the pro-apoptotic signal of Cyt-c under oxidative stress conditions at CL concentrations lower than for the unmodified protein.
Collapse
Affiliation(s)
- Daiana A Capdevila
- 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, C1428EHA Buenos Aires, 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, C1428EHA Buenos Aires, Argentina
| | - Florencia Tomasina
- Departamento de Bioquímica and Center for Free Radical and Biomedical Research, Facultad de Medicina, Universidad de la República , Montevideo, Uruguay
| | - Verónica Tortora
- Departamento de Bioquímica and Center for Free Radical and Biomedical Research, Facultad de Medicina, Universidad de la República , Montevideo, Uruguay
| | - Verónica Demicheli
- Departamento de Bioquímica and Center for Free Radical and Biomedical Research, Facultad de Medicina, Universidad de la República , Montevideo, Uruguay
| | - Rafael Radi
- Departamento de Bioquímica and Center for Free Radical and Biomedical Research, Facultad de Medicina, Universidad de la República , Montevideo, 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, C1428EHA Buenos Aires, Argentina
| |
Collapse
|
14
|
McClelland LJ, Seagraves SM, Khan MKA, Cherney MM, Bandi S, Culbertson JE, Bowler BE. The response of Ω-loop D dynamics to truncation of trimethyllysine 72 of yeast iso-1-cytochrome c depends on the nature of loop deformation. J Biol Inorg Chem 2015; 20:805-19. [PMID: 25948392 PMCID: PMC4485566 DOI: 10.1007/s00775-015-1267-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2015] [Accepted: 04/27/2015] [Indexed: 11/24/2022]
Abstract
Trimethyllysine 72 (tmK72) has been suggested to play a role in sterically constraining the heme crevice dynamics of yeast iso-1-cytochrome c mediated by the Ω-loop D cooperative substructure (residues 70-85). A tmK72A mutation causes a gain in peroxidase activity, a function of cytochrome c that is important early in apoptosis. More than one higher energy state is accessible for the Ω-loop D substructure via tier 0 dynamics. Two of these are alkaline conformers mediated by Lys73 and Lys79. In the current work, the effect of the tmK72A mutation on the thermodynamic and kinetic properties of wild-type iso-1-cytochrome c (yWT versus WT*) and on variants carrying a K73H mutation (yWT/K73H versus WT*/K73H) is studied. Whereas the tmK72A mutation confers increased peroxidase activity in wild-type yeast iso-1-cytochrome c and increased dynamics for formation of a previously studied His79-heme alkaline conformer, the tmK72A mutation speeds return of the His73-heme alkaline conformer to the native state through destabilization of the His73-heme alkaline conformer relative to the native conformer. These opposing behaviors demonstrate that the response of the dynamics of a protein substructure to mutation depends on the nature of the perturbation to the substructure. For a protein substructure which mediates more than one function of a protein through multiple non-native structures, a mutation could change the partitioning between these functions. The current results suggest that the tier 0 dynamics of Ω-loop D that mediates peroxidase activity has similarities to the tier 0 dynamics required to form the His79-heme alkaline conformer.
Collapse
Affiliation(s)
- Levi J McClelland
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Dynamics, University of Montana, Missoula, MT, 59812, USA
| | | | | | | | | | | | | |
Collapse
|
15
|
Babbitt SE, Sutherland MC, San Francisco B, Mendez DL, Kranz RG. Mitochondrial cytochrome c biogenesis: no longer an enigma. Trends Biochem Sci 2015; 40:446-55. [PMID: 26073510 DOI: 10.1016/j.tibs.2015.05.006] [Citation(s) in RCA: 87] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2015] [Revised: 05/13/2015] [Accepted: 05/18/2015] [Indexed: 12/31/2022]
Abstract
Cytochromes c (cyt c) and c1 are heme proteins that are essential for aerobic respiration. Release of cyt c from mitochondria is an important signal in apoptosis initiation. Biogenesis of c-type cytochromes involves covalent attachment of heme to two cysteines (at a conserved CXXCH sequence) in the apocytochrome. Heme attachment is catalyzed in most mitochondria by holocytochrome c synthase (HCCS), which is also necessary for the import of apocytochrome c (apocyt c). Thus, HCCS affects cellular levels of cyt c, impacting mitochondrial physiology and cell death. Here, we review the mechanisms of HCCS function and the roles of heme and residues in the CXXCH motif. Additionally, we consider concepts emerging within the two prokaryotic cytochrome c biogenesis pathways.
Collapse
Affiliation(s)
- Shalon E Babbitt
- Department of Biology, Washington University, St Louis, MO 63130, USA
| | | | | | - Deanna L Mendez
- Department of Biology, Washington University, St Louis, MO 63130, USA
| | - Robert G Kranz
- Department of Biology, Washington University, St Louis, MO 63130, USA.
| |
Collapse
|
16
|
Yanamala N, Kapralov AA, Djukic M, Peterson J, Mao G, Klein-Seetharaman J, Stoyanovsky DA, Stursa J, Neuzil J, Kagan VE. Structural re-arrangement and peroxidase activation of cytochrome c by anionic analogues of vitamin E, tocopherol succinate and tocopherol phosphate. J Biol Chem 2014; 289:32488-98. [PMID: 25278024 DOI: 10.1074/jbc.m114.601377] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Cytochrome c is a multifunctional hemoprotein in the mitochondrial intermembrane space whereby its participation in electron shuttling between respiratory complexes III and IV is alternative to its role in apoptosis as a peroxidase activated by interaction with cardiolipin (CL), and resulting in selective CL peroxidation. The switch from electron transfer to peroxidase function requires partial unfolding of the protein upon binding of CL, whose specific features combine negative charges of the two phosphate groups with four hydrophobic fatty acid residues. Assuming that other endogenous small molecule ligands with a hydrophobic chain and a negatively charged functionality may activate cytochrome c into a peroxidase, we investigated two hydrophobic anionic analogues of vitamin E, α-tocopherol succinate (α-TOS) and α-tocopherol phosphate (α-TOP), as potential inducers of peroxidase activity of cytochrome c. NMR studies and computational modeling indicate that they interact with cytochrome c at similar sites previously proposed for CL. Absorption spectroscopy showed that both analogues effectively disrupt the Fe-S(Met(80)) bond associated with unfolding of cytochrome c. We found that α-TOS and α-TOP stimulate peroxidase activity of cytochrome c. Enhanced peroxidase activity was also observed in isolated rat liver mitochondria incubated with α-TOS and tBOOH. A mitochondria-targeted derivative of TOS, triphenylphosphonium-TOS (mito-VES), was more efficient in inducing H2O2-dependent apoptosis in mouse embryonic cytochrome c(+/+) cells than in cytochrome c(-/-) cells. Essential for execution of the apoptotic program peroxidase activation of cytochrome c by α-TOS may contribute to its known anti-cancer pharmacological activity.
Collapse
Affiliation(s)
- Naveena Yanamala
- From the Center for Free Radical and Antioxidant Health, the Departments of Environmental and Occupational Health
| | - Alexander A Kapralov
- From the Center for Free Radical and Antioxidant Health, the Departments of Environmental and Occupational Health
| | - Mirjana Djukic
- From the Center for Free Radical and Antioxidant Health, the Departments of Environmental and Occupational Health
| | - Jim Peterson
- the Departments of Environmental and Occupational Health
| | - Gaowei Mao
- From the Center for Free Radical and Antioxidant Health, the Departments of Environmental and Occupational Health
| | - Judith Klein-Seetharaman
- the Division of Metabolic and Vascular Health, Medical School, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Detcho A Stoyanovsky
- From the Center for Free Radical and Antioxidant Health, the Departments of Environmental and Occupational Health
| | - Jan Stursa
- the Biomedical Research Center, University Hospital, Hradec Kralove 569810, Czech Republic
| | - Jiri Neuzil
- the Institute of Biotechnology, Academy of Sciences of the Czech Republic, Prague 14220, Czech Republic, and the School of Medical Science, Griffith University, Southport, Queensland 4222, Australia
| | - Valerian E Kagan
- From the Center for Free Radical and Antioxidant Health, the Departments of Environmental and Occupational Health, Pharmacology and Chemical Biology, Radiation Oncology, and Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260
| |
Collapse
|
17
|
Bashir Q, Meulenbroek EM, Pannu NS, Ubbink M. Engineering specificity in a dynamic protein complex with a single conserved mutation. FEBS J 2014; 281:4892-905. [DOI: 10.1111/febs.13028] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2014] [Revised: 07/09/2014] [Accepted: 08/27/2014] [Indexed: 11/27/2022]
Affiliation(s)
- Qamar Bashir
- Gorlaeus Laboratories; Leiden Institute of Chemistry; Leiden University; The Netherlands
| | | | - Navraj S. Pannu
- Gorlaeus Laboratories; Leiden Institute of Chemistry; Leiden University; The Netherlands
| | - Marcellus Ubbink
- Gorlaeus Laboratories; Leiden Institute of Chemistry; Leiden University; The Netherlands
| |
Collapse
|
18
|
Zhang Y, Stevens JM, Ferguson SJ. Substrate recognition of holocytochrome c synthase: N-terminal region and CXXCH motif of mitochondrial cytochrome c. FEBS Lett 2014; 588:3367-74. [PMID: 25084480 PMCID: PMC4158909 DOI: 10.1016/j.febslet.2014.07.026] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2014] [Revised: 07/18/2014] [Accepted: 07/22/2014] [Indexed: 11/25/2022]
Abstract
Holocytochrome c synthase (HCCS) does not attach heme to cytochromes lacking the histidine in the CXXCH motif. HCCS can recognise C-terminally truncated cytochromes c. The aromatic nature of, or possibly shape complementarity to, F15 in cytochrome c is important for recognition by HCCS. The spacing of the phenylalanine relative to the CXXCH is a recognition feature.
Holocytochrome c synthase (HCCS) attaches heme covalently to mitochondrial respiratory cytochromes c. Little is known about the reaction of heme attachment to apocytochromes c by HCCS, although recently it has been established that the CXXCH motif and the N-terminus of the apocytochrome polypeptide are important protein–protein recognition motifs. Here, we explore further the important features of the N-terminal sequence and investigate what variations in the CXXCH residues are productively recognised by HCCS in its substrate.
Collapse
Affiliation(s)
- Yulin Zhang
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Julie M Stevens
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom.
| | - Stuart J Ferguson
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom.
| |
Collapse
|
19
|
Marques BS, Nucci NV, Dodevski I, Wang KWC, Athanasoula EA, Jorge C, Wand AJ. Measurement and control of pH in the aqueous interior of reverse micelles. J Phys Chem B 2014; 118:2020-31. [PMID: 24506449 PMCID: PMC3983379 DOI: 10.1021/jp4103349] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
![]()
The
encapsulation of proteins and nucleic acids within the nanoscale
water core of reverse micelles has been used for over 3 decades as
a vehicle for a wide range of investigations including enzymology,
the physical chemistry of confined spaces, protein and nucleic acid
structural biology, and drug development and delivery. Unfortunately,
the static and dynamical aspects of the distribution of water in solutions
of reverse micelles complicate the measurement and interpretation
of fundamental parameters such as pH. This is a severe disadvantage
in the context of (bio)chemical reactions and protein structure and
function, which are generally highly sensitive to pH. There is a need
to more fully characterize and control the effective pH of the reverse
micelle water core. The buffering effect of titratable head groups
of the reverse micelle surfactants is found to often be the dominant
variable defining the pH of the water core. Methods for measuring
the pH of the reverse micelle aqueous interior using one-dimensional 1H and two-dimensional heteronuclear NMR spectroscopy are described.
Strategies for setting the effective pH of the reverse micelle water
core are demonstrated. The exquisite sensitivity of encapsulated proteins
to the surfactant, water content, and pH of the reverse micelle is
also addressed. These results highlight the importance of assessing
the structural fidelity of the encapsulated protein using multidimensional
NMR before embarking upon a detailed structural and biophysical characterization.
Collapse
Affiliation(s)
- Bryan S Marques
- Graduate Group in Biochemistry and Molecular Biophysics and Johnson Research Foundation and Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine , Philadelphia, Pennsylvania 19104-6059, United States
| | | | | | | | | | | | | |
Collapse
|
20
|
Zaidi S, Hassan MI, Islam A, Ahmad F. The role of key residues in structure, function, and stability of cytochrome-c. Cell Mol Life Sci 2014; 71:229-55. [PMID: 23615770 PMCID: PMC11113841 DOI: 10.1007/s00018-013-1341-1] [Citation(s) in RCA: 105] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2013] [Revised: 04/05/2013] [Accepted: 04/08/2013] [Indexed: 02/06/2023]
Abstract
Cytochrome-c (cyt-c), a multi-functional protein, plays a significant role in the electron transport chain, and thus is indispensable in the energy-production process. Besides being an important component in apoptosis, it detoxifies reactive oxygen species. Two hundred and eighty-five complete amino acid sequences of cyt-c from different species are known. Sequence analysis suggests that the number of amino acid residues in most mitochondrial cyts-c is in the range 104 ± 10, and amino acid residues at only few positions are highly conserved throughout evolution. These highly conserved residues are Cys14, Cys17, His18, Gly29, Pro30, Gly41, Asn52, Trp59, Tyr67, Leu68, Pro71, Pro76, Thr78, Met80, and Phe82. These are also known as "key residues", which contribute significantly to the structure, function, folding, and stability of cyt-c. The three-dimensional structure of cyt-c from ten eukaryotic species have been determined using X-ray diffraction studies. Structure analysis suggests that the tertiary structure of cyt-c is almost preserved along the evolutionary scale. Furthermore, residues of N/C-terminal helices Gly6, Phe10, Leu94, and Tyr97 interact with each other in a specific manner, forming an evolutionary conserved interface. To understand the role of evolutionary conserved residues on structure, stability, and function, numerous studies have been performed in which these residues were substituted with different amino acids. In these studies, structure deals with the effect of mutation on secondary and tertiary structure measured by spectroscopic techniques; stability deals with the effect of mutation on T m (midpoint of heat denaturation), ∆G D (Gibbs free energy change on denaturation) and folding; and function deals with the effect of mutation on electron transport, apoptosis, cell growth, and protein expression. In this review, we have compiled all these studies at one place. This compilation will be useful to biochemists and biophysicists interested in understanding the importance of conservation of certain residues throughout the evolution in preserving the structure, function, and stability in proteins.
Collapse
Affiliation(s)
- Sobia Zaidi
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025 India
| | - Md. Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025 India
| | - Asimul Islam
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025 India
| | - Faizan Ahmad
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025 India
| |
Collapse
|
21
|
Alvarez-Paggi D, Castro MA, Tórtora V, Castro L, Radi R, Murgida DH. Electrostatically Driven Second-Sphere Ligand Switch between High and Low Reorganization Energy Forms of Native Cytochrome c. J Am Chem Soc 2013; 135:4389-97. [DOI: 10.1021/ja311786b] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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, C1428EHA-Buenos Aires, Argentina
- Departamento
de Bioquímica and ⊥Center for Free Radical and Biomedical Research, Facultad de Medicina, Universidad de la República, Montevideo, 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, C1428EHA-Buenos Aires, Argentina
- Departamento
de Bioquímica and ⊥Center for Free Radical and Biomedical Research, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Verónica Tórtora
- 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, C1428EHA-Buenos Aires, Argentina
- Departamento
de Bioquímica and ⊥Center for Free Radical and Biomedical Research, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Laura 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, C1428EHA-Buenos Aires, Argentina
- Departamento
de Bioquímica and ⊥Center for Free Radical and Biomedical Research, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Rafael Radi
- 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, C1428EHA-Buenos Aires, Argentina
- Departamento
de Bioquímica and ⊥Center for Free Radical and Biomedical Research, Facultad de Medicina, Universidad de la República, Montevideo, 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, C1428EHA-Buenos Aires, Argentina
- Departamento
de Bioquímica and ⊥Center for Free Radical and Biomedical Research, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| |
Collapse
|
22
|
Cherney MM, Junior CC, Bowler BE. Mutation of trimethyllysine 72 to alanine enhances His79-heme-mediated dynamics of iso-1-cytochrome c. Biochemistry 2013; 52:837-46. [PMID: 23311346 DOI: 10.1021/bi301599g] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Trimethyllysine 72 (Tml72) of yeast iso-1-cytochrome c lies across the surface of the heme crevice loop (Ω-loop D, residues 70-85) like a brace. Lys72 is oriented similarly in horse cytochrome c (Cytc). To determine whether this residue affects the dynamics of opening the heme crevice loop, we have studied the effect of a Tml72 to Ala substitution on the formation of the His79-heme alkaline conformer near neutral pH using a variant of iso-1-Cytc including K72A and K79H mutations. Guanidine hydrochloride denaturation shows that the Tml72 to Ala substitution within error does not affect the global stability of the protein. The effect of the Tml72 to Ala substitution on the thermodynamics of the His79-heme alkaline transition is also small. However, pH-jump kinetic studies of the His79-heme alkaline transition show that both the forward and backward rates of conformational change are increased by the Tml72 to Ala substitution. The barrier for opening the heme crevice is reduced by 0.5 kcal/mol and for closing the heme crevice by 0.3 kcal/mol. The ability of Tml72 to modulate the heme crevice dynamics may indicate a crucial role in regulating function, such as in the peroxidase activity seen in the early stages of apoptosis.
Collapse
Affiliation(s)
- Melisa M Cherney
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Dynamics, University of Montana, Missoula, MT 59812, United States
| | | | | |
Collapse
|
23
|
Vincelli AJ, Pottinger DS, Zhong F, Hanske J, Rolland SG, Conradt B, Pletneva EV. Recombinant expression, biophysical characterization, and cardiolipin-induced changes of two Caenorhabditis elegans cytochrome c proteins. Biochemistry 2013; 52:653-66. [PMID: 23282202 DOI: 10.1021/bi3014938] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Cytochrome c (cyt c) is one of the most widely studied biomolecules, but not much is known about this protein from nematodes. Recombinant expression of Caenorhabditis elegans CYC-2.1 and CYC-2.2 allowed for detailed characterization of their structural features, redox properties, stabilities, and interactions with cardiolipin (CL)-containing liposomes. Using a variety of spectroscopic tools, we show that CYC-2.1 and CYC-2.2 adopt a globular α-helical fold with His/Met heme ligation. The longer CYC-2.2 has a lower thermodynamic stability than CYC-2.1 and lacks His residues to misligate to the heme in the protein's denatured state. Both C. elegans proteins bind to CL-containing liposomes, and these interactions promote the proteins' peroxidase activity but to a much greater degree for CYC-2.2. Dye-to-heme distance distributions from time-resolved fluorescence resonance energy transfer in bimane-labeled CYC-2.1 and CYC-2.2 revealed similar populations of extended and compact conformers for CL-bound proteins, suggesting that their distinct peroxidase activities in the presence of CL arise from differences in the local heme environments for the two polypeptide ensembles. Without inhibition from His misligation, a less stable and more prone to unfolding CYC-2.2 allows for better access of substrates to the heme and thus exhibits higher peroxidase activity. Similar features of the conformational ensembles of CYC-2.1 and CYC-2.2 to those of mammalian cyt c suggest that C. elegans proteins, particularly the former, could serve as useful models for examining the mechanism of cyt c-CL interactions in live organisms.
Collapse
Affiliation(s)
- Amber J Vincelli
- Department of Chemistry, Dartmouth College, Hanover, NH 03755, USA
| | | | | | | | | | | | | |
Collapse
|
24
|
Human mitochondrial holocytochrome c synthase's heme binding, maturation determinants, and complex formation with cytochrome c. Proc Natl Acad Sci U S A 2012; 110:E788-97. [PMID: 23150584 DOI: 10.1073/pnas.1213897109] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Proper functioning of the mitochondrion requires the orchestrated assembly of respiratory complexes with their cofactors. Cytochrome c, an essential electron carrier in mitochondria and a critical component of the apoptotic pathway, contains a heme cofactor covalently attached to the protein at a conserved CXXCH motif. Although it has been known for more than two decades that heme attachment requires the mitochondrial protein holocytochrome c synthase (HCCS), the mechanism remained unknown. We purified membrane-bound human HCCS with endogenous heme and in complex with its cognate human apocytochrome c. Spectroscopic analyses of HCCS alone and complexes of HCCS with site-directed variants of cytochrome c revealed the fundamental steps of heme attachment and maturation. A conserved histidine in HCCS (His154) provided the key ligand to the heme iron. Formation of the HCCS:heme complex served as the platform for interaction with apocytochrome c. Heme was the central molecule mediating contact between HCCS and apocytochrome c. A conserved histidine in apocytochrome c (His19 of CXXCH) supplied the second axial ligand to heme in the trapped HCCS:heme:cytochrome c complex. We also examined the substrate specificity of human HCCS and converted a bacterial cytochrome c into a robust substrate for the HCCS. The results allow us to describe the molecular mechanisms underlying the HCCS reaction.
Collapse
|
25
|
Asher WB, Bren KL. Cytochrome c heme lyase can mature a fusion peptide composed of the amino-terminal residues of horse cytochrome c. Chem Commun (Camb) 2012; 48:8344-6. [PMID: 22792539 DOI: 10.1039/c2cc31112g] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
It is shown that cytochrome c heme lyase (CCHL) attaches heme covalently to peptides composed of the N-terminal segment of cyt c fused to a non-heme containing protein, lending insight into the substrate specificity of CCHL and providing a new route to artificial heme proteins.
Collapse
Affiliation(s)
- Wesley B Asher
- Department of Chemistry, University of Rochester, Rochester, New York 14627-0216, USA
| | | |
Collapse
|
26
|
Verissimo AF, Sanders J, Daldal F, Sanders C. Engineering a prokaryotic apocytochrome c as an efficient substrate for Saccharomyces cerevisiae cytochrome c heme lyase. Biochem Biophys Res Commun 2012; 424:130-5. [PMID: 22732413 DOI: 10.1016/j.bbrc.2012.06.088] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2012] [Accepted: 06/18/2012] [Indexed: 12/11/2022]
Abstract
Cytochromes c are heme proteins that require multiple maturation components, such as heme lyases, for cofactor incorporation. Saccharomyces cerevisiae has two heme lyases that are specific for apocytochromes c (CCHL) or c(1) (CC(1)HL). CCHL can covalently attach heme b groups to apocytochrome c substrates of eukaryotic but not prokaryotic origin. Besides their conserved Cys-Xxx-Xxx-Cys-His heme-binding motifs, the amino-terminal regions of apocytochrome c substrates appear to be important for CCHL function. In this study, we show for the first time that only two amino acid changes in the amino-terminal region of the non-CCHL substrate apocytochrome c(2) from Rhodobacter capsulatus are necessary and sufficient for efficient holocytochrome c formation by CCHL. This finding led us to propose a consensus sequence located at the amino-terminus of apocytochromes c, and critical for substrate recognition and heme ligation by CCHL.
Collapse
Affiliation(s)
- Andreia F Verissimo
- Department of Biology, University of Pennsylvania, 433 South University Avenue, Philadelphia, PA 19104, USA
| | | | | | | |
Collapse
|
27
|
Direct electrochemistry of novel affinity-tag immobilized recombinant horse heart cytochrome c. Biosens Bioelectron 2012; 34:171-7. [DOI: 10.1016/j.bios.2012.01.039] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2011] [Revised: 01/26/2012] [Accepted: 01/27/2012] [Indexed: 02/07/2023]
|
28
|
Volkov AN, Vanwetswinkel S, Van de Water K, van Nuland NAJ. Redox-dependent conformational changes in eukaryotic cytochromes revealed by paramagnetic NMR spectroscopy. JOURNAL OF BIOMOLECULAR NMR 2012; 52:245-256. [PMID: 22318343 DOI: 10.1007/s10858-012-9607-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2011] [Accepted: 01/15/2012] [Indexed: 05/31/2023]
Abstract
Cytochrome c (Cc) is a soluble electron carrier protein, transferring reducing equivalents between Cc reductase and Cc oxidase in eukaryotes. In this work, we assessed the structural differences between reduced and oxidized Cc in solution by paramagnetic NMR spectroscopy. First, we have obtained nearly-complete backbone NMR resonance assignments for iso-1-yeast Cc and horse Cc in both oxidation states. These were further used to derive pseudocontact shifts (PCSs) arising from the paramagnetic haem group. Then, an extensive dataset comprising over 450 measured PCSs and high-resolution X-ray and solution NMR structures of both proteins were used to define the anisotropic magnetic susceptibility tensor, Δχ. For most nuclei, the PCSs back-calculated from the Δχ tensor are in excellent agreement with the experimental PCS values. However, several contiguous stretches-clustered around G41, N52, and A81-exhibit large deviations both in yeast and horse Cc. This behaviour is indicative of redox-dependent structural changes, the extent of which is likely conserved in the protein family. We propose that the observed discrepancies arise from the changes in protein dynamics and discuss possible functional implications.
Collapse
Affiliation(s)
- Alexander N Volkov
- Jean Jeener NMR Centre, Structural Biology Brussels, Vrije Universiteit Brussel, Belgium
| | | | | | | |
Collapse
|
29
|
Mitochondrial cytochromecsynthase: CP motifs are not necessary for heme attachment to apocytochromec. FEBS Lett 2011; 585:3415-9. [DOI: 10.1016/j.febslet.2011.08.042] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2011] [Revised: 08/25/2011] [Accepted: 08/26/2011] [Indexed: 11/20/2022]
|
30
|
Abstract
In c-type cytochromes, heme becomes covalently attached to the polypeptide chain by a reaction between the vinyl groups of the heme and cysteine thiols from the protein. There are two such cytochromes in mitochondria: cytochrome c and cytochrome c(1). The heme attachment is a post-translational modification that is catalysed by different biogenesis proteins in different organisms. Three types of biogenesis system are found or predicted in mitochondria: System I (the cytochrome c maturation system); System III (termed holocytochrome c synthase (HCCS) or heme lyase); and System V. This review focuses primarily on cytochrome c maturation in mitochondria containing HCCS (System III). It describes what is known about the enzymology and substrate specificity of HCCS; the role of HCCS in human disease; import of HCCS into mitochondria; import of apocytochromes c and c(1) into mitochondria and the close relationships with HCCS-dependent heme attachment; and the role of the fungal cytochrome c biogenesis accessory protein Cyc2. System V is also discussed; this is the postulated mitochondrial cytochrome c biogenesis system of trypanosomes and related organisms. No cytochrome c biogenesis proteins have been identified in the genomes of these organisms whose c-type cytochromes also have a unique mode of heme attachment.
Collapse
Affiliation(s)
- James W A Allen
- Department of Biochemistry, University of Oxford, Oxford, UK.
| |
Collapse
|
31
|
The mitochondrial cytochrome c
N-terminal region is critical for maturation by holocytochrome c
synthase. FEBS Lett 2011; 585:1891-6. [DOI: 10.1016/j.febslet.2011.04.058] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2011] [Revised: 04/18/2011] [Accepted: 04/20/2011] [Indexed: 11/19/2022]
|
32
|
Topography of tyrosine residues and their involvement in peroxidation of polyunsaturated cardiolipin in cytochrome c/cardiolipin peroxidase complexes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2011; 1808:2147-55. [PMID: 21356558 DOI: 10.1016/j.bbamem.2011.04.009] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2010] [Revised: 04/13/2011] [Accepted: 04/21/2011] [Indexed: 01/30/2023]
Abstract
Formation of cytochrome c (cyt c)/cardiolipin (CL) peroxidase complex selective toward peroxidation of polyunsaturated CLs is a pre-requisite for mitochondrial membrane permeabilization. Tyrosine residues - via the generation of tyrosyl radicals (Tyr) - are likely reactive intermediates of the peroxidase cycle leading to CL peroxidation. We used mutants of horse heart cyt c in which each of the four Tyr residues was substituted for Phe and assessed their contribution to the peroxidase catalysis. Tyr67Phe mutation was associated with a partial loss of the oxygenase function of the cyt c/CL complex and the lowest concentration of H(2)O(2)-induced Tyr radicals in electron paramagnetic resonance (EPR) spectra. Our MS experiments directly demonstrated decreased production of CL-hydroperoxides (CL-OOH) by Tyr67Phe mutant. Similarly, oxidation of a phenolic substrate, Amplex Red, was affected to a greater extent in Tyr67Phe than in three other mutants. Tyr67Phe mutant exerted high resistance to H(2)O(2)-induced oligomerization. Measurements of Tyr fluorescence, hetero-nuclear magnetic resonance (NMR) and computer simulations position Tyr67 in close proximity to the porphyrin ring heme iron and one of the two axial heme-iron ligand residues, Met80. Thus, the highly conserved Tyr67 is a likely electron-donor (radical acceptor) in the oxygenase half-reaction of the cyt c/CL peroxidase complex.
Collapse
|
33
|
Kleingardner JG, Bren KL. Comparing substrate specificity between cytochrome c maturation and cytochrome c heme lyase systems for cytochrome c biogenesis. Metallomics 2011; 3:396-403. [PMID: 21380436 PMCID: PMC3081496 DOI: 10.1039/c0mt00086h] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Hemes c are characterized by their covalent attachment to a polypeptide via a widely conserved CXXCH motif. There are multiple biological systems that facilitate heme c biogenesis. System I, the cytochrome c maturation (CCM) system, is found in many bacteria and is commonly employed in the maturation of bacterial cytochromes c in Escherichia coli-based expression systems. System III, cytochrome c heme lyase (CCHL), is an enzyme found in the mitochondria of many eukaryotes and is used for heterologous expression of mitochondrial holocytochromes c. To test CCM specificity, a series of Hydrogenobacter thermophilus cytochrome c(552) variants was successfully expressed and matured by the CCM system with CX(n)CH motifs where n = 1-4, further extending the known substrate flexibility of the CCM system by successful maturation of a bacterial cytochrome c with a novel CXCH motif. Horse cytochrome c variants with both expanded and contracted attachment motifs (n = 1-3) were also tested for expression and maturation by both CCM and CCHL, allowing direct comparison of CCM and CCHL substrate specificities. Successful maturation of horse cytochrome c by CCHL with an extended CXXXCH motif was observed, demonstrating that CCHL shares the ability of CCM to mature hemes c with extended heme attachment motifs. In contrast, two single amino acid mutants were found in horse cytochrome c that severely limit maturation by CCHL, yet were efficiently matured with CCM. These results identify potentially important residues for the substrate recognition of CCHL.
Collapse
|
34
|
|
35
|
Tai H, Munegumi T, Yamamoto Y. Control of the Stability of Hydrogenobacter Thermophilus Cytochrome c552 through Alteration of the Basicity of the N-Terminal Amino Group of the Polypeptide Chain. Inorg Chem 2010; 49:10840-6. [DOI: 10.1021/ic1005924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Hulin Tai
- Department of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan
| | - Toratane Munegumi
- Department of Materials Chemistry and Bioengineering, Oyama National College of Technology, Oyama, Tochigi 323-0806, Japan
| | - Yasuhiko Yamamoto
- Department of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan
| |
Collapse
|
36
|
Zang C, Stevens JA, Link JJ, Guo L, Wang L, Zhong D. Ultrafast proteinquake dynamics in cytochrome c. J Am Chem Soc 2010; 131:2846-52. [PMID: 19203189 DOI: 10.1021/ja8057293] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We report here our systematic studies of the heme dynamics and induced protein conformational relaxations in two redox states of ferric and ferrous cytochrome c upon femtosecond excitation. With a wide range of probing wavelengths from the visible to the UV and a site-directed mutation we unambiguously determined that the protein dynamics in the two states are drastically different. For the ferrous state the heme transforms from 6-fold to 5-fold coordination with ultrafast ligand dissociation in less than 100 fs, followed by vibrational cooling within several picoseconds, but then recombining back to its original 6-fold coordination in 7 ps. Such impulsive bond breaking and late rebinding generate proteinquakes and strongly perturb the local heme site and shake global protein conformation, which were found to completely recover in 13 and 42 ps, respectively. For the ferric state the heme however maintains its 6-fold coordination. The dynamics mainly occur at the local site, including ultrafast internal conversion in hundreds of femtoseconds, vibrational cooling on the similar picosecond time scale, and complete ground-state recovery in 10 ps, and no global conformation relaxation was observed.
Collapse
Affiliation(s)
- Chen Zang
- Department of Physics, Program of Biophysics, The Ohio State University, 191 West Woodruff Avenue, Columbus, Ohio, 43210, USA
| | | | | | | | | | | |
Collapse
|
37
|
Maturation of a eukaryotic cytochrome c in the cytoplasm of Escherichia coli without the assistance by a dedicated biogenesis apparatus. J Bioenerg Biomembr 2010; 42:125-33. [DOI: 10.1007/s10863-010-9276-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2010] [Accepted: 02/22/2010] [Indexed: 10/19/2022]
|
38
|
Schröper F, Baumann A, Offenhäusser A, Mayer D. Bidirectional immobilization of affinity-tagged cytochrome c on electrode surfaces. Chem Commun (Camb) 2010; 46:5295-7. [DOI: 10.1039/c0cc00850h] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
39
|
Kawai C, Pessoto FS, Rodrigues T, Mugnol KCU, Tórtora V, Castro L, Milícchio VA, Tersariol ILS, Di Mascio P, Radi R, Carmona-Ribeiro AM, Nantes IL. pH-sensitive binding of cytochrome c to the inner mitochondrial membrane. Implications for the participation of the protein in cell respiration and apoptosis. Biochemistry 2009; 48:8335-42. [PMID: 19650668 DOI: 10.1021/bi9006463] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cytochrome c exhibits two positively charged sites: site A containing lysine residues with high pKa values and site L containing ionizable groups with pKaobs values around 7.0. This protein feature implies that cytochrome c can participate in the fusion of mitochondria and have its detachment from the inner membrane regulated by cell acidosis and alkalosis. In this study, we demonstrated that both horse and tuna cytochrome c exhibited two types of binding to inner mitochondrial membranes that contributed to respiration: a high-affinity and low-efficiency pH-independent binding (microscopic dissociation constant Ksapp2, approximately 10 nM) and a low-affinity and high-efficiency pH-dependent binding that for horse cytochrome c had a pKa of approximately 6.7. For tuna cytochrome c (Lys22 and His33 replaced with Asn and Trp, respectively), the effect of pH on Ksapp1 was less striking than for the horse heme protein, and both tuna and horse cytochrome c had closed Ksapp1 values at pH 7.2 and 6.2, respectively. Recombinant mutated cytochrome c H26N and H33N also restored the respiration of the cytochrome c-depleted mitoplast in a pH-dependent manner. Consistently, the detachment of cytochrome c from nondepleted mitoplasts was favored by alkalinization, suggesting that site L ionization influences the participation of cytochrome c in the respiratory chain and apoptosis.
Collapse
Affiliation(s)
- Cintia Kawai
- Centro Interdisciplinar de Investigação Bioquímica (CIIB), Universidade de Mogi das Cruzes (UMC), Mogi das Cruzes, São Paulo, Brazil
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
40
|
Liu W, Rumbley JN, Englander SW, Wand AJ. Fast structural dynamics in reduced and oxidized cytochrome c. Protein Sci 2009; 18:670-4. [PMID: 19241377 DOI: 10.1002/pro.72] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The sub-nanosecond structural dynamics of reduced and oxidized cytochrome c were characterized. Dynamic properties of the protein backbone measured by amide (15)N relaxation and side chains measured by the deuterium relaxation of methyl groups change little upon change in the redox state. These results imply that the solvent reorganization energy associated with electron transfer is small, consistent with previous theoretical analyses. The relative rigidity of both redox states also implies that dynamic relief of destructive electron transfer pathway interference is not operational in free cytochrome c.
Collapse
Affiliation(s)
- Weixia Liu
- Department of Biochemistry and Biophysics, Johnson Research Foundation, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6059, USA
| | | | | | | |
Collapse
|
41
|
Duncan MG, Williams MD, Bowler BE. Compressing the free energy range of substructure stabilities in iso-1-cytochrome c. Protein Sci 2009; 18:1155-64. [PMID: 19472325 DOI: 10.1002/pro.120] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Evolutionary conservation of substructure architecture between yeast iso-1-cytochrome c and the well-characterized horse cytochrome c is studied with limited proteolysis, the alkaline conformational transition and global unfolding with guanidine-HCl. Mass spectral analysis of limited proteolysis cleavage products for iso-1-cytochrome c show that its least stable substructure is the same as horse cytochrome c. The limited proteolysis data yield a free energy of 3.8 +/- 0.4 kcal mol(-1) to unfold the least stable substructure compared with 5.05 +/- 0.30 kcal mol(-1) for global unfolding of iso-1-cytochrome c. Thus, substructure stabilities of iso-1-cytochrome c span only approximately 1.2 kcal mol(-1) compared with approximately 8 kcal mol(-1) for horse cytochrome c. Consistent with the less cooperative folding thus expected for the horse protein, the guanidine-HCl m-values are approximately 3 kcal mol(-1)M(-1) versus approximately 4.5 kcal mol(-1)M(-1) for horse versus yeast cytochrome c. The tight free energy spacing of the yeast cytochrome c substructures suggests that its folding has more branch points than for horse cytochrome c. Studies on a variant of iso-1-cytochrome c with an H26N mutation indicate that the least and most stable substructures unfold sequentially and the two least stable substructures unfold independently as for horse cytochrome c. Thus, important aspects of the substructure architecture of horse cytochrome c, albeit compressed energetically, are preserved evolutionally in yeast iso-1-cytochrome c.
Collapse
Affiliation(s)
- Michael G Duncan
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Dynamics, The University of Montana, Missoula, MT 59812, USA
| | | | | |
Collapse
|
42
|
Tai H, Munegumi T, Yamamoto Y. Stability of the heme Fe-N-terminal amino group coordination bond in denatured cytochrome c. Inorg Chem 2009; 48:331-8. [PMID: 19053349 DOI: 10.1021/ic801202d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In the denatured states of Hydrogenobacter thermophilus cytochrome c(552) (HT) and Pseudomonas aeruginosa cytochrome c(551) (PA), and their mutants, the N-terminal amino group of the polypeptide chain is coordinated to heme Fe in place of the axial Met, the His-N(term) form being formed. The coordination of the N-terminal amino group to heme Fe leads to loop formation by the N-terminal stretch preceding the first Cys residue bound to the heme, and the N-terminal stretches of HT and PA are different from each other in terms of both the sequence and the number of constituent amino acid residues. The His-N(term) form was shown to be rather stable, and hence it can influence the stability of the denatured state. We have investigated the heme Fe coordination structures and stabilities of the His-N(term) forms emerging upon guanidine hydrochloric acid-induced unfolding of the oxidized forms of the proteins. The Fe-N(term) coordination bond in the His-N(term) form with a 9-residue N-terminal stretch of HT proteins was found to be tilted to some extent away from the heme normal, as reflected by the great heme methyl proton shift spread. On the other hand, the small heme methyl proton shift spread of the His-N(term) form with an 11-residue stretch of PA proteins indicated that its Fe-N(term) bond is nearly parallel with the heme normal. The stability of the His-N(term) form was found to be affected by the structural properties of the N-terminal stretch, such as its length and the N-terminal residue. With a given N-terminal residue, the stability of the His-N(term) form is higher for a 9-residue N-terminal stretch than an 11-residue one. In addition, with a given length of the N-terminal stretch, the His-N(term) form with an N-terminal Glu is stabilized by a few kJ mol(-1) relative to that with an N-terminal Asn. These results provide a novel insight into the stabilizing interactions in the denatured cyts c that will facilitate elucidation of the folding/unfolding mechanisms of the proteins.
Collapse
Affiliation(s)
- Hulin Tai
- Department of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan
| | | | | |
Collapse
|
43
|
Abriata LA, Cassina A, Tórtora V, Marín M, Souza JM, Castro L, Vila AJ, Radi R. Nitration of solvent-exposed tyrosine 74 on cytochrome c triggers heme iron-methionine 80 bond disruption. Nuclear magnetic resonance and optical spectroscopy studies. J Biol Chem 2009; 284:17-26. [PMID: 18974097 PMCID: PMC2610516 DOI: 10.1074/jbc.m807203200] [Citation(s) in RCA: 86] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2008] [Revised: 10/28/2008] [Indexed: 02/04/2023] Open
Abstract
Cytochrome c, a mitochondrial electron transfer protein containing a hexacoordinated heme, is involved in other physiologically relevant events, such as the triggering of apoptosis, and the activation of a peroxidatic activity. The latter occurs secondary to interactions with cardiolipin and/or post-translational modifications, including tyrosine nitration by peroxynitrite and other nitric oxide-derived oxidants. The gain of peroxidatic activity in nitrated cytochrome c has been related to a heme site transition in the physiological pH region, which normally occurs at alkaline pH in the native protein. Herein, we report a spectroscopic characterization of two nitrated variants of horse heart cytochrome c by using optical spectroscopy studies and NMR. Highly pure nitrated cytochrome c species modified at solvent-exposed Tyr-74 or Tyr-97 were generated after treatment with a flux of peroxynitrite, separated, purified by preparative high pressure liquid chromatography, and characterized by mass spectrometry-based peptide mapping. It is shown that nitration of Tyr-74 elicits an early alkaline transition with a pKa = 7.2, resulting in the displacement of the sixth and axial iron ligand Met-80 and replacement by a weaker Lys ligand to yield an alternative low spin conformation. Based on the study of site-specific Tyr to Phe mutants in the four conserved Tyr residues, we also show that this transition is not due to deprotonation of nitro-Tyr-74, but instead we propose a destabilizing steric effect of the nitro group in the mobile Omega-loop of cytochrome c, which is transmitted to the iron center via the nearby Tyr-67. The key role of Tyr-67 in promoting the transition through interactions with Met-80 was further substantiated in the Y67F mutant. These results therefore provide new insights into how a remote post-translational modification in cytochrome c such as tyrosine nitration triggers profound structural changes in the heme ligation and microenvironment and impacts in protein function.
Collapse
Affiliation(s)
- Luciano A Abriata
- Instituto de Biología Molecular y Celular de Rosario (IBR), Biophysics Section, Universidad Nacional de Rosario, 2000 Rosario, Argentina, Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, 11800 Montevideo, Uruguay, Center for Free Radical and Biomedical Research, Facultad de Medicina, Universidad de la República, 11800 Montevideo, Uruguay, and Sección Bioquímica-Biología Molecular, Facultad de Ciencias, Universidad de la República, 11400 Montevideo, Uruguay
| | - Adriana Cassina
- Instituto de Biología Molecular y Celular de Rosario (IBR), Biophysics Section, Universidad Nacional de Rosario, 2000 Rosario, Argentina, Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, 11800 Montevideo, Uruguay, Center for Free Radical and Biomedical Research, Facultad de Medicina, Universidad de la República, 11800 Montevideo, Uruguay, and Sección Bioquímica-Biología Molecular, Facultad de Ciencias, Universidad de la República, 11400 Montevideo, Uruguay; Instituto de Biología Molecular y Celular de Rosario (IBR), Biophysics Section, Universidad Nacional de Rosario, 2000 Rosario, Argentina, Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, 11800 Montevideo, Uruguay, Center for Free Radical and Biomedical Research, Facultad de Medicina, Universidad de la República, 11800 Montevideo, Uruguay, and Sección Bioquímica-Biología Molecular, Facultad de Ciencias, Universidad de la República, 11400 Montevideo, Uruguay
| | - Verónica Tórtora
- Instituto de Biología Molecular y Celular de Rosario (IBR), Biophysics Section, Universidad Nacional de Rosario, 2000 Rosario, Argentina, Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, 11800 Montevideo, Uruguay, Center for Free Radical and Biomedical Research, Facultad de Medicina, Universidad de la República, 11800 Montevideo, Uruguay, and Sección Bioquímica-Biología Molecular, Facultad de Ciencias, Universidad de la República, 11400 Montevideo, Uruguay; Instituto de Biología Molecular y Celular de Rosario (IBR), Biophysics Section, Universidad Nacional de Rosario, 2000 Rosario, Argentina, Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, 11800 Montevideo, Uruguay, Center for Free Radical and Biomedical Research, Facultad de Medicina, Universidad de la República, 11800 Montevideo, Uruguay, and Sección Bioquímica-Biología Molecular, Facultad de Ciencias, Universidad de la República, 11400 Montevideo, Uruguay
| | - Mónica Marín
- Instituto de Biología Molecular y Celular de Rosario (IBR), Biophysics Section, Universidad Nacional de Rosario, 2000 Rosario, Argentina, Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, 11800 Montevideo, Uruguay, Center for Free Radical and Biomedical Research, Facultad de Medicina, Universidad de la República, 11800 Montevideo, Uruguay, and Sección Bioquímica-Biología Molecular, Facultad de Ciencias, Universidad de la República, 11400 Montevideo, Uruguay; Instituto de Biología Molecular y Celular de Rosario (IBR), Biophysics Section, Universidad Nacional de Rosario, 2000 Rosario, Argentina, Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, 11800 Montevideo, Uruguay, Center for Free Radical and Biomedical Research, Facultad de Medicina, Universidad de la República, 11800 Montevideo, Uruguay, and Sección Bioquímica-Biología Molecular, Facultad de Ciencias, Universidad de la República, 11400 Montevideo, Uruguay
| | - Josá M Souza
- Instituto de Biología Molecular y Celular de Rosario (IBR), Biophysics Section, Universidad Nacional de Rosario, 2000 Rosario, Argentina, Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, 11800 Montevideo, Uruguay, Center for Free Radical and Biomedical Research, Facultad de Medicina, Universidad de la República, 11800 Montevideo, Uruguay, and Sección Bioquímica-Biología Molecular, Facultad de Ciencias, Universidad de la República, 11400 Montevideo, Uruguay; Instituto de Biología Molecular y Celular de Rosario (IBR), Biophysics Section, Universidad Nacional de Rosario, 2000 Rosario, Argentina, Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, 11800 Montevideo, Uruguay, Center for Free Radical and Biomedical Research, Facultad de Medicina, Universidad de la República, 11800 Montevideo, Uruguay, and Sección Bioquímica-Biología Molecular, Facultad de Ciencias, Universidad de la República, 11400 Montevideo, Uruguay
| | - Laura Castro
- Instituto de Biología Molecular y Celular de Rosario (IBR), Biophysics Section, Universidad Nacional de Rosario, 2000 Rosario, Argentina, Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, 11800 Montevideo, Uruguay, Center for Free Radical and Biomedical Research, Facultad de Medicina, Universidad de la República, 11800 Montevideo, Uruguay, and Sección Bioquímica-Biología Molecular, Facultad de Ciencias, Universidad de la República, 11400 Montevideo, Uruguay; Instituto de Biología Molecular y Celular de Rosario (IBR), Biophysics Section, Universidad Nacional de Rosario, 2000 Rosario, Argentina, Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, 11800 Montevideo, Uruguay, Center for Free Radical and Biomedical Research, Facultad de Medicina, Universidad de la República, 11800 Montevideo, Uruguay, and Sección Bioquímica-Biología Molecular, Facultad de Ciencias, Universidad de la República, 11400 Montevideo, Uruguay
| | - Alejandro J Vila
- Instituto de Biología Molecular y Celular de Rosario (IBR), Biophysics Section, Universidad Nacional de Rosario, 2000 Rosario, Argentina, Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, 11800 Montevideo, Uruguay, Center for Free Radical and Biomedical Research, Facultad de Medicina, Universidad de la República, 11800 Montevideo, Uruguay, and Sección Bioquímica-Biología Molecular, Facultad de Ciencias, Universidad de la República, 11400 Montevideo, Uruguay.
| | - Rafael Radi
- Instituto de Biología Molecular y Celular de Rosario (IBR), Biophysics Section, Universidad Nacional de Rosario, 2000 Rosario, Argentina, Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, 11800 Montevideo, Uruguay, Center for Free Radical and Biomedical Research, Facultad de Medicina, Universidad de la República, 11800 Montevideo, Uruguay, and Sección Bioquímica-Biología Molecular, Facultad de Ciencias, Universidad de la República, 11400 Montevideo, Uruguay; Instituto de Biología Molecular y Celular de Rosario (IBR), Biophysics Section, Universidad Nacional de Rosario, 2000 Rosario, Argentina, Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, 11800 Montevideo, Uruguay, Center for Free Radical and Biomedical Research, Facultad de Medicina, Universidad de la República, 11800 Montevideo, Uruguay, and Sección Bioquímica-Biología Molecular, Facultad de Ciencias, Universidad de la República, 11400 Montevideo, Uruguay.
| |
Collapse
|
44
|
Bandi S, Bowler BE. Probing the bottom of a folding funnel using conformationally gated electron transfer reactions. J Am Chem Soc 2008; 130:7540-1. [PMID: 18494471 DOI: 10.1021/ja801941r] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The effect of global stability on the kinetics of interconversion between the native (N) and a compact, partially unfolded form (I) of iso-1-cytochrome c stabilized by His73-heme ligation is investigated using a novel conformationally gated ET method. For the K73H variant and the 2-fold less stable AcH73 variant, the N and I conformers are of nearly equal stability at pH 7.5. The pH jump kinetic data yield kobs = kNI + kIN of 35-40 s-1 at final pH values from 6 to 8 for the AcH73 variant, about 3-fold faster than for the more stable K73H variant. Gated ET measurements give kNI = 28 s-1 and kIN = 13 s-1 for the AcH73 variant, 10- and 2-fold greater than that for the more stable K73H variant. Thus, funneled landscapes have evolved such that loss of global stability lowers barriers at the bottom of a folding funnel, still allowing for efficient folding.
Collapse
Affiliation(s)
- Swati Bandi
- Department of Chemistry and Center for Biomolecular Structure and Dynamics, The University of Montana, Missoula, Montana 59812, USA
| | | |
Collapse
|
45
|
Xu X, Reinle W, Hannemann F, Konarev PV, Svergun DI, Bernhardt R, Ubbink M. Dynamics in a Pure Encounter Complex of Two Proteins Studied by Solution Scattering and Paramagnetic NMR Spectroscopy. J Am Chem Soc 2008; 130:6395-403. [DOI: 10.1021/ja7101357] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Xingfu Xu
- Institute of Chemistry, Leiden University, P.O. Box 9502, NL-2300RA Leiden, The Netherlands, Naturwissenschaftlich-Technische Fakultat III, Institut für Biochemie, Universität des Saarlandes, P.O. Box 151150, D-66041, Saarbrucken, Germany, EMBL Hamburg, Notkestrasse 85, D-22603 Hamburg, Germany, and Institute of Crystallography, Russian Academy of Sciences, Leninsky pr. 59, 117333, Moscow, Russia
| | - Wolfgang Reinle
- Institute of Chemistry, Leiden University, P.O. Box 9502, NL-2300RA Leiden, The Netherlands, Naturwissenschaftlich-Technische Fakultat III, Institut für Biochemie, Universität des Saarlandes, P.O. Box 151150, D-66041, Saarbrucken, Germany, EMBL Hamburg, Notkestrasse 85, D-22603 Hamburg, Germany, and Institute of Crystallography, Russian Academy of Sciences, Leninsky pr. 59, 117333, Moscow, Russia
| | - Frank Hannemann
- Institute of Chemistry, Leiden University, P.O. Box 9502, NL-2300RA Leiden, The Netherlands, Naturwissenschaftlich-Technische Fakultat III, Institut für Biochemie, Universität des Saarlandes, P.O. Box 151150, D-66041, Saarbrucken, Germany, EMBL Hamburg, Notkestrasse 85, D-22603 Hamburg, Germany, and Institute of Crystallography, Russian Academy of Sciences, Leninsky pr. 59, 117333, Moscow, Russia
| | - Peter V. Konarev
- Institute of Chemistry, Leiden University, P.O. Box 9502, NL-2300RA Leiden, The Netherlands, Naturwissenschaftlich-Technische Fakultat III, Institut für Biochemie, Universität des Saarlandes, P.O. Box 151150, D-66041, Saarbrucken, Germany, EMBL Hamburg, Notkestrasse 85, D-22603 Hamburg, Germany, and Institute of Crystallography, Russian Academy of Sciences, Leninsky pr. 59, 117333, Moscow, Russia
| | - Dmitri I. Svergun
- Institute of Chemistry, Leiden University, P.O. Box 9502, NL-2300RA Leiden, The Netherlands, Naturwissenschaftlich-Technische Fakultat III, Institut für Biochemie, Universität des Saarlandes, P.O. Box 151150, D-66041, Saarbrucken, Germany, EMBL Hamburg, Notkestrasse 85, D-22603 Hamburg, Germany, and Institute of Crystallography, Russian Academy of Sciences, Leninsky pr. 59, 117333, Moscow, Russia
| | - Rita Bernhardt
- Institute of Chemistry, Leiden University, P.O. Box 9502, NL-2300RA Leiden, The Netherlands, Naturwissenschaftlich-Technische Fakultat III, Institut für Biochemie, Universität des Saarlandes, P.O. Box 151150, D-66041, Saarbrucken, Germany, EMBL Hamburg, Notkestrasse 85, D-22603 Hamburg, Germany, and Institute of Crystallography, Russian Academy of Sciences, Leninsky pr. 59, 117333, Moscow, Russia
| | - Marcellus Ubbink
- Institute of Chemistry, Leiden University, P.O. Box 9502, NL-2300RA Leiden, The Netherlands, Naturwissenschaftlich-Technische Fakultat III, Institut für Biochemie, Universität des Saarlandes, P.O. Box 151150, D-66041, Saarbrucken, Germany, EMBL Hamburg, Notkestrasse 85, D-22603 Hamburg, Germany, and Institute of Crystallography, Russian Academy of Sciences, Leninsky pr. 59, 117333, Moscow, Russia
| |
Collapse
|
46
|
Fernandes AP, Couto I, Morgado L, Londer YY, Salgueiro CA. Isotopic labeling of c-type multiheme cytochromes overexpressed in E. coli. Protein Expr Purif 2008; 59:182-8. [PMID: 18343156 DOI: 10.1016/j.pep.2008.02.001] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2008] [Revised: 02/06/2008] [Accepted: 02/07/2008] [Indexed: 11/30/2022]
Abstract
Progresses made in bacterial genome sequencing show a remarkable profusion of multiheme c-type cytochromes in many bacteria, highlighting the importance of these proteins in different cellular events. However, the characterization of multiheme cytochromes has been significantly retarded by the numerous experimental challenges encountered by researchers who attempt to overexpress these proteins, especially if isotopic labeling is required. Here we describe a methodology for isotopic labeling of multiheme cytochromes c overexpressed in Escherichia coli, using the triheme cytochrome PpcA from Geobacter sulfurreducens as a model protein. By combining different strategies previously described and using E. coli cells containing the gene coding for PpcA and the cytochrome c maturation gene cluster, an experimental labeling methodology was developed that is based on two major aspects: (i) use of a two-step culture growth procedure, where cell growth in rich media was followed by transfer to minimal media containing (15)N-labeled ammonium chloride, and (ii) incorporation of the heme precursor delta-aminolevulinic acid in minimal culture media. The yields of labeled protein obtained were comparable to those obtained for expression of PpcA in rich media. Proper protein folding and labeling were confirmed by UV-visible and NMR spectroscopy. To our knowledge, this is the first report of a recombinant multiheme cytochrome labeling and it represents a major breakthrough for functional and structural studies of multiheme cytochromes.
Collapse
Affiliation(s)
- Ana P Fernandes
- Requimte-CQFB, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa (FCT/UNL), Campus Caparica, 2829-516 Caparica, Portugal
| | | | | | | | | |
Collapse
|
47
|
Krishna MMG, Maity H, Rumbley JN, Englander SW. Branching in the sequential folding pathway of cytochrome c. Protein Sci 2007; 16:1946-56. [PMID: 17660254 PMCID: PMC2206985 DOI: 10.1110/ps.072922307] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Previous results indicate that the folding pathways of cytochrome c and other proteins progressively build the target native protein in a predetermined stepwise manner by the sequential formation and association of native-like foldon units. The present work used native state hydrogen exchange methods to investigate a structural anomaly in cytochrome c results that suggested the concerted folding of two segments that have little structural relationship in the native protein. The results show that the two segments, an 18-residue omega loop and a 10-residue helix, are able to unfold and refold independently, which allows a branch point in the folding pathway. The pathway that emerges assembles native-like foldon units in a linear sequential manner when prior native-like structure can template a single subsequent foldon, and optional pathway branching is seen when prior structure is able to support the folding of two different foldons.
Collapse
Affiliation(s)
- Mallela M G Krishna
- Johnson Research Foundation, Department of Biochemistry and Biophysics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104-6059, USA.
| | | | | | | |
Collapse
|
48
|
Abe M, Ohno S, Yokogawa T, Nakanishi T, Arisaka F, Hosoya T, Hiramatsu T, Suzuki M, Ogasawara T, Sawasaki T, Nishikawa K, Kitamura M, Hori H, Endo Y. Detection of structural changes in a cofactor binding protein by using a wheat germ cell-free protein synthesis system coupled with unnatural amino acid probing. Proteins 2007; 67:643-52. [PMID: 17348022 DOI: 10.1002/prot.21341] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
A cell-free protein synthesis system is a powerful tool with which unnatural amino acids can be introduced into polypeptide chains. Here, the authors describe unnatural amino acid probing in a wheat germ cell-free translation system as a method for detecting the structural changes that occur in a cofactor binding protein on a conversion of the protein from an apo-form to a holo-form. The authors selected the FMN-binding protein from Desulfovibrio vulgaris as a model protein. The apo-form of the protein was synthesized efficiently in the absence of FMN. The purified apo-form could be correctly converted to the holo-form. Thus, the system could synthesize the active apo-form. Gel filtration chromatography, analytical ultracentrifugation, and circular dichroism-spectra studies suggested that the FMN-binding site of the apo-form is open as compared with the holo-form. To confirm this idea, the unnatural amino acid probing was performed by incorporating 3-azido-L-tyrosine at the Tyr35 residue in the FMN-binding site. The authors optimized three steps in their system. The introduced 3-azido-L-tyrosine residue was subjected to specific chemical modification by a fluorescein-triarylphosphine derivative. The initial velocity of the apo-form reaction was 20 fold faster than that of the holo-form, demonstrating that the Tyr35 residue in the apo-form is open to solvent.
Collapse
Affiliation(s)
- Masato Abe
- Department of Applied Chemistry, Faculty of Engineering, Ehime University, Matsuyama 790-8577, Japan
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
49
|
Abel CJ, Goldbeck RA, Latypov RF, Roder H, Kliger DS. Conformational equilibration time of unfolded protein chains and the folding speed limit. Biochemistry 2007; 46:4090-9. [PMID: 17352458 PMCID: PMC4327933 DOI: 10.1021/bi0622930] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The speed with which the conformers of unfolded protein chains interconvert is a fundamental question in the study of protein folding. Kinetic evidence is presented here for the time constant for interconversion of disparate unfolded chain conformations of a small globular protein, cytochrome c, in the presence of guanidine hydrochloride denaturant. The axial binding reactions of histidine and methionine residues with the Fe(II) heme cofactor were monitored with time-resolved magnetic circular dichroism spectroscopy after photodissociation of the CO complexes of unfolded protein obtained from horse and tuna and from several histidine mutants of the horse protein. A kinetic model fitting both the reaction rate constants and spectra of the intermediates was used to obtain a quantitative estimate of the conformational diffusion time. The latter parameter was approximated as a first-order time constant for exchange between conformational subensembles presenting either a methionine or a histidine residue to the heme iron for facile binding. The mean diffusional time constant of the wild type and variants was 3 +/- 2 mus, close to the folding "speed limit". The implications of the relatively rapid conformational equilibration time observed are discussed in terms of the energy landscape and classical pathway time regimes of folding, for which the conformational diffusion time can be considered a pivot point.
Collapse
Affiliation(s)
| | - Robert A. Goldbeck
- To whom correspondence should be addressed: Tel.: 831-459-4007, Fax: 831-459-2935.,
| | | | | | | |
Collapse
|
50
|
Abstract
Recent work on the thermodynamics of protein denatured states is providing insight into the stability of residual structure and the conformational constraints that affect the disordered states of proteins. Current data from native state hydrogen exchange and the pH dependence of protein stability indicate that residual structure can modulate the stability of the denatured state by up to 4 kcal mol(-1). NMR structural data have emphasized the role of hydrophobic clusters in stabilizing denatured state residual structures, however recent results indicate that electrostatic interactions, both favorable and unfavorable, are also important modulators of the stability of the denatured state. Thermodynamics methods that take advantage of histidine-heme ligation chemistry have also been developed to probe the conformational constraints that act on denatured states. These methods have provided insights into the role of excluded volume, chain stiffness, and loop persistence in modulating the conformational preferences of highly disordered proteins. New insights into protein folding and novel methods to manipulate protein stability are emerging from this work.
Collapse
Affiliation(s)
- Bruce E Bowler
- Department of Chemistry, University of Montana, Missoula, MT 59812, USA.
| |
Collapse
|