1
|
Brand SE, Scharlau M, Geren L, Hendrix M, Parson C, Elmendorf T, Neel E, Pianalto K, Silva-Nash J, Durham B, Millett F. Accelerated Evolution of Cytochrome c in Higher Primates, and Regulation of the Reaction between Cytochrome c and Cytochrome Oxidase by Phosphorylation. Cells 2022; 11:cells11244014. [PMID: 36552779 PMCID: PMC9777161 DOI: 10.3390/cells11244014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 11/24/2022] [Accepted: 12/01/2022] [Indexed: 12/14/2022] Open
Abstract
Cytochrome c (Cc) underwent accelerated evolution from the stem of the anthropoid primates to humans. Of the 11 amino acid changes that occurred from horse Cc to human Cc, five were at Cc residues near the binding site of the Cc:CcO complex. Single-point mutants of horse and human Cc were made at each of these positions. The Cc:CcO dissociation constant KD of the horse mutants decreased in the order: T89E > native horse Cc > V11I Cc > Q12M > D50A > A83V > native human. The largest effect was observed for the mutants at residue 50, where the horse Cc D50A mutant decreased KD from 28.4 to 11.8 μM, and the human Cc A50D increased KD from 4.7 to 15.7 μM. To investigate the role of Cc phosphorylation in regulating the reaction with CcO, phosphomimetic human Cc mutants were prepared. The Cc T28E, S47E, and Y48E mutants increased the dissociation rate constant kd, decreased the formation rate constant kf, and increased the equilibrium dissociation constant KD of the Cc:CcO complex. These studies indicate that phosphorylation of these residues plays an important role in regulating mitochondrial electron transport and membrane potential ΔΨ.
Collapse
Affiliation(s)
| | - Martha Scharlau
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, USA
| | - Lois Geren
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, USA
| | - Marissa Hendrix
- Independent Researcher, P.O. Box 603, Dardanelle, AR 72834, USA
| | - Clayre Parson
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, USA
| | - Tyler Elmendorf
- School of Medicine, University of Kansas Medical Center, 2060 W 39th Ave, Kansas City, KS 66103, USA
| | - Earl Neel
- Tulsa Bone and Joint Associates, Tulsa, OK 74146, USA
| | - Kaila Pianalto
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, USA
| | | | - Bill Durham
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, USA
| | - Francis Millett
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, USA
- Correspondence:
| |
Collapse
|
2
|
Brzezinski P, Moe A, Ädelroth P. Structure and Mechanism of Respiratory III-IV Supercomplexes in Bioenergetic Membranes. Chem Rev 2021; 121:9644-9673. [PMID: 34184881 PMCID: PMC8361435 DOI: 10.1021/acs.chemrev.1c00140] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Indexed: 12/12/2022]
Abstract
In the final steps of energy conservation in aerobic organisms, free energy from electron transfer through the respiratory chain is transduced into a proton electrochemical gradient across a membrane. In mitochondria and many bacteria, reduction of the dioxygen electron acceptor is catalyzed by cytochrome c oxidase (complex IV), which receives electrons from cytochrome bc1 (complex III), via membrane-bound or water-soluble cytochrome c. These complexes function independently, but in many organisms they associate to form supercomplexes. Here, we review the structural features and the functional significance of the nonobligate III2IV1/2 Saccharomyces cerevisiae mitochondrial supercomplex as well as the obligate III2IV2 supercomplex from actinobacteria. The analysis is centered around the Q-cycle of complex III, proton uptake by CytcO, as well as mechanistic and structural solutions to the electronic link between complexes III and IV.
Collapse
Affiliation(s)
- Peter Brzezinski
- Department of Biochemistry and Biophysics,
The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Agnes Moe
- Department of Biochemistry and Biophysics,
The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Pia Ädelroth
- Department of Biochemistry and Biophysics,
The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91 Stockholm, Sweden
| |
Collapse
|
3
|
Gideon DA, Nirusimhan V, E JC, Sudarsha K, Manoj KM. Mechanism of electron transfers mediated by cytochromes c and b5 in mitochondria and endoplasmic reticulum: classical and murburn perspectives. J Biomol Struct Dyn 2021; 40:9235-9252. [PMID: 33998974 DOI: 10.1080/07391102.2021.1925154] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
We explore the mechanism of electron transfers mediated by cytochrome c, a soluble protein involved in mitochondrial oxidative phosphorylation and cytochrome b5, a microsomal membrane protein acting as a redox aide in xenobiotic metabolism. We found minimal conservation in the sequence and surface amino acid residues of cytochrome c/b5 proteins among divergent species. Therefore, we question the evolutionary logic for electron transfer (ET) occurring through affinity binding via recognition of specific surface residues/topography. Also, analysis of putative protein-protein interactions in the crystal structures of these proteins and their redox partners did not point to any specific interaction logic. A comparison of the kinetic and thermodynamic constants of wildtype vs. mutants did not provide strong evidence to support the binding-based ET paradigm, but indicated support for diffusible reactive species (DRS)-mediated process. Topographically divergent cytochromes from one species have been substituted for reaction with proteins from other species, implying the involvement of non-specific interactions. We provide a viable alternative (murburn concept) to classical protein-protein binding-based long range ET mechanism. To account for the promiscuity of interactions and solvent-accessible hemes, we propose that the two proteins act as non- specific redox capacitors, mediating one-electron redox equilibriums involving DRS and unbound ions.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Daniel Andrew Gideon
- Satyamjayatu: The Science & Ethics Foundation, Palakkad District, Kerala State, India.,Department of Biotechnology and Bioinformatics, Bishop Heber College (Autonomous), Tiruchirappalli, Tamil Nadu, India
| | - Vijay Nirusimhan
- Department of Biotechnology and Bioinformatics, Bishop Heber College (Autonomous), Tiruchirappalli, Tamil Nadu, India
| | - Jesu Castin E
- Department of Biotechnology and Bioinformatics, Bishop Heber College (Autonomous), Tiruchirappalli, Tamil Nadu, India
| | - Karthik Sudarsha
- Department of Biotechnology and Bioinformatics, Bishop Heber College (Autonomous), Tiruchirappalli, Tamil Nadu, India
| | - Kelath Murali Manoj
- Satyamjayatu: The Science & Ethics Foundation, Palakkad District, Kerala State, India
| |
Collapse
|
4
|
Sarewicz M, Pintscher S, Pietras R, Borek A, Bujnowicz Ł, Hanke G, Cramer WA, Finazzi G, Osyczka A. Catalytic Reactions and Energy Conservation in the Cytochrome bc1 and b6f Complexes of Energy-Transducing Membranes. Chem Rev 2021; 121:2020-2108. [PMID: 33464892 PMCID: PMC7908018 DOI: 10.1021/acs.chemrev.0c00712] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Indexed: 12/16/2022]
Abstract
This review focuses on key components of respiratory and photosynthetic energy-transduction systems: the cytochrome bc1 and b6f (Cytbc1/b6f) membranous multisubunit homodimeric complexes. These remarkable molecular machines catalyze electron transfer from membranous quinones to water-soluble electron carriers (such as cytochromes c or plastocyanin), coupling electron flow to proton translocation across the energy-transducing membrane and contributing to the generation of a transmembrane electrochemical potential gradient, which powers cellular metabolism in the majority of living organisms. Cytsbc1/b6f share many similarities but also have significant differences. While decades of research have provided extensive knowledge on these enzymes, several important aspects of their molecular mechanisms remain to be elucidated. We summarize a broad range of structural, mechanistic, and physiological aspects required for function of Cytbc1/b6f, combining textbook fundamentals with new intriguing concepts that have emerged from more recent studies. The discussion covers but is not limited to (i) mechanisms of energy-conserving bifurcation of electron pathway and energy-wasting superoxide generation at the quinol oxidation site, (ii) the mechanism by which semiquinone is stabilized at the quinone reduction site, (iii) interactions with substrates and specific inhibitors, (iv) intermonomer electron transfer and the role of a dimeric complex, and (v) higher levels of organization and regulation that involve Cytsbc1/b6f. In addressing these topics, we point out existing uncertainties and controversies, which, as suggested, will drive further research in this field.
Collapse
Affiliation(s)
- Marcin Sarewicz
- Department
of Molecular Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
| | - Sebastian Pintscher
- Department
of Molecular Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
| | - Rafał Pietras
- Department
of Molecular Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
| | - Arkadiusz Borek
- Department
of Molecular Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
| | - Łukasz Bujnowicz
- Department
of Molecular Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
| | - Guy Hanke
- School
of Biological and Chemical Sciences, Queen
Mary University of London, London E1 4NS, U.K.
| | - William A. Cramer
- Department
of Biological Sciences, Purdue University, West Lafayette, Indiana 47907 United States
| | - Giovanni Finazzi
- Laboratoire
de Physiologie Cellulaire et Végétale, Université Grenoble Alpes, Centre National Recherche Scientifique,
Commissariat Energie Atomique et Energies Alternatives, Institut National
Recherche l’agriculture, l’alimentation et l’environnement, 38054 Grenoble Cedex 9, France
| | - Artur Osyczka
- Department
of Molecular Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
| |
Collapse
|
5
|
Singharoy A, Maffeo C, Delgado-Magnero KH, Swainsbury DJK, Sener M, Kleinekathöfer U, Vant JW, Nguyen J, Hitchcock A, Isralewitz B, Teo I, Chandler DE, Stone JE, Phillips JC, Pogorelov TV, Mallus MI, Chipot C, Luthey-Schulten Z, Tieleman DP, Hunter CN, Tajkhorshid E, Aksimentiev A, Schulten K. Atoms to Phenotypes: Molecular Design Principles of Cellular Energy Metabolism. Cell 2019; 179:1098-1111.e23. [PMID: 31730852 PMCID: PMC7075482 DOI: 10.1016/j.cell.2019.10.021] [Citation(s) in RCA: 92] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 09/04/2019] [Accepted: 10/21/2019] [Indexed: 01/01/2023]
Abstract
We report a 100-million atom-scale model of an entire cell organelle, a photosynthetic chromatophore vesicle from a purple bacterium, that reveals the cascade of energy conversion steps culminating in the generation of ATP from sunlight. Molecular dynamics simulations of this vesicle elucidate how the integral membrane complexes influence local curvature to tune photoexcitation of pigments. Brownian dynamics of small molecules within the chromatophore probe the mechanisms of directional charge transport under various pH and salinity conditions. Reproducing phenotypic properties from atomistic details, a kinetic model evinces that low-light adaptations of the bacterium emerge as a spontaneous outcome of optimizing the balance between the chromatophore's structural integrity and robust energy conversion. Parallels are drawn with the more universal mitochondrial bioenergetic machinery, from whence molecular-scale insights into the mechanism of cellular aging are inferred. Together, our integrative method and spectroscopic experiments pave the way to first-principles modeling of whole living cells.
Collapse
Affiliation(s)
- Abhishek Singharoy
- School of Molecular Sciences, Center for Applied Structural Discovery, Arizona State University at Tempe, Tempe, AZ 85282, USA.
| | - Christopher Maffeo
- Department of Physics, NSF Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Karelia H Delgado-Magnero
- Centre for Molecular Simulation and Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - David J K Swainsbury
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, UK
| | - Melih Sener
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Ulrich Kleinekathöfer
- Department of Physics and Earth Sciences, Jacobs University Bremen, 28759 Bremen, Germany
| | - John W Vant
- School of Molecular Sciences, Center for Applied Structural Discovery, Arizona State University at Tempe, Tempe, AZ 85282, USA
| | - Jonathan Nguyen
- School of Molecular Sciences, Center for Applied Structural Discovery, Arizona State University at Tempe, Tempe, AZ 85282, USA
| | - Andrew Hitchcock
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, UK
| | - Barry Isralewitz
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Ivan Teo
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Danielle E Chandler
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - John E Stone
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - James C Phillips
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Taras V Pogorelov
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Department of Chemistry, School of Chemical Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - M Ilaria Mallus
- Department of Physics and Earth Sciences, Jacobs University Bremen, 28759 Bremen, Germany
| | - Christophe Chipot
- Department of Physics, NSF Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Laboratoire International Associé CNRS-UIUC, UMR 7019, Université de Lorraine, 54506 Vandœuvre-lès-Nancy, France
| | - Zaida Luthey-Schulten
- Department of Physics, NSF Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Department of Chemistry, School of Chemical Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - D Peter Tieleman
- Centre for Molecular Simulation and Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - C Neil Hunter
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, UK.
| | - Emad Tajkhorshid
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Departments of Biochemistry, Chemistry, Bioengineering, and Pharmacology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
| | - Aleksei Aksimentiev
- Department of Physics, NSF Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
| | - Klaus Schulten
- Department of Physics, NSF Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| |
Collapse
|
6
|
Measuring the functionality of the mitochondrial pumping complexes with multi-wavelength spectroscopy. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2019; 1860:89-101. [DOI: 10.1016/j.bbabio.2018.11.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Revised: 10/04/2018] [Accepted: 11/07/2018] [Indexed: 12/24/2022]
|
7
|
Hagras MA, Hayashi T, Stuchebrukhov AA. Quantum Calculations of Electron Tunneling in Respiratory Complex III. J Phys Chem B 2015; 119:14637-51. [DOI: 10.1021/acs.jpcb.5b09424] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Muhammad A. Hagras
- Department of Chemistry, University of California, One Shields
Avenue, Davis, California 95616, United States
| | - Tomoyuki Hayashi
- Department of Chemistry, University of California, One Shields
Avenue, Davis, California 95616, United States
| | - Alexei A. Stuchebrukhov
- Department of Chemistry, University of California, One Shields
Avenue, Davis, California 95616, United States
| |
Collapse
|
8
|
Fry BA, Solomon LA, Leslie Dutton P, Moser CC. Design and engineering of a man-made diffusive electron-transport protein. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2015; 1857:513-521. [PMID: 26423266 DOI: 10.1016/j.bbabio.2015.09.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Revised: 09/12/2015] [Accepted: 09/25/2015] [Indexed: 11/18/2022]
Abstract
Maquettes are man-made cofactor-binding oxidoreductases designed from first principles with minimal reference to natural protein sequences. Here we focus on water-soluble maquettes designed and engineered to perform diffusive electron transport of the kind typically carried out by cytochromes, ferredoxins and flavodoxins and other small proteins in photosynthetic and respiratory energy conversion and oxido-reductive metabolism. Our designs were tested by analysis of electron transfer between heme maquettes and the well-known natural electron transporter, cytochrome c. Electron-transfer kinetics were measured from seconds to milliseconds by stopped-flow, while sub-millisecond resolution was achieved through laser photolysis of the carbon monoxide maquette heme complex. These measurements demonstrate electron transfer from the maquette to cytochrome c, reproducing the timescales and charge complementarity modulation observed in natural systems. The ionic strength dependence of inter-protein electron transfer from 9.7×10(6) M(-1) s(-1) to 1.2×10(9) M(-1) s(-1) follows a simple Debye-Hückel model for attraction between +8 net charged oxidized cytochrome c and -19 net charged heme maquette, with no indication of significant protein dipole moment steering. Successfully recreating essential components of energy conversion and downstream metabolism in man-made proteins holds promise for in vivo clinical intervention and for the production of fuel or other industrial products. This article is part of a Special Issue entitled Biodesign for Bioenergetics--the design and engineering of electronic transfer cofactors, proteins and protein networks, edited by Ronald L. Koder and J.L. Ross Anderson.
Collapse
Affiliation(s)
- Bryan A Fry
- Department of Biochemistry & Biophysics, Univ. of Pennsylvania, Philadelphia PA, USA
| | - Lee A Solomon
- Department of Biochemistry & Biophysics, Univ. of Pennsylvania, Philadelphia PA, USA
| | - P Leslie Dutton
- Department of Biochemistry & Biophysics, Univ. of Pennsylvania, Philadelphia PA, USA
| | - Christopher C Moser
- Department of Biochemistry & Biophysics, Univ. of Pennsylvania, Philadelphia PA, USA.
| |
Collapse
|
9
|
Sarewicz M, Osyczka A. Electronic connection between the quinone and cytochrome C redox pools and its role in regulation of mitochondrial electron transport and redox signaling. Physiol Rev 2015; 95:219-43. [PMID: 25540143 PMCID: PMC4281590 DOI: 10.1152/physrev.00006.2014] [Citation(s) in RCA: 97] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Mitochondrial respiration, an important bioenergetic process, relies on operation of four membranous enzymatic complexes linked functionally by mobile, freely diffusible elements: quinone molecules in the membrane and water-soluble cytochromes c in the intermembrane space. One of the mitochondrial complexes, complex III (cytochrome bc1 or ubiquinol:cytochrome c oxidoreductase), provides an electronic connection between these two diffusible redox pools linking in a fully reversible manner two-electron quinone oxidation/reduction with one-electron cytochrome c reduction/oxidation. Several features of this homodimeric enzyme implicate that in addition to its well-defined function of contributing to generation of proton-motive force, cytochrome bc1 may be a physiologically important point of regulation of electron flow acting as a sensor of the redox state of mitochondria that actively responds to changes in bioenergetic conditions. These features include the following: the opposing redox reactions at quinone catalytic sites located on the opposite sides of the membrane, the inter-monomer electronic connection that functionally links four quinone binding sites of a dimer into an H-shaped electron transfer system, as well as the potential to generate superoxide and release it to the intermembrane space where it can be engaged in redox signaling pathways. Here we highlight recent advances in understanding how cytochrome bc1 may accomplish this regulatory physiological function, what is known and remains unknown about catalytic and side reactions within the quinone binding sites and electron transfers through the cofactor chains connecting those sites with the substrate redox pools. We also discuss the developed molecular mechanisms in the context of physiology of mitochondria.
Collapse
Affiliation(s)
- Marcin Sarewicz
- Department of Molecular Biophysics, Faculty of Biochemistry, Biophysics, and Biotechnology, Jagiellonian University, Kraków, Poland
| | - Artur Osyczka
- Department of Molecular Biophysics, Faculty of Biochemistry, Biophysics, and Biotechnology, Jagiellonian University, Kraków, Poland
| |
Collapse
|
10
|
Moreno-Beltrán B, Díaz-Quintana A, González-Arzola K, Velázquez-Campoy A, De la Rosa MA, Díaz-Moreno I. Cytochrome c1 exhibits two binding sites for cytochrome c in plants. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2014; 1837:1717-29. [PMID: 25091281 DOI: 10.1016/j.bbabio.2014.07.017] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 03/17/2014] [Revised: 07/23/2014] [Accepted: 07/26/2014] [Indexed: 11/27/2022]
Abstract
In plants, channeling of cytochrome c molecules between complexes III and IV has been purported to shuttle electrons within the supercomplexes instead of carrying electrons by random diffusion across the intermembrane bulk phase. However, the mode plant cytochrome c behaves inside a supercomplex such as the respirasome, formed by complexes I, III and IV, remains obscure from a structural point of view. Here, we report ab-initio Brownian dynamics calculations and nuclear magnetic resonance-driven docking computations showing two binding sites for plant cytochrome c at the head soluble domain of plant cytochrome c1, namely a non-productive (or distal) site with a long heme-to-heme distance and a functional (or proximal) site with the two heme groups close enough as to allow electron transfer. As inferred from isothermal titration calorimetry experiments, the two binding sites exhibit different equilibrium dissociation constants, for both reduced and oxidized species, that are all within the micromolar range, thus revealing the transient nature of such a respiratory complex. Although the docking of cytochrome c at the distal site occurs at the interface between cytochrome c1 and the Rieske subunit, it is fully compatible with the complex III structure. In our model, the extra distal site in complex III could indeed facilitate the functional cytochrome c channeling towards complex IV by building a "floating boat bridge" of cytochrome c molecules (between complexes III and IV) in plant respirasome.
Collapse
Affiliation(s)
- Blas Moreno-Beltrán
- Instituto de Bioquímica Vegetal y Fotosíntesis, cicCartuja, Universidad de Sevilla - CSIC, Avda. Américo Vespucio 49, Sevilla 41092, Spain
| | - Antonio Díaz-Quintana
- Instituto de Bioquímica Vegetal y Fotosíntesis, cicCartuja, Universidad de Sevilla - CSIC, Avda. Américo Vespucio 49, Sevilla 41092, Spain
| | - Katiuska González-Arzola
- Instituto de Bioquímica Vegetal y Fotosíntesis, cicCartuja, Universidad de Sevilla - CSIC, Avda. Américo Vespucio 49, Sevilla 41092, Spain
| | - Adrián Velázquez-Campoy
- Institute of Biocomputation and Physics of Complex Systems (BIFI)-Joint Unit BIFI-IQFR (CSIC), Universidad de Zaragoza, Mariano Esquillor s/n, 50018, Zaragoza, Spain; Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, Pedro Cerbuna 12, 50009, Zaragoza, Spain; Fundacion ARAID, Government of Aragon, Maria de Luna 11, 50018, Zaragoza, Spain
| | - Miguel A De la Rosa
- Instituto de Bioquímica Vegetal y Fotosíntesis, cicCartuja, Universidad de Sevilla - CSIC, Avda. Américo Vespucio 49, Sevilla 41092, Spain
| | - Irene Díaz-Moreno
- Instituto de Bioquímica Vegetal y Fotosíntesis, cicCartuja, Universidad de Sevilla - CSIC, Avda. Américo Vespucio 49, Sevilla 41092, Spain.
| |
Collapse
|
11
|
Millett F, Havens J, Rajagukguk S, Durham B. Design and use of photoactive ruthenium complexes to study electron transfer within cytochrome bc1 and from cytochrome bc1 to cytochrome c. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2012; 1827:1309-19. [PMID: 22985600 DOI: 10.1016/j.bbabio.2012.09.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2012] [Revised: 08/29/2012] [Accepted: 09/03/2012] [Indexed: 10/27/2022]
Abstract
The cytochrome bc1 complex (ubiquinone:cytochrome c oxidoreductase) is the central integral membrane protein in the mitochondrial respiratory chain as well as the electron-transfer chains of many respiratory and photosynthetic prokaryotes. Based on X-ray crystallographic studies of cytochrome bc1, a mechanism has been proposed in which the extrinsic domain of the iron-sulfur protein first binds to cytochrome b where it accepts an electron from ubiquinol in the Qo site, and then rotates by 57° to a position close to cytochrome c1 where it transfers an electron to cytochrome c1. This review describes the development of a ruthenium photooxidation technique to measure key electron transfer steps in cytochrome bc1, including rapid electron transfer from the iron-sulfur protein to cytochrome c1. It was discovered that this reaction is rate-limited by the rotational dynamics of the iron-sulfur protein rather than true electron transfer. A conformational linkage between the occupant of the Qo ubiquinol binding site and the rotational dynamics of the iron-sulfur protein was discovered which could play a role in the bifurcated oxidation of ubiquinol. A ruthenium photoexcitation method is also described for the measurement of electron transfer from cytochrome c1 to cytochrome c. This article is part of a Special Issue entitled: Respiratory Complex III and related bc complexes.
Collapse
Key Words
- 2,2′-bipyrazine
- 2,2′-bipyridine
- 2,2′:4′,4″:2″,2‴-quaterpyridine
- 2Fe2S
- 3,3′-bipyridazine
- 4,4′-dimethyl-2,2′-bipridine
- Cc
- CcO
- Cytochrome bc(1)
- Cytochrome c
- Electron transfer
- ISP
- JG144
- MOAS
- P(f)
- P(m)
- Q
- Q(i)
- Q(o)
- Q(o) site inhibitor which fixes ISP in b state
- Q(o) site inhibitor which promotes mobile state of ISP
- QH(2)
- R. sphaeroides
- Rhodobacter sphaeroides
- Rieske iron–sulfur center
- Ru(2)D
- Ruthenium
- S-3-anilino-5-methyl-5-(4,6-difluorophenyl)-1,3-oxazolidine-2,4-dione
- [Ru(bpy)(2)](2)qpy(4+)
- bpd
- bpy
- bpz
- cyt bc(1)
- cytochrome bc(1)
- cytochrome c
- cytochrome c oxidase
- dmb
- inside ubiquinone binding site
- iron–sulfur protein
- methoxyacrylate stilbene
- outside ubiquinol binding site
- qpy
- ubiquinol
- ubiquionone
- yCc
- yeast Cc
Collapse
Affiliation(s)
- Francis Millett
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, USA.
| | | | | | | |
Collapse
|
12
|
Cytochrome c signalosome in mitochondria. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2011; 40:1301-15. [DOI: 10.1007/s00249-011-0774-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2011] [Revised: 10/12/2011] [Accepted: 10/21/2011] [Indexed: 10/15/2022]
|
13
|
Castellani M, Havens J, Kleinschroth T, Millett F, Durham B, Malatesta F, Ludwig B. The acidic domain of cytochrome c₁ in paracoccus denitrificans, analogous to the acidic subunits in eukaryotic bc₁ complexes, is not involved in the electron transfer reaction to its native substrate cytochrome c(552). BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2011; 1807:1383-9. [PMID: 21856278 DOI: 10.1016/j.bbabio.2011.08.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2011] [Revised: 08/03/2011] [Accepted: 08/05/2011] [Indexed: 11/19/2022]
Abstract
The cytochrome bc(1) complex is a key component in several respiratory pathways. One of the characteristics of the eukaryotic complex is the presence of a small acidic subunit, which is thought to guide the interaction of the complex with its electron acceptor and facilitate electron transfer. Paracoccus denitrificans represents the only example of a prokaryotic organism in which a highly acidic domain is covalently fused to the cytochrome c(1) subunit. In this work, a deletion variant lacking this acidic domain has been produced and purified by affinity chromatography. The complex is fully intact as shown by its X-ray structure, and is a dimer (Kleinschroth et al., subm.) compared to the tetrameric (dimer-of-dimer) state of the wild-type. The variant complex is studied by steady-state kinetics and flash photolysis, showing wild type turnover and a virtually identical interaction with its substrate cytochrome c(552).
Collapse
Affiliation(s)
- Michela Castellani
- Institute of Biochemistry, Molecular Genetics, Goethe University, D-60438 Frankfurt am Main and Cluster of Excellence "Macromolecular Complexes" (CEF-MC), D-60438 Frankfurt am Main, Germany
| | | | | | | | | | | | | |
Collapse
|
14
|
Sarewicz M, Pietras R, Froncisz W, Osyczka A. Reorientation of cytochrome c2 upon interaction with oppositely charged macromolecules probed by SR EPR: implications for the role of dipole moment to facilitate collisions in proper configuration for electron transfer. Metallomics 2011; 3:404-9. [PMID: 21431229 DOI: 10.1039/c0mt00105h] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The reaction of water-soluble cytochrome c (c(2)) with its physiological redox partners is facilitated by electrostatic attractions between the two protein surfaces. Using spin-labeled cytochrome c(2) from Rhodobacter capsulatus and pulse electron paramagnetic resonance (EPR) measurements we compared spatial orientation of cytochrome c(2) upon its binding to surfaces of opposite charge. We observed that cytochrome c(2) can use its negatively charged "back" side when exposed to interact with positively charged surfaces (DEAE resin) which is the opposite to the use of its positively charged "front" side in physiological interaction with negatively charged binding domain of cytochrome bc(1). The later orientation is also adopted upon non-physiological binding of cytochrome c(2) to negatively charged carboxymethyl cellulose resin. These results directly demonstrate how the electric dipolar nature of cytochrome c(2) influences its orientation in interactions with charged surfaces, which may facilitate collisions with other redox proteins in a proper orientation to support physiologically-competent electron transfer. Saturation recovery EPR provides an attractive tool for monitoring spatial orientation of proteins in their interaction with surfaces in liquid phase. It is particularly valuable for metalloproteins engaged in redox reactions as a means to monitor the geometry and dynamics of formation of protein complexes in measurements that are independent of electron transfer processes.
Collapse
Affiliation(s)
- Marcin Sarewicz
- Department of Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, ul Gronostajowa 7, 30-307 Kraków, Poland
| | | | | | | |
Collapse
|
15
|
Moser CC, Anderson JLR, Dutton PL. Guidelines for tunneling in enzymes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2010; 1797:1573-86. [PMID: 20460101 DOI: 10.1016/j.bbabio.2010.04.441] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2009] [Revised: 04/26/2010] [Accepted: 04/28/2010] [Indexed: 11/17/2022]
Abstract
Here we extend the engineering descriptions of simple, single-electron-tunneling chains common in oxidoreductases to quantify sequential oxidation-reduction rates of two-or-more electron cofactors and substrates. We identify when nicotinamides may be vulnerable to radical mediated oxidation-reduction and merge electron-tunneling expressions with the chemical rate expressions of Eyring. The work provides guidelines for the construction of new artificial oxidoreductases inspired by Nature but adopting independent design and redox engineering.
Collapse
Affiliation(s)
- Christopher C Moser
- Dept. Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | | | | |
Collapse
|
16
|
Janzon J, Yuan Q, Malatesta F, Hellwig P, Ludwig B, Durham B, Millett F. Probing the Paracoccus denitrificans cytochrome c(1)-cytochrome c(552) interaction by mutagenesis and fast kinetics. Biochemistry 2009; 47:12974-84. [PMID: 19006325 DOI: 10.1021/bi800932c] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Electron transfer (ET) between Paracoccus denitrificans cytochrome (cyt) c(1) and cytochrome c(552) was studied using the soluble redox fragments cyt c(1CF) and cyt c(552F). A new ruthenium cyt c(552F) derivative labeled at C23 (Ru(z)-23-c(552F)) was designed to measure rapid electron transfer with cyt c(1CF) in the physiological direction using flash photolysis. The bimolecular rate constant k(12) decreased rapidly with ionic strength above 40 mM, consistent with a diffusional process guided by long-range electrostatic interactions between the two proteins. However, a new kinetic phase was detected at an ionic strength of <35 mM with the ruthenium photoexcitation technique in which k(12) became very rapid (3 x 10(9) M(-1) s(-1)) and nearly independent of ionic strength, suggesting that the reaction became so fast that it was controlled by short-range diffusion along the protein surfaces guided by hydrophobic interactions. These results are consistent with a two-step model for formation of the final encounter complex. No intracomplex electron transfer between Ru(z)-23-c(552F) and c(1CF) was observed even at the lowest ionic strength, indicating that the dissociation constant of the complex was >30 microM. On the other hand, the ruthenium-labeled yeast cytochrome c derivative Ru(z)-39-Cc formed a tight 1:1 complex with cyt c(1CF) at ionic strengths of <60 mM with an intracomplex electron transfer rate constant of 50000 s(-1). A group of cyt c(1CF) variants in the presumed docking site were generated on the basis of information from the yeast cyt bc(1)-cyt c cocrystal structure. Kinetic analysis of cyt c(1CF) mutants located near the heme crevice provided preliminary identification of the interaction site for cyt c(552F) and suggested that formation of the encounter complex is guided primarily by the overall electrostatic surface potential rather than by defined ions.
Collapse
Affiliation(s)
- Julia Janzon
- Molecular Genetics, Institute of Biochemistry, Biocentre Goethe-University, 60438 Frankfurt/Main, Germany.
| | | | | | | | | | | | | |
Collapse
|
17
|
Sarewicz M, Borek A, Daldal F, Froncisz W, Osyczka A. Demonstration of short-lived complexes of cytochrome c with cytochrome bc1 by EPR spectroscopy: implications for the mechanism of interprotein electron transfer. J Biol Chem 2008; 283:24826-36. [PMID: 18617515 PMCID: PMC2529009 DOI: 10.1074/jbc.m802174200] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2008] [Revised: 07/08/2008] [Indexed: 11/18/2022] Open
Abstract
One of the steps of a common pathway for biological energy conversion involves electron transfer between cytochrome c and cytochrome bc1. To clarify the mechanism of this reaction, we examined the structural association of those two proteins using the electron transfer-independent electron paramagnetic resonance (EPR) techniques. Drawing on the differences in the continuous wave EPR spectra and saturation recoveries of spin-labeled bacterial and mitochondrial cytochromes c recorded in the absence and presence of bacterial cytochrome bc1, we have exposed a time scale of dynamic equilibrium between the bound and the free state of cytochrome c at various ionic strengths. Our data show a successive decrease of the bound cytochrome c fraction as the ionic strength increases, with a limit of approximately 120 mm NaCl above which essentially no bound cytochrome c can be detected by EPR. This limit does not apply to all of the interactions of cytochrome c with cytochrome bc1 because the cytochrome bc1 enzymatic activity remained high over a much wider range of ionic strengths. We concluded that EPR monitors just the tightly bound state of the association and that an averaged lifetime of this state decreases from over 100 micros at low ionic strength to less than 400 ns at an ionic strength above 120 mm. This suggests that at physiological ionic strength, the tightly bound complex on average lasts less than the time needed for a single electron exchange between hemes c and c1, indicating that productive electron transfer requires several collisions of the two molecules. This is consistent with an early idea of diffusion-coupled reactions that link the soluble electron carriers with the membranous complexes, which, we believe, provides a robust means of regulating electron flow through these complexes.
Collapse
Affiliation(s)
- Marcin Sarewicz
- Department of Biophysics, Faculty of
Biochemistry, Biophysics, and Biotechnology, Jagiellonian University, 30-387
Kraków, Poland and the Department of
Biology, Plant Science Institute, University of Pennsylvania, Philadelphia,
Pennsylvania 19104
| | - Arkadiusz Borek
- Department of Biophysics, Faculty of
Biochemistry, Biophysics, and Biotechnology, Jagiellonian University, 30-387
Kraków, Poland and the Department of
Biology, Plant Science Institute, University of Pennsylvania, Philadelphia,
Pennsylvania 19104
| | - Fevzi Daldal
- Department of Biophysics, Faculty of
Biochemistry, Biophysics, and Biotechnology, Jagiellonian University, 30-387
Kraków, Poland and the Department of
Biology, Plant Science Institute, University of Pennsylvania, Philadelphia,
Pennsylvania 19104
| | - Wojciech Froncisz
- Department of Biophysics, Faculty of
Biochemistry, Biophysics, and Biotechnology, Jagiellonian University, 30-387
Kraków, Poland and the Department of
Biology, Plant Science Institute, University of Pennsylvania, Philadelphia,
Pennsylvania 19104
| | - Artur Osyczka
- Department of Biophysics, Faculty of
Biochemistry, Biophysics, and Biotechnology, Jagiellonian University, 30-387
Kraków, Poland and the Department of
Biology, Plant Science Institute, University of Pennsylvania, Philadelphia,
Pennsylvania 19104
| |
Collapse
|
18
|
Dadak V, Holik M. Electrostatic attraction between cytochrome bc 1 and cytochrome c affects kinetics of cytochrome c reduction. BIOCHEMISTRY (MOSCOW) 2008; 73:870-80. [DOI: 10.1134/s000629790808004x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
19
|
Kano K, Watanabe K, Ishida Y. Porphyrin J-Aggregates Stabilized by Ferric Myoglobin in Neutral Aqueous Solution. J Phys Chem B 2008; 112:14402-8. [DOI: 10.1021/jp802567b] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Koji Kano
- Department of Molecular Chemistry and Biochemistry, Doshisha University, Kyotanabe, Kyoto 610-0321, Japan
| | - Kenji Watanabe
- Department of Molecular Chemistry and Biochemistry, Doshisha University, Kyotanabe, Kyoto 610-0321, Japan
| | - Yoshiyuki Ishida
- Department of Molecular Chemistry and Biochemistry, Doshisha University, Kyotanabe, Kyoto 610-0321, Japan
| |
Collapse
|
20
|
Distance metrics for heme protein electron tunneling. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2008; 1777:1032-7. [PMID: 18471429 DOI: 10.1016/j.bbabio.2008.04.021] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2008] [Revised: 03/17/2008] [Accepted: 04/13/2008] [Indexed: 11/20/2022]
Abstract
There is no doubt that distance is the principal parameter that sets the order of magnitude for electron-tunneling rates in proteins. However, there continue to be varying ways to measure electron-tunneling distances in proteins. This distance uncertainty blurs the issue of whether the intervening protein medium has been naturally selected to speed or slow any particular electron-tunneling reaction. For redox cofactors lacking metals, an edge of the cofactor can be defined that approximates the extent in space that includes most of the wavefunction associated with its tunneling electron. Beyond this edge, the wavefunction tails off much more dramatically in space. The conjugated porphyrin ring seems a reasonable edge for the metal-free pheophytins and bacteriopheophytins of photosynthesis. For a metal containing redox cofactor such as heme, an appropriate cofactor edge is more ambiguous. Electron-tunneling distance may be measured from the conjugated heme macrocycle edge or from the metal, which can be up to 4.8 A longer. In a typical protein medium, such a distance difference normally corresponds to a approximately 1000 fold decrease in tunneling rate. To address this ambiguity, we consider both natural heme protein electron transfer and light-activated electron transfer in ruthenated heme proteins. We find that the edge of the conjugated heme macrocycle provides a reliable and useful tunneling distance definition consistent with other biological electron-tunneling reactions. Furthermore, with this distance metric, heme axially- and edge-oriented electron transfers appear similar and equally well described by a simple square barrier tunneling model. This is in contrast to recent reports for metal-to-metal metrics that require exceptionally poor donor/acceptor couplings to explain heme axially-oriented electron transfers.
Collapse
|
21
|
Black KM, Wallace CJA. Probing the role of the conserved beta-II turn Pro-76/Gly-77 of mitochondrial cytochrome c. Biochem Cell Biol 2007; 85:366-74. [PMID: 17612631 DOI: 10.1139/o07-049] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The loop segment comprising residues 70-84 in mitochondrial cytochrome c serves to direct the polypeptide backbone to permit the functionally required heme Fe - S (Met-80) co-ordination. The primary sequence here is highly conserved, which is something rarely observed in surface loop segments and suggests that its purpose is more complex than its obvious structural role. The beta-II turn formed by Pro-76 and Gly-77 is postulated to be key to the redirection of the peptide backbone required to execute the loop. We assessed the importance of Pro-76 and Gly-77 by mutating 1 or both of these residues to alanine such that the range of allowable dihedral angles was altered, and this resulted in significant changes in physicochemical properties and biological activities. We observed structural perturbations using circular dichroism spectroscopy and thermal denaturation studies. Based on these changes, we propose that the Pro-76/Gly-77 beta-II turn precisely orients the 70s loop, not only to maintain the backbone orientation required for the formation of the axial heme ligand, but also to provide a complementary surface to physiological partners.
Collapse
Affiliation(s)
- Karen M Black
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4H7, Canada
| | | |
Collapse
|
22
|
Kano K, Ishida Y. Supramolecular Complex of Cytochromec with a Polyanionic β-Cyclodextrin. Angew Chem Int Ed Engl 2007. [DOI: 10.1002/ange.200603471] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
|
23
|
Kano K, Ishida Y. Supramolecular Complex of Cytochromec with a Polyanionic β-Cyclodextrin. Angew Chem Int Ed Engl 2007; 46:727-30. [PMID: 17154192 DOI: 10.1002/anie.200603471] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Koji Kano
- Department of Molecular Science and Technology, Doshisha University, Kyotanabe, Kyoto 610-0321, Japan.
| | | |
Collapse
|
24
|
Szaciłowski K, Macyk W, Drzewiecka-Matuszek A, Brindell M, Stochel G. Bioinorganic photochemistry: frontiers and mechanisms. Chem Rev 2005; 105:2647-94. [PMID: 15941225 DOI: 10.1021/cr030707e] [Citation(s) in RCA: 559] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
|
25
|
Abstract
The bc1 complexes are intrinsic membrane proteins that catalyze the oxidation of ubihydroquinone and the reduction of cytochrome c in mitochondrial respiratory chains and bacterial photosynthetic and respiratory chains. The bc1 complex operates through a Q-cycle mechanism that couples electron transfer to generation of the proton gradient that drives ATP synthesis. Genetic defects leading to mutations in proteins of the respiratory chain, including the subunits of the bc1 complex, result in mitochondrial myopathies, many of which are a direct result of dysfunction at catalytic sites. Some myopathies, especially those in the cytochrome b subunit, exacerbate free-radical damage by enhancing superoxide production at the ubihydroquinone oxidation site. This bypass reaction appears to be an unavoidable feature of the reaction mechanism. Cellular aging is largely attributable to damage to DNA and proteins from the reactive oxygen species arising from superoxide and is a major contributing factor in many diseases of old age. An understanding of the mechanism of the bc1 complex is therefore central to our understanding of the aging process. In addition, a wide range of inhibitors that mimic the quinone substrates are finding important applications in clinical therapy and agronomy. Recent structural studies have shown how many of these inhibitors bind, and have provided important clues to the mechanism of action and the basis of resistance through mutation. This paper reviews recent advances in our understanding of the mechanism of the bc1 complex and their relation to these physiologically important issues in the context of the structural information available.
Collapse
Affiliation(s)
- Antony R Crofts
- Department of Biochemistry, and Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA.
| |
Collapse
|
26
|
Blouin C, Guillemette JG, Wallace CJA. Probing electrostatic interactions in cytochrome c using site-directed chemical modification. Biochem Cell Biol 2002; 80:197-203. [PMID: 11989715 DOI: 10.1139/o01-238] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
This communication reports the generation of an electrostatic probe using chemical modification of methionine side chains. The alkylation of methionine by iodoacetamide was achieved in a set of Saccharomyces cerevisiae iso-1-cytochrome c mutants, introducing the nontitratable, nondelocalized positive charge of a carboxyamidomethylmethionine sulfonium (CAMMS) ion at five surface and one buried site in the protein. Changes in redox potential and its variation with temperature were used to calculate microscopic effective dielectric constants operating between the probe and the heme iron. Dielectric constants (epsilon) derived from deltadeltaG values were not useful due to entropic effects, but epsilon(deltadeltaH) gave results that supported the theory. The effect on biological activity of surface derivatization was interpreted in terms of protein-protein interactions. The introduction of an electrostatic probe in cytochrome c often resulted in marked effects on activity with one of two physiological partners: cytochrome c reductase, especially if introduced at position 65, and cytochrome c oxidase, if at position 28.
Collapse
Affiliation(s)
- Christian Blouin
- Department of Biochemistry, Dalhousie University, Halifax, NS, Canada
| | | | | |
Collapse
|
27
|
Hunte C, Solmaz S, Lange C. Electron transfer between yeast cytochrome bc(1) complex and cytochrome c: a structural analysis. BIOCHIMICA ET BIOPHYSICA ACTA 2002; 1555:21-8. [PMID: 12206886 DOI: 10.1016/s0005-2728(02)00249-9] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The structure of the complex between cytochrome c (CYC) and the cytochrome bc(1) complex (QCR) from yeast crystallized with an antibody fragment has been recently determined at 2.97 A resolution [Proc. Natl. Acad. Sci. U. S. A. 99 (2002) 2800]. CYC binds to subunit cytochrome c(1) of the enzyme stabilized by hydrophobic interactions surrounding the heme crevices creating a small, compact contact site. A central cation-pi interaction is an important and conserved feature of CYC binding. Peripheral patches with highly conserved complementary charges further stabilize the enzyme-substrate complex by long-range electrostatic forces and may affect the orientation of the substrate. Size and characteristics of the contact site are optimal for a transient electron transfer complex. Kinetic data show a bell-shaped ionic strength dependence of the cytochrome c reduction with a maximum activity near physiological ionic strength. The dependence is less pronounced in yeast compared to horse heart CYC indicating less impact of electrostatic interactions in the yeast system. Interestingly, a local QCR activity minimum is found for both substrates at 120-140 mM ionic strength. The architecture of the complex results in close distance of both c-type heme groups allowing the rapid reduction of cytochrome c by QCR via direct heme-to-heme electron transfer. Remarkably, CYC binds only to one of the two possible binding sites of the homodimeric complex and binding appears to be coordinated with the presence of ubiquinone at the Q(i) site. Regulatory aspects of CYC reduction are discussed.
Collapse
Affiliation(s)
- Carola Hunte
- Max-Planck-Institute of Biophysics, Dept. Molecular Membrane Biology, Heinrich-Hoffmann-Str. 7, 60528 Frankfurt/M., Germany.
| | | | | |
Collapse
|
28
|
Yu CA, Wen X, Xiao K, Xia D, Yu L. Inter- and intra-molecular electron transfer in the cytochrome bc(1) complex. BIOCHIMICA ET BIOPHYSICA ACTA 2002; 1555:65-70. [PMID: 12206893 DOI: 10.1016/s0005-2728(02)00256-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
In this review, we compare the intra-molecular and inter-molecular electron transfer rate constants of the high-potential branch of the cytochrome bc(1) complex. Several methods such as the conventional stopped-flow spectroscopy, pH-induced electron transfer, photoactivated ruthenium complex induced electron transfer and photoreleaseable caged quinol, have been used to determine reaction rates between redox centers in an attempt to elucidate the reaction mechanism of this vital energy conserving complex. Since the most active pure cytochrome bc(1) complex has a turnover number of 800 s(-1), any step with a rate constant much larger than this will not be rate-limiting. The most likely rate-limiting step is the cytochrome b redox state governed movement of the head domain of iron-sulfur protein from its electron-accepting site ("fixed" or "b-state" position) to its electron donating site ("c(1)-state" position).
Collapse
Affiliation(s)
- Chang-An Yu
- Department of Biochemistry and Molecular Biology, NRC-255, OAES, Oklahoma State University, Stillwater, OK74078, USA.
| | | | | | | | | |
Collapse
|
29
|
Engstrom G, Xiao K, Yu CA, Yu L, Durham B, Millett F. Photoinduced electron transfer between the Rieske iron-sulfur protein and cytochrome c(1) in the Rhodobacter sphaeroides cytochrome bc(1) complex. Effects of pH, temperature, and driving force. J Biol Chem 2002; 277:31072-8. [PMID: 12045199 DOI: 10.1074/jbc.m202594200] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Electron transfer from the Rieske iron-sulfur protein to cytochrome c(1) (cyt c(1)) in the Rhodobacter sphaeroides cytochrome bc(1) complex was studied using a ruthenium dimer complex, Ru(2)D. Laser flash photolysis of a solution containing reduced cyt bc(1), Ru(2)D, and a sacrificial electron acceptor results in oxidation of cyt c(1) within 1 micros, followed by electron transfer from the iron-sulfur center (2Fe-2S) to cyt c(1) with a rate constant of 80,000 s(-1). Experiments were carried out to evaluate whether the reaction was rate-limited by true electron transfer, proton gating, or conformational gating. The temperature dependence of the reaction yielded an enthalpy of activation of +17.6 kJ/mol, which is consistent with either rate-limiting conformational gating or electron transfer. The rate constant was nearly independent of pH over the range pH 7 to 9.5 where the redox potential of 2Fe-2S decreases significantly due to deprotonation of His-161. The rate constant was also not greatly affected by the Rieske iron-sulfur protein mutations Y156W, S154A, or S154A/Y156F, which decrease the redox potential of 2Fe-2S by 62, 109, and 159 mV, respectively. It is concluded that the electron transfer reaction from 2Fe-2S to cyt c(1) is controlled by conformational gating.
Collapse
Affiliation(s)
- Gregory Engstrom
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, USA
| | | | | | | | | | | |
Collapse
|
30
|
Lange C, Hunte C. Crystal structure of the yeast cytochrome bc1 complex with its bound substrate cytochrome c. Proc Natl Acad Sci U S A 2002; 99:2800-5. [PMID: 11880631 PMCID: PMC122428 DOI: 10.1073/pnas.052704699] [Citation(s) in RCA: 283] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Small diffusible redox proteins facilitate electron transfer in respiration and photosynthesis by alternately binding to integral membrane proteins. Specific and transient complexes need to be formed between the redox partners to ensure fast turnover. In respiration, the mobile electron carrier cytochrome c shuttles electrons from the cytochrome bc1 complex to cytochrome c oxidase. Despite extensive studies of this fundamental step of energy metabolism, the structures of the respective electron transfer complexes were not known. Here we present the crystal structure of the complex between cytochrome c and the cytochrome bc1 complex from Saccharomyces cerevisiae. The complex was crystallized with the help of an antibody fragment, and its structure was determined at 2.97-A resolution. Cytochrome c is bound to subunit cytochrome c1 of the enzyme. The tight and specific interactions critical for electron transfer are mediated mainly by nonpolar forces. The close spatial arrangement of the c-type hemes unexpectedly suggests a direct and rapid heme-to-heme electron transfer at a calculated rate of up to 8.3 x 10(6) s(-1). Remarkably, cytochrome c binds to only one recognition site of the homodimeric multisubunit complex. Interestingly, the occupancy of quinone in the Qi site is higher in the monomer with bound cytochrome c, suggesting a coordinated binding and reduction of both electron-accepting substrates. Obviously, cytochrome c reduction by the cytochrome bc1 complex can be regulated in response to respiratory conditions.
Collapse
Affiliation(s)
- Christian Lange
- Max Planck Institute for Biophysics, Heinrich-Hoffmann-Strasse 7, D-60528 Frankfurt am Main, Germany
| | | |
Collapse
|
31
|
Black KM, Clark-Lewis I, Wallace CJ. Conserved tryptophan in cytochrome c: importance of the unique side-chain features of the indole moiety. Biochem J 2001; 359:715-20. [PMID: 11672447 PMCID: PMC1222194 DOI: 10.1042/0264-6021:3590715] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The absolute conservation of tryptophan at position 59 in cytochrome c is related to the unique chemical nature of its indole moiety. The indole side chain of Trp-59 possesses three salient features: bulk, hydrophobicity and the ability of its indole nitrogen to act as a hydrogen-bond donor. Crystallographic evidence identifies the indole nitrogen of Trp-59 as having a stabilizing hydrogen-bonding interaction with the buried carboxylate group of haem propionate 7. Side-chain bulk is also likely to be important because a Phe or Leu residue can replace Trp to give an at least partly functional protein, whereas the smaller Gly or Ser cannot. Semisynthetic analogues were designed to test the importance of the side-chain features of tryptophan by using a recently developed method for stereoselective fragment religation in yeast cytochrome c. Three yeast iso-1 cytochrome c analogues were produced in which Trp-59 was replaced by a non-coded amino acid: p-iodophenylalanine, beta-(3-pyridyl)-alanine or beta-(2-naphthyl)-alanine. Replacement of Trp-59 with these non-coded amino acids allows the reasons for its conservation to be analysed, because they vary with respect to size, hydrophobicity and hydrogen-bond potential. Our results show that decreasing the bulk and hydrophobicity of the side chain at position 59 has a profound but different impact on physicochemical and biological parameters from those of abolishing hydrogen-bond donor potential. This suggests that Trp-59 has both a local and a global stability effect by solvating a buried charge and by having a key role in the packing of the cytochrome c hydrophobic core.
Collapse
Affiliation(s)
- K M Black
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada, B3H 4H7.
| | | | | |
Collapse
|
32
|
Hitomi Y, Hayashi T, Wada K, Mizutani T, Hisaeda Y, Ogoshi H. Interprotein Electron Transfer Reaction Regulated by an Artificial Interface We thank Prof. Dr. I. Morishima and his group for the arrangement of laser flash photolysis equipment. This work was supported by Nagase Science and Technology Foundation, and a Grant-in-Aid for Scientific Research from the Ministry of Education, Science and Culture, Japan. Y. H. was supported by Research Fellowships of the Japanese Society for the Promotion of Science for Young Scientists. Angew Chem Int Ed Engl 2001; 40:1098-1101. [PMID: 11268087 DOI: 10.1002/1521-3773(20010316)40:6<1098::aid-anie10980>3.0.co;2-g] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Yutaka Hitomi
- Department of Synthetic Chemistry and Biological Chemistry Graduate School of Engineering, Kyoto University Kyoto 606-8501 (Japan)
| | | | | | | | | | | |
Collapse
|
33
|
Hitomi Y, Hayashi T, Wada K, Mizutani T, Hisaeda Y, Ogoshi H. Interprotein Electron Transfer Reaction Regulated by an Artificial Interface. Angew Chem Int Ed Engl 2001. [DOI: 10.1002/1521-3757(20010316)113:6<1132::aid-ange11320>3.0.co;2-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|