1
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Lobez AP, Wu F, Di Trani JM, Rubinstein JL, Oliveberg M, Brzezinski P, Moe A. Electron transfer in the respiratory chain at low salinity. Nat Commun 2024; 15:8241. [PMID: 39300056 DOI: 10.1038/s41467-024-52475-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Accepted: 09/09/2024] [Indexed: 09/22/2024] Open
Abstract
Recent studies have established that cellular electrostatic interactions are more influential than assumed previously. Here, we use cryo-EM and perform steady-state kinetic studies to investigate electrostatic interactions between cytochrome (cyt.) c and the complex (C) III2-IV supercomplex from Saccharomyces cerevisiae at low salinity. The kinetic studies show a sharp transition with a Hill coefficient ≥2, which together with the cryo-EM data at 2.4 Å resolution indicate multiple cyt. c molecules bound along the supercomplex surface. Negatively charged loops of CIII2 subunits Qcr6 and Qcr9 become structured to interact with cyt. c. In addition, the higher resolution allows us to identify water molecules in proton pathways of CIV and, to the best of our knowledge, previously unresolved cardiolipin molecules. In conclusion, the lowered electrostatic screening renders engagement of multiple cyt. c molecules that are directed by electrostatically structured CIII2 loops to conduct electron transfer between CIII2 and CIV.
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Affiliation(s)
- Ana Paula Lobez
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, Stockholm, Sweden
| | - Fei Wu
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, Stockholm, Sweden
| | - Justin M Di Trani
- Molecular Medicine program, The Hospital for Sick Children, 686 Bay Street, Toronto, Ontario, Canada
- Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - John L Rubinstein
- Molecular Medicine program, The Hospital for Sick Children, 686 Bay Street, Toronto, Ontario, Canada
- Department of Medical Biophysics, The University of Toronto, 101 College Street, Toronto, Ontario, Canada
- Department of Biochemistry, The University of Toronto, 1 Kings College Circle, Toronto, Ontario, Canada
| | - Mikael Oliveberg
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, Stockholm, Sweden.
| | - Peter Brzezinski
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, Stockholm, Sweden.
| | - Agnes Moe
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, Stockholm, Sweden.
- Institute of Biochemistry and Molecular Medicine, University of Bern, Bühlstrasse 28, Bern, Switzerland.
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2
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Zhou Z, Arroum T, Luo X, Kang R, Lee YJ, Tang D, Hüttemann M, Song X. Diverse functions of cytochrome c in cell death and disease. Cell Death Differ 2024; 31:387-404. [PMID: 38521844 PMCID: PMC11043370 DOI: 10.1038/s41418-024-01284-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Revised: 03/13/2024] [Accepted: 03/18/2024] [Indexed: 03/25/2024] Open
Abstract
The redox-active protein cytochrome c is a highly positively charged hemoglobin that regulates cell fate decisions of life and death. Under normal physiological conditions, cytochrome c is localized in the mitochondrial intermembrane space, and its distribution can extend to the cytosol, nucleus, and extracellular space under specific pathological or stress-induced conditions. In the mitochondria, cytochrome c acts as an electron carrier in the electron transport chain, facilitating adenosine triphosphate synthesis, regulating cardiolipin peroxidation, and influencing reactive oxygen species dynamics. Upon cellular stress, it can be released into the cytosol, where it interacts with apoptotic peptidase activator 1 (APAF1) to form the apoptosome, initiating caspase-dependent apoptotic cell death. Additionally, following exposure to pro-apoptotic compounds, cytochrome c contributes to the survival of drug-tolerant persister cells. When translocated to the nucleus, it can induce chromatin condensation and disrupt nucleosome assembly. Upon its release into the extracellular space, cytochrome c may act as an immune mediator during cell death processes, highlighting its multifaceted role in cellular biology. In this review, we explore the diverse structural and functional aspects of cytochrome c in physiological and pathological responses. We summarize how posttranslational modifications of cytochrome c (e.g., phosphorylation, acetylation, tyrosine nitration, and oxidation), binding proteins (e.g., HIGD1A, CHCHD2, ITPR1, and nucleophosmin), and mutations (e.g., G41S, Y48H, and A51V) affect its function. Furthermore, we provide an overview of the latest advanced technologies utilized for detecting cytochrome c, along with potential therapeutic approaches related to this protein. These strategies hold tremendous promise in personalized health care, presenting opportunities for targeted interventions in a wide range of conditions, including neurodegenerative disorders, cardiovascular diseases, and cancer.
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Affiliation(s)
- Zhuan Zhou
- Department of Surgery, UT Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Tasnim Arroum
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, 48201, USA
| | - Xu Luo
- Eppley Institute for Research in Cancer and Allied Diseases, Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Rui Kang
- Department of Surgery, UT Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Yong J Lee
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, 8700 Beverly Blvd, Los Angeles, CA, 90048, USA
| | - Daolin Tang
- Department of Surgery, UT Southwestern Medical Center, Dallas, TX, 75390, USA.
| | - Maik Hüttemann
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, 48201, USA.
- Department of Biochemistry, Microbiology, and Immunology, Wayne State University, Detroit, MI, 48201, USA.
| | - Xinxin Song
- Department of Surgery, UT Southwestern Medical Center, Dallas, TX, 75390, USA.
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3
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Di Savino A, Foerster JM, Ullmann GM, Ubbink M. The Charge Distribution on a Protein Surface Determines Whether Productive or Futile Encounter Complexes Are Formed. Biochemistry 2021; 60:747-755. [PMID: 33646750 PMCID: PMC8041253 DOI: 10.1021/acs.biochem.1c00021] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
![]()
Protein complex formation
depends strongly on electrostatic interactions.
The distribution of charges on the surface of redox proteins is often
optimized by evolution to guide recognition and binding. To test the
degree to which the electrostatic interactions between cytochrome c peroxidase (CcP) and cytochrome c (Cc)
are optimized, we produced five CcP variants, each with a different
charge distribution on the surface. Monte Carlo simulations show that
the addition of negative charges attracts Cc to the new patches, and
the neutralization of the charges in the regular, stereospecific binding
site for Cc abolishes the electrostatic interactions in that region
entirely. For CcP variants with the charges in the regular binding
site intact, additional negative patches slightly enhance productive
complex formation, despite disrupting the optimized charge distribution.
Removal of the charges in the regular binding site results in a dramatic
decrease in the complex formation rate, even in the presence of highly
negative patches elsewhere on the surface. We conclude that additional
charge patches can result in either productive or futile encounter
complexes, depending on whether negative residues are located also
in the regular binding site.
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Affiliation(s)
- Antonella Di Savino
- Leiden University, Institute of Chemistry, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Johannes M Foerster
- University of Bayreuth, Computational Biochemistry, Universitätsstraße 30, NW I, 95447 Bayreuth, Germany
| | - G Matthias Ullmann
- University of Bayreuth, Computational Biochemistry, Universitätsstraße 30, NW I, 95447 Bayreuth, Germany
| | - Marcellus Ubbink
- Leiden University, Institute of Chemistry, Einsteinweg 55, 2333 CC Leiden, The Netherlands
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4
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Wheel and Deal in the Mitochondrial Inner Membranes: The Tale of Cytochrome c and Cardiolipin. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2020; 2020:6813405. [PMID: 32377304 PMCID: PMC7193304 DOI: 10.1155/2020/6813405] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 02/28/2020] [Indexed: 12/15/2022]
Abstract
Cardiolipin oxidation and degradation by different factors under severe cell stress serve as a trigger for genetically encoded cell death programs. In this context, the interplay between cardiolipin and another mitochondrial factor—cytochrome c—is a key process in the early stages of apoptosis, and it is a matter of intense research. Cytochrome c interacts with lipid membranes by electrostatic interactions, hydrogen bonds, and hydrophobic effects. Experimental conditions (including pH, lipid composition, and post-translational modifications) determine which specific amino acid residues are involved in the interaction and influence the heme iron coordination state. In fact, up to four binding sites (A, C, N, and L), driven by different interactions, have been reported. Nevertheless, key aspects of the mechanism for cardiolipin oxidation by the hemeprotein are well established. First, cytochrome c acts as a pseudoperoxidase, a process orchestrated by tyrosine residues which are crucial for peroxygenase activity and sensitivity towards oxidation caused by protein self-degradation. Second, flexibility of two weakest folding units of the hemeprotein correlates with its peroxidase activity and the stability of the iron coordination sphere. Third, the diversity of the mode of interaction parallels a broad diversity in the specific reaction pathway. Thus, current knowledge has already enabled the design of novel drugs designed to successfully inhibit cardiolipin oxidation.
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5
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de Vos WM, Lindhoud S. Overcharging and charge inversion: Finding the correct explanation(s). Adv Colloid Interface Sci 2019; 274:102040. [PMID: 31698305 DOI: 10.1016/j.cis.2019.102040] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 09/04/2019] [Accepted: 09/25/2019] [Indexed: 11/29/2022]
Abstract
Both overcharging and charge inversion denote a general observation that the sign of a surface charge can flip in the presence of interacting species such as surfactants, polyelectrolytes, proteins and multivalent ions. Moreover, charge inversion of proteins through charge regulation, is one explanation for protein adsorption to similarly charged surfaces. While overcharging and charge inversion have been long studied, the explanations for these phenomena are often still debated. Broadly these explanations can be categorized as "chemical" where specific attractive interactions are seen as the cause of charge inversion, and "physical" where purely electrostatic interactions and constraints of geometry are used as explanation. In this review, charge inversion is discussed from a very broad viewpoint, where we draw connections between the various explanations proposed for very different systems. Especially, we highlight the work of Johannes Lyklema, who always carefully balanced between the competing chemical and physical explanations, and demonstrated that only few experimental systems allow just a single explanation.
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Affiliation(s)
- Wiebe M de Vos
- Membrane Surface Science, University of Twente, MESA+ Institute for Nanotechnology, P.O. Box 217, 7500 AE Enschede, the Netherlands
| | - Saskia Lindhoud
- Nanobiophysics, University of Twente, MESA+ Institute for Nanotechnology, P.O. Box 217, 7500 AE Enschede, the Netherlands.
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6
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Wood MH, Humphreys EK, Welbourn RJL. Structural Changes in Adsorbed Cytochrome c upon Applied Potential Characterized by Neutron Reflectometry. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:6055-6063. [PMID: 30966748 DOI: 10.1021/acs.langmuir.9b00691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The structural behavior of an electron-transfer protein, cytochrome c, at the 316L stainless steel electrode/aqueous interface was investigated over a range of applied potentials using neutron reflectometry supported by solution depletion isotherms, X-ray reflectometry, and quartz crystal microbalance measurements. A custom-made electrochemical cell allowed in situ observation of the adsorbed protein across a range of applied potentials; models fitted to the NR data showed a compact inner protein layer at the metal/electrolyte interface and a further thicker but highly diffuse layer that could be removed by rinsing. The overall amount adsorbed was found to be strongly dependent on the applied potential and buffer pH. Subtle but significant changes in the structure of the adsorbed protein layer were seen as the potential was swept between ±0.40 V, reflecting changing attractive/repulsive interactions between the protein's charged side groups and the surface. At greater applied potentials, irreversible changes in the stainless steel film structure were also observed and attributed to deuterium absorption into the metal.
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Affiliation(s)
- Mary H Wood
- School of Chemistry , University of Birmingham , Birmingham B15 2TT , U.K
| | - Elizabeth K Humphreys
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB3 1EW , U.K
| | - Rebecca J L Welbourn
- ISIS Neutron & Muon Source, Rutherford Appleton Laboratory , Didcot OX11 0QX , U.K
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7
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Affiliation(s)
- Kazuo Kobayashi
- The Institute of Scientific and Industrial Research, Osaka University, Mihogaoka 8-1, Ibaraki, Osaka 567-0047, Japan
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8
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Melin F, Schoepp-Cothenet B, Abdulkarim S, Noor MR, Soulimane T, Hellwig P. Electrochemical study of an electron shuttle diheme protein: The cytochrome c from T. thermophilus. Inorganica Chim Acta 2017. [DOI: 10.1016/j.ica.2017.05.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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9
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Harper-Leatherman AS, Wallace JM, Rolison DR. Cytochrome c Stabilization and Immobilization in Aerogels. Methods Mol Biol 2016; 1504:149-163. [PMID: 27770420 DOI: 10.1007/978-1-4939-6499-4_12] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
Sol-gel-derived aerogels are three-dimensional, nanoscale materials that combine large surface area with high porosity. These traits make them useful for any rate-critical chemical process, particularly sensing or electrochemical applications, once physical or chemical moieties are incorporated into the gels to add their functionality to the ultraporous scaffold. Incorporating biomolecules into aerogels, other than such rugged species as lipases or cellulose, has been challenging due to the inability of most biomolecules to remain structurally intact within the gels during the necessary supercritical fluid (SCF) processing. However, the heme protein cytochrome c (cyt.c) forms self-organized superstructures around gold (or silver) nanoparticles in buffer that can be encapsulated into wet gels as the sol undergoes gelation. The guest-host wet gel can then be processed to form composite aerogels in which cyt.c retains its characteristic visible absorption. The gold (or silver) nanoparticle-nucleated superstructures protect the majority of the protein from the harsh physicochemical conditions necessary to form an aerogel. The Au~cyt.c superstructures exhibit rapid gas-phase recognition of nitric oxide (NO) within the bioaerogel matrix, as facilitated by the high-quality pore structure of the aerogel, while remaining viable for weeks at room temperature. More recently, careful control of synthetic parameters (e.g., buffer concentration, protein concentration, SCF extraction rate) have allowed for the preparation of cyt.c-silica aerogels, sans nucleating nanoparticles; these bioaerogels also exhibit rapid gas-phase sensing while retaining protein structural stability.
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Affiliation(s)
- Amanda S Harper-Leatherman
- Chemistry and Biochemistry Department, Fairfield University, 1073 North Benson Road, Fairfield, CT, 06824, USA.
| | - Jean Marie Wallace
- Nova Research, Inc., 1900 Elkin Street, Suite 230, Alexandria, VA, 22308, USA
| | - Debra R Rolison
- U.S. Naval Research Laboratory, Surface Chemistry Branch, Code 6170, Washington, DC, 20375, USA
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10
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Vogt S, Rhiel A, Weber P, Ramzan R. Revisiting Kadenbach: Electron flux rate through cytochrome c-oxidase determines the ATP-inhibitory effect and subsequent production of ROS. Bioessays 2016; 38:556-67. [PMID: 27171124 PMCID: PMC5084804 DOI: 10.1002/bies.201600043] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Mitochondrial respiration is the predominant source of ATP. Excessive rates of electron transport cause a higher production of harmful reactive oxygen species (ROS). There are two regulatory mechanisms known. The first, according to Mitchel, is dependent on the mitochondrial membrane potential that drives ATP synthase for ATP production, and the second, the Kadenbach mechanism, is focussed on the binding of ATP to Cytochrome c Oxidase (CytOx) at high ATP/ADP ratios, which results in an allosteric conformational change to CytOx, causing inhibition. In times of stress, ATP-dependent inhibition is switched off and the activity of CytOx is exclusively determined by the membrane potential, leading to an increase in ROS production. The second mechanism for respiratory control depends on the quantity of electron transfer to the Heme aa3 of CytOx. When ATP is bound to CytOx the enzyme is inhibited, and ROS formation is decreased, although the mitochondrial membrane potential is increased.
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Affiliation(s)
- Sebastian Vogt
- Cardiovascular Research Lab, Biochemical Pharmacological Research CenterPhilipps‐University MarburgMarburgGermany
| | - Annika Rhiel
- Cardiovascular Research Lab, Biochemical Pharmacological Research CenterPhilipps‐University MarburgMarburgGermany
| | - Petra Weber
- Cardiovascular Research Lab, Biochemical Pharmacological Research CenterPhilipps‐University MarburgMarburgGermany
| | - Rabia Ramzan
- Cardiovascular Research Lab, Biochemical Pharmacological Research CenterPhilipps‐University MarburgMarburgGermany
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11
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Vlasova II, Kapralov AA, Michael ZP, Burkert SC, Shurin MR, Star A, Shvedova AA, Kagan VE. Enzymatic oxidative biodegradation of nanoparticles: Mechanisms, significance and applications. Toxicol Appl Pharmacol 2016; 299:58-69. [PMID: 26768553 PMCID: PMC4811710 DOI: 10.1016/j.taap.2016.01.002] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Revised: 01/01/2016] [Accepted: 01/02/2016] [Indexed: 12/22/2022]
Abstract
Biopersistence of carbon nanotubes, graphene oxide (GO) and several other types of carbonaceous nanomaterials is an essential determinant of their health effects. Successful biodegradation is one of the major factors defining the life span and biological responses to nanoparticles. Here, we review the role and contribution of different oxidative enzymes of inflammatory cells - myeloperoxidase, eosinophil peroxidase, lactoperoxidase, hemoglobin, and xanthine oxidase - to the reactions of nanoparticle biodegradation. We further focus on interactions of nanomaterials with hemoproteins dependent on the specific features of their physico-chemical and structural characteristics. Mechanistically, we highlight the significance of immobilized peroxidase reactive intermediates vs diffusible small molecule oxidants (hypochlorous and hypobromous acids) for the overall oxidative biodegradation process in neutrophils and eosinophils. We also accentuate the importance of peroxynitrite-driven pathways realized in macrophages via the engagement of NADPH oxidase- and NO synthase-triggered oxidative mechanisms. We consider possible involvement of oxidative machinery of other professional phagocytes such as microglial cells, myeloid-derived suppressor cells, in the context of biodegradation relevant to targeted drug delivery. We evaluate the importance of genetic factors and their manipulations for the enzymatic biodegradation in vivo. Finally, we emphasize a novel type of biodegradation realized via the activation of the "dormant" peroxidase activity of hemoproteins by the nano-surface. This is exemplified by the binding of GO to cyt c causing the unfolding and 'unmasking' of the peroxidase activity of the latter. We conclude with the strategies leading to safe by design carbonaceous nanoparticles with optimized characteristics for mechanism-based targeted delivery and regulatable life-span of drugs in circulation.
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Affiliation(s)
- Irina I Vlasova
- Department of Environmental and Occupational Health, Center for Free Radical and Antioxidant Health, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA 15219, United States; Research Institute for Physico-Chemical Medicine, Federal Medico-Biological Agency, Moscow 119453, Russia
| | - Alexandr A Kapralov
- Department of Environmental and Occupational Health, Center for Free Radical and Antioxidant Health, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA 15219, United States
| | - Zachary P Michael
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, United States
| | - Seth C Burkert
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, United States
| | - Michael R Shurin
- Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, PA 15261, United States; Department of Immunology, University of Pittsburgh Medical Center, Pittsburgh, PA 15261, United States
| | - Alexander Star
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, United States
| | - Anna A Shvedova
- Pathology and Physiology Research Branch, Health Effects Laboratory Division (HELD), National Institute for Occupational Safety and Health (NIOSH) and Department of Physiology and Pharmacology, West Virginia University, Morgantown, WV 26505, United States.
| | - Valerian E Kagan
- Department of Environmental and Occupational Health, Center for Free Radical and Antioxidant Health, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA 15219, United States; Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, United States; Departments of Pharmacology and Chemical Biology and Radiation Oncology, University of Pittsburgh, Pittsburgh, PA 15260, United States.
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12
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Hannibal L, Tomasina F, Capdevila DA, Demicheli V, Tórtora V, Alvarez-Paggi D, Jemmerson R, Murgida DH, Radi R. Alternative Conformations of Cytochrome c: Structure, Function, and Detection. Biochemistry 2016; 55:407-28. [DOI: 10.1021/acs.biochem.5b01385] [Citation(s) in RCA: 89] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Luciana Hannibal
- Departamento
de Bioquímica, Facultad de Medicina, Universidad de la República, Avda. General Flores 2125, 11800 Montevideo, Uruguay
- Centro
de Investigaciones Biomédicas (CEINBIO), Facultad de Medicina, Universidad de la República, Avda. General Flores 2125, 11800 Montevideo, Uruguay
- Center
for Pediatrics and Adolescent Medicine, Medical Center, University of Freiburg, Mathildenstrasse 1, Freiburg D-79106, Germany
| | - Florencia Tomasina
- Departamento
de Bioquímica, Facultad de Medicina, Universidad de la República, Avda. General Flores 2125, 11800 Montevideo, Uruguay
- Centro
de Investigaciones Biomédicas (CEINBIO), Facultad de Medicina, Universidad de la República, Avda. General Flores 2125, 11800 Montevideo, Uruguay
| | - Daiana A. Capdevila
- Departamento
de Química Inorgánica, Analítica y Química
Física/INQUIMAE, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Pabellón 2, Ciudad Universitaria, C1428EHA Buenos Aires, Argentina
| | - Verónica Demicheli
- Departamento
de Bioquímica, Facultad de Medicina, Universidad de la República, Avda. General Flores 2125, 11800 Montevideo, Uruguay
- Centro
de Investigaciones Biomédicas (CEINBIO), Facultad de Medicina, Universidad de la República, Avda. General Flores 2125, 11800 Montevideo, Uruguay
| | - Verónica Tórtora
- Departamento
de Bioquímica, Facultad de Medicina, Universidad de la República, Avda. General Flores 2125, 11800 Montevideo, Uruguay
- Centro
de Investigaciones Biomédicas (CEINBIO), Facultad de Medicina, Universidad de la República, Avda. General Flores 2125, 11800 Montevideo, Uruguay
| | - Damián Alvarez-Paggi
- Departamento
de Química Inorgánica, Analítica y Química
Física/INQUIMAE, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Pabellón 2, Ciudad Universitaria, C1428EHA Buenos Aires, Argentina
| | - Ronald Jemmerson
- Department
of Microbiology and Immunology, University of Minnesota, MMC 196,
420 Delaware Street, Southeast, Minneapolis, Minnesota 55455, United States
| | - Daniel H. Murgida
- Departamento
de Química Inorgánica, Analítica y Química
Física/INQUIMAE, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Pabellón 2, Ciudad Universitaria, C1428EHA Buenos Aires, Argentina
| | - Rafael Radi
- Departamento
de Bioquímica, Facultad de Medicina, Universidad de la República, Avda. General Flores 2125, 11800 Montevideo, Uruguay
- Centro
de Investigaciones Biomédicas (CEINBIO), Facultad de Medicina, Universidad de la República, Avda. General Flores 2125, 11800 Montevideo, Uruguay
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13
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Hristova SH, Zhivkov AM. Adsorption of cytochrome c on montmorillonite nanoplates: Protein concentration dependence. J Colloid Interface Sci 2015; 446:252-62. [DOI: 10.1016/j.jcis.2015.01.039] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Revised: 01/05/2015] [Accepted: 01/13/2015] [Indexed: 11/25/2022]
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14
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Pandiscia LA, Schweitzer-Stenner R. Coexistence of Native-like and Non-Native Partially Unfolded Ferricytochrome c on the Surface of Cardiolipin-Containing Liposomes. J Phys Chem B 2015; 119:1334-49. [DOI: 10.1021/jp5104752] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Leah A. Pandiscia
- Department
of Chemistry, Drexel University, Philadelphia, PA 19104, United States
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15
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Rajabi K. Time-resolved pulsed hydrogen/deuterium exchange mass spectrometry probes gaseous proteins structural kinetics. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2015; 26:71-82. [PMID: 25318698 DOI: 10.1007/s13361-014-1004-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Revised: 09/10/2014] [Accepted: 09/11/2014] [Indexed: 06/04/2023]
Abstract
A pulsed hydrogen/deuterium exchange (HDX) method has been developed for rapid monitoring of the exchange kinetics of protein ions with D2O a few milliseconds after electrospray ionization (ESI). The stepwise gradual evolution of HDX of multiply charged protein ions was monitored using the pulsed HDX mass spectrometry technique. Upon introducing a very short pulse of D2O (in the μs to ms time scale) into the linear ion trap (LIT) of a time-of-flight (TOF) mass spectrometer, bimodal distributions were detected for the ions of cytochrome c and ubiquitin. Mechanistic details of HDX reactions for ubiquitin and cytochrome c in the gas phase were uncovered and the structural transitions were followed by analyzing the kinetics of HDX.
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Affiliation(s)
- Khadijeh Rajabi
- Department of Chemistry, University of British Columbia (UBC), 2036 Mail Mall, Vancouver, BC, V6T 1Z1, Canada,
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16
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Domazou AS, Gebicka L, Didik J, Gebicki JL, van der Meijden B, Koppenol WH. The kinetics of the reaction of nitrogen dioxide with iron(II)- and iron(III) cytochrome c. Free Radic Biol Med 2014; 69:172-80. [PMID: 24447894 DOI: 10.1016/j.freeradbiomed.2014.01.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/29/2013] [Revised: 12/13/2013] [Accepted: 01/09/2014] [Indexed: 02/05/2023]
Abstract
The reactions of NO2 with both oxidized and reduced cytochrome c at pH 7.2 and 7.4, respectively, and with N-acetyltyrosine amide and N-acetyltryptophan amide at pH 7.3 were studied by pulse radiolysis at 23 °C. NO2 oxidizes N-acetyltyrosine amide and N-acetyltryptophan amide with rate constants of (3.1±0.3)×10(5) and (1.1±0.1)×10(6) M(-1) s(-1), respectively. With iron(III)cytochrome c, the reaction involves only its amino acids, because no changes in the visible spectrum of cytochrome c are observed. The second-order rate constant is (5.8±0.7)×10(6) M(-1) s(-1) at pH 7.2. NO2 oxidizes iron(II)cytochrome c with a second-order rate constant of (6.6±0.5)×10(7) M(-1) s(-1) at pH 7.4; formation of iron(III)cytochrome c is quantitative. Based on these rate constants, we propose that the reaction with iron(II)cytochrome c proceeds via a mechanism in which 90% of NO2 oxidizes the iron center directly-most probably via reaction at the solvent-accessible heme edge-whereas 10% oxidizes the amino acid residues to the corresponding radicals, which, in turn, oxidize iron(II). Iron(II)cytochrome c is also oxidized by peroxynitrite in the presence of CO2 to iron(III)cytochrome c, with a yield of ~60% relative to peroxynitrite. Our results indicate that, in vivo, NO2 will attack preferentially the reduced form of cytochrome c; protein damage is expected to be marginal, the consequence of formation of amino acid radicals on iron(III)cytochrome c.
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Affiliation(s)
- Anastasia S Domazou
- Institute of Inorganic Chemistry, Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology, Zurich CH-8093, Switzerland.
| | - Lidia Gebicka
- Institute of Applied Radiation Chemistry, Faculty of Chemistry, Lodz University of Technology, 93-590 Lodz, Poland
| | - Joanna Didik
- Institute of Applied Radiation Chemistry, Faculty of Chemistry, Lodz University of Technology, 93-590 Lodz, Poland
| | - Jerzy L Gebicki
- Institute of Applied Radiation Chemistry, Faculty of Chemistry, Lodz University of Technology, 93-590 Lodz, Poland
| | - Benjamin van der Meijden
- Institute of Inorganic Chemistry, Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology, Zurich CH-8093, Switzerland
| | - Willem H Koppenol
- Institute of Inorganic Chemistry, Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology, Zurich CH-8093, Switzerland
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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.
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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
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Surface-enhanced resonance Raman scattering (SERRS) as a tool for the studies of electron transfer proteins attached to biomimetic surfaces: Case of cytochrome c. Electrochim Acta 2013. [DOI: 10.1016/j.electacta.2013.08.140] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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20
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Koppenol WH. Cytochrome c and superoxide. J Biol Inorg Chem 2013; 18:865-6. [DOI: 10.1007/s00775-013-1020-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2013] [Accepted: 06/20/2013] [Indexed: 10/26/2022]
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21
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Shiu YJ, Su C, Yeh YL, Liang KK, Hayashi M, Mo Y, Yan Y, Lin SH. Experimental and Theoretical Studies of Protein Folding-Unfolding. J CHIN CHEM SOC-TAIP 2013. [DOI: 10.1002/jccs.200400172] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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22
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Electrochemical characterization of dehaloperoxidase adsorbates on COOH/OH mixed self-assembled monolayers. J Electroanal Chem (Lausanne) 2013. [DOI: 10.1016/j.jelechem.2013.05.023] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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23
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Trana EN, Nocek JM, Knutson AK, Hoffman BM. Evolving the [myoglobin, cytochrome b(5)] complex from dynamic toward simple docking: charging the electron transfer reactive patch. Biochemistry 2012; 51:8542-53. [PMID: 23067206 DOI: 10.1021/bi301134f] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
We describe photoinitiated electron transfer (ET) from a suite of Zn-substituted myoglobin (Mb) variants to cytochrome b(5) (b(5)). An electrostatic interface redesign strategy has led to the introduction of positive charges into the vicinity of the heme edge through D/E → K charge-reversal mutation combinations at "hot spot" residues (D44, D60, and E85), augmented by the elimination of negative charges from Mb or b(5) by neutralization of heme propionates. These variations create an unprecedentedly large range in the product of the ET partners' total charges (-5 < -q(Mb)q(b(5)) < 40). The binding affinity (K(a)) increases 1000-fold as -q(Mb)q(b(5)) increases through this range and exhibits a surprisingly simple, exponential dependence on -q(Mb)q(b(5)). This is explained in terms of electrostatic interactions between a "charged reactive patch" (crp) on each partner's surface, defined as a compact region around the heme edge that (i) contains the total protein charge of each variant and (ii) encompasses a major fraction of the "reactive region" (Rr) comprising surface atoms with large matrix elements for electron tunneling to the heme. As -q(Mb)q(b(5)) increases, the complex undergoes a transition from fast to slow-exchange dynamics on the triplet ET time scale, with a correlated progression in the rate constants for intracomplex (k(et)) and bimolecular (k(2)) ET. This progression is analyzed by integrating the crp and Rr descriptions of ET into the textbook steady-state treatment of reversible binding between partners that undergo intracomplex ET and found to encompass the full range of behaviors predicted by the model. The generality of this approach is demonstrated by its application to the extensive body of data for the ET complex between the photosynthetic reaction center and cytochrome c(2). Deviations from this model also are discussed.
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Affiliation(s)
- Ethan N Trana
- Department of Chemistry, Northwestern University, Evanston, IL 60208, USA
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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]
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Tsou LK, Jain RK, Hamilton AD. Protein surface recognition by porphyrin-based receptors. J PORPHYR PHTHALOCYA 2012. [DOI: 10.1142/s1088424604000131] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Protein surface recognition is largely unexplored owing to the large solvent exposed surface and lack of proper molecular scaffolds to match the binding residues. This review describes the design, synthesis, and fluorescence binding studies of functionalized porphyrins aimed at targeting surface residues of proteins through complementary recognition. The pattern of lysine residues surrounding the heme-edge of horse heart cytochrome c has been targeted by tetraphenylporphyrin and tetrabiphenylporphyrin receptors that bind with nano- and sub-nanomolar affinity. Other designed porphyrin-based receptors also recognize potassium channel as a target. The strategies for protein surface recognition offer a new use for porphyrins as molecular scaffolds.
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Affiliation(s)
- Lun K. Tsou
- Department of Chemistry, Yale University, New Haven, CT 06520, USA
| | - Rishi K. Jain
- Department of Chemistry, Yale University, New Haven, CT 06520, USA
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Volkov AN, Nicholls P, Worrall JA. The complex of cytochrome c and cytochrome c peroxidase: The end of the road? BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2011; 1807:1482-503. [DOI: 10.1016/j.bbabio.2011.07.010] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2011] [Revised: 07/21/2011] [Accepted: 07/22/2011] [Indexed: 11/25/2022]
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Takashima H, Kitano M, Hirai C, Murakami H, Tsukahara K. Photophysical and DNA-binding properties of cytochrome c modified with a platinum(II) complex. J Phys Chem B 2011; 114:13889-96. [PMID: 20936831 DOI: 10.1021/jp106121n] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Cytochrome c (cyt c) derivatives modified with a platinum(II) complex at the lysine residue, cyt c(III)-[Pt(bpy)(dapap)](1) {bpy = 2,2'-bipyridine, and dapap = 3-(2,3-diaminopropionylamino)propionic acid}, have been prepared. The modified residues are Lys8, Lys13, Lys55, Lys60, Lys73, and Lys88. In the case of the cyt c(III)-[Pt(bpy)(dapap)](1) dyad, the photoexcited singlet state of (1)([Pt(bpy)(dapap)](1))* was quenched by the heme Fe(III) moiety through the intramolecular photoinduced energy-transfer reaction via a through-space mechanism. Next, in the presence of calf thymus (CT)-DNA, the DNA-responsive fluorescence properties of cyt c(III)-[Pt(bpy)(dapap)](1) isomers were investigated. The order of the obtained binding constants between the cyt c(III)-[Pt(bpy)(dapap)](1) isomer and CT-DNA in an aqueous solution suggested that the electrostatic interaction is one of the important factors to stabilize the cyt c-DNA complex. Finally, we discussed the rotational motion of the [Pt(bpy)(dapap)](2+) moiety at the surface of cyt c by fluorescence anisotropy measurement. The increase in the anisotropy parameter, r, for each cyt c isomer clearly revealed that the noncovalent recognition of the [Pt(bpy)(dapap)](2+) moiety by CT-DNA is an essential event in the formation of the cyt c-DNA complex and generation of DNA-sensitive fluorescence signals.
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Affiliation(s)
- Hiroshi Takashima
- Department of Chemistry, Faculty of Science, Nara Women's University, Nara, 630-8506 Japan.
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Harper-Leatherman AS, Wallace JM, Rolison DR. Cytochrome C stabilization and immobilization in aerogels. Methods Mol Biol 2011; 679:193-205. [PMID: 20865398 DOI: 10.1007/978-1-60761-895-9_16] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Sol-gel-derived aerogels are three-dimensional, nanoscale materials that combine large surface areas and high porosities. These traits make them useful for any rate-critical chemical process, particularly sensing or electrochemical applications, once physical or chemical moieties are incorporated into the gels to add their functionality into the ultraporous scaffold. Incorporating biomolecules into aerogels has been challenging due to the inability of most biomolecules to remain structurally intact within the gels during the necessary supercritical fluid processing. However, the heme protein cytochrome c (cyt. c) forms self-organized superstructures around gold (or silver) nanoparticles in buffer that can be encapsulated within silica and processed to form aerogels in which cyt. c retains its characteristic visible absorption. The gold (or silver) nanoparticle-nucleated superstructures protect the majority of the protein from the harsh physicochemical conditions necessary to form an aerogel. The Au∼cyt. c superstructures exhibit rapid gas-phase recognition of nitric oxide (NO) within the aerogel matrix, as facilitated by the high-quality pore structure of the aerogel, and remain viable for weeks at room temperature.
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29
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Jankowska KI, Pagba CV, Piatnitski Chekler EL, Deshayes K, Piotrowiak P. Electrostatic docking of a supramolecular host-guest assembly to cytochrome c probed by bidirectional photoinduced electron transfer. J Am Chem Soc 2010; 132:16423-31. [PMID: 21038913 DOI: 10.1021/ja102188e] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A water-soluble octacarboxyhemicarcerand was used as a shuttle to transport redox-active substrates across the aqueous medium and deliver them to the target protein. The results show that weak multivalent interactions and conformational flexibility can be exploited to reversibly bind complex supramolecular assemblies to biological molecules. Hydrophobic electron donors and acceptors were encapsulated within the hemicarcerand, and photoinduced electron transfer (ET) between the Zn-substituted cytochrome c (MW = 12.3 kD) and the host-guest complexes (MW = 2.2 kD) was used to probe the association between the negatively charged hemicarceplex and the positively charged protein. The behavior of the resulting ternary protein-hemicarcerand-guest assembly was investigated in two binding limits: (1) when K(encaps) ≫ K(assoc), the hemicarcerand transports the ligand to the protein while protecting it from the aqueous medium; and (2) when K(assoc) > K(encaps), the hemicarcerand-protein complex is formed first, and the hemicarcerand acts as an artificial receptor site that intercepts ligands from solution and positions them close to the active site of the metalloenzyme. In both cases, ET mediated by the protein-bound hemicarcerand is much faster than that due to diffusional encounters with the respective free donor or acceptor in solution. The measured ET rates suggest that the dominant binding region of the host-guest complex on the surface of the protein is consistent with the docking area of the native redox partner of cytochrome c. The strong association with the protein is attributed to the flexible conformation and adaptable charge distribution of the hemicarcerand, which allow for surface-matching with the cytochrome.
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Affiliation(s)
- Katarzyna I Jankowska
- Department of Chemistry, Rutgers University, 73 Warren Street, Newark, New Jersey 07102, United States
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Wei-Guo J, Chang-Wei L, Ji-Lin T, Zheng-Yan W, Shao-Jun D, Er-Kang W. Electrochemical and Spectroscopic Study on the Interaction of Cytochrome c with Anionic Lipid Vesicles. CHINESE J CHEM 2010. [DOI: 10.1002/cjoc.20030210514] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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31
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Kleiger G, Hao B, Mohl DA, Deshaies RJ. The acidic tail of the Cdc34 ubiquitin-conjugating enzyme functions in both binding to and catalysis with ubiquitin ligase SCFCdc4. J Biol Chem 2009; 284:36012-36023. [PMID: 19875449 PMCID: PMC2794717 DOI: 10.1074/jbc.m109.058529] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2009] [Revised: 10/22/2009] [Indexed: 12/15/2022] Open
Abstract
Ubiquitin ligases, together with their cognate ubiquitin-conjugating enzymes, are responsible for the ubiquitylation of proteins, a process that regulates a myriad of eukaryotic cellular functions. The first cullin-RING ligase discovered, yeast SCF(Cdc4), functions with the conjugating enzyme Cdc34 to regulate the cell cycle. Cdc34 orthologs are notable for their highly acidic C-terminal extension. Here we confirm that the Cdc34 acidic C-terminal tail has a role in Cdc34 binding to SCF(Cdc4) and makes a major contribution to the submicromolar K(m) of Cdc34 for SCF(Cdc4). Moreover, we demonstrate that a key functional property of the tail is its acidity. Our analysis also uncovers an unexpected new function for the acidic tail in promoting catalysis. We demonstrate that SCF is functional when Cdc34 is fused to the C terminus of Cul1 and that this fusion retains partial function even when the acidic tail has been deleted. The Cdc34-SCF fusion proteins that lack the acidic tail must interact in a fundamentally different manner than unfused SCF and wild type Cdc34, demonstrating that distinct mechanisms of E2 recruitment to E3, as is seen in nature, can sustain substrate ubiquitylation. Finally, a search of the yeast proteome uncovered scores of proteins containing highly acidic stretches of amino acids, hinting that electrostatic interactions may be a common mechanism for facilitating protein assembly.
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Affiliation(s)
- Gary Kleiger
- Howard Hughes Medical Institute and the Division of Biology, California Institute of Technology, Pasadena, California 91125
| | - Bing Hao
- Department of Molecular, Microbial and Structural Biology, University of Connecticut Health Center, Farmington, Connecticut 06030
| | - Dane A Mohl
- Howard Hughes Medical Institute and the Division of Biology, California Institute of Technology, Pasadena, California 91125
| | - Raymond J Deshaies
- Howard Hughes Medical Institute and the Division of Biology, California Institute of Technology, Pasadena, California 91125.
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Lenaz G, Genova ML. Structural and functional organization of the mitochondrial respiratory chain: a dynamic super-assembly. Int J Biochem Cell Biol 2009; 41:1750-1772. [PMID: 19711505 DOI: 10.1016/j.biocel.2009.04.003] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The structural organization of the mitochondrial oxidative phosphorylation (OXPHOS) system has received large attention in the past and most investigations led to the conclusion that the respiratory enzymatic complexes are randomly dispersed in the lipid bilayer of the inner membrane and functionally connected by fast diffusion of smaller redox components, Coenzyme Q and cytochrome c. More recent investigations by native gel electrophoresis, however, have shown the existence of supramolecular associations of the respiratory complexes, confirmed by electron microscopy analysis and single particle image processing. Flux control analysis has demonstrated that Complexes I and III in mammalian mitochondria and Complexes I, III, and IV in plant mitochondria kinetically behave as single units with control coefficients approaching unity for each single component, suggesting the existence of substrate channelling within the supercomplexes. The reasons why the presence of substrate channelling for Coenzyme Q and cytochrome c was overlooked in the past are analytically discussed. The review also discusses the forces and the conditions responsible for the formation of the supramolecular units. The function of the supercomplexes appears not to be restricted to kinetic advantages in electron transfer: we discuss evidence on their role in the stability and assembly of the individual complexes and in preventing excess oxygen radical formation. Finally, there is increasing evidence that disruption of the supercomplex organization leads to functional derangements responsible for pathological changes.
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Affiliation(s)
- Giorgio Lenaz
- Dipartimento di Biochimica G. Moruzzi, Università di Bologna, Via Irnerio 48, 40126 Bologna, Italy.
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Bracco LL, Einschlag FSG, Wolcan E, Ferraudi GJ. On the mechanism of the photoinduced reduction of an adduct of ferricytochrome C with a poly(4-vinylpyridine) polymer containing –ReI (CO)3(3,4,7,8-tetramethyl-1,10-phenanthroline) pendants. J Photochem Photobiol A Chem 2009. [DOI: 10.1016/j.jphotochem.2009.08.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Kantardjiev AA, Atanasov BP. PHEMTO: protein pH-dependent electric moment tools. Nucleic Acids Res 2009; 37:W422-7. [PMID: 19420068 PMCID: PMC2703894 DOI: 10.1093/nar/gkp336] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2009] [Revised: 04/17/2009] [Accepted: 04/21/2009] [Indexed: 11/13/2022] Open
Abstract
PHEMTO (protein pH-dependent electric moment tools) is released in response to the high demand in protein science community for evaluation of electrostatic characteristics in relations to molecular recognition. PHEMTO will serve protein scientists with new advanced features for analysis of protein molecular interactions: Electric/dipole moments, their pH-dependence and in silico charge mutagenesis effects on these properties as well as alternative algorithms for electric/dipole moment computation--Singular value decomposition of electrostatic potential (EP) to account for reaction field. The implementation is based on long-term experience--PHEI mean field electrostatics and PHEPS server for evaluation of global and local pH-dependent properties. However, PHEMTO is not just an update of our PHEPS server. Besides standard electrostatics, we offer new, advanced and useful features for analysis of protein molecular interactions. In addition our algorithms are very fast. Special emphasis is given to the interface--intuitive and user-friendly. The input is comprised of the atomic coordinate file in Protein Data Bank format. The advanced user is provided with a special input section for addition of non-polypeptide charges. The output covers actually full electrostatic characteristics but special emphasis is given to electric/dipole moments and their interactive visualization. PHEMTO server can be accessed at http://phemto.orgchm.bas.bg/.
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Affiliation(s)
| | - Boris P. Atanasov
- Biophysical Chemistry Group, Institute of Organic Chemistry, Bulgarian Academy of Sciences, Sofia-1113, Bulgaria
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Steinberg MZ, Elber R, McLafferty FW, Gerber RB, Breuker K. Early structural evolution of native cytochrome c after solvent removal. Chembiochem 2008; 9:2417-23. [PMID: 18785672 DOI: 10.1002/cbic.200800167] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Electrospray ionization transfers thermally labile biomolecules, such as proteins, from solution into the gas phase, where they can be studied by mass spectrometry. Covalent bonds are generally preserved during and after the phase transition, but it is less clear to what extent noncovalent interactions are affected by the new gaseous environment. Here, we present atomic-level computational data on the structural rearrangement of native cytochrome c immediately after solvent removal. The first structural changes after desolvation occur surprisingly early, on a timescale of picoseconds. For the time segment of up to 4.2 ns investigated here, we observed no significant breaking of native noncovalent bonds; instead, we found formation of new noncovalent bonds. This generally involves charged residues on the protein surface, resulting in transiently stabilized intermediate structures with a global fold that is essentially the same as that in solution. Comparison with data from native electron capture dissociation experiments corroborates both its mechanistic postulations and our computational predictions, and suggests that global structural changes take place on a millisecond timescale not covered by our simulations.
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Affiliation(s)
- Michal Z Steinberg
- Department of Physical Chemistry, Fritz Haber Research Center, Hebrew University, Jerusalem 91904, Israel
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Laia CAT, Costa SMB. Interaction of Zinc Tetrasulfonated Phthalocyanine with Cytochromecin Water and Triton-X 100 Micelles. J Phys Chem B 2008; 112:4276-82. [DOI: 10.1021/jp076100+] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Aubin-Tam ME, Zhou H, Hamad-Schifferli K. Structure of cytochrome c at the interface with magnetic CoFe 2O 4nanoparticles. SOFT MATTER 2008; 4:554-559. [PMID: 32907220 DOI: 10.1039/b711937b] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Yeast and horse cytochrome c are attached to 6 nm CoFe2O4 nanoparticles and their structure is studied as a function of the nanoparticle surface chemistry. For yeast cytochrome c, the attachment is covalent and site-specific via dithiol cross-linkage between cysteine 102 and dimercaptosuccinic acid, the nanoparticle ligand. To control site-specificity and allow better characterization of non-specific interactions, horse cytochrome c is non-specifically linked to the nanoparticle. Circular dichroism shows that the structure of both proteins is affected by linkage to the CoFe2O4 nanoparticle. Non-specific adsorption depends strongly on the surface properties of the nanoparticles. Co-functionalization with lysine improves protein folding, most likely by decreasing the nanoparticle net charge and impeding carboxylic acids residues from binding to surface cobalt and iron atoms. Higher protein coverage also helps folding for both yeast and horse cytochrome c.
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Affiliation(s)
- Marie-Eve Aubin-Tam
- Biological Engineering Department, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
| | - Hui Zhou
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Kimberly Hamad-Schifferli
- Biological Engineering Department, Massachusetts Institute of Technology, Cambridge, MA 02139, USA. and Mechanical Engineering Department, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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Janzon J, Eichhorn AC, Ludwig B, Malatesta F. Electron transfer kinetics between soluble modules of Paracoccus denitrificans cytochrome c1 and its physiological redox partners. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2008; 1777:250-9. [PMID: 18241666 DOI: 10.1016/j.bbabio.2008.01.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2007] [Revised: 01/07/2008] [Accepted: 01/09/2008] [Indexed: 11/17/2022]
Abstract
The transient electron transfer (ET) interactions between cytochrome c1 of the bc1-complex from Paracoccus denitrificans and its physiological redox partners cytochrome c552 and cytochrome c550 have been characterized functionally by stopped-flow spectroscopy. Two different soluble fragments of cytochrome c1 were generated and used together with a soluble cytochrome c552 module as a model system for interprotein ET reactions. Both c1 fragments lack the membrane anchor; the c1 core fragment (c1CF) consists of only the hydrophilic heme-carrying domain, whereas the c1 acidic fragment (c1AF) additionally contains the acidic domain unique to P. denitrificans. In order to determine the ionic strength dependencies of the ET rate constants, an optimized stopped-flow protocol was developed to overcome problems of spectral overlap, heme autoxidation and the prevalent non-pseudo first order conditions. Cytochrome c1 reveals fast bimolecular rate constants (10(7) to 10(8) M(-1) s(-1)) for the ET reaction with its physiological substrates c552 and c550, thus approaching the limit of a diffusion-controlled process, with 2 to 3 effective charges of opposite sign contributing to these interactions. No direct involvement of the N-terminal acidic c1-domain in electrostatically attracting its substrates could be detected. However, a slight preference for cytochrome c550 over c552 reacting with cyochrome c1 was found and attributed to the different functions of both cytochromes in the respiratory chain of P. denitrificans.
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Affiliation(s)
- Julia Janzon
- Molecular Genetics Group, Institute of Biochemistry, Biocentre J. W. Goethe-University Frankfurt/Main, Germany
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Wheeler KE, Nocek JM, Cull DA, Yatsunyk LA, Rosenzweig AC, Hoffman BM. Dynamic Docking of Cytochrome b5 with Myoglobin and α-Hemoglobin: Heme-Neutralization “Squares” and the Binding of Electron-Transfer-Reactive Configurations. J Am Chem Soc 2007; 129:3906-17. [PMID: 17343378 DOI: 10.1021/ja067598g] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Intracomplex electron transfer (ET) occurs most often in intrinsically transient, low affinity complexes. As a result, the means by which adequate specificity and reactivity are obtained to support effective ET is still poorly understood. We report here on two such ET complexes: cytochrome b5 (cyt b5) in reaction with its physiological partners, myoglobin (Mb) and hemoglobin (Hb). These complexes obey the Dynamic Docking (DD) paradigm: a large ensemble of weakly bound protein-protein configurations contribute to binding in the rapid-exchange limit, but only a few are ET-active. We report the ionic-strength dependence of the second-order rate constant, k2, for photoinitiated ET from within all four combinations of heme-neutralized Zn deuteroporphyrin-substituted Mb/alphaHb undergoing ET with cyt b5, the four "corners" of a "heme-neutralization square". These experiments provide insights into the relative importance of both global and local electrostatic contributions to the binding of reactive configurations, which are too few to be observed directly. To interpret the variations of k2 arising from heme neutralization, we have developed a procedure by which comparisons of the ET rate constants for a heme-neutralization square permit us to decompose the free energy of reactive binding into individual local electrostatic contributions associated with interactions between (i) the propionates of the two hemes and (ii) the heme of each protein with the polypeptide of its partner. Most notably, we find the contribution from the repulsion between propionates of partner hemes to the reactive binding free energy to be surprisingly small, DeltaG(Hb) approximately +1 kcal/mol at ambient temperature, 18 mM ionic strength, and we speculate about possible causes of this observation. To confirm the fundamental assumption of these studies, that the structure of a heme-neutralized protein is unaltered either by substitution of Zn or by heme neutralization, we have obtained the X-ray structure of ZnMb prepared with the porphyrin dimethyl ester and find it to be nearly isostructural with the native protein.
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Affiliation(s)
- Korin E Wheeler
- Department of Chemistry and Department of Biochemistry, Molecular Biology and Cell Biology, Northwestern University, 2145 North Sheridan Road, Evanston, IL 60208, USA
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Yin H, Hamilton AD. Strategies for targeting protein-protein interactions with synthetic agents. Angew Chem Int Ed Engl 2006; 44:4130-63. [PMID: 15954154 DOI: 10.1002/anie.200461786] [Citation(s) in RCA: 375] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The development of small-molecule modulators of protein-protein interactions is a formidable goal, albeit one that possesses significant potential for the discovery of novel therapeutics. Despite the daunting challenges, a variety of examples exists for the inhibition of two large protein partners with low-molecular-weight ligands. This review discusses the strategies for targeting protein-protein interactions and the state of the art in the rational design of molecules that mimic the structures and functions of their natural targets.
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Affiliation(s)
- Hang Yin
- Yale University, New Haven, CT, USA
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42
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Lenaz G, Genova ML. Kinetics of integrated electron transfer in the mitochondrial respiratory chain: random collisions vs. solid state electron channeling. Am J Physiol Cell Physiol 2006; 292:C1221-39. [PMID: 17035300 DOI: 10.1152/ajpcell.00263.2006] [Citation(s) in RCA: 110] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Recent evidence, mainly based on native electrophoresis, has suggested that the mitochondrial respiratory chain is organized in the form of supercomplexes, due to the aggregation of the main respiratory chain enzymatic complexes. This evidence strongly contrasts the previously accepted model, the Random Diffusion Model, largely based on kinetic studies, stating that the complexes are randomly distributed in the lipid bilayer of the inner membrane and functionally connected by lateral diffusion of small redox molecules, i.e., coenzyme Q and cytochrome c. This review critically examines the experimental evidence, both structural and functional, pertaining to the two models and attempts to provide an updated view of the organization of the respiratory chain and of its kinetic consequences. The conclusion that structural respiratory assemblies exist is overwhelming, whereas the expected functional consequence of substrate channeling between the assembled enzymes is controversial. Examination of the available evidence suggests that, although the supercomplexes are structurally stable, their kinetic competence in substrate channeling is more labile and may depend on the system under investigation and the assay conditions.
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Affiliation(s)
- Giorgio Lenaz
- Dipartimento di Biochimica "G. Moruzzi," Via Irnerio 48, 40126 Bologna, Italy.
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Lojou E, Bianco P. Assemblies of dendrimers and proteins on carbon and gold electrodes. Bioelectrochemistry 2006; 69:237-47. [PMID: 16707279 DOI: 10.1016/j.bioelechem.2006.03.028] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2005] [Revised: 03/23/2006] [Accepted: 03/23/2006] [Indexed: 11/19/2022]
Abstract
Dendritic macromolecules of two adjacent (G3.5 and G4) generations have been used to modify gold or carbon electrodes. The structure and stability of deposited films have been explored by quartz crystal microbalance (QCM), Surface Plasma Resonance (SPR) and electrochemistry. Dendrimers have been shown to adsorb spontaneously on electrode materials as compressed macromolecular films. They are able to inhibit (G3.5) or promote (G4) electroactive anionic species such as Fe(CN)(6)(3-/4-) used as a probe system. Mixed protein/dendrimer assemblies have been constructed with proteins differing in charge, nature of the prosthetic groups and sizes such as lysozyme, cytochrome c, polyhemic cytochrome c(3) or glucose oxidase. Generally, the stability of adsorbed films seems to be limited to one dendrimer/protein bilayer. Owing to the satisfactory stability of composite cytochrome c(3)/G3.5 or glucose oxidase/G4 films, biosensing applications are described for metal bioremediation and glucose detection, respectively.
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Affiliation(s)
- E Lojou
- Unité de Bioénergétique et Ingénierie des Protéines, CNRS, 31, chemin Joseph Aiguier - 13402 Marseille cedex 20, France.
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Domazou AS, Koppenol WH. Oxidation-state-dependent reactions of cytochrome c with the trioxidocarbonate(•1−) radical: a pulse radiolysis study. J Biol Inorg Chem 2006; 12:118-25. [PMID: 17004073 DOI: 10.1007/s00775-006-0172-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2006] [Accepted: 08/29/2006] [Indexed: 10/24/2022]
Abstract
The reaction of the trioxidocarbonate(*1-) radical (CO (3) (*-) , "carbonate radical anion") with cytochrome c was studied by pulse radiolysis at alkaline pH and room temperature. With iron(III) cytochrome c, CO (3) (*-) reacts with the protein moiety with rate constants of (5.1 +/- 0.6) x 10(7) M(-1) s(-1) (pH 8.4, I approximately 0.27 M) and (1.0 +/- 0.2) x 10(8) M(-1) s(-1) (pH 10, I = 0.5 M). The absorption spectrum of the haem moiety was not changed, thus, amino acid radicals produced on the protein do not reduce the haem. The pH-dependent difference in rate constants may be attributed to differences in ionization states of amino acids and to the change in the conformation of the protein. With iron(II) cytochrome c, CO (3) (*-) oxidizes the haem quantitatively, presumably via electrostatic guidance of the radical to the solvent-accessible haem edge, with a different pH dependence: at pH 8.4, the rate constant is (1.1 +/- 0.1) x 10(9) M(-1) s(-1) and, at pH 10, (7.6 +/- 0.6) x 10(8) M(-1) s(-1). We propose that CO (3) (*-) oxidizes the iron center directly, and that the lower rate observed at pH 10 is due to the different charge distribution of iron(II) cytochrome c.
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Affiliation(s)
- Anastasia S Domazou
- Institute of Inorganic Chemistry, Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology, ETH Zurich, Wolfgang-Pauli-Strasse 10, 8093, Zurich, Switzerland
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Affiliation(s)
- Donald T. Edmonds
- a The Clarendon Laboratory, Department of Physics , Parks Road, Oxford , OX1 2PU , England
| | - Neil K. Rogers
- b Laboratory of Molecular Biophysics, Department of Zoology , South Parks Road, Oxford , OX1 3PS , England
| | - Michael J.E. Sternberg
- b Laboratory of Molecular Biophysics, Department of Zoology , South Parks Road, Oxford , OX1 3PS , England
- c Department of Crystallography , Birkbeck College , Malet Street, London , WC1E 7HX , England
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Laia CAT, Costa SMB, Vieira Ferreira LF. Electron-transfer mechanism of the triplet state quenching of aluminium tetrasulfonated phthalocyanine by cytochrome c. Biophys Chem 2006; 122:143-55. [PMID: 16624476 DOI: 10.1016/j.bpc.2006.03.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2005] [Revised: 03/09/2006] [Accepted: 03/09/2006] [Indexed: 11/19/2022]
Abstract
The mechanism of electron-transfer from aluminium tetrasulfonated phthalocyanine triplet state to cytochrome c was investigated in this work. This reaction successfully quenches the dye triplet state due to the formation of complexes between the solute and the protein at the active site. The electron-transfer rate constant is around 3x10(7) s(-1), and is in accordance with previous results for the singlet excited state quenching [C.A.T. Laia, S.M.B. Costa, D. Phillips, A. Beeby. Electron-transfer kinetics in sulfonated aluminum phthalocyanines/cytochrome c complexes, J. Phys. Chem. B 108 (2004) 7506-7514.] in the framework of the Marcus theory, with a reorganization energy equal to 0.94 eV. The complex formation is diffusion controlled, but heterogeneities of the protein surface charge distribution lead to quenching rate constants smaller than predicted on a hard-spheres model with electrostatic interactions. Also the binding equilibrium constant is strongly affected by this phenomenon. Ionic strength plays an important role on the complex formation, but its effect on the unimolecular electron-transfer rate constant is negligible within experimental error.
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Affiliation(s)
- César A T Laia
- Centro de Química-Estrutural, Complexo 1, Instituto Superior Técnico, 1049-001 Lisboa, Portugal.
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Xu J, Bowden EF. Determination of the Orientation of Adsorbed Cytochrome c on Carboxyalkanethiol Self-Assembled Monolayers by In Situ Differential Modification. J Am Chem Soc 2006; 128:6813-22. [PMID: 16719461 DOI: 10.1021/ja054219v] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The contact domain utilized by horse cytochrome c when adsorptively bound to a C(10)COOH self-assembled monolayer (SAM) was delineated using a chemical method based on differential modification of surface amino acids. Horse cytochrome c was adsorbed at low ionic strength (pH 7.0, 4.4 mM potassium phosphate) onto 10 microm diameter gold particles coated with HS(CH(2))(10)COOH SAMs. After in situ modification of lysyl groups by reductive Schiff-base methylation, the protein was desorbed, digested using trypsin, and the peptide mapped using LC/MS. Relative lysyl reactivities were ascertained by comparing the resulting peptide frequencies to control samples of solution cytochrome c modified to the same average extent. The least reactive lysines in adsorbed cytochrome c were found to be 13, 72, 73, 79, and 86-88, consistent with a contact region located up and to the left (Met-80 side) of the solvent-exposed heme edge (conventional front face view). The most reactive lysines were 39, 53, 55, and 60, located on the lower backside. The proposed orientation features a heme tilt angle of approximately 35-40 degrees with respect to the substrate surface normal. Factors that can complicate or distort data interpretation are discussed, and the generality of differential modification relative to existing in situ methods for protein orientation determination is also addressed.
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Affiliation(s)
- Jishou Xu
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695-8204, USA
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Ataka K, Richter B, Heberle J. Orientational Control of the Physiological Reaction of Cytochrome c Oxidase Tethered to a Gold Electrode. J Phys Chem B 2006; 110:9339-47. [PMID: 16671753 DOI: 10.1021/jp0534131] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The physiological reaction of a membrane protein is reconstituted on a solid-supported electrode by orientational control via the position of an affinity tag. Recombinant cytochrome c oxidase (CcO) from Rhodobacter sphaeroides is immobilized on a chemically modified gold surface via the affinity of a histidine tag (His-tag) to a nickel chelating nitrilotriacetic acid surface. Control of the orientation is achieved by the adsorption of CcO through the His-tag engineered into the two opposite sites of the membrane protein surface. After reconstitution into a lipid layer, the functionality of this enzyme film electrode is probed by surface-enhanced infrared absorption spectroscopy and cyclic voltammetry. We demonstrate that cytochrome c (Cc) binds and initiates the catalytic reaction of CcO only when the latter is orientated with subunit II facing the bulk aqueous phase while Cc does not interact with the oppositely orientated CcO. We infer from the observed catalytic dioxygen reduction at potentials below 240 mV (vs a normal hydrogen electrode) that reduced Cc mediates electron input into CcO in a way similar to the physiological pathway. The quantitative analysis of the IR spectra indicates the presence of an inactive population of Cc bound to CcO at equal amounts as the redox-active population. This methodological approach demonstrates that the orientation of the membrane protein can be controlled depending on the position of the affinity tag. The approach is considered to be of general applicability as the introduction of affinity tags is routine in current biochemistry.
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Affiliation(s)
- Kenichi Ataka
- Forschungszentrum Jülich, IBI-2: Structural Biology, 52425 Jülich, Germany
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Bijeire L, Elias B, Souchard JP, Gicquel E, Moucheron C, Kirsch-De Mesmaeker A, Vicendo P. Photoelectron Transfer Processes with Ruthenium(II) Polypyridyl Complexes and Cu/Zn Superoxide Dismutase. Biochemistry 2006; 45:6160-9. [PMID: 16681388 DOI: 10.1021/bi060005u] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The processes that are photoinduced by [Ru(bpz)(3)](2+) (bpz = 2,2'-bipyrazyl) in the presence of Cu/Zn superoxide dismutase (Cu/Zn SOD) are investigated by laser flash photolysis and electron paramagnetic resonance (EPR) spectroscopy; they are compared to those of the system [Ru(bpy)(3)(2+)-Cu/Zn SOD]. Although the mechanism is complicated, primary and secondary reactions can be evidenced. First, the excited [Ru(bpz)(3)](2+) complex is quenched reductively by Cu/Zn SOD with the production of a reduced complex and an oxidized enzyme. The oxidation site of Cu/Zn SOD is proposed to correspond to amino acids located on the surface of the protein. Afterward and only when this reductive electron transfer to the excited complex has produced enough oxidized protein, another electron-transfer process can be evidenced. In this case, however, the charge-transfer process takes place in the other direction, i.e., from the excited complex to the Cu(II) center of the SOD with the formation of Ru(III) and Cu(I) species. This proposed mechanism is supported by the fact that [Ru(bpy)(3)](2+), which is less photo-oxidizing than [Ru(bpz)(3)](2+), exhibits no photoreaction with Cu/Zn SOD. Because Ru(III) species are generated as intermediates with [Ru(bpz)(3)](2+), they are proposed to be responsible for the enhancement of [poly(dG-dC)](2) and [poly(dA-dT)](2) oxidation observed when Cu/Zn SOD is added to the [Ru(bpz)(3)](2+)-DNA system.
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Affiliation(s)
- Laurent Bijeire
- Laboratoire des IMRCP, UMR 5623 au CNRS, Université Paul Sabatier, 31062 Toulouse Cedex 09, France
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Runge AF, Mendes SB, Saavedra SS. Order Parameters and Orientation Distributions of Solution Adsorbed and Microcontact Printed Cytochrome c Protein Films on Glass and ITO. J Phys Chem B 2006; 110:6732-9. [PMID: 16570979 DOI: 10.1021/jp056049e] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The structure of solution adsorbed and microcontact printed (muCP) cytochrome c (cyt c) films on glass and indium tin oxide (ITO) was investigated using attenuated total reflectance (ATR) and total internal reflectance fluorescence (TIRF) spectroscopies to determine the orientation of the heme groups in the films. The second and fourth order parameters of the heme as well as information on the angle between the absorption and emission dipoles of the heme, gamma, were experimentally determined. The order parameters of the heme are related to the order parameters of the protein molecule using the known angle between the heme plane and the electrostatic dipole moment of the cyt c protein. The effect of the surface roughness of the substrates (glass and ITO) was also taken into account quantitatively using AFM data. Physically possible order parameters were obtained for the heme group in both solution adsorbed and muCP films, but not for the electrostatic dipole moment of the protein. In addition, the experimental values of {cos2 gamma} for immobilized zinc-substituted cyt c are greater than the values of {cos2 gamma} determined in viscous solutions, which could be an indication that the environment of the heme groups changes upon adsorption. The electron transfer behavior of solution adsorbed and muCP films on ITO, determined using electrochemical methods, is compared to their orientation distribution and surface coverage as determined by spectroscopic methods.
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Affiliation(s)
- Anne F Runge
- Department of Chemistry and College of Optical Sciences, University of Arizona, Tucson, Arizona 85721, USA
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