BBA - Bioenergetics (v.1807, #5)
Editorial Board (i).
Molecular environments of divinyl chlorophylls in Prochlorococcus and Synechocystis: Differences in fluorescence properties with chlorophyll replacement by Mamoru Mimuro; Akio Murakami; Tatsuya Tomo; Tohru Tsuchiya; Kazuyuki Watabe; Makio Yokono; Seiji Akimoto (471-481).
A marine cyanobacterium, Prochlorococcus, is a unique oxygenic photosynthetic organism, which accumulates divinyl chlorophylls instead of the monovinyl chlorophylls. To investigate the molecular environment of pigments after pigment replacement but before optimization of the protein moiety in photosynthetic organisms, we compared the fluorescence properties of the divinyl Chl a-containing cyanobacteria, Prochlorococcus marinus (CCMP 1986, CCMP 2773 and CCMP 1375), by a Synechocystis sp. PCC 6803 (Synechocystis) mutant in which monovinyl Chl a was replaced with divinyl Chl a. P. marinus showed a single fluorescence band for photosystem (PS) II at 687 nm at 77 K; this was accompanied with change in pigment, because the Synechocystis mutant showed the identical shift. No fluorescence bands corresponding to the PS II 696-nm component and PS I longer-wavelength component were detected in P. marinus, although the presence of the former was suggested using time-resolved fluorescence spectra. Delayed fluorescence (DF) was detected at approximately 688 nm with a lifetime of approximately 29 ns. In striking contrast, the Synechocystis mutant showed three fluorescence bands at 687, 696, and 727 nm, but suppressed DF. These differences in fluorescence behaviors might not only reflect differences in the molecular structure of pigments but also differences in molecular environments of pigments, including pigment–pigment and/or pigment–protein interactions, in the antenna and electron transfer systems.► Three cultured strains of Prochlorococcus marinus showed characteristic fluorescence. ► Synechocystis sp. PCC 6803 with divinyl chlorophyll a changed fluorescence spectrum. ► We discuss the molecular environments of the pigments following replacement of a photosynthetic pigment, monovinyl chlorophyll to divinyl chlorophyll.
Keywords: Cyanobacteria; Divinyl chlorophyll; Evolution; Fluorescence; Photosynthesis; Time-resolved spectroscopy; Prochlorococcus;
Shedding light on the mitochondrial permeability transition by Fernanda Ricchelli; Justina Šileikytė; Paolo Bernardi (482-490).
The mitochondrial permeability transition is an increase of permeability of the inner mitochondrial membrane to ions and solutes with an exclusion size of about 1500 Da. It is generally accepted that the permeability transition is due to opening of a high-conductance channel, the permeability transition pore. Although the molecular nature of the permeability transition pore remains undefined, a great deal is known about its regulation and role in pathophysiology. This review specifically covers the characterization of the permeability transition pore by chemical modification of specific residues through photoirradiation of mitochondria after treatment with porphyrins. The review also illustrates the basic principles of the photodynamic effect and the mechanisms of phototoxicity and discusses the unique properties of singlet oxygen generated by specific porphyrins in discrete mitochondrial domains. These experiments provided remarkable information on the role, interactions and topology of His and Cys residues in permeability transition pore modulation and defined an important role for the outer membrane 18 kDa translocator protein (formerly known as the peripheral benzodiazepine receptor) in regulation of the permeability transition.► The permeability transition pore (PTP) is an inner membrane mitochondrial channel. ► The PTP is a major target in degenerative disease. ► The photodynamic effect is a useful tool to study biological systems. ► The use of dicarboxylic porphyrins and light allowed to dissect regulatory sites of the PTP. ► This review is a synthesis of the photodynamic approach applied to the PTP.
Keywords: Mitochondria; Permeability transition pore; Photodynamic effect;
Excess no predisposes mitochondrial succinate–cytochrome c reductase to produce hydroxyl radical by Jingfeng Chen; Chwen-Lih Chen; B. Rita Alevriadou; Jay L. Zweier; Yeong-Renn Chen (491-502).
Mitochondria-derived oxygen-free radical(s) are important mediators of oxidative cellular injury. It is widely hypothesized that excess NO enhances O2 •− generated by mitochondria under certain pathological conditions. In the mitochondrial electron transport chain, succinate–cytochrome c reductase (SCR) catalyzes the electron transfer reaction from succinate to cytochrome c. To gain the insights into the molecular mechanism of how NO overproduction may mediate the oxygen-free radical generation by SCR, we employed isolated SCR, cardiac myoblast H9c2, and endothelial cells to study the interaction of NO with SCR in vitro and ex vivo. Under the conditions of enzyme turnover in the presence of NO donor (DEANO), SCR gained pro-oxidant function for generating hydroxyl radical as detected by EPR spin trapping using DEPMPO. The EPR signal associated with DEPMPO/•OH adduct was nearly completely abolished in the presence of catalase or an iron chelator and partially inhibited by SOD, suggesting the involvement of the iron–H2O2-dependent Fenton reaction or O2 •−-dependent Haber–Weiss mechanism. Direct EPR measurement of SCR at 77 K indicated the formation of a nonheme iron–NO complex, implying that electron leakage to molecular oxygen was enhanced at the FAD cofactor, and that excess NO predisposed SCR to produce •OH. In H9c2 cells, SCR-dependent oxygen-free radical generation was stimulated by NO released from DEANO or produced by the cells following exposure to hypoxia/reoxygenation. With shear exposure that led to overproduction of NO by the endothelium, SCR-mediated oxygen-free radical production was also detected in cultured vascular endothelial cells.Display Omitted► Excess NO promotes the pro-oxidant activity of SCR to produce hydroxyl radical in vitro. ► SCR-mediated hydroxyl radical production depends on dinitroso iron intermediate formation at the S1 center. ► Excess NO induced by shear exposure or hypoxia/reoxygenation enhances oxygen-free radicals production by mitochondrial SCR in living cells.
Keywords: Mitochondria; Electron transport chain; SCR; NO; Hydroxyl radical; EPR spin trapping;
Catalytic intermediates of cytochrome bd terminal oxidase at steady-state: Ferryl and oxy-ferrous species dominate by Vitaliy B. Borisov; Elena Forte; Paolo Sarti; Alessandro Giuffrè (503-509).
The cytochrome bd ubiquinol oxidase from Escherichia coli couples the exergonic two-electron oxidation of ubiquinol and four-electron reduction of O2 to 2H2O to proton motive force generation by transmembrane charge separation. The oxidase contains two b-type hemes (b 558 and b 595) and one heme d, where O2 is captured and converted to water through sequential formation of a few intermediates. The spectral features of the isolated cytochrome bd at steady-state have been examined by stopped-flow multiwavelength absorption spectroscopy. Under turnover conditions, sustained by O2 and dithiothreitol (DTT)-reduced ubiquinone, the ferryl and oxy-ferrous species are the mostly populated catalytic intermediates, with a residual minor fraction of the enzyme containing ferric heme d and possibly one electron on heme b 558. These findings are unprecedented and differ from those obtained with mammalian cytochrome c oxidase, in which the oxygen intermediates were not found to be populated at detectable levels under similar conditions [M.G. Mason, P. Nicholls, C.E. Cooper, The steady-state mechanism of cytochrome c oxidase: redox interactions between metal centres, Biochem. J. 422 (2009) 237–246]. The data on cytochrome bd are consistent with the observation that the purified enzyme has the heme d mainly in stable oxy-ferrous and ferryl states. The results are here discussed in the light of previously proposed models of the catalytic cycle of cytochrome bd.► Spectral features of cytochrome bd terminal oxidase examined at steady-state by time-resolved spectrophotometry ► Ferryl and oxy-ferrous catalytic intermediates dominate ► Model of the catalytic cycle proposed.
Keywords: Respiration; Chlorin; Catalytic turnover; Reaction mechanism; Hemoprotein; Oxygen chemistry;
On understanding proton transfer to the biocatalytic [Fe―Fe]H sub-cluster in [Fe―Fe]H2ases: QM/MM MD simulations by G. Hong; A.J. Cornish; E.L. Hegg; R. Pachter (510-517).
Proton transfer to the [Fe―Fe]H sub-cluster in the Desulfovibrio desulfuricans (DdH) and Clostridium pasteurianum (CpI) [Fe―Fe] hydrogenases was investigated by a combination of first principles and empirical molecular dynamics simulations. Pathways that can be inferred from the X-ray crystal structures of DdH and CpI, i.e., (Glu159 → Ser198 → Glu156 → water460 → Cys178 → DTMA([Fe―Fe]H) and (Glu282 → Ser319 → Glu279 → water612 → Cys299), respectively, were considered. Proton transfer from Cys178 to DTMA in the [Fe―Fe]H sub-cluster in DdH was readily observed in our results, specifically when [Fe―Fe]H was in the reduced state ([FeI―FeI]) or in the mixed valence state for the protonated distal iron Fed ([FeI―FeII―H−]H). A concerted mechanism is proposed, where proton transfer in DdH from Glu159 to Glu156 via Ser198 and Glu156 to Cys178 via water460 readily occurred, as well as from Glu282 to Glu279 via Ser319 and Glu279 to Cys299 via water612 in CpI. The theoretical prediction of the proton transfer characteristics is consistent with the assumed biocatalytic mechanism of the [Fe―Fe] hydrogenases in which the proton binds at Fed, providing confirmation that has not been explored so far. The computational results were qualitatively validated by the agreement with experimental hydrogen production activity data for mutated CpI enzymes, relative to the wild-type protein. Finally, the insight provided by the simulations, combined, in part, with experimental validation, are important for establishing an approach in future exploration of proton transfer to the active site in this class of enzymes, and possibly also for biomimetic analogs.► Theoretical investigation of proton transfer to Fed offered mechanistic understanding. ► A concerted mechanism of proton transfer in DdH and CpI was theoretically elucidated. ► Computational results consistent with experimental hydrogen production of mutated CpI.
Keywords: Fe―Fe; Hydrogenases; QM/MM MD simulation; Proton transfer; Hydrogen production activity;
Energy transfer in an LH4-like light harvesting complex from the aerobic purple photosynthetic bacterium Roseobacter denitrificans by Dariusz M. Niedzwiedzki; Marcel Fuciman; Harry A. Frank; Robert E. Blankenship (518-528).
A peripheral light-harvesting complex from the aerobic purple bacterium Roseobacter (R.) denitrificans was purified and its photophysical properties characterized. The complex contains two types of pigments, bacteriochlorophyll (BChl) a and the carotenoid (Car) spheroidenone and possesses unique spectroscopic properties. It appears to lack the B850 bacteriochlorophyll a Qy band that is typical for similar light-harvesting complex 2 antennas. Circular dichroism and low temperature steady-state absorption spectroscopy revealed that the B850 band is present but is shifted significantly to shorter wavelengths and overlaps with the B800 band at room temperature. Such a spectral signature classifies this protein as a member of the light-harvesting complex 4 class of peripheral light-harvesting complexes, along with the previously known light-harvesting complex 4 from Rhodopseudomonas palustris. The influence of the spectral change on the light-harvesting ability was studied using steady-state absorption, fluorescence, circular dichroism, femtosecond and microsecond time-resolved absorption and time-resolved fluorescence spectroscopies. The results were compared to the properties of the similar (in pigment composition) light-harvesting complex 2 from aerobically grown Rhodobacter sphaeroides and are understood within the context of shared similarities and differences and the putative influence of the pigments on the protein structure and its properties.Display Omitted► Spectroscopic studies of unusual LH complex from R. denitrificans were performed. ► We performed transient absorption spectroscopy at room temperature and at 10 K. ► Results classify this complex to a LH4 class. ► We compared LH complexes from R. denitrificans and aerobically grown Rb. sphaeroides.
Keywords: LH4; LH2; Carotenoids; Bacteriochlorophyll; Transient absorption; Light harvesting;
Corrigendum to “Analysis of high temperature stress on the dynamics of antenna size and reducing side heterogeneity of Photosystem II in Wheat leaves (Triticum aestivum)” [Biochim. Biophys. Acta 1807 (2011) 22–29] by Sonal Mathur; Suleyman I. Allakhverdiev; Anjana Jajoo (529).
Corrigendum to “A novel functional element in the N-terminal region of Arum concinnatum alternative oxidase is indispensable for catalytic activity of the enzyme in HeLa cells” [Biochim. Biophys. Acta 1797 (2010) 20–28] by Yusuke Kakizaki; Roger S. Seymour; Kikukatsu Ito (530-531).