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BBA - Bioenergetics (v.1787, #9)
Protein–cofactor interactions in bioenergetic complexes: The role of the A1A and A1B phylloquinones in Photosystem I by Nithya Srinivasan; John H. Golbeck ⁎ (pp. 1057-1088).
This review focuses on phylloquinone as an indispensable link between light-induced charge separation and subsequent charge stabilization in Photosystem I (PS I). Here, the role of the polypeptide in conferring the necessary kinetic and thermodynamic properties to phylloquinone so as to specify its functional role in PS I electron transfer is discussed. Photosynthetic electron transfer and the role of quinones in Type I and Type II reaction centers are introduced at the outset with particular emphasis on the determination of redox potentials of the cofactors. Currently used methodologies, particularly time-resolved optical spectroscopy and varieties of magnetic resonance spectroscopy that have become invaluable in uncovering the details of phylloquinone function are described in depth. Recent studies on the selective alteration of the protein environment and on the incorporation of foreign quinones either by chemical or genetic means are explored to assess how these studies have improved our understanding of protein–quinone interactions. Particular attention is paid to the function of the H-bond, methyl group and phytyl tail of the phylloquinone in interacting with the protein environment.
Keywords: Abbreviations; PS I; Photosystem I; PS II; Photosystem II; ATP; Adenosine triphosphate; NADPH; Nicotinamide adenine dinucleotide phosphate; RC; Reaction center; EPR; Electron paramagnetic resonance; ENDOR; Electron nuclear double resonance; FTIR; Fourier transform infrared; hfc; Hyperfine coupling; H-bond; Hydrogen bond; ESEEM; Electron spin echo envelope modulationPhotosystem I; Phylloquinone; Electron transfer; Redox potential
Regulation of respiration controlled by mitochondrial creatine kinase in permeabilized cardiac cells in situ by Rita Guzun; Natalja Timohhina; Kersti Tepp; Claire Monge; Tuuli Kaambre; Peeter Sikk; Andrey V. Kuznetsov; Christophe Pison; Valdur Saks (pp. 1089-1105).
The main focus of this investigation is steady state kinetics of regulation of mitochondrial respiration in permeabilized cardiomyocytes in situ. Complete kinetic analysis of the regulation of respiration by mitochondrial creatine kinase was performed in the presence of pyruvate kinase and phosphoenolpyruvate to simulate interaction of mitochondria with glycolytic enzymes. Such a system analysis revealed striking differences in kinetic behaviour of the MtCK-activated mitochondrial respiration in situ and in vitro. Apparent dissociation constants of MgATP from its binary and ternary complexes with MtCK, Kia and Ka (1.94±0.86 mM and 2.04±0.14 mM, correspondingly) were increased by several orders of magnitude in situ in comparison with same constants in vitro (0.44±0.08 mM and 0.016±0.01 mM, respectively). Apparent dissociation constants of creatine, Kib and Kb (2.12±0.21 mM 2.17±0.40 Mm, correspondingly) were significantly decreased in situ in comparison with in vitro mitochondria (28±7 mM and 5±1.2 mM, respectively). Dissociation constant for phosphocreatine was not changed. These data may indicate selective restriction of metabolites' diffusion at the level of mitochondrial outer membrane. It is concluded that mechanisms of the regulation of respiration and energy fluxes in vivo are system level properties which depend on intracellular interactions of mitochondria with cytoskeleton, intracellular MgATPases and cytoplasmic glycolytic system.
Keywords: Respiration; Cardiomyocyte; Mitochondria; Creatine kinase; Creatine
Exploring the binding site of acetogenin in the ND1 subunit of bovine mitochondrial complex I by Koji Sekiguchi; Masatoshi Murai; Hideto Miyoshi ⁎ (pp. 1106-1111).
125I-labeled ( trifluoromethyl)phenyl diazirinyl acetogenin, [125I]TDA, a photoaffinity labeling probe of acetogenin, photo-cross-links to the ND1 subunit of bovine heart mitochondrial NADH–ubiquinone oxidoreductase (complex I) with high specificity [ The ND1 subunit constructs the inhibitor binding domain in bovine heart mitochondrial complex I, Biochemistry 46 6409–6416.]. To identify the binding site of [125I]TDA in the ND1 subunit, we carried out limited proteolysis of the subunit cross-linked by [125I]TDA using various proteases and carefully analyzed the fragmentation patterns. Our results revealed that the cross-linked residue is located within the region of the 4th to 5th transmembrane helices (Val144–Glu192) of the subunit. It is worth noting that an excess amount of short-chain ubiquinones such as ubiquinone-2 (Q2) and 2-azido-Q2 suppressed the cross-linking by [125I]TDA in a concentration-dependent way. Although the question of whether the binding sites for ubiquinone and different inhibitors in complex I are identical remains to be answered, the present study provided, for the first time, direct evidence that an inhibitor (acetogenin) and ubiquinone competitively bind to the enzyme. Considering the present results along with earlier photoaffinity labeling studies, we propose that not all inhibitors acting at the terminal electron transfer step of complex I necessarily bind to the ubiquinone binding site itself.
Keywords: Mitochondrial complex I; Acetogenin; Respiratory inhibitor; Photoaffinity labeling; ND1 subunit
Photo-catalytic oxidation of a di-nuclear manganese centre in an engineered bacterioferritin ‘reaction centre’ by Brendon Conlan ⁎; Nicholas Cox; Ji-Hu Su; Warwick Hillier; Johannes Messinger; Wolfgang Lubitz; P. Leslie Dutton; Tom Wydrzynski ⁎ (pp. 1112-1121).
Photosynthesis involves the conversion of light into chemical energy through a series of electron transfer reactions within membrane-bound pigment/protein complexes. The Photosystem II (PSII) complex in plants, algae and cyanobacteria catalyse the oxidation of water to molecular O2. The complexity of PSII has thus far limited attempts to chemically replicate its function. Here we introduce a reverse engineering approach to build a simple, light-driven photo-catalyst based on the organization and function of the donor side of the PSII reaction centre. We have used bacterioferritin (BFR) (cytochrome b1) from Escherichia coli as the protein scaffold since it has several, inherently useful design features for engineering light-driven electron transport. Among these are: ( i.) a di-iron binding site; ( ii.) a potentially redox-active tyrosine residue; and ( iii.) the ability to dimerise and form an inter-protein heme binding pocket within electron tunnelling distance of the di-iron binding site. Upon replacing the heme with the photoactive zinc–chlorin e6 (ZnCe6) molecule and the di-iron binding site with two manganese ions, we show that the two Mn ions bind as a weakly coupled di-nuclear Mn2II,II centre, and that ZnCe6 binds in stoichiometric amounts of 1:2 with respect to the dimeric form of BFR. Upon illumination the bound ZnCe6 initiates electron transfer, followed by oxidation of the di-nuclear Mn centre possibly via one of the inherent tyrosine residues in the vicinity of the Mn cluster. The light dependent loss of the MnII EPR signals and the formation of low field parallel mode Mn EPR signals are attributed to the formation of MnIII species. The formation of the MnIII is concomitant with consumption of oxygen. Our model is the first artificial reaction centre developed for the photo-catalytic oxidation of a di-metal site within a protein matrix which potentially mimics water oxidation centre (WOC) photo-assembly.
Keywords: Abbreviations; BFR; wild type bacterioferritin; BFR; 1; bacterioferritin double mutant H46R, H112R without cofactors; BFR; 1; –M; BFR; 1; with two manganese ions bound; BFR; 1; –Z; BFR; 1; with ZnCe; 6; bound; BFR; 1; –ZM; BFR; 1; with stoichiometric amounts of ZnCe; 6; and manganese bound; EPR; electron paramagnetic resonance; ITC; isothermal titration calorimetry; PSII; Photosystem II; ZnCe; 6; zinc; II; chlorin e; 6Artificial photosynthesis; EPR; Manganese; Electron transfer; Protein engineering; Bacterioferritin; Zinc chlorin e; 6
ApcD is necessary for efficient energy transfer from phycobilisomes to photosystem I and helps to prevent photoinhibition in the cyanobacterium Synechococcus sp. PCC 7002 by Chunxia Dong; Aihui Tang; Jindong Zhao ⁎; Conrad W. Mullineaux; Gaozhong Shen; Donald A. Bryant ⁎ (pp. 1122-1128).
Phycobilisomes (PBS) are the major light-harvesting, protein–pigment complexes in cyanobacteria and red algae. PBS absorb and transfer light energy to photosystem (PS) II as well as PS I, and the distribution of light energy from PBS to the two photosystems is regulated by light conditions through a mechanism known as state transitions. In this study the quantum efficiency of excitation energy transfer from PBS to PS I in the cyanobacterium Synechococcus sp. PCC 7002 was determined, and the results showed that energy transfer from PBS to PS I is extremely efficient. The results further demonstrated that energy transfer from PBS to PS I occurred directly and that efficient energy transfer was dependent upon the allophycocyanin-B alpha subunit, ApcD. In the absence of ApcD, cells were unable to perform state transitions and were trapped in state 1. Action spectra showed that light energy transfer from PBS to PS I was severely impaired in the absence of ApcD. An apcD mutant grew more slowly than the wild type in light preferentially absorbed by phycobiliproteins and was more sensitive to high light intensity. On the other hand, a mutant lacking ApcF, which is required for efficient energy transfer from PBS to PS II, showed greater resistance to high light treatment. Therefore, state transitions in cyanobacteria have two roles: (1) they regulate light energy distribution between the two photosystems; and (2) they help to protect cells from the effects of light energy excess at high light intensities.
Keywords: Cyanobacteria; Phycobilisome; Photosynthesis; State transition; Photosystem I; Photosystem II; Synechococcus; sp. PCC 7002
A more robust version of the Arginine 210-switched mutant in subunit a of the Escherichia coli ATP synthase by Leon Bae; Steven B. Vik ⁎ (pp. 1129-1134).
Previous work has shown that the essential R210 of subunit a in the Escherichia coli ATP synthase can be switched with a conserved glutamine Q252 with retention of a moderate level of function, that a third mutation P204T enhances this function, and that the arginine Q252R can be replaced by lysine without total loss of activity. In this study, the roles of P204T and R210Q were examined. It was concluded that the threonine in P204T is not directly involved in function since its replacement by alanine did not significantly affect growth properties. Similarly, it was concluded that the glutamine in R210Q is not directly involved with function since replacement by glycine results in significantly enhanced function. Not only did the rate of ATP-driven proton translocation increase, but also the sensitivity of ATP hydrolysis to inhibition by N,N′-dicyclohexylcarbodiimide (DCCD) rose to more than 50%. Finally, mutations at position E219, a residue near the proton pathway, were used to test whether the Arginine-switched mutant uses the normal proton pathway. In a wild type background, the E219K mutant was confirmed to have greater function than the E219Q mutant, as has been shown previously. This same unusual result was observed in the triple mutant background, P204T/R210Q/Q252R, suggesting that the Arginine-switched mutants are using the normal proton pathway from the periplasm.
Keywords: Abbreviations; ACMA; 9-amino-6-chloro-2-methoxyacridine; DCCD; N,N′-dicyclohexylcarbodiimide; FCCP; carbonyl cyanide; p; -(trifluoromethoxy) phenylhydrazone; HA; Hemaglutinin epitope; TM4; the fourth transmembrane span of subunit; a; , for exampleATP synthase; F; 1; F; o; Subunit; a; Proton translocation; Rotary motor; ATPase
Control of choline oxidation in rat kidney mitochondria by Niaobh O'Donoghue; Trevor Sweeney; Robin Donagh; Kieran J. Clarke; Richard K. Porter ⁎ (pp. 1135-1139).
Choline is a quaternary amino cationic organic alcohol that is oxidized to betaine in liver and kidney mitochondria. Betaine acts as an intracellular organic osmolyte in the medulla of the kidney. Evidence is provided that kidney mitochondria have a choline transporter in their inner membrane. The transporter has a Km of 173±64 μM and a Vmax of 0.4±0.1 nmol/min/mg mitochondrial protein (at 10 °C). Uptake of choline is not coupled to betaine efflux. Transporter activity demonstrates a dependence on membrane potential and choline transport is inhibited by hemicholinium-3. Steady-state oxygen consumption due to choline oxidation in kidney mitochondria was measurable at 37 °C (125±6 pmolO2/min/mg mitochondrial protein), in the absence of other mitochondrial electron transport chain substrates and the choline transporter was shown to be the major site of control (96±4%) over choline oxidation flux in isolated kidney mitochondria. We conclude that the choline transporter in rat kidney mitochondria is the major site of control over the production of the organic osmolyte, betaine.
Keywords: Abbreviations; EGTA; ethylenebis(oxethylenenitrilo)tetraacetic acid; FCCP; carbonyl cyanide p-trifluoromethoxyphenylhyrazone; HEPES; 4-(2-hydroxyethyl)-1-peiperazine-ethanesulfonic acid; MOPS; (3-[N}-morphilino)propane sulphonic acid; TPMP; methyltriphenylphosphoniumCholine; Betaine; Mitochondria; Osmolyte; Kidney; Transporter
Molecular dynamics simulation of water in cytochrome c oxidase reveals two water exit pathways and the mechanism of transport by Ryogo Sugitani; Alexei A. Stuchebrukhov ⁎ (pp. 1140-1150).
We have examined the network of connected internal cavities in cytochrome c oxidase along which water produced at the catalytic center is removed from the enzyme. Using combination of structural analysis, molecular dynamics simulations, and free energy calculations we have identified two exit pathways that connect the Mg2+ ion cavity to the outside of the enzyme. Each pathway has a well-defined bottleneck, which determines the overall rate of water traffic along the exit pathway, and a specific cooperative mechanism of passing it. One of the pathways is going via Arg438/439 (in bovine numbering) toward the CuA center, approaching closely its His204B ligand and Lys171B residue; and the other is going toward Asp364 and Thr294. Comparison of the pathways among different aa3-type enzymes shows that they are well conserved. Possible connections of the finding to redox-coupled proton pumping mechanism are discussed. We propose specific mutations near the bottlenecks of the exit pathways that can test some of our hypotheses.
Keywords: Cytochrome; c; oxidase; Water exit channel; Proton pumping mechanism; Potential of mean force; Computer simulation; Molecular dynamics