On the value of knowing a z* ion for what it is

Computer simulation of database searches of electron transfer dissociation (ETD) spectra using both "bottom up" and "top down" approaches was performed to evaluate the utility of knowing a priori which product ions contain the C-terminus (i.e., the z* ions). In this work, knowledge of the identities of the z* ions was used to exclude putative identifications that are based solely on the mass matching of undifferentiated product ions derived from an experiment with those derived from in silico fragmentation. The benefit from knowing which ions are z* ions was found to be heavily dependent on the quality of the ETD spectra, in terms of sequence coverage afforded by the product ions, the amount of noise in the spectra (i.e., extraneous peaks that do not directly reflect primary structure), and mass measurement accuracy. Under conditions in which the likelihood for misidentifications are high without a priori knowledge of ion types (e.g., b-, y-, c-, or z-ions), a knowledge of which product ions are z* ions allows discrimination against false-positive identifications. Relatively little benefit from knowing which ions are z* ions was noted when product spectra reflected relatively high sequence coverage and when a low fraction of the products ions were due to extraneous peaks (i.e., spectra with relatively little noise). In all cases, specificity is higher with higher mass measurement accuracy with the consequent reduction in benefit from knowledge of which ions are z* ions.     

The influence of potassium- and sodium-free solutions on sodium efflux from squid giant axons

The sensitivity of sodium efflux to the removal of potassium ions from the external solution and the change in sodium efflux occurring when sodium ions are also removed were observed to be related. When Tris was used to replace external sodium ions, increases in sodium efflux were always observed whether the sensitivity of sodium efflux to external potassium ions was weak or strong. Greater percentage increases in sodium efflux occurred, however, the greater the sensitivity of sodium efflux to external potassium ions. When lithium ions were used to replace external sodium ions, increases in sodium efflux occurred if the sensitivity of efflux to external potassium ions was strong whereas decreases in sodium efflux took place if the sensitivity of efflux to external potassium ions was weak. Intermediate sensitivities of efflux to external potassium resulted in no change in efflux upon substitution of lithium ions for external sodium ions. In the presence of 10^-5 M ouabain, substitution of Tris for external sodium ions always resulted in a small decrease in sodium efflux. The data can be described in terms of a model which assumes the presence of efflux stimulation sites that are about 98% selective to potassium ions and about 2% selective to sodium or lithium ions.     

The effect of the pH and phosphate ions on the precipitate formation reaction of sodium ions with pyroantimonate

Summary The effect of phosphate ions and the pH of the solution on the precipitation of Na-pyroantimonate was studied by a quantitative method. The presence of phosphate ions has an inhibitory effect on the formation of Na-pyroantimonate precipitate. The inhibiting effect decreases with the increasing concentration of hydroxyl ions. In the absence of phosphate ions at pH 9.5 Na⁺-ions precipitate completely. The inhibiting effect is explained by a complex formation reaction of the phosphate ions with the antimony (V) ions.     

Fast Diffusion of Multivalent Ions Facilitated by Concerted Interactions in Dual‐Ion Battery Systems

Sluggish solid‐phase diffusion has been an essential issue in developing intercalation electrode materials using multivalent ions. Compared to monovalent Li ions, the diffusion of multivalent ions is still not well understood. Here, combining first‐principles calculations with electrochemical experiments, it is shown that the diffusion of divalent Mg ions is significantly facilitated in Li–Mg dual‐ion systems, and the activation energy is remarkably reduced by the concerted interactions of the preceding Li ions and following Mg ions. Thus, making dual‐ion systems is a promising way to construct high‐energy‐density, rechargeable batteries with multivalent ions. This work will provide a new perspective on solid‐phase diffusion that is typically a rate‐controlling process in battery systems and fuel cell devices.     

Neoplastic cell transformation by heavy ions

We have studied the induction of morphological transformation by heavy ions. Golden hamster embryo cells were irradiated with 95 MeV 14N ions (530 keV/microns), 22 MeV 4He ions (36 keV/microns), and 22 MeV 4He ions with a 100-microns Al absorber (77 keV/microns) which were generated by a cyclotron at the Institute of Physical and Chemical Research in Japan. Colonies were considered to contain neoplastically transformed cells when the cells were densely stacked and made a crisscross pattern. It was shown that the induction of transformation was much more effective with 14N and 4He ions than with gamma or X rays. The relative biological effectiveness (RBE) relative to 60Co gamma rays was 3.3 for 14N ions, 2.4 for 4He ions, and 3.3 for 4He ions with a 100-microns Al absorber. The relationship between RBE and linear energy transfer was qualitatively similar for both cell death and transformation.     

Interactions between rare-earth ions and DNA of Bashibai sheep

The interaction between rare-earth ions and DNA from Bashibai sheep was studied by microcalorimetry and electrochemistry. The DNA chain was found to have four to five binding sites for rare-earth ions. The binding affinity was about 10??-10?? M. It was also found that smaller ions caused more heat to be released in the process of binding and bound more readily to the nucleic acid chain. This is attributed to the enhanced ability of polarization of smaller ions and reduced steric hindrance compared to larger ions. The electrochemistry results show that rare-earth ions could be inserted into the DNA helix, producing a new complex with electrochemically active groups. The rare-earth ions and DNA complex reached equilibrium after a 90-min incubation at room temperature.     

Optimal conditions for bio-oxidation of ferrous ions to ferric ions using Thiobacillus ferrooxidans

A chemo-biochemical process using Thiobacillus ferrooxidans for desulphurization of gaseous fuels and emissions containing hydrogen sulphide (H2S) has been developed. In the first stage, H2S present in fuel gas and emissions is selectively oxidized to elemental sulphur using ferric sulphate. The ferrous sulphate produced in the first stage of the process is oxidized to ferric sulphate using Thiobacillus ferrooxidans for recycle and reuse in the process. The effects of process variables, temperature, pH, total dissolved solids (TDS), elemental sulphur, ferric and magnesium ions on bio-oxidation of ferrous ions to ferric ions were investigated using flask culture experiments. The bio-oxidation of ferrous ions to ferric ions could be achieved efficiently in the temperature range of 20(+/-1)-44(+/-1) degrees C. A pH range of 1.8(+/-0.02)-2.2(+/-0.02) was optimum for the growth of culture and effective bio-oxidation of ferrous ions to ferric ions. The effect of TDS on bio-oxidation of ferrous ions indicated that a preacclimatized culture in a growth medium containing high dissolved solid was required to achieve effective bio-oxidation of ferrous ions. Elemental sulphur ranging from 1000 to 100,000 mg/l did not have any effect on efficiency of ferrous ion oxidation. The efficiency of bio-oxidation of ferrous ions to ferric ions was not affected in the presence of ferric ions up to a concentration of 500 mg/l while 3 mg/l of magnesium ion was optimal for achieving effective bio-oxidation.     

Patchwork peptide sequencing: extraction of sequence information from accurate mass data of peptide tandem mass spectra recorded at high resolution

The accurate mass values of all immonium, y(1), y(2), a(2), and b(2) ions of tryptic peptides composed of the 20 standard amino acids were calculated. The differences between adjacent masses in this data set are greater than 10 mDa for more than 80% of the values. Using this mass list, the majority of low mass ions in quadrupole-time of flight tandem mass spectra of peptides from tryptic digests and from an elastase digest could be assigned. Besides the a(2)/b(2) ions, which carry residues 1-2 from the N-terminus, a variety of internal dipeptide b ions were regularly observed. In case internal proline was present, corresponding dipeptide b ions carrying proline at the N-terminal position occurred. By assigning the dipeptide b ions on the basis of their accurate mass, bidirectional or unidirectional sequence information was obtained, which is localized to the peptide N-terminus (a(2)/b(2) ions) or not localized (internal b ions). Identification of the y(1) and y(2) ions by their accurate mass provides unidirectional sequence information localized to the peptide C-terminus. It is shown that this patchwork-type sequence information extractable from accurate mass data of low-mass ions is highly efficient for protein identification.     

Engineering of microorganisms towards recovery of rare metal ions

The bioadsorption of metal ions using microorganisms is an attractive technology for the recovery of rare metal ions as well as removal of toxic heavy metal ions from aqueous solution. In initial attempts, microorganisms with the ability to accumulate metal ions were isolated from nature and intracellular accumulation was enhanced by the overproduction of metal-binding proteins in the cytoplasm. As an alternative, the cell surface design of microorganisms by cell surface engineering is an emerging strategy for bioadsorption and recovery of metal ions. Cell surface engineering was firstly applied to the construction of a bioadsorbent to adsorb heavy metal ions for bioremediation. Cell surface adsorption of metal ions is rapid and reversible. Therefore, adsorbed metal ions can be easily recovered without cell breakage, and the bioadsorbent can be reused or regenerated. These advantages are suitable for the recovery of rare metal ions. Actually, the cell surface display of a molybdate-binding protein on yeast led to the enhanced adsorption of molybdate, one of the rare metal ions. An additional advantage is that the cell surface display system allows high-throughput screening of protein/peptide libraries owing to the direct evaluation of the displayed protein/peptide without purification and concentration. Therefore, the creation of novel metal-binding protein/peptide and engineering of microorganisms towards the recovery of rare metal ions could be simultaneously achieved.     

Models of active transport of ions in biomembranes of various types of cells

Nonequilibrium statistical models of the active transport of ions in biomembranes have been constructed. Differences of chemical potentials of the ATP-ADP reaction and the electrochemical potential of ions were taken as the thermodynamic forces responsible for the flow of ions through the membrane. The active transport of ions was viewed as a cross phenomenon arising from the chemical reaction of the ATP hydrolysis. These models provide independent calculations of the resting potential at the biomembrane and concentrations of ions in a cell on the assumption the free energy of the ATP-ADP reaction is fully (without the dissipation loss) converted to the free energy of transported ions. They take into account the presence of nonpenetrating ions in a cell. It was shown that different concentrations of nonpenetrating ions have a considerable effect on the resting potential. The proposed models were compared with experimental data obtained for different types of cells including neurons, muscular cells, bacteria, plants, and mitochondria. Calculated values of the membrane potential and ion concentrations were in good qualitative agreement with experimental data.     

Effect of cGMP and cations on the permeability of cattle retinal disks

Guanosine 3',5'-monophosphate and Na or Ca ions affect the transmembrane movements of the same pool of intradiskal ions. Extradiskal Na ions activate the efflux of intradiskal Na ions. Extradiskal Ca ions activate the efflux of intradiskal Rb ions. Na and Ca ions activate Na/Ca or Ca/Ca exchange, as previously described. cGMP activates a membrane permeability for all the cations tested, as previously described. The reciprocal relations between cGMP and the other pathways for ion movements through disk membranes are systematically examined. Some analogies between the cGMP-activated permeability of the disk membranes and the light-sensitive conductance of the rod plasma outer membrane are discussed.     

Hydrogen ion block of the sodium pore in squid giant axons

The block of squid axon sodium channels by H ions was studied using voltage-clamp and internal perfusion techniques. An increase in the concentration of internal permeant ions decreased the block produced by external H ions. The voltage dependence of the block was found to be nonmonotonic: it was reduced by both large positive and large negative potentials. The ability of internal ions to modify the block by external H+ is explained by a competition among these ions for a binding site within the pore. The nonmonotonic voltage dependence is consistent with this picture if the hydrogen ions are allowed to be permeant.     

Properties of microsolvated ions: from the microenvironment of chromophore and alkali metal ions in proteins to negative ions in water clusters

Here we discuss the fascinating chemistry and physics of microsolvated ions that bridge the transition from bare ions in gas phase to ions in solution. Such ions occur in many situations in biochemistry and are crucial for several functions; metal ions, for example, must remove their water shell to pass through ion pumps in membranes. Furthermore, only a few water molecules are buried in the hydrophobic pockets of proteins where they are bound to charged amino acid residues or ionic chromophores. Another aspect is the reactivity of microsolvated ions and the importance in atmospheric, organic and inorganic chemistry. We close by a discussion of the stability of molecular dianions, and how hydration affects the electronic binding energy. There is a vast literature on microsolvated ions, and in this review we are far from being comprehensive, rather we mainly bring examples of our own work.     

抗Cu2+嗜酸氧化亚铁硫杆菌的驯化及诱变育种

从我国三大铜矿的酸性矿坑水中富集分离出9个具有较强活性的嗜酸氧化亚铁硫杆菌菌株,经过Cu~(2 )的系列浓度梯度的培养,选出其中天然抗铜能力最强的菌株26~#,在Cu~(2 )浓度为0．20mol/L的9K培养基中能在72h内完全氧化培养基中的Fe~(2 ),在含0．22mol/L Cu2~(2 )的9K培养基中能在192h内完全氧化培养基中的Fe~(2 )。以CuSO_4·5H_2O为单变量驯化介质驯化该26~#抗铜菌株,26~#驯化菌株的Fe~(2 )氧化能力明显增强:在含0．25mol/LCu~(2 )的9K培养基中能在84h内完全氧化其中的Fe~(2 )。为了提高驯化菌的稳定性,将驯化后的26~#菌株用紫外线进行诱变。研究结果表明:驯化诱变对菌种的改良有重要的作用,诱变后菌株的生长性能稳定,氧化活性进一步提高,26~#驯化诱变菌在0．25mol/LCu~(2 )存在的条件下完全氧化9K培养基中Fe~(2 )的时间约为60h,对Fe~(2 )氧化能力明显强于驯化菌及野生菌。     

Modulation of gill Na+,K+-ATPase activity by ammonium ions: Putative coupling of nitrogen excretion and ion uptake in the freshwater shrimp Macrobrachium olfersii

The effect of NH4+ ions on (Na+,K+)-ATPase hydrolytic activity was examined in a gill microsomal fraction from M. olfersii. In the absence of NH4+ ions, K+ ions stimulated ATP hydrolysis, exhibiting cooperative kinetics (nH=0.8), to a maximal specific activity of V=556.1+/-22.2 nmol.min(-1).mg(-1) with K(0.5)=2.4+/-0.1 mmol.L(-1). No further stimulation by K+ ions was observed in the presence of 50 mmol.L(-1) NH4+ ions. ATP hydrolysis was also stimulated by NH4+ ions obeying Michaelian kinetics to a maximal specific activity of V=744.8+/-22.3 nmol.min(-1).mg(-1) and KM=8.4+/-0.2 mmol.L(-1). In the presence of 10 mmol.L(-1) K+ ions, ATP hydrolysis was synergistically stimulated by NH4+ ions to V=689.8+/-13.8 nmol.min(-1).mg(-1) and K(0.5)=6.6+/-0.1 mmol.L(-1), suggesting that NH4+ ions bind to different sites than K+ ions. PNPP hydrolysis was also stimulated cooperatively by K+ or NH4+ ions to maximal values of V= 235.5+/-11.8 nmol.min(-1).mg(-1) and V=234.8+/-7.0 nmol.min(-1).mg(-1), respectively. In contrast to ATP hydrolysis, K(+)-phosphatase activity was not synergistically stimulated by NH4+ and K+ ions. These data suggest that at high NH4+ ion concentrations, the (Na+, K+)-ATPase exposes a new site; the subsequent binding of NH4+ ions stimulates ATP hydrolysis to rates higher than those for K+ ions alone. This is the first demonstration that (Na+, K+)-ATPase activity in a freshwater shrimp gill is modulated by ammonium ions, independently of K+ ions, an effect that may constitute a fine-tuning mechanism of physiological relevance to osmoregulatory and excretory processes in palaemonid shrimps.     

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.     

K(+) versus Na(+) ions in a K channel selectivity filter: a simulation study

Molecular dynamics simulations of a bacterial potassium channel (KcsA) embedded in a phospholipid bilayer reveal significant differences in interactions of the selectivity filter with K(+) compared with Na(+) ions. K(+) ions and water molecules within the filter undergo concerted single-file motion in which they translocate between adjacent sites within the filter on a nanosecond timescale. In contrast, Na(+) ions remain bound to sites within the filter and do not exhibit translocation on a nanosecond timescale. Furthermore, entry of a K(+) ion into the filter from the extracellular mouth is observed, whereas this does not occur for a Na(+) ion. Whereas K(+) ions prefer to sit within a cage of eight oxygen atoms of the filter, Na(+) ions prefer to interact with a ring of four oxygen atoms plus two water molecules. These differences in interactions in the selectivity filter may contribute to the selectivity of KcsA for K(+) ions (in addition to the differences in dehydration energy between K(+) and Na(+)) and the block of KcsA by internal Na(+) ions. In our simulations the selectivity filter exhibits significant flexibility in response to changes in ion/protein interactions, with a somewhat greater distortion induced by Na(+) than by K(+) ions.     

Influence of copper(II) and magnesium(II) ions on the ciprofloxacin binding to DNA

The influence of magnesium(II) and copper(II) ions on the binding of ciprofloxacin to double stranded calf thymus DNA was studied by fluorescence emission spectroscopy, ultraviolet- and circular dichroism (CD) spectroscopy. The interaction of ciprofloxacin and copper(II) ions was followed by strong fluorescence quenching which was almost unaffected by the presence of DNA. On the other hand, only a slight decrease in fluorescence emission intensity, which was enhanced in the presence of DNA, was observed for ciprofloxacin interaction with magnesium(II) ions. Furthermore, magnesium(II) ions increase the thermal stability of the DNA, while, in the presence of ciprofloxacin, the degree of stabilisation is smaller. In contrast, copper(II) ions destabilise double helical DNA to heat, while ciprofloxacin slightly affects only the second transition of the biphasic melting curve of calf thymus DNA. Magnesium(II) ions at 25 degrees C induce conformational transitions of DNA at concentrations of 1.5 mM and 2.5 M, as monitored by CD. On the other hand copper(II) ions induce only one conformational transition, at a concentration of 12.7 microM. At higher concentrations of copper(II) ions (c>700 microM) DNA starts to precipitate. Significant changes in the CD spectra of DNA were observed after addition of ciprofloxacin to a solution containing DNA and copper(II) ions, but not to DNA and magnesium(II) ions. Based on our spectroscopic results, we propose that copper(II) ions are not directly involved into ciprofloxacin binding to DNA via phosphate groups as it has been suggested for magnesium(II) ions.     

Structural characterization of underivatized arabino-xylo-oligosaccharides by negative-ion electrospray mass spectrometry

Various arabino-xylo-oligosaccharides with known substitution patterns were assessed by negative ESI-Q-TOFMS and ESI-ITMS. The CID spectra of linear xylo-oligosaccharides and of nine isomeric mono- and disubstituted arabino-xylo-oligosaccharides established that structures differing in their substitution pattern can be differentiated by this approach. The negative-ion fragmentation spectra of the deprotonated quasi-molecular ions are mainly characterized by glycosidic cleavage ions from the C-series, which provide sequence informations, and by cross-ring cleavage (0,2)A(i) ions, which provide partial linkage information. When the collision energy increased, the cross-ring cleavage (0,2)A(i) ions underwent consecutive loss of water to produce (0,2)A(i)-18 fragment ions and glycosidic cleavage ions of the B-series are also produced besides the C(i) ions. Contrary to linear xylo-oligosaccharides, C(i) ions, which originate from C-3 monosubstituted xylosyl residues never produce the related cross-ring cleavage (0,2)A(i) ions. Disubstitution at O-2 and O-3 of xylosyl residues appears to enhance the production of the (0,2)A(i) ions compared to monosubstitution. For the differentiation of the mono- and disubstitution patterns of the penultimate xylosyl residue, the relative abundance of the glycosidic cleavage ions at m/z 263 and 299 found on Q-TOF CID spectra plays a relevant role and appears to be more informative than MS(n) spectra obtained on a ion trap instrument.     

Substoichiometric levels of Cu2+ ions accelerate the kinetics of fiber formation and promote cell toxicity of amyloid-{beta} from Alzheimer disease

A role for Cu(2+) ions in Alzheimer disease is often disputed, as it is believed that Cu(2+) ions only promote nontoxic amorphous aggregates of amyloid-β (Aβ). In contrast with currently held opinion, we show that the presence of substoichiometric levels of Cu(2+) ions in fact doubles the rate of production of amyloid fibers, accelerating both the nucleation and elongation of fiber formation. We suggest that binding of Cu(2+) ions at a physiological pH causes Aβ to approach its isoelectric point, thus inducing self-association and fiber formation. We further show that Cu(2+) ions bound to Aβ are consistently more toxic to neuronal cells than Aβ in the absence of Cu(2+) ions, whereas Cu(2+) ions in the absence of Aβ are not cytotoxic. The degree of Cu-Aβ cytotoxicity correlates with the levels of Cu(2+) ions that accelerate fiber formation. We note the effect appears to be specific for Cu(2+) ions as Zn(2+) ions inhibit the formation of fibers. An active role for Cu(2+) ions in accelerating fiber formation and promoting cell death suggests impaired copper homeostasis may be a risk factor in Alzheimer disease.