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1.
A new 3D, spin-state-selective coherence transfer NMR experiment is described that yields accurate measurements for eight scalar or dipolar couplings within a spin system composed of a methylene adjacent to a methine group. Implementations of the experiment have been optimized for proteins and for nucleic acids. The experiments are demonstrated for C–C moieties of the third IgG-binding domain from Streptococcal Protein G (GB3) and for C –C groups in a 24-nt RNA oligomer. Chemical shifts of C, C and H (respectively C , C and H ) are dispersed in the three orthogonal dimensions, and the absence of heteronuclear decoupling leads to distinct and well-resolved E.COSY multiplet patterns. In an isotropic sample, the E.COSY displacements correspond to 1JCH, 2JCH2+2JCH3, 2JCH, 1JCH2+1JCH3, 1JCH22JH2H3, 1JCH32JH2H3, 3JHH2 and 3JHH3 for proteins, and 1J , 2J J , 2J , 1J +1J , 1J J , 1J J , 3J and 3J in nucleic acids. The experiment, based on relaxation-optimized spectroscopy, yields best results when applied to residues where the methine–methylene group corresponds to a reasonably isolated spin system, as applies for C, F, Y, W, D, N and H residues in proteins, or the C –C groups in nucleic acids. Splittings can be measured under either isotropic or weakly aligned conditions, yielding valuable structural information both through the 3J couplings and the one-, two- and three-bond dipolar interactions. Dipolar couplings for 10 out of 13 sidechains in GB3 are found to be in excellent agreement with its X-ray structure, whereas one residue adopts a different backbone geometry, and two residues are subject to extensive 1 rotamer averaging. The abundance of dipolar couplings can also yield stereospecific assignments of the non-equivalent methylene protons. For the RNA oligomer, dipolar data yielded stereospecific assignments for six out of the eight C H2 groups in the loop region of the oligomer, in all cases confirmed by 1J ^{1} $$" align="middle" border="0"> J , and H resonating downfield of H .Supplementary material to this paper is available in electronic form at http://dx.doi.org/10.1007/s10858-005-0175-z.  相似文献   

2.
It is proposed to obtain effective Lipari–Szabo order parameters and local correlation times for relaxation vectors of protein 13CO nuclei by carrying out a 13CO-R1 auto relaxation experiment, a transverse CSA/dipolar cross correlation and a transverse 13CO CSA/13CO–15N CSA/dipolar cross correlation experiment. Given the global rotational correlation time from 15N relaxation experiments, a new program COMFORD (CO-Modelfree Fitting Of Relaxation Data) is presented to fit the 13CO data to an effective order parameter , an effective local correlation time and the orientation of the CSA tensor with respect to the molecular frame. It is shown that the effective is least sensitive to rotational fluctuations about an imaginary axis and most sensitive to rotational fluctuations about an imaginary axis parallel to the NH bond direction. As such, the information is fully complementary to the 15N relaxation order parameter, which is least sensitive to fluctuations about the NH axis and most sensitive to fluctuations about the axis. The new paradigm is applied on data of Ca2+ saturated Calmodulin, and on available literature data for Ubiquitin. Our data indicate that the order parameters rapport on slower, and sometimes different, motions than the 15N relaxation order parameters. The CO local correlation times correlate well with the calmodulin’s secondary structure. Electronic Supplementary Material Supplementary material is available to authorized users in the online version of this article at .  相似文献   

3.
We recently introduced a new line of reduced-dimensionality experiments making constructive use of axial peak magnetization, which has so far been suppressed as an undesirable artifact in multidimensional NMR spectra [Szyperski, T., Braun, D., Banecki, B. and Wüthrich, K. (1996) J. Am. Chem. Soc., 118, 8146–8147]. The peaks arising from the axial magnetization are located at the center of the doublets resulting from projection. Here we describe the use of such projected four-dimensional (4D) triple resonance experiments for the efficient sequential resonance assignment of 15N/13C-labeled proteins. A 3D / /(CO)NHN experiment is recorded either in conjunction with 3D HNN< > or with the newly presented 3D HNN scheme. The first combination yields sequential assignments based on the measurement of13 C chemical shifts and provides a complete 1H, 13C and 15N resonance assignment of polypeptide backbone and CHn moieties. When employing the second combination, 13C=O chemical shifts are not measured, but the sequential assignment relies on both 13C and1 H chemical shifts. The assignment is performed in a semi-automatic fashion using the program XEASY in conjunction with the newly implemented program SPSCAN. This program package offers routines for the facile mutual interconversion of single-quantum and zero/double-quantum frequencies detected in conventional and reduced-dimensionality spectra, respectively. In particular, SPSCAN comprises a peak picking routine tailored to cope with the distinct peak patterns of projected NMR experiments performed with simultaneous acquisition of central peaks. Data were acquired at 13 °C for the N-terminal 63-residue polypeptide fragment of the 434 repressor. Analysis of these spectra, which are representative for proteins of about 15 kDa when working at commonly used temperatures around 30 °C , demonstrates the efficiency of our approach for the assignment of medium-sized15 N/13C doubly labeled proteins.  相似文献   

4.
Biocycling of sulfur (S) has been proposed to play an important role in the recovery of ecosystems following anthropogenic S deposition. Here, we investigated the importance of the humus layer in the biocycling of S in three forested catchments in the Gårdsjön area of southwestern Sweden with differing S inputs and S isotope signature values. These experimental sites consisted of two reference catchments and the Gårdsjön roof experiment catchment (G1), where anthropogenic deposition was intercepted from 1991 until May 2002 by a roof placed over the entire catchment area. Under the roof, controlled levels of deposition were applied, using a sprinkler system, and the only form of S added was marine SO42− with a δ of +19.5‰.We installed ion exchange resin bags at the interface between the humus layer and mineral soil at each of the catchments to collect SO42− passing through the humus. The resin bags were installed on four occasions, in 1999 and 2000, covering two summer and two winter periods. The ions collected by each bag during these sampling periods were then eluted and their δ values and SO42− concentrations determined. The most striking result is that the average δ value in the resin bags was more than 12‰ lower compared to that of the sprinkler water in the G1 roof catchment. There was no increasing trend in the isotope value in the resin bag SO42− despite that the roof treatment has been on-going for almost 10 years; the average value for all resin bags was +7.1‰. The highest δ values found in the G1 roof catchment were between +11‰ and +12‰. However, these values were all obtained from resin bags installed at a single sampling location. Throughfall and resin bag δ values were more similar in the two reference catchments: about +7.5‰ in both cases. There was, however, an increase in resin bag δ values during the first winter period, from about +7‰ to +9‰. The resin bag δ value was linearly and positively related (r2 = 0.26, p < 0.001) to the amount of SO42− extracted from the resin bags, if relatively high amounts (>50 mmol m−2) were excluded. High amounts of resin bag SO42− seemed to be related to groundwater inputs, as indicated by the δ value. Our results suggest that rapid immobilization of SO42− into a large organic S pool may alter the S isotope value and affect the δ values measured in the mineral soil and runoff.  相似文献   

5.
Formate and phosphate affect substantially the rate of tyrosine D (TyrD) oxidation and the stability of the radical Tyr in Photosystem II [Hienerwadel R, Boussac A, Breton J and Berthomieu C (1996) Biochemistry 35: 15447–15460]. This observation prompted us to analyze the influence of formate and phosphate on the environment of TyrD using FTIR spectroscopy. The ν (CO) IR mode of Tyr at 1503 cm−1 remains unchanged whatever the buffer used at pH 6 and whether formate is present or not in the sample. Similarly, the main IR mode of reduced TyrD remains at ≈1250 cm−1 in all tested conditions. We thus conclude that formate does not modify the hydrogen-bonded interactions of TyrD and Tyr with neighbouring D2His189 and D2Gln164. In the TyrD-state, an IR mode of formate significantly different from that observed in solution, is detected using 13C-formate, showing that formate forms a strong electrostatic interaction within PS II. The presence of formate affects also IR bands that may be assigned to an arginine side chain. Upon Tyr formation, formate does not protonate but its binding interaction weakens. A proton uptake by Mes or phosphate buffer is detected, which is not observed when BisTris is used as a buffer. In these latter conditions, IR bands characteristic of the protonation of a carboxylate group of the protein are detected instead. The present IR data and the recent structural model of the TyrD environment proposed by Ferreira KN, Iverson TM, Maghlaoui K, Barber J and Iwata S [(2004) Science 303: 1831–1838], suggest that the proton released upon Tyr formation is shared within a hydrogen bonding network including D2Arg294, and CP47Glu364 and that perturbation of this network by formate – possibly binding near D2Arg294 – substantially affects the properties of TyrD.  相似文献   

6.
Summary A set of three-dimensional triple-resonance experiments is described which provide , , and coupling constants. The pulse sequences generate E.COSY-like multiplet patterns and comprise a magnetization transfer from the amide proton to the α-proton or vice versa via the directly bound heteronuclei. For residues with the 1Hα spin resonating close to the H2O signal, a modified HNCA experiment can be employed to measure the vicinal 1HN,1Hα couplings. Ambiguities associated with the conversion of values into ϕ-angle constraints for protein structure determination can be resolved with the knowledge of the heteronuclear 3J-couplings. In favourable cases, stereospecific assignments of glycine α-protons can be obtained by employing the experiments described here in combination with NOE data. The methods are applied to flavodoxin from Desulfovibrio vulgaris.  相似文献   

7.
Novel cross-correlated spin relaxation (CCR) experiments are described, which measure pairwise CCR rates for obtaining peptide dihedral angles Φ. The experiments utilize intra-HNCA type coherence transfer to refocus 2-bond coupling evolution and generate the or multiple quantum coherences which are required for measuring the desired CCR rates. The contribution from other coherences is also discussed and an appropriate setting of the evolution delays is presented. These CCR experiments were applied to 15N- and 13C-labeled human ubiquitin. The relevant CCR rates showed a high degree of correlation with the Φ angles observed in the X-ray structure. By utilizing these CCR experiments in combination with those previously established for obtaining dihedral angle Ψ, we can determine high resolution structures of peptides that bind weakly to large target molecules.  相似文献   

8.
It has been commonly recognized that residual dipolar coupling data provide a measure of quality for protein structures. To quantify this observation, a database of 100 single-domain proteins has been compiled where each protein was represented by two independently solved structures. Backbone 1H–15N dipolar couplings were simulated for the target structures and then fitted to the model structures. The fits were characterized by an R-factor which was corrected for the effects of non-uniform distribution of dipolar vectors on a unit sphere. The analyses show that favorable values virtually guarantee high accuracy of the model structure (where accuracy is defined as the backbone coordinate rms deviation). On the other hand, unfavorable values do not necessarily suggest low accuracy. Based on the simulated data, a simple empirical formula is proposed to estimate the accuracy of protein structures. The method is illustrated with a number of examples, including PDZ2 domain of human phosphatase hPTP1E. Electronic supplementary material Electronic supplementary material is available for this article at and accessible for authorised users.  相似文献   

9.
A simple linear relationship between the J coupling constant and the linewidth (1/2) of in-phase NMR peaks has been identified. This relationship permits the rapid and accurate determination of polypeptide J coupling constants from a simple inspection of amide cross peaks in homonuclear 1H TOCSY or 1H NOESY spectra. By using the appropriate set of processing parameters we show that J = 0.5(1/2) – MW/5000 + 1.8 for TOCSY spectra and J = 0.6(1/2) – MW/5000 – 0.9 for NOESY spectra, where 1/2 is the half-height linewidth in Hz and MW is the molecular weight of the protein in Da. The simplicity of this relationship, combined with the ease with which 1/2 measurements can be made, means that J coupling constants can now be rapidly determined (up to 100 measurements in less than 30 min) without the need for any complex curve-fitting algorithms. Tests on 11 different polypeptides involving more than 650 separate J measurements have shown that this method yields coupling constants with an rmsd error (relative to X-ray data) of less than 0.9 Hz. Furthermore, the correlation coefficient between the predicted NMR coupling constants and those derived from high-resolution X-ray crystal structures is typically better than 0.89. These simple linear relationships have been found to be valid for peptides as small as 1 kDa to proteins as large as 20 kDa. Despite the method's simplicity, these results are comparable to the accuracy and precision of the best techniques published to date.  相似文献   

10.
13C NMR spectra of several carbon monoxide (99.7% 13C and 11.8% 18O enriched) hemoprotein models with varying polar and steric effects of the distal organic superstructure and constraints of the proximal side are reported. This enables the 57Fe-13C(O) coupling constants ( ), 13C shieldings ((13C)), and 18O isotope effects on13 C shieldings (113C(18O/16O)) to be measured and hence comparisons with hemoproteins, C-O vibrational frequencies and X-ray structural data to be made. Negative polar interactions in the binding pocket and inhibition of Fe//CO back-donation or positive distal polar interactions with amide NH groups appear to have little direct effect on couplings. Similarly, the axial hindered base 1,2-dimethylimidazole has a minor effect on the values despite higher rates of CO desorption being observed for such complexes. On the contrary,13 C shieldings vary widely and an excellent correlation was found between the infrared C-O vibrational frequencies ((C-O)) and13 C shieldings and a reasonable correlation with18 O isotope effects on 13C shieldings. This suggests that (13C), (C-O) and1 13 C(18O/16O) are accurate monitors of the multiple mechanisms by which steric and electronic interactions are released in superstructured heme model compounds. The 13C shieldings of heme models cover a 4.0 ppm range which is extended to 7.0 ppm when several HbCO and MbCO species at different pH values are included. The latter were found to obey a similar linear (13 (13C) versus (C-O) relationship, which proves that both heme models and heme proteins are homogeneous from the structural and electronic viewpoint. Our results suggest that (C-O), (13C) and 113C(18O/16O) measurements reflect similar interaction which is primarily the modulation of back-bonding from the Fe d to the CO * orbital by the distal pocket polar interactions. The lack of correlation between1 13 C(18O/16O) and crystallographic CO bond lengths (r(C-O)) reflects significant uncertainties in the X-ray determination of the carbon and oxygen positions.  相似文献   

11.
A novel NMR pulse sequence is introduced to determine the glycosidic torsion angle χ in 13C,15N-labeled oligonucleotides. The quantitative Γ-HCNCH measures the dipolar cross-correlated relaxation rates (pyrimidines) and (purines). Cross-correlated relaxation rates of a 13C,15N-labeled RNA 14mer containing a cUUCGg tetraloop were determined and yielded χ-angles that agreed remarkably well with data derived from the X-ray structure of the tetraloop. In addition, the method was applied to the larger stemloop D (SLD) subdomain of the Coxsackievirus B3 cloverleaf 30mer RNA and the effect of anisotropic rotational motion was examined for this molecule. It could be shown that the χ-angle determination especially for nucleotides in the anti conformation was very accurate and the method was ideally suited to distinguish between the syn and the anti-conformation of all four types of nucleotides. Electronic Supplementary Material The online version of this article (doi:) contains supplementary material, which is available to authorized users.  相似文献   

12.
The motional properties of the cyclic enterobacterial common antigen (cECA), consisting of four trisaccharide repeat units, have been investigated by carbon-13 spin relaxation. R1, R2 and NOE relaxation parameters have been determined at three magnetic field strengths. The data were interpreted within the model-free framework to include the possibility of motional anisotropy, and overall as well as local dynamical parameters were fitted separately for each ring carbon. The motional anisotropy was addressed by assuming an axially symmetric diffusion tensor, which was fitted from the overall correlation times for each site in the sugar residues using the previously determined crystal structure. The data were found to be in agreement with an oblate shape of the molecule, and the values for Diso and were in good agreement with translational diffusion data and an estimate based on calculation of the moment of inertia tensor, respectively. The local dynamics in cECA were found to be residue-dependent. Somewhat lower values for the order parameters, as well as longer local correlation times, were observed for the -linked ManNAcA residue compared to the two -linked residues in the trisaccharide repeat unit.  相似文献   

13.
A method is presented to determine both and backbone angles in proteins simultaneously. This is achieved by measuring the effect on two-spin coherences of cross-correlation between 15 N-1HN and 13 vectors. The cross-correlation rates are obtained by comparing two complementary three-dimensional experiments.  相似文献   

14.
Summary A simple heteronuclear relayed E.COSY pulse sequence with a minimum number of pulses is proposed for the quantitative determination of heteronuclear three-bond J-coupling constants in uniformly 13C-enriched polypeptide samples. Numerous heteronuclear three-bond coupling constants, including , , , and , can be determined for each residue from a single heteronuclear relayed E.COSY spectrum. Couplings relevant for stereospecific assignments as well as for the determination of dihedral angles in the amino acid backbone and in side chains are obtained. The method is demonstrated on the uniformly 13C-enriched decapeptide antamanide (-Val1-Pro2-Pro3-Ala4-Phe5-Phe6-Pro7-Pro8-Phe9-Phe10-).  相似文献   

15.
Heteronuclear NMR spin relaxation studies of conformational dynamics are coming into increasing use to help understand the functions of ribozymes and other RNAs. Due to strong magnetic interactions within the ribose ring, however, these studies have thus far largely been limited to 13C and 15N resonances on the nucleotide base side chains. We report here the application of the alternate-site 13C isotopic labeling scheme, pioneered by LeMaster for relaxation studies of amino acid side chains, to nucleic acid systems. We have used different strains of E. coli to prepare mononucleotides containing 13C label in one of two patterns: Either C1′ or C2′ in addition to C4′, termed (1′/2′,4′) labeling, or nearly complete labeling at the C2′ and C4′ sites only, termed (2′,4′) labeling. These patterns provide isolated H spin systems on the labeled carbon atoms and thus allow spin relaxation studies without interference from scalar or dipolar coupling. Using relaxation studies of AMP dissolved in glycerol at varying temperature to produce systems with correlation times characteristic of different size RNAs, we demonstrate the removal of errors due to interaction in T 1 measurements of larger nucleic acids and in T measurements in RNA molecules. By extending the applicability of spin relaxation measurements to backbone ribose groups, this technology should greatly improve the flexibility and completeness of NMR analyses of conformational dynamics in RNA.  相似文献   

16.
Summary Quantitative J-correlation and triple-resonance ECOSY-type experiments are used to unambiguously establish the presence of four-bond sequential HN-H J-couplings in the protein staphylococcal nuclease. Substantially negative values, ranging from -0.8 to -2.3 Hz, are observed when the angle is near +120°, and the following angle near +60°. For other conformations, the four-bond HN-H J-couplings fall between -0.5 and +0.5 Hz.  相似文献   

17.
During the last 60 years, pollution of the groundwater with has greatly increased in many parts of Europe, as a consequence of excessive use of manure and synthetic fertilisers. Monitoring of groundwater-fed wetlands indicated that sediments with high concentrations had the lowest Fe and concentrations in the pore water. A comparison of two restored open water fens, differing in supply via the groundwater, indicated that the redox potential and the sulphate ( ) reduction rate were lower when the groundwater contained not only but also high concentrations. The lower reduction rates in the -rich open water fen were associated with lower concentrations and the presence of plant species characteristic of clear water. In contrast, the higher reduction rates in the -poor open water fen were associated with very high concentrations and massive development of plant species characteristic of eutrophic environments. Investigations at -rich seepage sites in black alder carrs, showed that high concentrations in the pore water caused chlorosis in the alder carr vegetation, due to lower availability of Fe in the pore water and less Fe uptake by the plants. Experimental desiccation of sediments proved that the -rich seepage sites contained no oxidisable FeS x , contrary to -poor locations, which became acidified and mobilised extremely high amounts of due to FeS x oxidation. A laboratory experiment showed that addition to sediments led to reduced releases of Fe, and S2–, very likely due to the oxidation of reduced Fe and S compounds. Overall, the results confirmed that is an energetically more favourable electron acceptor in anaerobic sediments than Fe and , and that high loads function as a redox buffer, preventing reduction of Fe and . Limited reduction prevents S2– -mediated mobilisation of from Fe- complexes. At a higher redox potential, reduced Fe, including FeS x , was oxidised, increasing the content of Fe(III) capable of binding . This prevented increased availability and the concomitant massive development of plant species characteristic of eutrophic environments.  相似文献   

18.
Summary Toluene diisocyanate (TDI) is widely used as a chemical intermediate in the production of polyurethane products such as foams, coatings, and elastomers. In exposed workers, chronic inhalation of TDI has resulted in significant decreases in lung function. TDI-induced asthma is related to its disturbance of acetylcholine in most affected workers but the actions of TDI on nicotinic acetylcholine receptors (nAChR) are unclear. In order to understand the role of TDI acting on nAChR, we used human neuroblastoma SH-SY5Y cells to investigate the effects of TDI on cytosolic free calcium concentration ([Ca ) changes under the stimulation of nAChR. The results showed that TDI was capable of inhibiting the [Ca rise induced by nicotinic ligands, epibatidine, DMPP and nicotine. The inhibition was remained, even increased after chronic treatment of TDI. Our study of TDI acting on human nAChR suggests a possibility that the human nerve system plays some role in the toxicity of TDI in the pulmonary system.  相似文献   

19.
Summary The PR-like proteins, class I -1,3-glucanase (GLU I) and chitinase (CHN I), are induced as part of a stereotypic response that can provide protection against viral, bacterial, and fungal pathogens. We have identified two Nicotiana plumbaginifolia ankyrin-repeat proteins, designated lucanohydrolase inding roteins (GBP) 1 and 2, that bind GLU I and CHN I both in vitro and when expressed in yeast cells. Sense as well as antisense transformants of tobacco carrying the GBP1 gene elaborated graft-transmissible acropetally moving signals that induced the downward curling of young leaves. This phenotype was associated with reduced starch, sucrose, and fructose accumulation; the formation of necrotic lesions; and, the induction of markers for the hypersensitive response. GBP1/2 are members of a conserved lant-specific yrin- repeat (PANK) family that includes proteins implicated in carbohydrate allocation, reactive oxygen metabolism, hypersensitive cell death, rapid elicitor responses, virus pathogenesis, and auxin signaling. The similarity in phenotype of PANK transformants and transformants altered in carbohydrate metabolism leads us to propose that PANK family members are multifunctional proteins involved in linking plant defense responses and carbohydrate metabolism.  相似文献   

20.
We previously showed that activation of the cystic fibrosis (CF) transmembrane conductance regulator (CFTR) Cl conductance (gCFTR) supports parallel activation of amiloride-sensitive epithelial Na+ channel (ENaC) in the native human sweat duct. However, it is not clear whether phosphorylated CFTR, phosphorylated ENaC, or only Cl -channel function is required for activation. We used basilaterally α-toxin-permeabilized human sweat ducts to test the hypothesis that ENaC activation depends only on Cl -channel function and not on phosphorylation of either CFTR or ENaC. CFTR is classically activated by PKA plus millimolar ATP, but cytosolic glutamate activation of gCFTR is independent of ATP and phosphorylation. We show here that both phosphorylation-dependent (PKA) and phosphorylation-independent (glutamate) activation of CFTR Cl channel function support gENaC activation. We tested whether cytosolic application of 5 mM ATP alone, phosphorylation by cAMP, cGMP, G-protein dependent kinases (all in the presence of 100 μM ATP), or glutamate could support ENaC activation in the absence of gCFTR. We found that none of these agonists activated gENaC by themselves when Cl current ( ) through CFTR was blocked by: 1) Cl removal, 2) DIDS inhibition, 3) lowering the ATP concentration to 100 μM (instead of 5 mM required to support CFTR channel function), or 4) mutant CFTR (homozygous ΔF508 CF ducts). However, Cl gradients in the direction of absorption supported, while Cl gradients in the direction of secretion prevented ENaC activation. We conclude that the interaction between CFTR and ENaC is dependent on activated through CFTR in the direction of absorption (Cl gradient from lumen to cell). But such activation of ENaC is independent of phosphorylation and ATP. However, reversing through CFTR in the direction of secretion (Cl gradient from cell to lumen) prevents ENaC activation even in the presence of through CFTR. An erratum to this article is available at .  相似文献   

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