Browsing by Subject "ELECTRON-TRANSFER"

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  • Postila, Pekka A.; Kaszuba, Karol; Kuleta, Patryk; Vattulainen, Ilpo; Sarewicz, Marcin; Osyczka, Artur; Rog, Tomasz (2016)
    The cytochrome (cyt) bc(1) complex is an integral component of the respiratory electron transfer chain sustaining the energy needs of organisms ranging from humans to bacteria. Due to its ubiquitous role in the energy metabolism, both the oxidation and reduction of the enzyme's substrate co-enzyme Q has been studied vigorously. Here, this vast amount of data is reassessed after probing the substrate reduction steps at the Q(i)-site of the cyt bc(1) complex of Rhodobacter capsulatus using atomistic molecular dynamics simulations. The simulations suggest that the Lys251 side chain could rotate into the Q(i)-site to facilitate binding of half-protonated semiquinone - a reaction intermediate that is potentially formed during substrate reduction. At this bent pose, the Lys251 forms a salt bridge with the Asp252, thus making direct proton transfer possible. In the neutral state, the lysine side chain stays close to the conserved binding location of cardiolipin (CL). This back-and-forth motion between the CL and Asp252 indicates that Lys251 functions as a proton shuttle controlled by pH-dependent negative feedback. The CL/K/D switching, which represents a refinement to the previously described CL/K pathway, fine-tunes the proton transfer process. Lastly, the simulation data was used to formulate a mechanism for reducing the substrate at the Q(i)-site.
  • Kuleta, Patryk; Lasham, Jonathan; Sarewicz, Marcin; Ekiert, Iwona; Sharma, Vivek; Ekiert, Robert; Osyczka, Artur (2021)
    Hemes are common elements of biological redox cofactor chains involved in rapid electron transfer. While the redox properties of hemes and the stability of the spin state are recognized as key determinants of their function, understanding the molecular basis of control of these properties is challenging. Here, benefiting from the effects of one mitochondrial disease-related point mutation in cytochrome b, we identify a dual role of hydrogen bonding (H-bond) to the propionate group of heme bH of cytochrome bc1, a common component of energy-conserving systems. We found that replacing conserved glycine with serine in the vicinity of heme bH caused stabilization of this bond, which not only increased the redox potential of the heme but also induced structural and energetic changes in interactions between Fe ion and axial histidine ligands. The latter led to a reversible spin conversion of the oxidized Fe from 1/2 to 5/2, an effect that potentially reduces the electron transfer rate between the heme and its redox partners. We thus propose that H-bond to the propionate group and heme-protein packing contribute to the fine-tuning of the redox potential of heme and maintaining its proper spin state. A subtle balance is needed between these two contributions: While increasing the H-bond stability raises the heme potential, the extent of increase must be limited to maintain the low spin and diamagnetic form of heme. This principle might apply to other native heme proteins and can be exploited in engineering of artificial hemecontaining protein maquettes.
  • Wirtanen, T.; Muuronen, M.; Hurmalainen, J.; Tuononen, H. M.; Nieger, M.; Helaja, J. (2016)
    With an excess of a strong acid, 2,3-dichloro-5,6-dicyano-1,4-quinone (DDQ) is shown to promote metal-free intermolecular oxidative dehydrogenative (ODH) 3,3'-coupling of 2-aryl-benzo[b]furans and 2-aryl-benzo[b]thiophenes up to 92% yield as demonstrated with 9 substrates. Based on the analysis of oxidation potentials and molecular orbitals combined with EPR, NMR and UV-Vis observations, the studied reaction is initiated by a DDQ-substrate charge transfer complex and presumably proceeds via oxidation of the substrate into an electrophilic radical cation that further reacts with another molecule of a neutral substrate. The coupling reactivity can easily be predicted from the oxidation potential of the substrate and the morphology of its frontier molecular orbitals. The intermolecular ODH coupling reaction allowed a concise total synthesis of the natural product shandougenine B.
  • Warnau, Judith; Sharma, Vivek; Gamiz-Hernandez, Ana P.; Di Luca, Andrea; Haapanen, Outi; Vattulainen, Ilpo; Wikström, Mårten; Hummer, Gerhard; Kaila, Ville R. I. (2018)
    Complex I couples the free energy released from quinone (Q) reduction to pump protons across the biological membrane in the respiratory chains of mitochondria and many bacteria. The Q reduction site is separated by a large distance from the proton-pumping membrane domain. To address the molecular mechanism of this long-range proton-electron coupling, we perform here full atomistic molecular dynamics simulations, free energy calculations, and continuum electrostatics calculations on complex I from Thermus thermophilus. We show that the dynamics of Q is redox-state-dependent, and that quinol, QH(2), moves out of its reduction site and into a site in the Q tunnel that is occupied by a Q analog in a crystal structure of Yarrowia lipolytica. We also identify a second Q-binding site near the opening of the Q tunnel in the membrane domain, where the Q headgroup forms strong interactions with a cluster of aromatic and charged residues, while the Q tail resides in the lipid membrane. We estimate the effective diffusion coefficient of Q in the tunnel, and in turn the characteristic time for Q to reach the active site and for QH2 to escape to the membrane. Our simulations show that Q moves along the Q tunnel in a redox-state-dependent manner, with distinct binding sites formed by conserved residue clusters. The motion of Q to these binding sites is proposed to be coupled to the proton-pumping machinery in complex I.
  • Grabsztunowicz, Magda; Rantala, Marjaana; Ivanauskaite, Aiste; Blomster, Tiina; Koskela, Minna M.; Vuorinen, Katariina; Tyystjarvi, Esa; Burow, Meike; Overmyer, Kirk; Mähönen, Ari P.; Mulo, Paula (2021)
    In Arabidopsis, two leaf-type ferredoxin-NADP(+) oxidoreductase (LFNR) isoforms function in photosynthetic electron flow in reduction of NADP(+), while two root-type FNR (RFNR) isoforms catalyse reduction of ferredoxin in non-photosynthetic plastids. As the key to understanding, the function of RFNRs might lie in their spatial and temporal distribution in different plant tissues and cell types, we examined expression of RFNR1 and RFNR2 genes using beta-glucuronidase (GUS) reporter lines and investigated accumulation of distinct RFNR isoforms using a GFP approach and Western blotting upon various stresses. We show that while RFNR1 promoter is active in leaf veins, root tips and in the stele of roots, RFNR2 promoter activity is present in leaf tips and root stele, epidermis and cortex. RFNR1 protein accumulates as a soluble protein within the plastids of root stele cells, while RFNR2 is mainly present in the outer root layers. Ozone treatment of plants enhanced accumulation of RFNR1, whereas low temperature treatment specifically affected RFNR2 accumulation in roots. We further discuss the physiological roles of RFNR1 and RFNR2 based on characterization of rfnr1 and rfnr2 knock-out plants and show that although the function of these proteins is partly redundant, the RFNR proteins are essential for plant development and survival.
  • Gholami, Peyman; Khataee, Alireza; Vahid, Behrouz; Karimi, Afzal; Golizadeh, Mortaza; Ritala, Mikko (2020)
    This research aimed to prepare a recoverable sonophotocatalyst, in which microfibrillated carboxymethyl cellulose (MFC) acted as the Zn-Cu-Mg-mixed metal hydroxide/graphitic carbon nitride (MMH/g-C3N4) carrier. The characteristics of bare and composite sonophotocatalysts were analyzed by the XRD, FT-IR, BET, DRS, PL and FE-SEM equipped with the EDX mapping. The performance of prepared composites (MMH/g-C3N4@MFC) with various weight ratios of the MMH/g-C3N4 was studied for the sonophotocatalytic degradation of sulfadiazine (SDZ) as the model emerging contaminant. 93% of SDZ was degraded using the most effective catalyst (MMH/gC(3)N(4)@MFC3) with 15% weight ratio of the MMH/g-C3N4 under the desired operating conditions including solution pH of 6.5, SDZ concentration of 0.15 mM and ultrasonic power of 300 W. The MMH addition to the gC(3)N(4) structure increased the separation of charge carriers generated via the visible light or ultrasound irradiations. Moreover, the MMH/g-C3N4 was dispersed uniformly on the MFC and consequently, more active sites were available to form reactive oxygen species (ROS), compared to powder form. Hydroxyl radicals ((OH)-O-center dot) were determined as the main ROS in the SDZ degradation by performing a series of scavenging experiments. Less than 10% decrease in the degradation efficiency of SDZ was observed during five subsequent experiments, which indicated the proper retention of the MMH/g-C3N4 particles in the MFC. The adequate mineralization of SDZ (83% decrease in chemical oxygen demand (COD)) was obtained after 200 min of treatment. Eventually, ten degradation intermediates were identified by the GC-MS analysis and a plausible degradation mechanism for the contaminant was proposed.
  • Gholami, Peyman; Khataee, Alireza; Vahid, Behrouz; Karimi, Afzal; Golizadeh, Mortaza; Ritala, Mikko (2020)
    This research aimed to prepare a recoverable sonophotocatalyst, in which microfibrillated carboxymethyl cellulose (MFC) acted as the Zn-Cu-Mg-mixed metal hydroxide/graphitic carbon nitride (MMH/g-C3N4) carrier. The characteristics of bare and composite sonophotocatalysts were analyzed by the XRD, FT-IR, BET, DRS, PL and FE-SEM equipped with the EDX mapping. The performance of prepared composites (MMH/g-C3N4@MFC) with various weight ratios of the MMH/g-C3N4 was studied for the sonophotocatalytic degradation of sulfadiazine (SDZ) as the model emerging contaminant. 93% of SDZ was degraded using the most effective catalyst (MMH/gC(3)N(4)@MFC3) with 15% weight ratio of the MMH/g-C3N4 under the desired operating conditions including solution pH of 6.5, SDZ concentration of 0.15 mM and ultrasonic power of 300 W. The MMH addition to the gC(3)N(4) structure increased the separation of charge carriers generated via the visible light or ultrasound irradiations. Moreover, the MMH/g-C3N4 was dispersed uniformly on the MFC and consequently, more active sites were available to form reactive oxygen species (ROS), compared to powder form. Hydroxyl radicals ((OH)-O-center dot) were determined as the main ROS in the SDZ degradation by performing a series of scavenging experiments. Less than 10% decrease in the degradation efficiency of SDZ was observed during five subsequent experiments, which indicated the proper retention of the MMH/g-C3N4 particles in the MFC. The adequate mineralization of SDZ (83% decrease in chemical oxygen demand (COD)) was obtained after 200 min of treatment. Eventually, ten degradation intermediates were identified by the GC-MS analysis and a plausible degradation mechanism for the contaminant was proposed.
  • Gholami, Peyman; Khataee, Alireza; Vahid, Behrouz; Karimi, Afzal; Golizadeh, Mortaza; Ritala, Mikko (2020)
    This research aimed to prepare a recoverable sonophotocatalyst, in which microfibrillated carboxymethyl cellulose (MFC) acted as the Zn-Cu-Mg-mixed metal hydroxide/graphitic carbon nitride (MMH/g-C3N4) carrier. The characteristics of bare and composite sonophotocatalysts were analyzed by the XRD, FT-IR, BET, DRS, PL and FE-SEM equipped with the EDX mapping. The performance of prepared composites (MMH/g-C3N4@MFC) with various weight ratios of the MMH/g-C3N4 was studied for the sonophotocatalytic degradation of sulfadiazine (SDZ) as the model emerging contaminant. 93% of SDZ was degraded using the most effective catalyst (MMH/gC(3)N(4)@MFC3) with 15% weight ratio of the MMH/g-C3N4 under the desired operating conditions including solution pH of 6.5, SDZ concentration of 0.15 mM and ultrasonic power of 300 W. The MMH addition to the gC(3)N(4) structure increased the separation of charge carriers generated via the visible light or ultrasound irradiations. Moreover, the MMH/g-C3N4 was dispersed uniformly on the MFC and consequently, more active sites were available to form reactive oxygen species (ROS), compared to powder form. Hydroxyl radicals ((OH)-O-center dot) were determined as the main ROS in the SDZ degradation by performing a series of scavenging experiments. Less than 10% decrease in the degradation efficiency of SDZ was observed during five subsequent experiments, which indicated the proper retention of the MMH/g-C3N4 particles in the MFC. The adequate mineralization of SDZ (83% decrease in chemical oxygen demand (COD)) was obtained after 200 min of treatment. Eventually, ten degradation intermediates were identified by the GC-MS analysis and a plausible degradation mechanism for the contaminant was proposed.
  • Rytioja, Johanna; Hilden, Kristiina; Di Falco, Marcos; Zhou, Miaomiao; Aguilar-Pontes, Maria Victoria; Sietiö, Outi-Maaria; Tsang, Adrian; de Vries, Ronald; Mäkelä, Miia R. (2017)
    The ability to obtain carbon and energy is a major requirement to exist in any environment. For several ascomycete fungi, (post-)genomic analyses have shown that species that occupy a large variety of habitats possess a diverse enzymatic machinery, while species with a specific habitat have a more focused enzyme repertoire that is well-adapted to the prevailing substrate. White-rot basidiomycete fungi also live in a specific habitat, as they are found exclusively in wood. In this study, we evaluated how well the enzymatic machinery of the white-rot fungus Dichomitus squalens is tailored to degrade its natural wood substrate. The transcriptome and exoproteome of D. squalens were analyzed after cultivation on two natural substrates, aspen and spruce wood, and two non-woody substrates, wheat bran and cotton seed hulls. D. squalens produced ligninolytic enzymes mainly at the early time point of the wood cultures, indicating the need to degrade lignin to get access to wood polysaccharides. Surprisingly, the response of the fungus to the non-woody polysaccharides was nearly as good a match to the substrate composition as observed for the wood polysaccharides. This indicates that D. squalens has preserved its ability to efficiently degrade plant biomass types not present in its natural habitat.