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1.
NMR relaxation of arginine (Arg) 15Nε nuclei is useful for studying side-chain dynamics of proteins. In this work, we studied the impact of two geminal 15N–15N scalar couplings on measurements of transverse relaxation rates (R 2 ) for Arg side-chain 15Nε nuclei. For 12 Arg side chains of the DNA-binding domain of the Antp protein, we measured the geminal 15N–15N couplings ( 2 J NN ) of the 15Nε nuclei and found that the magnitudes of the 2 J NN coupling constants were virtually uniform with an average of 1.2 Hz. Our simulations, assuming ideal 180° rotations for all 15N nuclei, suggested that the two 2 J NN couplings of this magnitude could in principle cause significant modulation in signal intensities during the Carr–Purcell-Meiboom–Gill (CPMG) scheme for Arg 15Nε R 2 measurements. However, our experimental data show that the expected modulation via two 2 J NN couplings vanishes during the 15N CPMG scheme. This quenching of J modulation can be explained by the mechanism described in Dittmer and Bodenhausen (Chemphyschem 7:831–836, 2006). This effect allows for accurate measurements of R 2 relaxation rates for Arg side-chain 15Nε nuclei despite the presence of two 2 J NN couplings. Although the so-called recoupling conditions may cause overestimate of R 2 rates for very mobile Arg side chains, such conditions can readily be avoided through appropriate experimental settings.  相似文献   

2.
The limits of resolution that can be obtained in 1H–15N 2D NMR spectroscopy of isotopically enriched nanocrystalline proteins are explored. Combinations of frequency switched Lee–Goldburg (FSLG) decoupling, fast magic angle sample spinning (MAS), and isotopic dilution via deuteration are investigated as methods for narrowing the amide 1H resonances. Heteronuclear decoupling of 15N from the 1H resonances is also studied. Using human ubiquitin as a model system, the best resolution is most easily obtained with uniformly 2H and 15N enriched protein where the amides have been exchanged in normal water, MAS at 20 kHz, and WALTZ-16 decoupling of the 15N nuclei. The combination of these techniques results in average 1H lines of only 0.26 ppm full width at half maximum. Techniques for optimizing instrument stability and 15N decoupling are described for achieving the best possible performance in these experiments.  相似文献   

3.
We present a highly sensitive pulse sequence, carbonyl carbon label selective 1H–15N HSQC (CCLS-HSQC) for the detection of signals from 1H–15N units involved in 13C′–15N linkages. The CCLS-HSQC pulse sequence utilizes a modified 15N CT evolution period equal to 1/( ) (∼33 ms) to select for 13C′–15N pairs. By collecting CCLS-HSQC and HNCO data for two proteins (8 kDa ubiquitin and 20 kDa HscB) at various temperatures (5–40°C) in order to vary correlation times, we demonstrate the superiority of the CCLS-HSQC pulse sequence for proteins with long correlation times (i.e. higher molecular weight). We then show that the CCLS-HSQC experiment yields assignments in the case of a 41 kDa protein incorporating pairs of 15N- and 13C′-labeled amino acids, where a TROSY 2D-HN(CO) had failed. Although the approach requires that the 1H–15N HSQC cross peaks be observable, it does not require deuteration of the protein. The method is suitable for larger proteins and is less affected by conformational exchange than HNCO experiments, which require a longer period of transverse 15N magnetization. The method also is tolerant to the partial loss of signal from isotopic dilution (scrambling). This approach will be applicable to families of proteins that have been resistant to NMR structural and dynamic analysis, such as large enzymes, and partially folded or unfolded proteins.  相似文献   

4.
A TROSY-based NMR experiment is described for simultaneous measurement of the 15N longitudinal relaxation rate constant R1 and the {1H}–15N nuclear Overhauser enhancement. The experiment is based on the observation that the TROSY mixing pulse sequence element symmetrically exchanges 1H and 15N magnetizations. The accuracy of the proposed technique is validated by comparison to independent measurements of both relaxation parameters for the protein ubiquitin. The simultaneous experiment is approximately 20–33% shorter than conventional sequential measurements.  相似文献   

5.
A confined aquifer in the Malm Karst of the Franconian Alb, South Germany was investigated in order to understand the role of the vadose zone in denitrifiaction processes. The concentrations of chemical tracers Sr2+ and Cl and concentrations of stable isotope 18O were measured in spring water and precipitation during storm events. Based on these measurements a conceptual model for runoff was constructed. The results indicate that pre-event water, already stored in the system at the beginning of the event, flows downslope on vertical and lateral preferential flow paths. Chemical tracers used in a mixing model for hydrograph separation have shown that the pre-event water contribution is up to 30%. Applying this information to a conceptual runoff generation model, the values of 15N and 18O in nitrate could be calculated. Field observations showed the occurence of significant microbial denitrification processes above the soil/bedrock interface before nitrate percolates through to the deeper horizon of the vadose zone. The source of nitrate could be determined and denitrification processes were calculated. Assuming that the nitrate reduction follows a Rayleigh process one could approximate a nitrate input concentration of about 170 mg/l and a residual nitrate concentration of only about 15%. The results of the chemical and isotopic tracers postulate fertilizers as nitrate source with some influence of atmospheric nitrate. The combined application of hydrograph separation and determination of isotope values in 15N and 18O of nitrate lead to an improved understanding of microbial processes (nitrification, denitrification) in dynamic systems.  相似文献   

6.
Arginine side-chains are often key for enzyme catalysis, protein–ligand and protein–protein interactions. The importance of arginine stems from the ability of the terminal guanidinium group to form many key interactions, such as hydrogen bonds and salt bridges, as well as its perpetual positive charge. We present here an arginine 13Cζ-detected NMR experiment in which a double-quantum coherence involving the two 15Nη nuclei is evolved during the indirect chemical shift evolution period. As the precession frequency of the double-quantum coherence is insensitive to exchange of the two 15Nη; this new approach is shown to eliminate the previously deleterious line broadenings of 15Nη resonances caused by the partially restricted rotation about the Cζ–Nε bond. Consequently, sharp and well-resolved 15Nη resonances can be observed. The utility of the presented method is demonstrated on the L99A mutant of the 19 kDa protein T4 lysozyme, where the measurement of small chemical shift perturbations, such as one-bond deuterium isotope shifts, of the arginine amine 15Nη nuclei becomes possible using the double-quantum experiment.  相似文献   

7.
A comparison of the effects of foliar and soil N application was made in field-grown mature fruiting Gala/M9 apple trees (Malus domestica Borkh) in 2001 and 2002 growing seasons under Pacific Northwest growing conditions in southern British Columbia, Canada. The trees, six years old at the start of the experiment, were treated: (1) with 5 g/l urea sprays supplied every two weeks (7 times) from mid May to mid August (total about 50 g N/tree/year), (2) with the same amount of N applied to the soil with the same timing and quantity as for the foliar treatment, and (3) with no N (control). Leaf color (as SPAD readings) and N concentrations (mg/g), and soil NH4+-N and NO3-N were measured periodically throughout the two seasons. Leached NO3-N was monitored monthly via an anion exchange probe from June to October in 2001 and from May to November in 2002. Shoot length was measured in October and N concentration of one-year-old wood and roots was determined in December of each growing s eason. Soil N application significantly increased shoot length relative to control or foliar N application. Leaf color, leaf N, and N concentration of one-year-old wood and roots were similarly increased relative to control by both soil and foliar N application. These treatments also increased fruit yield relative to control. There was no significant difference in yield and fruit quality between soil and foliar N applications. Soil N application increased soil NH4+-N and NO3-N content in the root zone, and also increased the NO3 leaching loss below the root zone especially late in the growing season. Our results suggested that tree N status and yield and fruit quality could be maintained by multiple urea sprays during the growing season in apple orchards, and foliar N application will reduce the risk of soil NO3-N leaching.  相似文献   

8.
In two mountain ecosystems at the Alptal research site in central Switzerland, pulses of 15NO3 and 15NH4 were separately applied to trace deposited inorganic N. One forested and one litter meadow catchment, each approximately 1600 m2, were delimited by trenches in the Gleysols. K15NO3 was applied weekly or fortnightly over one year with a backpack sprayer, thus labelling the atmospheric nitrate deposition. After the sampling and a one-year break, 15NH4Cl was applied as a second one-year pulse, followed by a second sampling campaign. Trees (needles, branches and bole wood), ground vegetation, litter layer and soil (LF, A and B horizon) were sampled at the end of each labelling period. Extractable inorganic N, microbial N, and immobilised soil N were analysed in the LF and A horizons. During the whole labelling period, the runoff water was sampled as well. Most of the added tracer remained in both ecosystems. More NO3 than NH4+ tracer was retained, especially in the forest. The highest recovery was in the soil, mainly in the organic horizon, and in the ground vegetation, especially in the mosses. Event-based runoff analyses showed an immediate response of 15NO3 in runoff, with sharp 15N peaks corresponding to discharge peaks. NO3 leaching showed a clear seasonal pattern, being highest in spring during snowmelt. The high capacity of N retention in these ecosystems leads to the assumption that deposited N accumulates in the soil organic matter, causing a progressive decline of its C:N ratio.  相似文献   

9.
New 3D HCN quantitative J (QJ) pulse schemes are presented for the precise and accurate measurement of one-bond 15N1/913C1, 15N1/913C6/8, and 15N1/913C2/4 residual dipolar couplings (RDCs) in weakly aligned nucleic acids. The methods employ 1H–13C multiple quantum (MQ) coherence or TROSY-type pulse sequences for optimal resolution and sensitivity. RDCs are obtained from the intensity ratio of H1–C1–N1/9 (MQ-HCN-QJ) or H6/8–C6/8–N1/9 (TROSY-HCN-QJ) correlations in two interleaved 3D NMR spectra, with dephasing intervals of zero (reference spectrum) and 1/(2JNC) (attenuated spectrum). The different types of 15N–13C couplings can be obtained by using either the 3D MQ-HCN-QJ or TROSY-HCN-QJ pulse scheme, with the appropriate setting of the duration of the constant-time 15N evolution period and the offset of two frequency-selective 13C pulses. The methods are demonstrated for a uniformly 13C, 15N-enriched 24-nucleotide stem-loop RNA sequence, helix-35, aligned in the magnetic field using phage Pf1. For measurements of RDCs systematic errors are found to be negligible, and experiments performed on a 1.5 mM helix-35 sample result in an estimated precision of ca. 0.07 Hz for 1DNC, indicating the utility of the measured RDCs in structure validation and refinement. Indeed, for a complete set of 15N1/913C1, 15N1/913C6/8, and 15N1/913C2/4 dipolar couplings obtained for the stem nucleotides, the measured RDCs are in excellent agreement with those predicted for an NMR structure of helix-35, refined using independently measured observables, including 13C–1H, 13C–13C and 1H–1H dipolar couplings.Supplementary material to this paper is available in electronic form at http://dx.doi.org/10.1007/s10858-005-0646-2.  相似文献   

10.
The heteronuclear 15N–{1H} NOE values are typically determined by taking the ratio of 15N signal intensities recorded in the presence and absence of 1H saturation prior to evolution of 15N magnetization. Since the intensity ratio of two independent experiments is taken, complete recovery of 15N magnetization during the scan repetition delay is critical to obtain reliable NOE values. Because it may not be practical to wait for the complete recovery of magnetization at high magnetic fields, Solomon equations may be used to correct measured NOE values. Here, based on experiments and simulations, we show that since the cross-correlation between 1H–15N dipole and 15N chemical shift anisotropy becomes significant at high fields for small or deuterated proteins, measured NOE values can not be accurately corrected based on the Solomon equations. We also discuss ranges of rotational correlation times and proton spin-flip rate, in which the NOE values can be corrected by the equations.  相似文献   

11.
Interleukin-36α (IL-36α) is a recently characterised member of the interleukin-1 superfamily. It is involved in the pathogenesis of inflammatory arthritis in one third of psoriasis patients. By binding of IL-36α to its receptor IL-36R via the NF-κB pathway other cytokines involved in inflammatory and apoptotic cascade are activated. The efficacy of complex formation is controlled by N-terminal processing. To obtain a more detailed view on the structure function relationship we performed a heteronuclear multidimensional NMR investigation and here report the 1H, 13C, and 15N resonance assignments for the backbone and side chain nuclei of the pro-inflammatory cytokine interleukin-36α.  相似文献   

12.

Key message

For long-term environmental investigations, tree-ring δ 15 N values are inappropriate proxies for foliar δ 15 N for both Fagus sylvatica and Picea abies under moderate N loads.

Abstract

Currently it is unclear whether stable nitrogen isotope signals of tree-rings are related to those in foliage, and whether they can be used to infer tree responses to environmental changes. We studied foliar and tree-ring nitrogen (δ15N) and carbon (δ13C) isotope ratios in European beech (Fagus sylvatica L.) and Norway spruce (Picea abies L.) from six long-term forest monitoring sites in Switzerland together with data on N deposition and soil N availability, as well as a drought response index over the last two decades. For both species, tree-ring δ15N and δ13C values were less negative compared to foliar δ15N and δ13C values, most likely due to recycling and reallocation of N within the tree and fractionation processes associated with the transport of sucrose and the formation of tree-rings, respectively. Temporal trends recorded in foliar δ15N were not reflected in tree-ring δ15N, with much higher variations in tree-rings compared to foliage. Soil N availability and N deposition were partially able to explain changes in foliar δ13C, while there were no significant correlations between environmental variables and either tree-ring or foliar δ15N. Our results suggest an uncoupling between the N isotopic composition of tree-rings and foliage. Consequently, tree-ring δ15N values are inappropriate proxies of foliar δ15N values under low-to-moderate N deposition loads. Furthermore, at such low levels of deposition, tree-ring δ15N values are not recommended as archives of tree responses to soil C/N or bulk N deposition.
  相似文献   

13.
We present a simple method, ARTSY, for extracting 1JNH couplings and 1H–15N RDCs from an interleaved set of two-dimensional 1H–15N TROSY-HSQC spectra, based on the principle of quantitative J correlation. The primary advantage of the ARTSY method over other methods is the ability to measure couplings without scaling peak positions or altering the narrow line widths characteristic of TROSY spectra. Accuracy of the method is demonstrated for the model system GB3. Application to the catalytic core domain of HIV integrase, a 36 kDa homodimer with unfavorable spectral characteristics, demonstrates its practical utility. Precision of the RDC measurement is limited by the signal-to-noise ratio, S/N, achievable in the 2D TROSY-HSQC spectrum, and is approximately given by 30/(S/N) Hz.  相似文献   

14.
15.
Massive anthropogenic acceleration of the global nitrogen (N) cycle has stimulated interest in understanding the fate of excess N loading to aquatic ecosystems. Nitrate (NO3 ) is traditionally thought to be removed mainly by microbial respiratory denitrification coupled to carbon (C) oxidation, or through biomass assimilation. Alternatively, chemolithoautotrophic bacterial metabolism may remove NO3 by coupling its reduction with the oxidation of sulfide to sulfate (SO4 2−). The NO3 may be reduced to N2 or to NH4 +, a form of dissimilatory nitrate reduction to ammonium (DNRA). The objectives of this study were to investigate the importance of S oxidation as a NO3 removal process across diverse freshwater streams, lakes, and wetlands in southwestern Michigan (USA). Simultaneous NO3 removal and SO4 2− production were observed in situ using modified “push-pull” methods in nine streams, nine wetlands, and three lakes. The measured SO4 2− production can account for a significant fraction (25–40%) of the overall NO3 removal. Addition of 15NO3 and measurement of 15NH4 + production using the push–pull method revealed that DNRA was a potentially important process of NO3 removal, particularly in wetland sediments. Enrichment cultures suggest that Thiomicrospira denitrificans may be one of the organisms responsible for this metabolism. These results indicate that NO3 -driven SO4 2− production could be widespread and biogeochemically important in freshwater sediments. Removal of NO3 by DNRA may not ameliorate problems such as eutrophication because the N remains bio-available. Additionally, if sulfur (S) pollution enhances NO3 removal in freshwaters, then controls on N processing in landscapes subject to S and N pollution are more complex than previously appreciated. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.  相似文献   

16.
Abstract Stable isotope ratios of terrestrial ecosystem nitrogen (N) pools reflect internal processes and input–output balances. Disturbance generally increases N cycling and loss, yet few studies have examined ecosystem δ15N over a disturbance-recovery sequence. We used a chronosequence approach to examine N distribution and δ15N during forest regrowth after agricultural abandonment. Site ages ranged from 10 to 115 years, with similar soils, climate, land-use history, and overstory vegetation (white pine Pinus strobus). Foliar N and δ15N decreased as stands aged, consistent with a progressive tightening of the N cycle during forest regrowth on agricultural lands. Over time, foliar δ15N became more negative, indicating increased fractionation along the mineralization–mycorrhizal–plant uptake pathway. Total ecosystem N was constant across the chronosequence, but substantial internal N redistribution occurred from the mineral soil to plants and litter over 115 years (>25% of ecosystem N or 1,610 kg ha−1). Temporal trends in soil δ15N generally reflected a redistribution of depleted N from the mineral soil to the developing O horizon. Although plants and soil δ15N are coupled over millennial time scales of ecosystem development, our observed divergence between plants and soil suggests that they can be uncoupled during the disturbance-regrowth sequence. The approximate 2‰ decrease in ecosystem δ15N over the century scale suggests significant incorporation of atmospheric N, which was not detected by traditional ecosystem N accounting. Consideration of temporal trends and disturbance legacies can improve our understanding of the influence of broader factors such as climate or N deposition on ecosystem N balances and δ15N. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.  相似文献   

17.
18.
γS-crystallin is a major structural component of the human eye lens, which maintains its stability over the lifetime of an organism with negligible turnover. The G57W mutant of human γS-crystallin (abbreviated hereafter as γS-G57W) is associated with dominant congenital cataracts. In order to provide a structural basis for the ability of γS-G57W causing cataract, we have cloned, overexpressed, isolated and purified the protein. The 2D [15N–1H]-HSQC spectrum recorded with uniformly 13C/15N-labelled γS-G57W was highly dispersed indicating the protein to adopt an ordered conformation. In this paper, we report almost complete sequence-specific 1H, 13C and 15N resonance assignments of γS-G57W using a suite of heteronuclear 3D NMR experiments.  相似文献   

19.
Two novel HSQC-IPAP approaches are proposed to achieve α/β spin-state editing simultaneously for 13C and 15N in a single NMR experiment. The pulse schemes are based on a time-shared (TS) 2D 1H,13C/1H,15N-HSQC correlation experiment that combines concatenated echo elements for simultaneous J(CH) and J(NH) coupling constants evolution, TS evolution of 13C and 15N chemical shifts in the indirect dimension and heteronuclear α/β-spin-state selection by means of the IPAP principle. Heteronuclear α/β-editing for all CH n (n = 1–3) and NH n (1–2) multiplicities can be achieved in the detected F2 dimension of a single TS-HSQC-F2-IPAP experiment. On the other hand, an alternative TS-HSQC-F1-IPAP experiment is also proposed to achieve α/β-editing in the indirect F1 dimension. Experimental and simulated data is provided to evaluate these principles in terms of sensitivity and performance simultaneously on backbone and side-chain CH, CH2, CH3, NH, and NH2 spin systems in uniformly 13C/15N-labeled proteins and in small natural-abundance peptides.  相似文献   

20.
Biogeochemical theory emphasizes nitrogen (N) limitation and the many factors that can restrict N accumulation in temperate forests, yet lacks a working model of conditions that can promote naturally high N accumulation. We used a dynamic simulation model of ecosystem N and δ15N to evaluate which combination of N input and loss pathways could produce a range of high ecosystem N contents characteristic of forests in the Oregon Coast Range. Total ecosystem N at nine study sites ranged from 8,788 to 22,667 kg ha−1 and carbon (C) ranged from 188 to 460 Mg ha−1, with highest values near the coast. Ecosystem δ15N displayed a curvilinear relationship with ecosystem N content, and largely reflected mineral soil, which accounted for 96–98% of total ecosystem N. Model simulations of ecosystem N balances parameterized with field rates of N leaching required long-term average N inputs that exceed atmospheric deposition and asymbiotic and epiphytic N2-fixation, and that were consistent with cycles of post-fire N2-fixation by early-successional red alder. Soil water δ15NO3 patterns suggested a shift in relative N losses from denitrification to nitrate leaching as N accumulated, and simulations identified nitrate leaching as the primary N loss pathway that constrains maximum N accumulation. Whereas current theory emphasizes constraints on biological N2-fixation and disturbance-mediated N losses as factors that limit N accumulation in temperate forests, our results suggest that wildfire can foster substantial long-term N accumulation in ecosystems that are colonized by symbiotic N2-fixing vegetation.  相似文献   

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