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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: 61] [Impact Index Per Article: 20.3] [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.
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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
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Singharoy A, Barragan AM, Thangapandian S, Tajkhorshid E, Schulten K. Binding Site Recognition and Docking Dynamics of a Single Electron Transport Protein: Cytochrome c2. J Am Chem Soc 2016; 138:12077-89. [PMID: 27508459 PMCID: PMC5518707 DOI: 10.1021/jacs.6b01193] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Small diffusible redox proteins facilitate electron transfer in respiration and photosynthesis by alternately binding to their redox partners and integral membrane proteins and exchanging electrons. Diffusive search, recognition, binding, and unbinding of these proteins often amount to kinetic bottlenecks in cellular energy conversion, but despite the availability of structures and intense study, the physical mechanisms controlling redox partner interactions remain largely unknown. The present molecular dynamics study provides an all-atom description of the cytochrome c2-docked bc1 complex in Rhodobacter sphaeroides in terms of an ensemble of favorable docking conformations and reveals an intricate series of conformational changes that allow cytochrome c2 to recognize the bc1 complex and bind or unbind in a redox state-dependent manner. In particular, the role of electron transfer in triggering a molecular switch and in altering water-mediated interface mobility, thereby strengthening and weakening complex formation, is described. The results resolve long-standing discrepancies between structural and functional data.
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Affiliation(s)
- Abhishek Singharoy
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana–Champaign, 405 N. Mathews Ave., Urbana, IL 61801, USA
| | - Angela M. Barragan
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana–Champaign, 405 N. Mathews Ave., Urbana, IL 61801, USA
- Department of Physics, University of Illinois at Urbana–Champaign, 1110 W. Green St., Urbana, IL 61801, USA
| | - Sundarapandian Thangapandian
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana–Champaign, 405 N. Mathews Ave., Urbana, IL 61801, USA
| | - Emad Tajkhorshid
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana–Champaign, 405 N. Mathews Ave., Urbana, IL 61801, USA
- Department of Biochemistry, University of Illinois Urbana–Champaign, 600 S. Mathews Ave., Urbana, IL 61801, USA
| | - Klaus Schulten
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana–Champaign, 405 N. Mathews Ave., Urbana, IL 61801, USA
- Department of Physics, University of Illinois at Urbana–Champaign, 1110 W. Green St., Urbana, IL 61801, USA
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3
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Infante-Rodriguez C, Domon L, Breuilles P, Uguen D. Asymmetric Synthesis of Stigmatellin and Crocacin C. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2015. [DOI: 10.1246/bcsj.20140271] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Carolina Infante-Rodriguez
- Laboratoire de Synthèse Organique (associé au CNRS; UMR 7509), Ecole Européenne de Chimie, Polymères et Matériaux, Université de Strasbourg
| | - Lisianne Domon
- Laboratoire de Synthèse Organique (associé au CNRS; UMR 7509), Ecole Européenne de Chimie, Polymères et Matériaux, Université de Strasbourg
| | - Pascal Breuilles
- Laboratoire de Synthèse Organique (associé au CNRS; UMR 7509), Ecole Européenne de Chimie, Polymères et Matériaux, Université de Strasbourg
| | - Daniel Uguen
- Laboratoire de Synthèse Organique (associé au CNRS; UMR 7509), Ecole Européenne de Chimie, Polymères et Matériaux, Université de Strasbourg
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4
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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: 106] [Impact Index Per Article: 11.8] [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.
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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
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5
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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.
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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.
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Kokhan O, Ponomarenko N, Pokkuluri PR, Schiffer M, Tiede DM. Multimerization of solution-state proteins by tetrakis(4-sulfonatophenyl)porphyrin. Biochemistry 2014; 53:5070-9. [PMID: 25028772 DOI: 10.1021/bi500278g] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Surface binding and interactions of anionic porphyins bound to cationic proteins have been studied for nearly three decades and are relevant as models for protein surface molecular recognition and photoinitiated electron transfer. However, interpretation of data in nearly all reports explicitly or implicitly assumed interaction of porphyrin with monodisperse proteins in solutions. In this report, using small-angle X-ray scattering with solution phase samples, we demonstrate that horse heart cytochrome (cyt) c, triheme cytochrome c7 PpcA from Geobacter sulfurreducens, and hen egg lysozyme multimerize in the presence of zinc tetrakis(4-sulfonatophenyl)porphyrin (ZnTPPS). Multimerization of cyt c showed a pH dependence with a stronger apparent binding affinity under alkaline conditions and was weakened in the presence of a high salt concentration. Ferric-cyt c formed complexes larger than those formed by ferro-cyt c. Free base TPPS and FeTPPS facilitated formation of complexes larger than those of ZnTPPS. No increase in protein aggregation state for cationic proteins was observed in the presence of cationic porphyrins. All-atom molecular dynamics simulations of cyt c and PpcA with free base TPPS corroborated X-ray scattering results and revealed a mechanism by which the tetrasubstituted charged porphyrins serve as bridging ligands nucleating multimerization of the complementarily charged protein. The final aggregation products suggest that multimerization involves a combination of electrostatic and hydrophobic interactions. The results demonstrate an overlooked complexity in the design of multifunctional ligands for protein surface recognition.
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Affiliation(s)
- Oleksandr Kokhan
- Chemical Sciences and Engineering Division, Argonne National Laboratory , Lemont, Illinois 60439, United States
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7
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Pietras R, Sarewicz M, Osyczka A. Molecular organization of cytochrome c2 near the binding domain of cytochrome bc1 studied by electron spin-lattice relaxation enhancement. J Phys Chem B 2014; 118:6634-43. [PMID: 24845964 PMCID: PMC4065165 DOI: 10.1021/jp503339g] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
![]()
Measurements
of specific interactions between proteins are challenging.
In redox systems, interactions involve surfaces near the attachment
sites of cofactors engaged in interprotein electron transfer (ET).
Here we analyzed binding of cytochrome c2 to cytochrome bc1 by measuring paramagnetic
relaxation enhancement (PRE) of spin label (SL) attached to cytochrome c2. PRE was exclusively induced by the iron atom
of heme c1 of cytochrome bc1, which guaranteed that only the configurations with
SL to heme c1 distances up to ∼30
Å were detected. Changes in PRE were used to qualitatively and
quantitatively characterize the binding. Our data suggest that at
low ionic strength and under an excess of cytochrome c2 over cytochrome bc1, several
cytochrome c2 molecules gather near the
binding domain forming a “cloud” of molecules. When
the cytochrome bc1 concentration increases,
the cloud disperses to populate additional available binding domains.
An increase in ionic strength weakens the attractive forces and the
average distance between cytochrome c2 and cytochrome bc1 increases. The spatial
arrangement of the protein complex at various ionic strengths is different.
Above 150 mM NaCl the lifetime of the complexes becomes so short that
they are undetectable. All together the results indicate that cytochrome c2 molecules, over the range of salt concentration
encompassing physiological ionic strength, do not form stable, long-lived
complexes but rather constantly collide with the surface of cytochrome bc1 and ET takes place coincidentally with one
of these collisions.
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Affiliation(s)
- Rafał Pietras
- Department of Molecular Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University , 30-387 Kraków, Poland
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8
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Lin MT, Gennis RB. Product-controlled steady-state kinetics between cytochrome aa(3) from Rhodobacter sphaeroides and equine ferrocytochrome c analyzed by a novel spectrophotometric approach. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2012; 1817:1894-900. [PMID: 22516686 DOI: 10.1016/j.bbabio.2012.04.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2012] [Revised: 03/30/2012] [Accepted: 04/02/2012] [Indexed: 11/29/2022]
Abstract
Cytochrome c oxidase (CcO) catalyzes the reduction of molecular oxygen to water using ferrocytochrome c (cyt c(2+)) as the electron donor. In this study, the oxidation of horse cyt c(2+) by CcO from Rhodobacter sphaeroides, was monitored using stopped-flow spectrophotometry. A novel analytic procedure was applied in which the spectra were deconvoluted into the reduced and oxidized forms of cyt c by a least-squares fitting method, yielding the reaction rates at various concentrations of cyt c(2+) and cyt c(3+). This allowed an analysis of the effects of cyt c(3+) on the steady-state kinetics between CcO and cyt c(2+). The results show that cyt c(3+) exhibits product inhibition by two mechanisms: competition with cyt c(2+) at the catalytic site and, in addition, an interaction at a second site which further modulates the reaction of cyt c(2+) at the catalytic site. These results are generally consistent with previous reports, indicating the reliability of the new procedure. We also find that a 6×His-tag at the C-terminus of the subunit II of CcO affects the binding of cyt c at both sites. The approach presented here should be generally useful in spectrophotometric studies of complex enzyme kinetics. This article is part of a Special Issue entitled: 17th European Bioenergetics Conference (EBEC 2012).
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Affiliation(s)
- Myat T Lin
- Center for Biophysics and Computational Biology, University of Illinois, Urbana, IL 61801, USA
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9
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Kyndt JA, Fitch JC, Berry RE, Stewart MC, Whitley K, Meyer TE, Walker FA, Cusanovich MA. Tyrosine triad at the interface between the Rieske iron-sulfur protein, cytochrome c1 and cytochrome c2 in the bc1 complex of Rhodobacter capsulatus. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2012; 1817:811-8. [PMID: 22306765 DOI: 10.1016/j.bbabio.2012.01.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2011] [Revised: 01/20/2012] [Accepted: 01/20/2012] [Indexed: 11/25/2022]
Abstract
A triad of tyrosine residues (Y152-154) in the cytochrome c(1) subunit (C1) of the Rhodobacter capsulatus cytochrome bc(1) complex (BC1) is ideally positioned to interact with cytochrome c(2) (C2). Mutational analysis of these three tyrosines showed that, of the three, Y154 is the most important, since its mutation to alanine resulted in significantly reduced levels, destabilization, and inactivation of BC1. A second-site revertant of this mutant that regained photosynthetic capacity was found to have acquired two further mutations-A181T and A200V. The Y152Q mutation did not change the spectral or electrochemical properties of C1, and showed wild-type enzymatic C2 reduction rates, indicating that this mutation did not introduce major structural changes in C1 nor affect overall activity. Mutations Y153Q and Y153A, on the other hand, clearly affect the redox properties of C1 (e.g. by lowering the midpoint potential as much as 117 mV in Y153Q) and the activity by 90% and 50%, respectively. A more conservative Y153F mutant on the other hand, behaves similarly to wild-type. This underscores the importance of an aromatic residue at position Y153, presumably to maintain close packing with P184, which modeling indicates is likely to stabilize the sixth heme ligand conformation.
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Affiliation(s)
- John A Kyndt
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721, USA.
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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.
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Affiliation(s)
- Marcin Sarewicz
- Department of Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, ul Gronostajowa 7, 30-307 Kraków, Poland
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YAMAGUCHI A, ARAFUNE H, HOTTA K, ITOH T, TERAMAE N. Adsorption and Desorption Dynamics of Sodium Dodecyl Sulfate at the Octadecylsilane Layer on the Pore Surface of a Mesoporous Silica Film Observed in-situ by Optical Waveguide Spectroscopy. ANAL SCI 2011; 27:597-603. [DOI: 10.2116/analsci.27.597] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- Akira YAMAGUCHI
- College of Science, Ibaraki University
- Frontier Research Center for Applied Atomic Sciences, Ibaraki University
| | - Hiroyuki ARAFUNE
- Department of Chemistry, Graduate School of Science, Tohoku University
| | - Kazuhiro HOTTA
- Department of Chemistry, Graduate School of Science, Tohoku University
| | - Tetsuji ITOH
- Research Center for Compact Chemical System, National Institute of Advanced Industrial Science and Technology (AIST)
| | - Norio TERAMAE
- Department of Chemistry, Graduate School of Science, Tohoku University
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12
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Hotta K, Yamaguchi A, Teramae N. Properties of A Metal Clad Waveguide Sensor Based on A Nanoporous-Metal-Oxide/Metal Multilayer Film. Anal Chem 2010; 82:6066-73. [DOI: 10.1021/ac100654b] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Kazuhiro Hotta
- Department of Chemistry, Graduate School of Science, Tohoku University, Aoba-ku, Sendai 980-8578, Japan
| | - Akira Yamaguchi
- Department of Chemistry, Graduate School of Science, Tohoku University, Aoba-ku, Sendai 980-8578, Japan
| | - Norio Teramae
- Department of Chemistry, Graduate School of Science, Tohoku University, Aoba-ku, Sendai 980-8578, Japan
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Salamon Z, Fitch J, Cai M, Tumati S, Navratilova E, Tollin G. Plasmon-waveguide resonance studies of ligand binding to integral proteins in membrane fragments derived from bacterial and mammalian cells. Anal Biochem 2009; 387:95-101. [PMID: 19454250 DOI: 10.1016/j.ab.2009.01.019] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2008] [Revised: 01/12/2009] [Accepted: 01/14/2009] [Indexed: 11/19/2022]
Abstract
A procedure has been developed for directly depositing membrane fragments derived from bacterial cells (chromatophores from Rhodopseudomonas sphaeroides) and mammalian cells (mu-opioid receptor- and MC4 receptor-transfected human embryonic kidney (HEK) cells and rat trigeminal ganglion cells) on the silica surface of a plasmon-waveguide resonance (PWR) spectrometer. Binding of ligands (cytochrome c(2) for the chromatophores, the peptide agonists DAMGO and melanotan-II that are specific for the mu-opioid and MC4 receptors, and two nonpeptide agonists that are specific for the CB1 receptor) to these membrane fragments has been observed and characterized with high sensitivity using PWR spectral shifts. The K(D) values obtained are in excellent agreement with conventional pharmacological assays and with prior PWR studies using purified receptors inserted into deposited lipid bilayer membranes. These studies provide a new tool for obtaining useful biological information about receptor-mediated processes in real biological membranes.
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Affiliation(s)
- Zdzislaw Salamon
- Department of Biochemistry and Molecular Biophysics, University of Arizona, Tucson, AZ 85721, USA
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14
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A structural analysis of the transient interaction between the cytochrome bc1 complex and its substrate cytochrome c. Biochem Soc Trans 2008; 36:981-5. [PMID: 18793174 DOI: 10.1042/bst0360981] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
In cellular respiration, cytochrome c transfers electrons from the cytochrome bc1 complex to cytochrome c oxidase by transiently binding to the membrane proteins. The first X-ray structure of the yeast cytochrome bc1 complex with bound cytochrome c revealed the general architecture of the electron-transfer complex. The interface of the complex is small. The haem moieties are centrally located in a mainly non-polar contact site, which includes a cation-pi interaction and is surrounded by complementary charged residues. Only one cytochrome c1-docking site of the dimeric complex is occupied with cytochrome c. The recent 1.9 A (1 A=0.1 nm) resolution structure of the complex showed that the interface is highly hydrated. With cytochrome c bound, a higher number of interfacial water molecules are present on the cytochrome c1 interface, whereas its protein surface is not affected. Remarkably, the dimer structure is slightly asymmetric. Univalent cytochrome c binding coincides with conformational changes of the Rieske head domain and subunit QCR6p. Pronounced hydration and a mobility mismatch at the interface with disordered charged residues on the cytochrome c side are favourable for transient binding. Comparison with a new structure of the complex with bound isoform-2 cytochrome c led to the definition of a core interface, which refers to four common interaction pairs including the cation-pi interaction. They encircle the haem groups and are surrounded by variable interactions. The core interface may be a feature to gain specificity for formation of the reactive complex. The consistency in the binding interaction despite differences in primary sequence, redox state and crystal contacts, together with crystallization at physiological ionic strength, clearly suggest that the structures show the native bound state of the electron-transfer complex.
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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.
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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
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