Phosphoglucoisomerase-catalyzed interconversion of hexose phosphates

Summary The exchange of protons and deuterons by phosphoglucoisomerase during the single passage conversion of D-[2-¹³C,1-²H]fructose 6-phosphate in H₂O or D-[2-¹³C]fructose 6-phosphate in D₂O to D-[2-¹³C]glucose 6-phosphate, as coupled with the further generation of 6-phospho-D-[2-¹³C]gluconate in the presence of excess glucose-6-phosphate dehydrogenase was investigated by ¹³C NMR spectroscopy of the latter metabolite. In H₂O, the intramolecular deuteron transfer from the C₁ of D-fructose 6-phosphate to the C₂ of D-glucose 6-phosphate amounted to 65%, a value only slightly lower than the 72% intramolecular proton transfer in D₂O. Both percentages, especially the latter one, were lower than those previously recorded during the single passage conversion of D-[1-¹³C,2-²H]glucose 6-phosphate in H₂O or D-[1-¹³C]glucose 6-phosphate in D₂O to D-fructose 6-phosphate and then to D-fructose 1,6-bisphosphate. These differences indicate that the sequence of interactions between the hexose esters and the binding sites of phosphoglucoisomerase is not strictly in mirror image during, respectively, the conversion of the aldose phosphate to ketose phosphate and the opposite process.     

Phosphoglucoisomerase-catalyzed interconversion of hexose-phosphates

Summary The rate of conversion of D-glucose 6-phosphate to D-fructose 6-phosphate as catalyzed by yeast phosphoglucoisomerase is about fourfold lower when ³H, rather than ¹H, is present on the C2 of D-glucose 6-phosphate. This difference appears to be due mainly to a change in maximal velocity, rather than affinity. Phosphoglucoisomerase also distinguishes between ¹H and ³H in terms of either their intramolecular transfer from C2 to C1 or their incorporation from water on the C1 of D-fructose 6-phosphate.     

Phosphoglucoisomerase-catalyzed interconversion of hexose phosphates; comparison with phosphomannoisomerase

The isotopic discrimination, diastereotopic specificity and intramolecular hydrogen transfer characterizing the reaction catalyzed by phosphomannoisomerase are examined. During the monodirectional conversion of D-[2-3H]mannose 6-phosphate to D-fructose 6-phosphate and D-fructose 1,6-bisphosphate, the reaction velocity is one order of magnitude lower than with D-[U-14C]mannose 6-phosphate and little tritium (less than 6%) is transferred intramolecularly. Inorganic phosphate decreases the reaction velocity but favours the intramolecular transfer of tritium. Likewise, when D-[1-3H]fructose 6-phosphate prepared from D-[1-3H]glucose is exposed solely to phosphomannoisomerase, the generation of tritiated metabolites is virtually restricted to 3H2O and occurs at a much lower rate than the production of D-[U-14C]mannose 6-phosphate from D-[U-14C]fructose 6-phosphate. However, no 3H2O is formed when D-[1-3H]fructose 6-phosphate generated from D-[2-3H]glucose is exposed to phosphomannoisomerase, indicating that the diastereotopic specificity of the latter enzyme represents a mirror image of that of phosphoglucoisomerase. Advantage is taken of such a contrasting enzymic behaviour to assess the back-and-forth flow through the reaction catalyzed by phosphomannoisomerase in intact cells exposed to D-[1-3H]glucose, D-[5-3H]glucose or D-[6-3H]glucose. Relative to the rate of glycolysis, this back-and-forth flow amounted to approx. 4% in human erythrocytes and rat parotid cells, 9% in tumoral cells of the RINm5F line and 47% in rat pancreatic islets.     

Phosphoglucoisomerase-catalyzed interconversion of hexose phosphates: distinction of the 1-monodeutero-isotopomers of D-fructose 6-phosphate by 1H NMR spectroscopy.

The 1H NMR spectrum obtained with the alpha- and beta-anomers of D-[1-2H]fructose 6-phosphate generated from D-glucose 6-phosphate sequentially exposed in D2O to phosphoglucoisomerase, phosphofructokinase and fructose-1,6-diphosphatase differed from that recorded when the deuterated ketohexose phosphate was produced from D-mannose 6-phosphate sequentially exposed in D2O to phosphomannoisomerase, phosphofructokinase and fructose-1,6-diphosphatase. The identification of the 2 isotopomers of D-fructose 6-phosphate by 1H NMR spectroscopy provides a new tool to assess the relative extent of interconversion of hexose phosphates in the reactions catalyzed by phosphoglucoisomerase and phosphomannoisomerase, respectively.     

Phosphoglucoisomerase-catalyzed interconversion of hexose phosphates. A model for D-[2-3H]glucose metabolism in human erythrocytes

When D-[2-3H]glucose 6-phosphate mixed with the unlabeled ester is converted to D-[1-3H]fructose 6-phosphate and 3HOH in the phosphoglucoisomerase reaction and then to D-[1-3H]fructose 1,6-bisphosphate in the phosphofructokinase reaction, the specific radioactivity of the latter metabolite and the production of 3HOH relative to the total generation of tritiated end products are both inversely related to the concentration of phosphofructokinase. In human erythrocytes, the modeling of D-[2-3H]glucose metabolism, based on the activity of phosphoglucoisomerase in cell homogenates and on the steady-state content of D-glucose 6-phosphate and D-fructose 6-phosphate in intact cells, indicates that the back-and-forth interconversion of these esters is about five-times higher than the net glycolytic flux. Yet, the production of 3HOH from D-[2-3H]glucose is about 20% lower than the net glycolytic flux, as judged from the production of 3HOH from D-[5-3H]glucose. Thus, an incomplete detriation of D-[2-3H]glucose is not incompatible with an extensive interconversion of hexose 6-phosphates in the reaction catalyzed by phosphoglucoisomerase.     

Nitrogen partitioning and isotopic discrimination are affected by age and dietary protein content in growing lambs

It is difficult to separate an age-dependent fall in nitrogen use efficiency (NUE; N balance/N intake) in growing ruminants from a progressively decrease in animal protein requirements over time. This study examined the effect of dietary protein content on N partitioning, digestibility and N isotopic discrimination between the animal and its diet (Δ¹⁵N_animal-diet) evaluated at two different fattening periods (early v. late). Twenty-four male Romane lambs (age: 19 ± 4.0 days; BW: 8.3 ± 1.39 kg) were equally allocated to three dietary CP treatments (15%, 17% and 20% CP on a DM basis). Lambs were reared with their mothers until weaning, thereafter housed in individual pens until slaughter (45 kg BW). During the post-weaning period, lambs were allocated twice (early fattening (30 days post-weaning) and late fattening (60 days post-weaning)) to metabolic cages for digestibility and N balance study. When diet CP content increased, the average daily gain of lambs increased (P < 0.05) while the age at slaughter decreased (P = 0.01), but no effect was observed on feed efficiency (P > 0.10). Diet CP content had limited effect on lamb carcass traits. Higher fibre digestibility was observed at the early v. late fattening period (P < 0.001). The N intake and the urinary N excretion increased when diet CP content increased (P < 0.001) and when shifting from early to late fattening period (P < 0.001). Faecal N excretion (P = 0.14) and N balance (P > 0.10) were not affected by diet CP content. Nitrogen digestibility increased (P < 0.001) as the diet CP content increased and on average it was greater at late v. early fattening period (P = 0.02). The NUE decreased (P = 0.001) as the diet CP content increased and as the lamb became older (P < 0.001). However, the age-dependent fall in NUE observed was lower at high v. low dietary CP content (CP × age interaction; P = 0.04). The Δ¹⁵N_animal-diet was positively correlated (P < 0.05) with N intake (r = 0.59), excretion of faecal N (r = 0.41), urinary N (r = 0.69) and total manure N (r = 0.64), while negatively correlated with NUE (r = −0.57). Overall, the experiment showed NUE was lower in older lambs and when lambs were fed high diet CP content, and that Δ¹⁵N_animal-diet was a useful indicator not only for NUE but also for urinary N excretion, which is a major environmental pollution factor on farm.     

Phosphoglucoisomerase-catalyzed interconversion of hexose phosphates: a model for the interconversion of D-[2-3H]glucose 6-phosphate and D-[1-3H]fructose 6-phosphate

Based on experimental data, a model is proposed for the interconversion of either unlabelled hexose phosphates or D-[2-3H]glucose 6-phosphate and D-[1-3H]fructose 6-phosphate in the reaction catalyzed by phosphoglucoisomerase. This model takes into account the known differences in maximal velocity and affinity for each substrate, the intramolecular transfer of tritium between C1 and C2, and the isotopic discrimination between unlabelled and tritiated esters. This model reveals that, in a close system characterized by the progressive detritiation of hexose phosphates, the concentration ratio of D-glucose 6-phosphate to D-fructose 6-phosphate is much higher with the tritiated than unlabelled esters, a paradoxical increase in the specific radioactivity of D-glucose 6-phosphate above its initial value being even observed during the initial period of exposure of D-[2-3H]glucose 6-phosphate to phosphoglucoisomerase. The extension of this model to an open system may be essential for the correct interpretation of radioactive data collected in intact cells exposed to D-[2-3H]glucose.     

Diet quality influences isotopic discrimination among amino acids in an aquatic vertebrate

Stable nitrogen isotopic composition of amino acids (δ¹⁵N_AA) has recently been employed as a powerful tool in ecological food web studies, particularly for estimating the trophic position (TP) of animal species in food webs. However, the validity of these estimates depends on the consistency of the trophic discrimination factor (TDF; = Δδ¹⁵N_AA at each shift of trophic level) among a suite of amino acids within the tissues of consumer species. In this study, we determined the TDF values of amino acids in tadpoles (the Japanese toad, Bufo japonicus) reared exclusively on one of three diets that differed in nutritional quality. The diets were commercial fish‐food pellets (plant and animal biomass), bloodworms (animal biomass), and boiled white rice (plant carbohydrate), representing a balanced, protein‐rich, and protein‐poor diet, respectively. The TDF values of two “source amino acids” (Src‐AAs), methionine and phenylalanine, were close to zero (0.3–0.5‰) among the three diets, typifying the values reported in the literature (~0.5‰ and ~0.4‰, respectively). However, TDF values of “trophic amino acids” (Tr‐AAs) including alanine, valine, leucine, isoleucine, and glutamic acid varied by diet: for example, the glutamic acid TDF was similar to the standard value (~8.0‰) when tadpoles were fed either the commercial pellets (8.0‰) or bloodworms (7.9‰), but when they were fed boiled rice, the TDF was significantly reduced (0.6‰). These results suggest that a profound lack of dietary protein may alter the TDF values of glutamic acid (and other Tr‐AAs and glycine) within consumer species, but not the two Src‐AAs (i.e., methionine and phenylalanine). Knowledge of how a nutritionally poor diet can influence the TDF of Tr‐ and Src‐AAs will allow amino acid isotopic analyses to better estimate TP among free‐roaming animals.     

Isotopic discrimination of zinc in higher plants

* The extent of isotopic discrimination of transition metals in biological processes is poorly understood but potentially has important applications in plant and biogeochemical studies. * Using multicollector inductively coupled plasma (ICP) mass spectrometry, we measured isotopic fractionation of zinc (Zn) during uptake from nutrient solutions by rice (Oryza sativa), lettuce (Lactuca sativa) and tomato (Lycopersicon esculentum) plants. * For all three species, the roots showed a similar extent of heavy Zn enrichment relative to the nutrient solution, probably reflecting preferential adsorption on external root surfaces. By contrast, a plant-species specific enrichment of the light Zn isotope occurred in the shoots, indicative of a biological, membrane-transport controlled uptake into plant cells. The extent of the fractionation in the shoots further depended on the Zn speciation in the nutrient solution. * The observed isotopic depletion in heavy Zn from root to shoot (-0.13 to -0.26 per atomic mass unit) is equivalent to roughly a quarter of the total reported terrestrial variability of Zn isotopic compositions (c. 0.84 per atomic mass unit). Plant uptake therefore represents an important source of isotopic variation in biogeochemical cycling of Zn.     

近缘细菌细胞间的相互识别与相互作用

亲缘识别是细菌细胞间竞争与合作的前提和基础。细菌通过亲缘识别分辨自我细胞和非自我细胞;非同类的细菌细胞相互分离或被排除,而亲缘种群内的细菌细胞进行群体运动、生物膜和子实体形成等社会性合作行为。细菌的自我识别机制可能有助于不同亲缘类群在混杂的自然系统中的共存。近些年来,细菌亲缘识别及相互作用的机制研究工作成为热点,本文总结了近缘细菌细胞间相互识别和作用机制的研究进展。     

QUDeX-MS: hydrogen/deuterium exchange calculation for mass spectra with resolved isotopic fine structure

Background

Hydrogen/deuterium exchange (HDX) coupled to mass spectrometry permits analysis of structure, dynamics, and molecular interactions of proteins. HDX mass spectrometry is confounded by deuterium exchange-associated peaks overlapping with peaks of heavy, natural abundance isotopes, such as carbon-13. Recent studies demonstrated that high-performance mass spectrometers could resolve isotopic fine structure and eliminate this peak overlap, allowing direct detection and quantification of deuterium incorporation.

Results

Here, we present a graphical tool that allows for a rapid and automated estimation of deuterium incorporation from a spectrum with isotopic fine structure. Given a peptide sequence (or elemental formula) and charge state, the mass-to-charge ratios of deuterium-associated peaks of the specified ion is determined. Intensities of peaks in an experimental mass spectrum within bins corresponding to these values are used to determine the distribution of deuterium incorporated. A theoretical spectrum can then be calculated based on the estimated distribution of deuterium exchange to confirm interpretation of the spectrum. Deuterium incorporation can also be detected for ion signals without a priori specification of an elemental formula, permitting detection of exchange in complex samples of unidentified material such as natural organic matter. A tool is also incorporated into QUDeX-MS to help in assigning ion signals from peptides arising from enzymatic digestion of proteins. MATLAB-deployable and standalone versions are available for academic use at qudex-ms.sourceforge.net and agarlabs.com.

Conclusion

Isotopic fine structure HDX-MS offers the potential to increase sequence coverage of proteins being analyzed through mass accuracy and deconvolution of overlapping ion signals. As previously demonstrated, however, the data analysis workflow for HDX-MS data with resolved isotopic fine structure is distinct. QUDeX-MS we hope will aid in the adoption of isotopic fine structure HDX-MS by providing an intuitive workflow and interface for data analysis.     

Parasites and stable isotopes: a comparative analysis of isotopic discrimination in parasitic trophic interactions

Stable isotopes are widely used to identify trophic interactions and to determine trophic positions of organisms in food webs. Comparative studies have provided general insights into the variation in isotopic composition between consumers and their diet (discrimination factors) in predator–prey and herbivore–plant relationships while other major components of food webs such as host–parasite interactions have been largely overlooked. In this study, we conducted a literature‐based comparative analysis using phylogenetically‐controlled mixed effects models, accounting for both parasite and host phylogenies, to investigate patterns and potential drivers in Δ¹³C and Δ¹⁵N discrimination factors in metazoan parasitic trophic interactions. Our analysis of 101 parasite–host pairs revealed a large range in Δ¹³C (–8.2 to 6.5) and Δ¹⁵N (–6.7 to 9.0) among parasite species, with no significant overall depletion or enrichment of ¹³C and ¹⁵N in parasites. As previously found in other trophic interactions, we identified a scaling relationship between the host isotopic value and both discrimination factors with Δ¹³C and Δ¹⁵N decreasing with increasing host δ¹³C and δ¹⁵N, respectively. Furthermore, parasite phylogenetic history explained a large fraction (>60%) of the observed variation in the Δ¹⁵N discrimination factor. Our findings suggest that the traditional isotope ecology framework (using an average Δ¹⁵N of 3.4‰) applies poorly to parasitic trophic interactions. They further indicate the need for a scaled rather than a fixed trophic discrimination factor framework along gradients of host δ¹⁵N. We also identified several conceptual and methodological issues which should to be considered in future research to help integrate parasitic interactions into a holistic isotope ecology framework across diverse trophic interactions.     

The effect of dietary water soluble carbohydrate to nitrogen ratio on nitrogen partitioning and isotopic fractionation of lactating goats offered a high-nitrogen diet

The objective of this study was to investigate the relationship between nitrogen (N) partitioning and isotopic fractionation in lactating goats consuming diets with a constant high concentration of N and increasing levels of water soluble carbohydrate (WSC). Eight lactating goats were offered four different ratios of WSC : N in the diet. A two-period incomplete cross-over design was used, with two goats assigned to each treatment in each period. N balance measurements were conducted, with measurement of feed N intake and total output of N in milk, faeces and urine. Treatment, period and infusion effects were tested using general ANOVA; the relationships between variables were analysed by linear regression. Dietary treatment and period had significant effects on dry matter (DM) intake (g/day). DM digestibility (g/kg DM) and N digestibility (g/kg N) increased as the ratio of WSC : N increased in the diet. No treatment effect was observed on milk urea N concentration (g/l) or urinary excretion of purine derivatives (mM/day). Although dietary treatment and period had significant effects on N intake, the change of N intake was small; no effect was observed for N partitioning among faeces, milk and urine. Milk, plasma and faeces were enriched in ¹⁵N compared with feed, whilst urine was depleted in ¹⁵N relative to feed. No significant relationship was established between N partitioning and isotopic fractionation. This study failed to confirm the potential to use N isotopic fractionation as an indicator of N partitioning in dairy goats when diets provided N in excess to requirements, most likely because the range of milk N output/N intake and urinary N output/N intake were narrow.     

On the significance of hydrogen bonds for the discrimination between CO and O2 by myoglobin

 Quantum chemical geometry optimisations have been performed on realistic models of the active site of myoglobin using density functional methods. The energy of the hydrogen bond between the distal histidine residue and CO or O₂ has been estimated to be 8 kJ/mol and 32 kJ/mol, respectively. This 24 kJ/mol energy difference accounts for most of the discrimination between CO and O₂ by myoglobin (about 17 kJ/mol). Thus, steric effects seem to be of minor importance for this discrimination. The Fe—C and C—O vibrational frequencies of CO-myoglobin have also been studied and the results indicate that CO forms hydrogen bonds to either the distal histidine residue or a water molecule during normal conditions. We have made several attempts to optimise structures with the deprotonated nitrogen atom of histidine directed towards CO. However, all such structures lead to unfavourable interactions between the histidine and CO, and to ν_CO frequencies higher than those observed experimentally. Received: 7 July 1998 / Accepted: 26 October 1998     

Non-climatic variations in the oxygen isotopic compositions of plants

The ¹⁸O content of leaf water strongly influences the ¹⁸O contents of atmospheric CO₂ and O₂. The ¹⁸O signatures of these atmospheric gases, in turn, emerge as important indicators of large-scale gas exchange processes. Better understanding of the factors that influence the isotopic composition of leaf water is still required, however, for the quantitative utilization of these tracers. The ¹⁸O enrichment of leaf water relative to local meteoric water, is known to reflect climatic conditions. Less is known about the extent variations in the ¹⁸O content of leaf water are influenced by nonclimatic, species-specific characteristics. In a collection of 90 plant species from all continents grown under the same climatic conditions in the Jerusalem Botanical Garden we observed variations of about 9‰ in the δ¹⁸O values of stem water, δ_s, and of about 14‰ in the mid-day δ¹⁸O enrichment of bulk leaf water, δ_LW–δ_s. Differences between δ¹⁸O values predicted by a conventional evaporation model, δ_M, and δ_LW ranged between – 3.3‰ and + 11.8‰. The δ¹⁸O values of water in the chloroplasts (δ_ch) in leaves of 10 selected plants were estimated from on-line CO₂ discrimination measurements. Although much uncertainty is still involved in these estimates, the results indicated that δ_ch can significantly deviate from δ_M in species with high leaf peclet number. The δ¹⁸O values of bulk leaf water significantly correlated with δ¹⁸O values of leaf cellulose (directly) and with instantaneous water use efficiency (A/E, inversely). Differences in isotopic characteristics among conventionally defined vegetation types were not significant, except for conifers that significantly differed from shrubs in δ¹⁸O and δ¹³C values of cellulose and in their peclet numbers, and from deciduous woodland species in their δ¹⁸O and δ¹³C values of cellulose. The results indicated that predictions of the δ¹⁸O values of leaf water (δ_LW, δ_M and δ_ch) could be improved by considering plant species-specific characteristics.     

Chiral discrimination and interaction mechanism between enantiomers and serum albumins

The chiral discrimination studies of biological system are theoretically and practically significant for the development of chiral drugs and life science. Our work has embarked upon the interaction between serum albumin (SA) (including human SA and bovine SA), R,S‐1‐(4‐methoxyphenyl)ethylamine, and R,S‐1‐(3‐methoxyphenyl)ethylamine. The formation of intermediate transition state, binding sites, and chiral discrimination ability can be investigated by ultraviolet‐visible spectra and fluorescence spectra. Moreover, both the changes of hydrophobic microenvironment and energy transfer can be detected by synchronous fluorescence spectra and fluorescence lifetime. Copyright © 2013 John Wiley & Sons, Ltd.