Conformational characteristics of polypeptides containing isolated L-proline residues with cis peptide bonds

The conformational characteristics of the peptide sequence X-l-Pro, where X  Gly or l-Ala and the peptide bond joining X and l-Pro is cis, are evaluated. Semi-empirical potential functions are used to estimate the contributions to the conformational energy made by the non-bonded van der Waals' and electrostatic interactions and the intrinsic torsional potentials about the NC^a and C^aC′ bonds. Rotations φ₁ and ψ₁ about the NC^a and C^aC′ bonds in residue X and rotation ψ₂ about the C^aC′ bond in l-Pro are permitted, while the angle of rotation φ₂ about the NC^a bond in l-Pro is fixed at 120 ° by the pyrrolidine ring. The presence of the cis peptide bond connecting X and l-Pro renders the backbone rotations φ₁, ψ₁ in X dependent upon the rotation ψ₂ about the C^aC′ bond in l-Pro. (Interdependence of rotations in neighboring residues joined by a cis peptide bond was previously observed in l-alanine oligomers.) The number of energetically allowed conformations for the Gly and l-Ala residues preceding a cis peptide bond l-Pro residue are found to be substantially reduced from those permitted when the peptide bond is trans or when l-Pro is replaced by an amino acid residue. On the other hand, ψ₂ = 100 to 160 ° (cis′) and 300 to 0 ° (trans′) are found to be the lowest energy conformations of the l-Pro residue irrespective of the cis or trans conformation of the X-l-Pro peptide bond.     

Jasmonate: A decision maker between cell death and acclimation in the response of plants to singlet oxygen

Under stress conditions that bring about excessive absorption of light energy in the chloroplasts, the formation of singlet oxygen (¹O₂) can be strongly enhanced, triggering programmed cell death. However, the ¹O₂ signaling pathway can also lead to acclimation to photooxidative stress, when ¹O₂ is produced in relatively low amounts. This acclimatory response is associated with a strong downregulation of the jasmonate biosynthesis pathway and the maintenance of low jasmonate levels, even under high light stress conditions that normally induce jasmonate synthesis. These findings suggest a central role for this phytohormone in the orientation of the ¹O₂ signaling pathway toward cell death or acclimation. This conclusion is confirmed here in an Arabidopsis double mutant obtained by crossing the ¹O₂-overproducing mutant ch1 and the jasmonate-deficient mutant dde2. This double mutant was found to be constitutively resistant to ¹O₂ stress and to display a strongly stimulated growth rate compared with the single ch1 mutant. However, the involvement of other phytohormones, such as ethylene, cannot be excluded.     

Energy status,growth and nitrogenase activity in continuous cultures of Rhizobium sp. strain CB756 supplied with NH+4 and various rates of aeration

Continuous cultures of the cowpea-type Rhizobium sp., strain CB756, were grown in the presence of NH⁺₄ at automatically controlled concentrations of dissolved O₂ and rates of aeration. Nitrogenase activity of steady-state cultures was only detected under microaeration conditions (dissolved O₂ typically <0.03 μM; aeration rate typically 0.6 μmol O₂/ml per h), when the cellular ATP pool size was 0.8–1.8 nmol/mg dry wt., (optimum 1.1) and the energy charge 0.6–0.7. At twice this aeration rate and dissolved O₂ concentration of about 0.15 μM, the yield of bacteria doubled, the ATP pool increased and energy charge increased to 0.8. With similar rates of O₂ supply but high concentration of dissolved O₂ (approx. 150 μM), cultures were NH⁺₄-limited and the ATP pool and energy charge were slightly reduced. Amongst all of these O₂ supply conditions the total pool of adenosine phosphates was not significantly different (2.6 S.D. 0.7 nmol/mg dry wt.). In steady-state, O₂-limited cultures, concentrations of cyclic GMP were higher when nitrogenase was present. When rates of O₂ supply to steady-state cultures were changed, oscillations in bacterial energy status and growth rate were induced decreasing in amplitude until a new steady state was reached. This made it difficult to discern precisely the energy status in which nitrogenase activity was derepressed or repressed. However, generally, increases in nitrogenase activity followed decreases in ATP and energy charge and decreased nitrogenase activity accompanied increases in these energy parameters. These results are discussed in relation to the possible involvement of adenylation or deadenylation of glutamine synthetase and to the control of nitrogenase synthesis in the presence of NH⁺₄. It is concluded that the small ATP pool size is responsible for failure of adenylylation of glutamine synthetase and is related to nitrogenase synthesis at microaeration rates.     

Effects of carbohydrate-structure changes on induced shifts in differential isotope-shift 13C-N.M.R.

Deuterium-induced, ¹³C-isotope shifts are shown to vary considerably from the initially predicted values calculated for ordinary pyranose and furanose sugars, when minor structural changes are introduced into the carbohydrate ring. Both substitution of C-OH groups or reduction of C-OH to CH₂ permitted the evaluation of γ effects of OD without the contribution of β-OD-induced shifting. The observed γ-shift values for these modified structures were twice as large as those previously noted. This difference is most probably due to favored salvation. Substitution of OH at C-6 led to the predicted loss of differential isotope-shift (d.i.s.) at C-6 because of its isolation from all β and γ OD groups. The ³¹P resonances of d-glucose 6-phosphate show downfield deuterium shifts. Based on d.i.s. values, new ¹³C-shift assignments are proposed for isomaltose and 2-amino-2-deoxy-α-d-glucose. A study of acidic carbohydrates has demonstrated that isotope shifts are somewhat larger for sp²-hybridized carbon atoms whose OH groups are acidic. Relaxation times for sp² carbon atoms isolated from dipolar interaction with protons were very long in D₂O relative to their relaxation time in the H₂O environment.     

Production of singlet oxygen in a non-self-sustained discharge

The production of O₂(a¹Δ_g) singlet oxygen in non-self-sustained discharges in pure oxygen and mixtures of oxygen with noble gases (Ar or He) was studied experimentally. It is shown that the energy efficiency of O₂(a¹Δ_g production can be optimized with respect to the reduced electric field E/N. It is shown that the optimal E/N values correspond to electron temperatures of 1.2–1.4 eV. At these E/N values, a decrease in the oxygen percentage in the mixture leads to an increase in the excitation rate of singlet oxygen because of the increase in the specific energy deposition per O₂ molecule. The onset of discharge instabilities not only greatly reduces the energy efficiency of singlet oxygen production but also makes it impossible to achieve high energy deposition in a non-self-sustained discharge. A model of a non-self-sustained discharge in pure oxygen is developed. It is shown that good agreement between the experimental and computed results for a discharge in oxygen over a wide range of reduced electric fields can be achieved only by taking into account the ion component of the discharge current. The cross section for the electron-impact excitation of O₂(a¹Δ_g and the kinetic scheme of the discharge processes with the participation of singlet oxygen are verified by comparing the experimental and computed data on the energy efficiency of the production of O₂(a¹Δ_g and the dynamics of its concentration. It is shown that, in the dynamics of O₂(a¹Δ_g molecules in the discharge afterglow, an important role is played by their deexcitation in a three-body reaction with the participation of O(³P) atoms. At high energy depositions in a non-self-sustained discharge, this reaction can reduce the maximal attainable concentration of singlet oxygen. The effect of a hydrogen additive to an Ar: O₂ mixture is analyzed based on the results obtained using the model developed. It is shown that, for actual electron beam current densities, a significant energy deposition in a non-self-sustained discharge in the mixtures under study can be achieved due to the high rate of electron detachment from negative ions. In this case, however, significant heating of the mixture can lead to a rapid quenching of O₂(a¹Δ_g molecules by atomic hydrogen.     

ATP synthases from archaea: The beauty of a molecular motor

Archaea live under different environmental conditions, such as high salinity, extreme pHs and cold or hot temperatures. How energy is conserved under such harsh environmental conditions is a major question in cellular bioenergetics of archaea. The key enzymes in energy conservation are the archaeal A₁A_O ATP synthases, a class of ATP synthases distinct from the F₁F_O ATP synthase ATP synthase found in bacteria, mitochondria and chloroplasts and the V₁V_O ATPases of eukaryotes. A₁A_O ATP synthases have distinct structural features such as a collar-like structure, an extended central stalk, and two peripheral stalks possibly stabilizing the A₁A_O ATP synthase during rotation in ATP synthesis/hydrolysis at high temperatures as well as to provide the storage of transient elastic energy during ion-pumping and ATP synthesis/-hydrolysis. High resolution structures of individual subunits and subcomplexes have been obtained in recent years that shed new light on the function and mechanism of this unique class of ATP synthases. An outstanding feature of archaeal A₁A_O ATP synthases is their diversity in size of rotor subunits and the coupling ion used for ATP synthesis with H⁺, Na⁺ or even H⁺ and Na⁺ using enzymes. The evolution of the H⁺ binding site to a Na⁺ binding site and its implications for the energy metabolism and physiology of the cell are discussed.     

Superoxide radicals and phagocytosis

Escherichia coli B, grown in iron-rich media, were more resistant toward the aerobic bactericidal action of the formed elements of blood than were comparable iron-deficient cells. The iron replete cells contained 2.5 times more ferrisuperoxide dismutase, 12 times more peroxidase, and 1.5 times more catalase than did the iron-deficient cells. The iron-deficient cells were more susceptible to exogenous O₂^? and to H₂O₂ than were iron-replete cells. Cyanide permitted a differentiation between ferrisuperoxide dismutase and catalase or peroxidase since it inhibited the latter peroxide-consuming enzymes but had no effect on the superoxide-utilizing enzyme. In the presence of 2 mm cyanide, the iron-replete E. coli were much more resistant toward phagocytic kill than were the iron-deficient cells even though this level of cyanide completely inhibited catalase and peroxidase. It can be concluded that a large part of the enhanced resistance toward phagocytic kill, exhibited by iron-replete E. coli B, was due to their increased content of the periplasmic ferrisuperoxide dismutase. It follows that O₂^? is probably an important agent in the killing of phagocytized E. coli B.     

Reduction of patient dose in medical radiography by utilizing scattered X-rays: Relation between permissible limit of scatter fraction,viewer brightness,and perceptibility of vision

This paper proposes a new technique for reducing the patient dose when employing medical radiographs prepared by using screen-film systems. In this technique the patient dose can be reduced by employing scattered X-rays in order to obtain the same film density as that realized without the use of scattered X-rays. The minimum perceptible thickness difference ΔX_min, which can be recognized by liminal vision, was psychophysically calculated by considering the energy spectrum of incident X-ray, sensitivity spectrum of the screen layer, and the perception capability of human vision. From the calculated ΔX_mins in various conditions, the permissible upper limit of scatter fraction for obtaining the same ΔX_min for three kinds of luminances, and the fraction of reduction in the primary X-rays were determined.As an example of the results, when the object size required for perception is 1.3 mm, a scatter fraction up to 42% can be permitted at a density D of 1.0 for a luminance of 2548 cd m^?2. When we increase the luminance of the viewer from 478 cd m^?2 to 2548 cd m^?2, the upper limit of the permitted scatter fraction varies from 30% to 42% at a D of 1.0, i.e., the patient dose can be reduced by 17% under the same perceptibility of ΔX_min by utilizing scattered X-rays. This reduction can be successfully achieved by changing the lead content of the grid from 0.45 to 0.38 g cm^?2.     

Comparative studies of mucopolysaccharides from marine animals. I. Raja eglanteria Bosc.

A mucopolysaccharide (MPS) was extracted from the pectoral fins of the skate, Raja eglanteria Bosc. The purified MPS had an anticoagulant activity of 28 IU/mg and an optical rotation value, [α]_D²⁵, of ?9°. The MPS was analyzed for uronic acid, hexosamine, N-sulfate, O-sulfate, O-sulfate, and neutral sugar. This analysis suggests that this MPS is an over-sulfated chondroitin sulfate, the electrophoretic pattern and infra-red spectrum of which are similar to chondroitin sulfate.     

Photooxidation of ferrocyanide and iodide ions and associated phosphorylation in NH2OH-treated chloroplasts

NH₂OH-treated, non-water oxidizing chloroplasts are shown to be capable of oxidizing ferrocyanide and I^? via Photosystem II at appreciable rates (? 200 μequiv/h per mg chlorophyll). Using methylviologen as electron acceptor, ferrocyanide oxidation can be measured as O₂ uptake, as ferricyanide formation, or as H⁺ consumption (2 Fe²⁺ + 2H⁺ + O₂ → 2 Fe³⁺ + H₂O₂). I^? oxidation can be measured as methylviologen-mediated O₂ uptake, or spectrophotometrically, using ferricyanide as electron acceptor. The oxidation product I₂ is re-reduced, as it is formed, by unknown reducing substances in the reaction system.The rate-saturating concentrations of these donors are very high: 30 mM with ferricyanide and 15 mM with I^?. Relatively lipophilic Photosystem II donors such as catechol, benzidine and p-aminophenol saturate the photooxidation rate at much lower concentrations (< 0.5 mM). It thus seems that the oxidation of hydrophilic reductants such as ferricyanide and I^? is limited by permeability barriers. Very likely the site of Photosystem II oxidation is embedded in the thylakoid membrane or is situated on the inner surface of the membrane.The efficiency of phosphorylation (P/e₂) is 0.5 to 0.6 with ferrocyanide and about 0.5 with I^?. In contrast the P/e₂ ratio is 1.0 to 1.2 when water, catechol, p-aminophenol or benzidine serves as electron donor. These differences imply that only one of two phosphorylation sites operate when ferrocyanide and I^? are oxidized. Ferrocyanide and I^? are also chemically distinct from other Photosystem II donors in that their oxidation does not involve proton release. It is suggested that the mechanism of energy conservation associated with Photosystem II may be only operative when the removal of electrons from the donor results in release of protons (i.e. with water, hydroquinones, phenylamines, etc.).     

Flux through mitochondrial redox circuits linked to nicotinamide nucleotide transhydrogenase generates counterbalance changes in energy expenditure

Compensatory changes in energy expenditure occur in response to positive and negative energy balance, but the underlying mechanism remains unclear. Under low energy demand, the mitochondrial electron transport system is particularly sensitive to added energy supply (i.e. reductive stress), which exponentially increases the rate of H₂O₂ (JH₂O₂) production. H₂O₂ is reduced to H₂O by electrons supplied by NADPH. NADP⁺ is reduced back to NADPH by activation of mitochondrial membrane potential–dependent nicotinamide nucleotide transhydrogenase (NNT). The coupling of reductive stress-induced JH₂O₂ production to NNT-linked redox buffering circuits provides a potential means of integrating energy balance with energy expenditure. To test this hypothesis, energy supply was manipulated by varying flux rate through β-oxidation in muscle mitochondria minus/plus pharmacological or genetic inhibition of redox buffering circuits. Here we show during both non-ADP– and low-ADP–stimulated respiration that accelerating flux through β-oxidation generates a corresponding increase in mitochondrial JH₂O₂ production, that the majority (∼70–80%) of H₂O₂ produced is reduced to H₂O by electrons drawn from redox buffering circuits supplied by NADPH, and that the rate of electron flux through redox buffering circuits is directly linked to changes in oxygen consumption mediated by NNT. These findings provide evidence that redox reactions within β-oxidation and the electron transport system serve as a barometer of substrate flux relative to demand, continuously adjusting JH₂O₂ production and, in turn, the rate at which energy is expended via NNT-mediated proton conductance. This variable flux through redox circuits provides a potential compensatory mechanism for fine-tuning energy expenditure to energy balance in real time.     

Anaerobiosis in Echinochloa crus-galli (Barnyard Grass) Seedlings : Intermediary Metabolism and Ethanol Tolerance

Tolerance to ethanol and the ability to metabolize key intermediary substrates under anaerobiosis were studied in Echinochloa crus-galli (L.) Beauv. var oryzicola seeds to further characterize the mechanisms which enable it to germinate and grow without O₂.

Our results indicate that E. crus-galli var oryzicola possesses an inherently high tolerance to ethanol and is able to metabolize low levels of ethanol in the absence of O₂. Concentrations of ethanol 45-fold greater than endogenous levels did not prove toxic to germinating seeds.

Five-day anaerobically grown seedlings of E. crus-galli var oryzicola metabolized added [¹⁴C]sucrose primarily to CO₂ and ethanol. Of the soluble compounds labeled, the phosphorylated intermediates of glycolysis and the oxidative pentose phosphate pathway predominated more under anaerobiosis than in air. In addition, organic acids and lipids were labeled from [¹⁴C]sucrose, the latter indicating that metabolism of carbohydrate via acetyl-CoA occurred in the absence of O₂. Lipids were also labeled when seeds were supplied with [¹⁴C]ethanol or [¹⁴C]acetate. Labeling experiments using the above compounds plus [¹⁴C]NaHCO₃, showed further labeling of organic acids; succinate and citrate being labeled under nitrogen, while fumarate was formed in air.

The above metabolic characteristics would allow for the maintenance of an active alcoholic fermentation system which, along with high alcohol dehydrogenase activity, would continue to recycle NAD and result in continued energy production without O₂. In addition, Echinochloa's ability to metabolize carbohydrate intermediates and to synthesize lipids indicates that mechanisms exist for providing the carbon intermediates for biosynthesis, particularly membrane synthesis for growth, even in the absence of O₂.

     

Flavonoids from Mimosa xanthocentra (Leguminosae: Mimosoideae) and molecular modeling studies for isovitexin-2″-O-α-l-rhamnopyranoside rotamers

Phytochemical investigation of Mimosa xanthocentra Mart. (Leguminosae: Mimosoideae), an herb comprising the diet of marsh deer and pampas deer in the Brazilian Pantanal, led to the isolation of flavones isovitexin-2″-O-α-l-rhamnopyranoside 1 and vitexin-2″-O-α-l-rhamnopyranoside 2, and a mixture of flavonols avicularin 3a and reynoutrin 3b. At room temperature, compound 1 was observed in the ¹H and ¹³C NMR spectra as a mixture of two rotamers in equilibrium in a DMSO-d₆ solution. Molecular modeling using MM2 calculations led to the first proposal of three-dimensional solution structure of both observed conformers. The energy barrier between both rotamers was evaluated theoretically by molecular modeling and experimentally by variable-temperature NMR studies and calculation of ΔG3 of rotation using Eyring equation. This is the first report on flavonoids from M. xanthocentra.     

Met23Lys mutation in subunit gamma of FOF1-ATP synthase from Rhodobacter capsulatus impairs the activation of ATP hydrolysis by protonmotive force

H⁺-F_OF₁-ATP synthase couples proton flow through its membrane portion, F_O, to the synthesis of ATP in its headpiece, F₁. Upon reversal of the reaction the enzyme functions as a proton pumping ATPase. Even in the simplest bacterial enzyme the ATPase activity is regulated by several mechanisms, involving inhibition by MgADP, conformational transitions of the ε subunit, and activation by protonmotive force. Here we report that the Met23Lys mutation in the γ subunit of the Rhodobacter capsulatus ATP synthase significantly impaired the activation of ATP hydrolysis by protonmotive force. The impairment in the mutant was due to faster enzyme deactivation that was particularly evident at low ATP/ADP ratio. We suggest that the electrostatic interaction of the introduced γLys23 with the DELSEED region of subunit β stabilized the ADP-inhibited state of the enzyme by hindering the rotation of subunit γ rotation which is necessary for the activation.     

The ins and outs of Na bioenergetics in Acetobacterium woodii

The acetogenic bacterium Acetobacterium woodii uses a transmembrane electrochemical sodium ion potential for bioenergetic reactions. A primary sodium ion potential is established during carbonate (acetogenesis) as well as caffeate respiration. The electrogenic Na⁺ pump connected to the Wood-Ljungdahl pathway (acetogenesis) still remains to be identified. The pathway of caffeate reduction with hydrogen as electron donor was investigated and the only membrane-bound activity was found to be a ferredoxin-dependent NAD⁺ reduction. This exergonic electron transfer reaction may be catalyzed by the membrane-bound Rnf complex that was discovered recently and is suggested to couple exergonic electron transfer from ferredoxin to NAD⁺ to the vectorial transport of Na⁺ across the cytoplasmic membrane. Rnf may also be involved in acetogenesis. The electrochemical sodium ion potential thus generated is used to drive endergonic reactions such as flagellar rotation and ATP synthesis. The ATP synthase is a member of the F₁F_O class of enzymes but has an unusual and exceptional feature. Its membrane-embedded rotor is a hybrid made of F_O and V_O-like subunits in a stoichiometry of 9:1. This stoichiometry is apparently not variable with the growth conditions. The structure and function of the Rnf complex and the Na⁺ F₁F_O ATP synthase as key elements of the Na⁺ cycle in A. woodii are discussed.     

Chiral-at-metal tetrahydrosalen complexes of resolved titanium(IV) sec-butoxides: Ligand wrapping and multiple asymmetric catalytic induction

The reaction of the racemic and resolved tetrahydrosalen derivative LH₂ (LH₂ = N,N’-bis(3,5-dichloro-2-hydroxybenzyl)-trans-1,2-diaminocyclohexane) with the resolved titanium(IV) sec-butoxides Ti(O^R-2Bu)₄ or Ti(O^S-2Bu)₄ yielded a series of four compounds, LTi(O²Bu)₂ (1-4), which have been characterized by IR, elemental analysis, ¹H and ¹³C NMR and X-ray crystallography. X-ray crystallography revealed the co-crystallization of two pseudo-C₂-symmetric products from racemic LH₂, whereas a perfect chiral induction of the ligand to the metal occurred when resolved (R,R)-LH₂ was used, resulting in a Δ fac-fac wrapping mode of the tetradentate ligand about the titanium center. Ab initio electronic structure calculations (DFT) are in agreement that the lowest energy isomer is that which is experimentally observed. Catalysis screenings show that Ti(O^S-2Bu)₄, in conjunction with (R,R)-LH₂, forms a matched pair that catalyzes the addition of dimethyl zinc to benzaldehyde with higher enantioselectivity than that observed for resolved (R,R)-LH₂ with Ti(O^R-2Bu)₄ or achiral Ti(OⁱPr)₄. Increasing the temperature of the system results in slightly increased enantiomeric excess.     

Modelling O2 and O2 unidirectional fluxes in plants. IV: Role of conductance and laws of its regulation in C3 plants

Numerous studies focus on the measurement of conductances for CO₂ transfer in plants and especially on their regulatory effects on photosynthesis. Measurement accuracy is strongly dependent on the model used and on the knowledge of the flow of photochemical energy generated by light in chloroplasts. The only accurate and precise method to quantify the linear electron flux (responsible for the production of reductive energy) is the direct measurement of O₂ evolution, by ¹⁸O₂ labelling and mass spectrometry. The sharing of this energy between the carboxylation (P) and the oxygenation of photorespiration (PR) depends on the plant specificity factor (Sp) and on the corresponding atmospheric concentrations of CO₂ and O₂ ( André, 2013). The concept of plant specificity factor simplifies the equations of the model. It gives a new expression of the effect of the conductance (g) between atmosphere and chloroplasts. Its quantitative effect on photosynthesis is easy to understand because it intervenes in the ratio of the plant specificity factor (Sp) to the specificity of Rubisco (Sr). Using this ‘simple’ model with the data of ¹⁸O₂ experiments, the calculation of conductance variations in response to CO₂ and light was carried out.