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1.
A general method for improving of the sensitivity of the TROSY-type triple resonance experiments in the presence of conformational exchange-induced (CSX) relaxation is proposed based on the use of CPMG-INEPT (Müller et al., J. Am. Chem. Soc., 1995, 117, 11043–11048) during the N–C polarization transfer periods. Significantly improved sensitivity is demonstrated for the majority of cross-peaks in the new [15N,1H]-TROSY-XY-HNCA experiment, measured with partially folded RNase AS-Protein, with negligible loss of sensitivity for resonances unaffected by CSX relaxation. In addition, a comparison of cross-peak amplitudes in [15N,1N]-TROSY-XY-HNCA and conventional [15N,1H]-TROSY-HNCA spectra provides a quick and sensitive estimation of the CSX relaxation contribution.  相似文献   

2.
Relaxation compensated constant-time Carr–Purcell–Meiboom–Gill relaxation dispersion experiments for amide protons are presented that detect s-ms time-scale dynamics of protein backbone amide sites. Because of their ten-fold larger magnetogyric ratio, much shorter 180° pulses can be applied to 1H than to 15N spins; therefore, off-resonance effects are reduced and a wider range of effective rf fields can often be used in the case of 1H experiments. Applications to [1H-15N]-ubiquitin and [1H-15N]-perdeuterated HIV-1 protease are discussed. In the case of ubiquitin, we present a pulse sequence that reduces artifacts that arise from homonuclear 3J(HN-H) coupling. In the case of the protease, we show that relaxation dispersion of both 1H and 15N spins provides a more comprehensive picture of slow backbone dynamics than does the relaxation dispersion of either spin alone. We also compare the relative merits of 1H versus 15N transverse relaxation measurements and note the benefits of using a perdeuterated protein to measure the relaxation dispersion of both spin types.  相似文献   

3.
This study experimentally determined the turnover rates of δ13C and δ15N as a function of growth and metabolism and isotopic fractionation for different tissues in captive populations of red rock lobster (Jasus edwardsii) and blue cod (Parapercis colias). Isotopic turnover was estimated using the model of Hesslein et al. [Hesslein, R., Hallard, K., Ramlal, P., 1993. Replacement of sulfur, carbon, and nitrogen in tissue of growing broad whitefish (Coregonus nasus) in response to a change in diet traced by δ34S, δ13C, and δ15N. Can. J. Fish. Aquat. Sci. 50, 2071–2076.]. Isotopic fractionations relative to diet differed among tissues and isotopes. Lobster muscle was more enriched than hemolymph and blue cod fin tissue was more enriched than blood for δ13C and δ15N. The metabolic component of turnover accounted for > 90% of the total isotopic turnover in lobster tissues and 30%–60% in blue cod tissues. Lobster muscle (half-life 147 d) and hemolymph (half-life 117 d) turnover rates were not significantly different but were faster than turnover rates of blue cod tissues. Whole blood, blood plasma fraction, and the blood cellular fraction had similar turnover rates; the whole blood half-life was 240 d for blue cod. Measuring turnover in larger, slower growing animals allowed for a more precise estimate of the metabolic component of isotopic turnover than in fast growing animals in which change is predominantly the result of dilution through growth. The differences in fractionation values among tissues observed here demonstrate that using generic trophic fractionation values would introduce error into diet reconstruction or migration studies. We demonstrate that a modified version of Hesslein et al.'s [Hesslein, R., Hallard, K., Ramlal, P., 1993. Replacement of sulfur, carbon, and nitrogen in tissue of growing broad whitefish (Coregonus nasus) in response to a change in diet traced by δ34S, δ13C, and δ15N. Can. J. Fish. Aquat. Sci. 50, 2071–2076.] turnover model could be used to estimate the temporal component of migration.  相似文献   

4.
Mg(II)–porphyrin–ligand and (bacterio)chlorophyl–ligand coordination interactions have been studied by solution and solid-state MAS NMR spectroscopy. 1H, 13C and 15N coordination shifts due to ring currents, electronic perturbations and structural effects are resolved for imidazole (Im) and 1-methylimidazole (1-MeIm) coordinated axially to Mg(II)-OEP and (B)Chl a. As a consequence of a single axial coordination of Im or 1-MeIm to the Mg(II) ion, 0.9–5.2 ppm 1H, 0.2–5.5 ppm 13C and 2.1–27.2 ppm 15N coordination shifts were measured for selectively labeled [1,3-15N]-Im, [1,3-15N,2-13C]-Im and [1,3-15N,1,2-13C]-1-MeIm. The coordination shifts depend on the distance of the nuclei to the porphyrin plane and the perturbation of the electronic structure. The signal intensities in the 1H NMR spectrum reveal a five-coordinated complex, and the isotropic chemical shift analysis shows a close analogy with the electronic structure of the BChl a–histidine in natural light harvesting 2 complexes. The line broadening of the ligand responses support the complementary IR data and provide evidence for a dynamic coordination bond in the complex.Abbreviations (B)Chl a (bacterio)chlorophyll a - HMBC heteronuclear multiple bond correlation - Im imidazole - LH light-harvesting - 1-MeIm 1-methylimidazole - Mg(II)-Por Mg(II)-porphyrin macrocycle - OEP 2,3,7,8,12,13,17,18-octaethylporphyrin  相似文献   

5.
Coherences were observed between 15N3 of cytosine and its trans amino proton (H42) using a modified gradient-based heteronuclear single quantum coherence (HSQC) pulse sequence optimized for three-bond proton-nitrogen couplings. The method is demonstrated with a 22-nucleotide RNA fragment of the P5abc region of a group I intron uniformly labeled with 15N. Use of intraresidue 15 N3-amino proton couplings to assign cytosine 15 N3 signals complements the recently proposed JNN HNN COSY [Dingley, A.J. and Grzesiek, S. (1998) J. Am. Chem. Soc., 120, 8293–8297] method of identifying hydrogen-bonded base pairs in RNA.  相似文献   

6.
Under the condition that the longitudinal relaxation time of spin I is shorter than the longitudinal relaxation time of spin S the steady-state magnetization in [S,I]-TROSY-type experiments can be enhanced by intermediate storage of a part of the steady-state magnetization of spin I on spin S with a pulse sequence element during the relaxation delay. It is demonstrated with samples ranging in size from the 1 kDa cyclosporin to the 110 kDa 15N,2H-labeled dihydroneopterin Aldolase that intermediate storage of steady-state magnetization in a [15N,1H]-TROSY experiment yields a signal gain of 10–25%. The method proposed here for intermediate storage of steady-state magnetization can be implemented in any [15N,1H]-TROSY-type experiments.  相似文献   

7.
The structure of a pair of modules (6F11F2), that forms part of the collagen-binding region of fibronectin, is refined using heteronuclear relaxation data. A structure of the pair was previously derived from 1H-1H NOE and 3 J HHN data [Bocquier et al. (1999) Structure, 7, 1451–1460] and a weak module–module interface, comprising Leu19 and Leu28, in 6F1, and Tyr68 in 2F1, was identified. In this study, the definition of the average relative orientation of the two modules is improved using the dependence of 15N relaxation on rotational diffusion anisotropy. This structure refinement is based on the selection of a subset of structures from sets calculated with NOE and 3 J HHN data alone, using the quality of the fits to the relaxation data as the selection criterion. This simple approach is compared to a refinement strategy where 15N relaxation data are included in the force field as additional restraints [Tjandra et al. (1997) Nat. Struct. Biol., 4, 443–449].  相似文献   

8.
The backbone dynamics of a 15N-labeled recombinant PAK pilin peptide spanning residues 128–144 in the C-terminal receptor binding domain of Pseudomonas aeruginosa pilin protein strain PAK (Lys128-Cys-Thr-Ser-Asp-Gln-Asp-Glu-Gln-Phe-Ile-Pro-Lys-Gly-Cys-Ser-Lys144) were probed by measurements of 15N NMR relaxation. This PAK(128–144) sequence is a target for the design of a synthetic peptide vaccine effective against multiple strains of P. aeruginosa infection. The 15N longitudinal (T1) and transverse (T2) relaxation rates and the steady-state heteronuclear {1H}-15N NOE were measured at three fields (7.04, 11.74 and 14.1 Tesla), five temperatures (5, 10, 15, 20, and 25°C ) and at pH 4.5 and 7.2. Relaxation data was analyzed using both the `model-free' formalism [Lipari, G. and Szabo, A. (1982) J. Am. Chem. Soc., 104, 4546–4559 and 4559–4570] and the reduced spectral density mapping approach [Farrow, N.A., Szabo, A., Torchia, D.A. and Kay, L.E. (1995) J. Biomol. NMR, 6, 153–162]. The relaxation data, spectral densities and order parameters suggest that the type I and type II -turns spanning residues Asp134-Glu-Gln-Phe137 and Pro139-Lys-Gly-Cys142, respectively, are the most ordered and structured regions of the peptide. The biological implications of these results will be discussed in relation to the role that backbone motions play in PAK pilin peptide immunogenicity, and within the framework of developing a pilin peptide vaccine capable of conferring broad immunity across P. aeruginosa strains.  相似文献   

9.
The backbone dynamics of the bacteriorhodopsin fragment (1–36)BR solubilized in a 1:1 chloroform/methanol mixture were investigated by heteronuclear 1H-15N NMR spectroscopy. The heteronuclear 15N longitudinal and transverse relaxation rates and 15N{1H} steady-state NOEs were measured at three magnetic fields (11.7, 14.1, and 17.6 T). Careful statistical analysis resulted in the selection of the extended model-free form of the spectral density function [Clore et al. (1990) J. Am. Chem. Soc., 112, 4989–4991] for all the backbone amides of (1–36)BR. The peptide exhibits motions on the micro-, nano-, and picosecond time scales. The dynamics of the -helical part of the peptide (residues 9–31) are characterised by nanosecond and picosecond motions with mean order parameters S s 2 = 0.60 and S f 2 = 0.84, respectively. The nanosecond motions were attributed to the peptide's helix-coil transitions in equilibrium. Residues 3–7 and 30–35 also exhibit motions on the pico- and nanosecond time scales, but with lower order parameters. Residue 10 at the beginning of the -helix and residues 30–35 at the C-terminus are involved in conformational exchange processes on the microsecond time scale. The implications of the obtained results for the studies of helix-coil transitions and the dynamics of membrane proteins are discussed.  相似文献   

10.
Summary The assignments of1H–15N magnetic resonances of the -cro repressor are presented. Individual15N-amino acids were incorporated into the protein, or it was uniformly labeled with15N. For the13C–15N double-labeling experiments,13C-amino acids were incorporated into the uniformly15N-labeled protein. All the amide1H–15N resonances could be assigned with such specific labeling, and sequential connectivities obtained by two-dimensional (2D)1H–15N reverse correlation spectroscopies and three-dimensional (3D)1H/15N NOESY-HMQC spectroscopy. Conventional 2D1H–1H correlation spectroscopies were applied to the assignment of the side-chain protons. Some of the1H resonance assignments are inconsistent with those previously reported [Weber, P.L., Wemmer, D.E. and Reid, B.R. (1985)Biochemistry,24, 4553–4562]. The sequential NOE connectivities and H-D exchange rates indicate several elements of the secondary structure, including -helices consisting of residues 8–15, 19–25 and 28–37, and three extended strands consisting of residues 4–7, 39–45 and 49–55. Based on several long-range NOEs, the three extended strands could be combined to form an antiparallel -sheet. The amide proton resonances of the C-terminal residues except Ala66 (residues 60–65) were hardly observed at neutral pH, indicating that the arm is flexible. The identified secondary structure elements in solution show good agreement with those in the crystal structure of the cro protein [Anderson, W.F., Ohlendorf, D.H., Takeda, Y. and Matthews, B.W. (1981)Nature,290, 754–758].  相似文献   

11.
Liu Z  Yuan Q  Wang W 《Amino acids》2009,36(1):71-73
A new method for synthesizing the labeled l-tryptophan is described in this work. l-Tryptophan, labeled with 98% 15N at position 1 was synthesized from the labeled anthranilic acid using Candida utilis mutants. The conversion ratio of 15N of 50% was achieved. The labeled anthranilic acid was synthesized by [15N] phthalimide that was prepared by 99.34% [15N] urea and phthalic anhydride in ortho-xylene medium at 140°C and under atmospheric pressure.  相似文献   

12.
To examine the effect of organic amendment application on the fate of inorganic-N accumulated in a vegetable field soil during conversion from inorganic to organic input, a pot experiment using 15N-labeled soil was conducted. The soil was labeled with 15N through addition of urea-15N (98 atom % 15N) and was then incubated for 1 year resulting in inorganic soil-N concentration and 15N abundance of 211 mg kg–1 soil and 4.950 atom %, respectively. Chinese cabbage [Brassica campestris (L.) Samjin] plants were grown in the labeled soil for 30 and 60 days after application of organic amendment at the rates of 0 (control), 200, 400, and 600 mg N kg–1 soil. Although organic amendment application did not show any significant effect on the uptake efficiency of inorganic-N by Chinese cabbage during the first 30 days, it significantly (P<0.05) increased inorganic-N uptake efficiency as well as total-N uptake and dry matter yield at the end of the 60-day growth period. Application of the organic amendment also increased microbial immobilization of inorganic-N in both growth periods. Between 30 and 60 days of growth, however, the amount of immobilized N from the inorganic-15N pool decreased, indicating re-mineralization of previously immobilized N. Although the amount of inorganic-15N lost was virtually the same among treatments at day 30, increased immobilization of inorganic-15N caused by organic amendment application led to the higher retention of inorganic-N in the soil and less loss of N at day 60 as compared to the control. These results indicate that increased immobilization by organic amendment application in the early growth season and the subsequent gradual re-mineralization may play an important role in increasing plant uptake of inorganic-15N, while minimizing N loss.  相似文献   

13.
In vivo and in vitro (tissue slices) incorporation of labeled precursors into DNA, RNA, and proteins was measured in mitochondria obtained from cerebral hemispheres, cerebellum, and brain stem of rats at different days of postnatal development. To compare the synthesis of macromolecules in mitochondria with that in other subcellular fractions, the incorporation of labeled precursors into DNA, RNA, and proteins extracted from nuclei and into RNA and proteins extracted from microsomes and cytoplasmic soluble fractions was also measured.The results obtained showed that the incorporation of [3H]thymidine into DNA and of [14C]leucine into proteins of nuclei and mitochondria from the various brain regions examined decreased during postnatal development, however, at 30 days of age the specific radioactivity of mitochondrial DNA was higher than that of nuclear DNA. [3H]Uridine incorporation into RNA decreased from 10 to 30 days of age in nuclei while in mitochondria it was quite similar at both ages. This result may be due to a faster turnover of mitochondrial RNA compared to that of mitochondrial DNA and proteins. The results obtained suggest an active biosynthesis of macromolecules in brain mitochondria and might indicate an intense biogenesis of these organelles in rat brain during postnatal development.Preliminary reports of these results were presented at the XI FEBS Meeting, Copenhagen, August 14–19, 1977, Poster number A2-2-155-3, and at III Meeting of Italian Biochem. Soc., Siena, October 3–5, 1977, Abstract C6.  相似文献   

14.
The advantages of using off-resonance rf fields in heteronuclear self-relaxation experiments are explored on a fully 15N-enriched protein. It is firstly shown that in the absence of slow motions the longitudinal and transverse 15N self-relaxation rate values derived with this method are in agreement with the ones measured by the classical inversion-recovery and Carr–Purcell–Meiboom–Gill (CPMG) sequences, respectively. Secondly, by comparing the 15N transverse self-relaxation rates obtained by the proposed off-resonance sequence and by the CPMG sequence, 11 residues out of the 61 of toxin are shown to exhibit a chemical exchange phenomenon in water on a time scale ranging from 1 µs to 100 ms. By varying the effective field amplitude, chemical exchange processes involving these residues are measured and the corresponding correlation times are evaluated without having assumed any motion model. Similar, though less precise, results are given by the analysis of the 15N off-resonance self-relaxation rates on the basis of the Lipari–Szabo model to describe the fast internal dynamics of toxin .  相似文献   

15.
For the quantification of nitrite and nitrate, the stable metabolites of -arginine-derived nitric oxide (NO) in human urine and plasma, we developed a gas chromatographic—mass spectrometric (GC—MS) method in which [15N]nitrite and [15N]nitrate were used as internal standards. Endogenous nitrite and [15N]nitrite added to acetone-treated plasma and urine samples were converted into their pentafluorobenzyl (PFB) derivatives using PFB bromide as the alkylating agent. For the analysis of endogenous nitrate and [15N]nitrate they were reduced to nitrite and [15N]nitrite, respectively, by cadmium in acidified plasma and urine samples prior to PFB alkylation. Reaction products were extracted with toluene and 1-μl aliquots were analyzed by selected-ion monitoring at m/z 46 for endogenous nitrite (nitrate) and m/z 47 for [15N]nitrite ([15N]nitrate). The intra- and inter-assay relative standard deviations for the determination of nitrite and nitrate in urine and plasma were below 3.8%. The detection limit of the method was 22 fmol of nitrite. Healthy subjects (n = 12) excreted into urine 0.49 ± 0.25 of nitrite and 109.5 ± 61.7 of nitrate (mean ± S.D., μmol/mmol creatinine) with a mean 24-h output of 5.7 μmol for nitrite and 1226 μmol for nitrate. The concentrations of nitrite and nitrate in the plasma of these volunteers were determined to be (mean ± S.D., μmol/l) 3.6 ± 0.8 and 68 ± 17, respectively.  相似文献   

16.
Improved relaxation-compensated Carr–Purcell–Meiboom-Gill pulse sequences are reported for studying chemical exchange of backbone 15N nuclei. In contrast to the original methods [J. P. Loria, M. Rance, and A. G. Palmer, J. Am. Chem. Soc. 121, 2331–2332 (1999)], phenomenological relaxation rate constants obtained using the new sequences do not contain contributions from 1H-1H dipole-dipole interactions. Consequently, detection and quantification of chemical exchange processes are facilitated because the relaxation rate constant in the limit of fast pulsing can be obtained independently from conventional 15N spin relaxation measurements. The advantages of the experiments are demonstrated using basic pancreatic trypsin inhibitor.  相似文献   

17.
Partly biosynthetic site-directed isotopically 13C enriched photosynthetic light-harvesting 2(LH2) complexes have been prepared from Rhodopseudomonas acidophila strain 10050 by using chemically labeled [1,2,3,4–13C], [1,4–13C] and [2,3–13C] succinic acid as a precursor in the growth medium. Two-dimensional proton driven spin diffusion (PDSD) solid state NMR correlation spectroscopy has been used to trace each individual 13C isotope from the labeled succinic acid precursor to its destination into the protein and into the embedded major light-absorbing bacteriochlorophyll cofactors. For both the residues of the protein and for the cofactors distinct labeling patterns have been deduced, for protein complexes prepared from [1,4–13C]-succinic acid or [2,3–13C]-succinic labeled media. All residues, except isoleucine and leucine, have been labeled almost homogeneously by the succinic acid precursor. Carbonyl carbons in the protein backbone were labeled by [1,4–13C]-succinic acid, while the C and C carbons of the residues were labeled by [2,3 13C]-succinic acid. Leucine and isoleucine residues were labeled using a uniformly labeled amino acid mixture in the medium. The pattern labeling yields an increase of the resolution and less spectral crowding. The partial labeling technique in combination with conventional solid state NMR methods at ultra high magnetic fields provides an attractive route to resolve chemical shifts for -helical transmembrane protein structures.  相似文献   

18.
19.
Maize (Zea mays L.) and pearl millet (Pennisetum americanum (L.) Leeke) seedlings were exposed to [15N]nitrate for 1-h periods at eight times during a 24-h period (16–8 h light-dark for maize; 14–10 h for millet). Influx of [15N]nitrate as well as its reduction and translocation were determined during each period. The efflux of previously absorbed [14N]nitrate to the uptake solution was also estimated. No marked diurnal changes in [14N]nitrate efflux or [15N]nitrate influx were evident in maize. In contrast, [14N]nitrate efflux from millet increased and eventually exceeded [15N]nitrate influx during the late dark and early light periods, resulting in net nitrate efflux from the roots. The dissimilarity of their diurnal patterns indicates that influx and efflux are independently regulated. In both species, [15N]nitrate reduction and 15N translocation to shoots were curtailed more by darkness than was [15N]nitrate influx. In the light, maize reduced 15% and millet 24% of the incoming [15N]nitrate. In darkness, reduction dropped to 11 and 17%, respectively. Since the accumulation of reduced-15N in shoots declined abruptly in darkness, whereas that in roots was little affected, it is suggested that in darkness [15N]nitrate reduction occurred primarily in roots. The decrease in nitrate uptake and reduction in darkness was not related to efflux, which remained constant in maize and did not respond immediately to darkness in pearl millet.Paper No. 6722 of the Journal Series of the North Carolina Agricultural Research Service, Raleigh  相似文献   

20.
Triple resonance HCN and HCNCH experiments are reliable methods of establishing sugar-to-base connectivity in the NMR spectra of isotopicaly labeled oligonucleotides. However, with larger molecules the sensitivity of the experiments is drastically reduced due to relaxation processes. Since the polarization transfer between 13C and 15N nuclei relies on rather small heteronuclear coupling constants (11–12 Hz), the long evolution periods (up to 30–40 ms) in the pulse sequences cannot be avoided. Therefore any effort to enhance sensitivity has to concentrate on manipulating the spin system in such a way that the spin–spin relaxation rates would be minimized. In the present paper we analyze the efficiency of the two known approaches of relaxation rate control, namely the use of multiple-quantum coherence (MQ) and of the relaxation interference between chemical shift anisotropy and dipolar relaxation – TROSY. Both theoretical calculations and experimental results suggest that for the sugar moiety (H1-C1-N1/9) the MQ approach is clearly preferable. For the base moiety (H6/8-C6/8-N1/9), however, the TROSY shows results superior to the MQ suppression of the dipole–dipole relaxation at moderate magnetic fields (500 MHz) and the sensitivity improvement becomes dramatically more pronounced at very high fields (800 MHz). The pulse schemes of the triple-resonance HCN experiments with sensitivity optimized performance for unambiguous assignments of intra-residual sugar-to-base connectivities combining both approaches are presented.  相似文献   

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