Non-equilibrium thermodynamic assessment of redox-driven H+ pumps in mitochondria

Isolated mitochondria suspended in an aerobic medium with 3-hydroxybutyrate or succinate serving as electron donor attain a stationary state with vanishing net flow of H+ ions (state 4). Adding valinomycin to such a suspension in the presence of various concentrations of K+ ions and a weak acid system such as acetate or phosphate creates new stationary states for the mitochondria which are characterized by a constant influx of K+ ions, while the net flow of H+ ions again vanishes due to the recycling of these ions by the weak acid system. Sufficiently low concentrations of K+ ions (less than 4 mM) cause these stationary states to last long enough for a separation of the mitochondria by centrifugation. The difference in electrochemical potential for H+ ions can then be determined by means of the partitioning of radioactively labelled markers. Suitable procedures to correct for binding of the markers are described. It is found that, for a constant affinity of the electron in the suspending medium, electron flow and the flow of K+ ions, which indicates the flow of pumped H+ ions, are linearly dependent on the electrochemical potential difference of H+ ions. The phenomenological coefficients obtained from these correlations are discussed with respect to the contributions of additive constants in the linear relations. It is found that, under the present experimental condition, such constants most likely vanish thus yielding symmetric flow-force relations. It is concluded that the redox-driven H+ pumps are not tightly coupled due to molecular slipping in the pumps and that the molecular stoichiometry is 2 H+ ions/electron for coupling site I and 4 H+ ions/electron for coupling sites II and III together.     

Fabrication of Gold Nanostructures and Studies of Their Morphological and Surface Plasmonic Properties

We report fabrication of gold nanostructures on glass and indium tin oxide (ITO)-coated glass substrates using high fluence and highly energetic gold ions generated by hot, dense, and strongly non-equilibrium plasma. Nanodots and nanorods are observed in scanning electron microscopy (SEM) of nanostructures grown on glass substrate with single and double shots of gold ions which is in conformity with the transmission electron microscopy image. SEM images for single and double shots of gold ions on ITO-coated glass substrate show only nanodots. The mean diameter of nanodots obtained on both glass and ITO-coated glass is found to increase with increase in the number of gold ions shot from one to two. The gold nanostructures exhibit red shift in surface plasmon resonance with increased interaction which is in agreement with other reported work.     

Effect of high magnesium ion concentration on the electron transport rate and proton exchange in thylakoid membranes in higher plants]

The effects of magnesium ion concentration on the rate of electron transport in isolated pea thylakoids were investigated in the pH range from 4.0 up to 8.0. In the absence of magnesium ions in the medium and in the presence of 5 mM MgCl2 in the experiments not only without added artificial acceptors but also with ferricyanide or methylviologen as an acceptor, this rate had a well-expressed maximum at pH 5.0. It was shown that, after depression to minimal values at pH 5.5-6.5, it gradually rose with increasing pH. An increase in magnesium ion concentration up to 20 mM essentially affected the electron transfer rate: it decreased somewhat at pH 4.0-5.0 but increased at higher pH values. At this magnesium ion concentration, the maximum rate was at pH 6.0-6.5 and the minimum, at pH 7.0. Subsequent rise upon increasing pH to 8.0 was expressed more sharply. The influence of high magnesium ion concentration on the rate of electron transport was not observed in the presence of gramicidin D. It was found that without uncoupler, the changes in the electron transfer rate under the influence of magnesium ions correlated to the changes in the first-order rate constant of the proton efflux from thylakoids. It is supposed that the change in the ability of thylakoids to keep protons by the action of magnesium ions is the result of electrostatic interactions of these ions with the charges on the external surface of membranes. A possible role of regulation of the electron transport rate by magnesium ions in vivo is discussed.     

On the minimal set of plasma parameters to determine the dispersion law of electron whistler waves

The minimal sufficient set of plasma parameters is presented to describe the dispersion properties of electron whistler waves (helicons) in a wide frequency range above the ion cutoff frequency, provided that the wave frequency is significantly lower than the electron plasma frequency. When the gyrofrequency of the lightest ions is much higher than those of heavier ions, it is sufficient to know the relative content of the lightest ions, the highest ion cutoff frequency, the lower hybrid resonance frequency, and the electron gyro- and plasma frequencies. In this case, the frequency of electron whistler waves is determined by the upper root of the biquadratic equation derived, whereas the lower root corresponds to a resonant mode with its refractive index increasing when the frequency tends toward the highest ion gyrofrequency from below. The developed approach is also efficient in plasmas containing a substantial amount of negative ions and/or heavy dust particulates. The accuracy of the approximate solution of the total cold plasma dispersion relation is illustrated graphically.     

Ascaris lumbricoides suum: morphological characterization of apparent cuticular pores by ionic permeability and electron microscopy

The cuticle of the parasitic roundworm Ascaris lumbricoides suum has been found to contain apparent pores, using scanning and transmission electron microscopy. However, X-ray spectral analysis and dot mapping analysis of diffusing divalent cations in the cuticle found these ions to be randomly distributed on the pseudocoelomic surface of the cuticle. This indicates that the pores seen with the electron microscope were not true structural pores and that the cuticle is homogeneously permeable to ions.     

Chelation ability of spironaphthoxazine with metal ions in silica gel

Spironaphthoxazine (SNO) and three metal ions, Mg(2+), Zn(2+), and Al(3+), were dispersed in silica gels by the sol-gel method. The chelation ability of SNO with the metal ions in silica gels was investigated by measuring the fluorescence spectra and was compared to that of 8-hydroxyquinoline (8-HQ) in ethanol and silica gels. A merocyanine-type isomer photoderived from SNO as well as 8-HQ easily formed complexes of the metal ions in the order of Al(3+), Zn(2+), and Mg(2+) because the coordination ability of the metal ions to such ligands depended on their electron affinity. The changes in the fluorescence spectra of the silica gel samples during light irradiation were also investigated. The relative band intensity due to the intermediate species between the original SNO and the merocyanine species decreased and that of the complex increased with the UV irradiation time. The reverse process was observed during visible irradiation. The UV irradiation effects on the chelation of SNO and its photochromic property also depended on the electron affinity of the metal ions.     

Mass spectrometry of the phosphatidylcholines: fragmentation processes for dioleoyl and stearoyl-oleoyl glycerylphosphorylcholine

Mass spectra for the various phosphatidylcholines, together with accurate mass measurements on the more abundant fragment ions, have been described in a previous paper (Ref. 5). No detailed fragmentation sequence was proposed on the evidence available. In the case of dioleoyl glycerylphosphorylcholine, some question arose as to whether certain ions were produced by electron impact or by pyrolysis. In this paper, results are reported which enable a more detailed fragmentation sequence to be proposed. By observing metastable transitions in the first field free region of a double-focusing mass spectrometer, it can be shown that the major ions in the spectrum are produced by electron impact processes, and not by pyrolysis; moreover, many of these ions are directly related to one another by metastable processes. In particular, it has been demonstrated that the ions at m/e 603 for dioleoyl glycerylphosphorylcholine and at m/e 604 for stearoyl-oleoyl glycerylphosphorylcholine are derived from the appropriate molecular ions by an electron impact-induced process. From measurements of the metastable ion intensities, as well as from the appearance potentials and ionization efficiency curves, conclusions may be drawn about many of the fragmentation mechanisms, allowing a distinction to be made between rearrangement and cleavage reactions.     

金属离子胁迫产生植物膜脂过氧化的能力与离子的极化能力正相关

金属离子胁迫导致植物产生多种生理损伤,其中包括膜脂的过氧化。不同的金属离子诱导植物产生膜脂过氧化差异很大,迄今对这些差异与金属离子性质之间的具体关系所知甚少。金属离子对阴离子和其他分子的作用主要取决于其电荷数量、半径大小和电子层结构,亦即取决于其极化作用。作者以水培拟南芥与油菜为材料,以不同极化作用的金属离子（Li^＋、Na^＋、K^＋、ca^2＋、Fe^2＋与Fe^3＋）为研究对象,检测了极化作用不同的金属离子胁迫拟南芥与油菜1、3、5 d后膜脂过氧化产物丙二醛（Malondialdehyde,MDA）的含量变化。结果发现,相同浓度的一价离子Li^＋、Na^＋与K^＋’胁迫5 d后,离子半径较小的Li^＋诱导拟南芥与油菜产生的丙二醛比Na^＋与K^＋高2倍以上;相同浓度下电子层结构相同的Fe^3＋与Fe^2＋胁迫5 d后,电荷高的Fe^3＋诱导拟南芥产生的丙二醛比Fe^2＋高2倍以上,而Fe^3＋诱导油菜产生的丙二醛比Fe^2＋高5倍以上;相同浓度的二离子Fe^2＋与ca^2＋胁迫,电子层结构复杂的Fe^2＋比ca^2＋诱导更多的丙二醛产生。运用离子势综合表征离子极化能力,则丙二醛的含量与离子势大小显著正相关。上述结果说明,金属离子诱导膜脂过氧化的胁迫能力与金属极化作用正相关,即电荷越高、离子半径越小及电子层越复杂,产生氧化胁迫程度越强。     

The relation between the unit thread of chromosomes and isolated nucleohistone

Changes in the physical properties and molecular structure of isolated nucleohistone, induced by binding magnesium or other ions, have been studied. Nucleohistone has a net negative charge. Added magnesium binds tightly to the DNA phosphate groups that are not already complexed with histone. This results in neutralization of the net negative charge, a reduction in intermolecular repulsion, aggregation and compaction of the nucleohistone gel. The “unit thread” of nucleohistone observed in the electron microscope changes diameter from 110 Å to 230 Å on addition of magnesium before drying. However, X-ray diffraction studies fail to detect any changes in regular tertiary structure on adding divalent ions. The methods for dehydration commonly used in specimen preparation for electron microscopy appear to cause a complete loss of regular tertiary structure.We conclude that the DNA in hydrated nucleohistone is supercoiled, that the degree of regular supercoiling is independent of the presence of ions and that both the 110 Å and 230 Å threads observed in the electron microscope probably contain the distorted remnant of a single supercoil.     

Effects of magnesium and chloride ions on light-induced electron transport in membrane fragments from a blue-green alga

The effects of magnesium and chloride ions on photosynthetic electron transport were investigated in membrane fragments of a blue-green alga, Nostoc muscorum (Strain 7119), noted for their stability and high rates of electron transport from water or reduced dichlorophenolindophenol to NADP⁺. Magnesium ions were required not only for light-induced electron transport from water to NADP⁺ but also for protection in the dark of the integrity of the water-photooxidizing system (Photosystem II). Membrane fragments suspended in the dark in a medium lacking Mg²⁺ lost the capacity to photoreduce NADP⁺ with water on subsequent illumination. Chloride ions could substitute, but less effectively, for each of these two effects of magnesium ions. By contrast, the photoreduction of NADP⁺ by DCIPH₂ was independent of Mg²⁺ (or Cl^?) for the protection of the electron transport system in the dark or during the light reaction proper. Furthermore, high concentrations of MgCl₂ produced a strong inhibition of NADP⁺ photoreduction with DCIPH₂ without significantly affecting the rate of NADP⁺ photoreduction with water. The implications of these findings for the differential involvement of Photosystem I and Photosystem II in the photoreduction of NADP⁺ with different electron donors are discussed.     

Investigation of Ion-Acoustic Solitons in Magnetosphere and Tokamak Warm Plasma with Two-Temperature Electrons

The properties of oblique propagation of small amplitude ion-acoustic soliton are investigated in a plasma containing weakly relativistic ions and two-temperature electrons (cold and hot electrons). The reductive perturbation method is used to derive the Korteweg?de Vries equation for the present plasma model. It is found that the parameters determining the nature of soliton are different for compressive or rarefactive structures. Moreover, the effects of weakly relativistic ions, the temperature ratio, and the density ratio of hot-to-cold electron species on soliton characters are studied. The theory is applied on the case of relativistic ions observed in the magnetosphere and in the case of nonrelativistic ions observed in tokamaks.     

Effect of air ions on submicron t1 bacteriophage aerosols

The effect of a high concentration of ionized air molecules on sampling T1 phage aerosols of submicron particle size was evaluated by comparing the phage recoveries of all-glass impingers (AGI-4) and type 6 filter papers. Sampler recoveries of all ionized aerosols were less than the recoveries of nonionized control aerosols. These reductions in recovery were greater with positive ions than with negative ions or ions of mixed polarity. The AGI-4 allowed considerable slippage, which was not affected by the air ions. Type 6 filter paper recoveries were less than AGI-4 recoveries. The air ions did not appear to affect the aerosol particle size as determined by an electron microscope.     

Plasma decay in the afterglow of a high-voltage nanosecond discharge in air

The decay of air plasma produced by a high-voltage nanosecond discharge at room temperature and gas pressures in the range of 1–10 Torr was studied experimentally and theoretically. The time dependence of the electron density was measured with a microwave interferometer. The initial electron density was about 10¹² cm⁻³. The discharge homogeneity was monitored using optical methods. The dynamics of the charged particle densities in the discharge afterglow was simulated by numerically solving the balance equations for electron and ions and the equation for the electron temperature. It was shown that, under these experimental conditions, plasma electrons are mainly lost due to dissociative and three-body recombination with ions. Agreement between the measured and calculated electron densities was achieved only when the rate constant of the three-body electron-ion recombination was increased by one order of magnitude and the temperature dependence of this rate constant was modified. This indicates that the mechanism for three-body recombination of molecular ions differs from that of the well-studied mechanism of atomic ion recombination.     

Formation of an anisotropic electron velocity distribution function and production of multicharged ions in the micropinch discharge plasma

Analysis of the results of polarimetric measurements of X-ray line radiation of multicharged ions in a Z-pinch discharge indicates that the formation of an anisotropic electron velocity distribution in the neck of the current channel and the generation of highly charged ions are separated in time. The generation of a fast electron beam in the longitudinal ohmic electric field in the stage of plasma compression in the neck results in the polarization of X-ray bremsstrahlung continuum. In the stage of expansion of the hot dense micropinch plasma, the radial electric field prevails, due to which X-ray line radiation of multicharged ions becomes linearly polarized.     

Electron transfer dissociation of iTRAQ labeled peptide ions

Triply and doubly charged iTRAQ ( isobaric tagging for relative and absolute quantitation) labeled peptide cations from a tryptic peptide mixture of bovine carbonic anhydrase II were subjected to electron transfer ion/ion reactions to investigate the effect of charge bearing modifications associated with iTRAQ on the fragmentation pattern. It was noted that electron transfer dissociation (ETD) of triply charged or activated ETD (ETD and supplemental collisional activation of intact electron transfer species) of doubly charged iTRAQ tagged peptide ions yielded extensive sequence information, in analogy with ETD of unmodified peptide ions. That is, addition of the fixed charge iTRAQ tag showed relatively little deleterious effect on the ETD performance of the modified peptides. ETD of the triply charged iTRAQ labeled peptide ions followed by collision-induced dissociation (CID) of the product ion at m/ z 162 yielded the reporter ion at m/ z 116, which is the reporter ion used for quantitation via CID of the same precursor ions. The reporter ion formed via the two-step activation process is expected to provide quantitative information similar to that directly produced from CID. A 103 Da neutral loss species observed in the ETD spectra of all the triply and doubly charged iTRAQ labeled peptide ions is unique to the 116 Da iTRAQ reagent, which implies that this process also has potential for quantitation of peptides/proteins. Therefore, ETD with or without supplemental collisional activation, depending on the precursor ion charge state, has the potential to directly identify and quantify the peptides/proteins simultaneously using existing iTRAQ reagents.     

Assessment of the anti-biofouling potentials of a copper iodide-doped nylon mesh

We propose a copper iodide (CuI)-doped nylon mesh prepared using polyiodide ions as a precursor toward anti-biofouling polymer textile. The CuI-doped nylon mesh was subjected to the prevention of biofouling in marine environments. The attachment of the marine organisms was markedly inhibited on the CuI-doped nylon mesh surface until 249 days. Scanning electron microscopy-energy dispersive X-ray analysis indicated that copper compounds were maintained in the nylon mesh after the field experiment, although copper content in the nylon mesh was reduced. Therefore, the copper ions slowly dissolved from nylon mesh will contribute to the long-term prevention of biofouling. Furthermore, electron spin resonance analysis revealed the generation of reactive oxygen species (ROS) from CuI-doped nylon mesh after the field experiment. One of the possibilities for toxic action of copper ions will be the direct effect of Cu+ -induced ROS on biofilm forming on nylon mesh surface. The proposed polymer textile can be applied to fishing and aquafarming nets, mooring rope for ship, or silt fence to restrict polluted water in marine environments.     

Location of high-affinity metal binding sites in the profile structure of the Ca+2-ATPase in the sarcoplasmic reticulum by resonance x-ray diffraction.

Resonance x-ray diffraction measurements on the lamellar diffraction from oriented multilayers of isolated sarcoplasmic reticulum (SR) membranes containing a small concentration of lanthanide (III) ions (lanthanide/protein molar ratio approximately 4) have allowed us to calculate both the electron density profile of the SR membrane and the separate electron density profile of the resonant lanthanide atoms bound to the membrane to a relatively low spatial resolution of approximately 40 A. Analysis of the membrane electron density profile and modeling of the separate low resolution lanthanide atom profile, using step-function electron density models based on the assumption that metal binding sites in the membrane profile are discrete and localized, resulted in the identification of a minimum of three such binding sites in the membrane profile. Two of these sites are low-affinity, low-occupancy sites identified with the two phospholipid polar headgroup regions of the lipid bilayer within the membrane profile. Up to 20% of the total lanthanide (III) ions bind to these low-affinity sites. The third site has relatively high affinity for lanthanide ion binding; its Ka is roughly an order of magnitude larger than that for the lower affinity polar headgroup sites. Approximately 80% of the total lanthanide ions present in the sample are bound to this high-affinity site, which is located in the "stalk" portion of the "headpiece" within the profile structure of the Ca+2 ATPase protein, approximately 12 A outside of the phospholipid polar headgroups on the extravesicular side of the membrane profile. Based on the nature of our results and on previous reports in the literature concerning the ability of lanthanide (III) ions to function as Ca+2 analogues for the Ca+2 ATPase we suggest that we have located a high-affinity metal binding site in the membrane profile which is involved in the active transport of Ca+2 ions across the SR membrane by the Ca+2 ATPase.     

ETMB-RBF: Discrimination of Metal-Binding Sites in Electron Transporters Based on RBF Networks with PSSM Profiles and Significant Amino Acid Pairs

Background

Cellular respiration is the process by which cells obtain energy from glucose and is a very important biological process in living cell. As cells do cellular respiration, they need a pathway to store and transport electrons, the electron transport chain. The function of the electron transport chain is to produce a trans-membrane proton electrochemical gradient as a result of oxidation–reduction reactions. In these oxidation–reduction reactions in electron transport chains, metal ions play very important role as electron donor and acceptor. For example, Fe ions are in complex I and complex II, and Cu ions are in complex IV. Therefore, to identify metal-binding sites in electron transporters is an important issue in helping biologists better understand the workings of the electron transport chain.

Methods

We propose a method based on Position Specific Scoring Matrix (PSSM) profiles and significant amino acid pairs to identify metal-binding residues in electron transport proteins.

Results

We have selected a non-redundant set of 55 metal-binding electron transport proteins as our dataset. The proposed method can predict metal-binding sites in electron transport proteins with an average 10-fold cross-validation accuracy of 93.2% and 93.1% for metal-binding cysteine and histidine, respectively. Compared with the general metal-binding predictor from A. Passerini et al., the proposed method can improve over 9% of sensitivity, and 14% specificity on the independent dataset in identifying metal-binding cysteines. The proposed method can also improve almost 76% sensitivity with same specificity in metal-binding histidine, and MCC is also improved from 0.28 to 0.88.

Conclusions

We have developed a novel approach based on PSSM profiles and significant amino acid pairs for identifying metal-binding sites from electron transport proteins. The proposed approach achieved a significant improvement with independent test set of metal-binding electron transport proteins.     

The three-dimensional morphology of aggregates of native cotton cellulose microfibrils

The three-dimensional morphology of native bacterial cellulose is confirmed by scanning electron microscopy. In addition, it is shown by scanning electron microscopy, and transmission electron microscopy with positive staining by phosphotungstic acid ions that aggregates of microfibrils of native cotton cellulose have a similar structure. The results are consistent with previous reports on microfibrils of algal cellulose. These observations exclude a simple spinneret process as a mechanism of formation of the microfibrils of these sources of cellulose.