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1.
2.
Dynamics and structure of (1–36)bacteriorhodopsin solubilized in chloroform/methanol mixture (1:1) were investigated by 1H-15N NMR spectroscopy under a hydrostatic pressure of 2000 bar. It was shown that the peptide retains its spatial structure at high pressure. 15N transverse and longitudinal relaxation times, 15N{1H} nuclear Overhauser effects, chemical shifts and the translation diffusion rate of the peptide at 2000 bar were compared with the respective data at ambient pressure [Orekhov et al. (1999) J. Biomol. NMR, 14, 345–356]. The model free analysis of the relaxation data for the helical 9–31 fragment revealed that the high pressure decreases the overall rotation and translation diffusion, as well as apparent order parameters of fast picosecond internal motions (S2 f) but has no effect on internal nanosecond motions (S2 s and s) of the peptide. The decrease of translation and overall rotation diffusion was attributed to the increase in solvent viscosity and the decrease of apparent order parameters S2 f to a compression of hydrogen bonds. It is suggested that this compression causes an elongation of H-N bonds and a decrease of absolute values of chemical shift anisotropy (CSA). In particular, the observed decrease of S2 f at 2000 bar can be explained by 0.001 nm increase of N-H bond lengths and 10 ppm decrease of 15N CSA values.  相似文献   

3.
We present NMR and μ+SR study of spin dynamics in one-dimensional and quasi-one-dimensional molecular magnets of recent synthesis. In particular, we focus on the so called Gd(hfac)3NIT-R and CoPhOMe magnetic chains families. For Gd-R helimagnets we show some differences between “weakly frustrated systems” and “fully frustrated systems”. The different behaviour is due to the different radical inserted in the chains (R = Me, Ph for “weakly frustrated systems” and R = iPr, Et for “fully frustrated systems”). The existence of different phase transitions, particularly to 3D long-range magnetic order in Gd-Ph and to chiral order in Gd-iPr, is remarked together with a comparison between results obtained from macroscopic and microscopic investigating techniques. As regards CoPhOMe slowly relaxing chain, the 1H NMR measurements confirm the freezing of the spins at low temperature, which prevents the 3D long-range order, and display the presence of two relaxation mechanisms related to distinct contributions to the local spin relaxation.  相似文献   

4.
Molecular dynamics simulations of the structurally homologous proteins TNfn3 and FNfn10 have been used to investigate the contributions to side-chain dynamics measured by NMR relaxation experiments. The results reproduce the variation in core side-chain dynamics observed by NMR and highlight the relevance of anharmonic motion and transitions between local minima for explaining NMR side-chain order parameters. A method is described for calculating converged order parameters by use of replica exchange molecular dynamics in conjunction with an implicit solvent model. These simulations allow the influence of various factors, such as the flexibility of side-chains and their free volume, on the mobility to be tested by perturbing the system. Deletion mutations are found to have the largest effect on the more densely packed FNfn10. Some counterintuitive effects are seen, such as an increase in order parameters close to deletion mutation sites, but these can be rationalized in terms of direct interactions with the modified side-chains. A statistical analysis of published order parameters supports the conclusions drawn from the simulations.  相似文献   

5.
Amyloid β-peptide (Aβ) is a major component of plaques in Alzheimer's disease, and formation of senile plaques has been suggested to originate from regions of neuronal membrane rich in gangliosides. We analyzed the mode of interaction of Aβ with lipid bilayers by multinuclear NMR using 31P nuclei. We found that Aβ (1-40) strongly perturbed the bilayer structure of dimyristoylphosphatidylcholine (DMPC), to form a non-lamellar phase (most likely micellar). The ganglioside GM1 potentiated the effect of Aβ (1-40), as viewed from 31P NMR. The difference of the isotropic peak intensity between DMPC/Aβ and DMPC/GM1/Aβ suggests a specific interaction between Aβ and GM1. We show that in the DMPC/GM1/Aβ system there are three lipid phases, namely a lamellar phase, a hexagonal phase and non-oriented lipids. The latter two phases are induced by the presence of the Aβ peptide, and facilitated by GM1.  相似文献   

6.
Summary The backbone dynamics of uniformly 15N-labelled fragments (residues 1–71 and 1–36) of bacterioopsin, solubilized in two media (methanol-chloroform (1:1), 0.1 M 2HCO2NH4, or SDS micelles) have been investigated using 2D proton-detected heteronuclear 1H-15N NMR spectroscopy at two spectrometer frequencies, 600 and 400 MHz. Contributions of the conformational exchange to the transverse relaxation rates of individual nitrogens were elucidated using a set of different rates of the CPMG spin-lock pulse train and were essentially suppressed by the high-frequency CPMG spin-lock. We found that most of the backbone amide groups of (1–71)bacterioopsin in SDS micelles are involved in the conformational exchange process over a rate range of 103 to 104 s-1. This conformational exchange is supposed to be due to an interaction between two -helixes of (1–71)bacterioopsin, since the hydrolysis of the peptide bond in the loop region results in the disappearance of exchange line broadening. 15N relaxation rates and 1H-15N NOE values were interpreted using the model-free approach of Lipari and Szabo [Lipari, G. and Szabo, A. (1982) J. Am. Chem. Soc., 104, 4546–4559]. In addition to overall rotation of the molecule, the backbone N-H vectors of the peptides are involved in two types of internal motions: fast, on a time scale <20 ps, and intermediate, on a time scale close to 1 ns. The intermediate dynamics in the -helical stretches was mostly attributed to bending motions. A decrease in the order parameter of intermediate motions was also observed for residues next to Pro50, indicating an anisotropy of the overall rotational diffusion of the molecule. Distinctly mobile regions are identified by a large decrease in the order parameter of intermediate motions and correspond to the N- and C-termini, and to a loop connecting the -helixes of (1–71)bacterioopsin. The internal dynamics of the -helixes on the millisecond and nanosecond time scales should be taken into account in the development of a model of the functioning bacteriorhodopsin.Abbreviations BO bacterioopsin - 2D two-dimensional - CPMG Carr-Purcell-Meiboom-Gill (Carr and Purcell, 1954) - SDS sodium dodecyl(2H25) sulfate - R(Sx), R(Sz) 15N transverse and longitudinal relaxation rates, respectively  相似文献   

7.
The structure and bonding properties of a number of closely related tetraphenyltin- and triphenyltin chloride compounds have been studied by the 119Sn Mössbauer effect and multinuclear NMR spectroscopy. The comparison of liquid and solid state 13C and 119Sn NMR spectra and of glassy solution matrix and neat solid state Mössbauer spectra provides information about the extent of intermolecular association effects in these compounds. The results indicate that all materials with the exception of (p-CF3Ph)3SnCl are adequately described as monomeric solids with tetrahedral geometry around the metal atom. For the latter compound spectroscopic evidence for the presence of a five-coordinated tin species is presented.  相似文献   

8.
This report describes the backbone amide dynamics of the uniformly 15N labeled catalytic domain of human stromelysin complexed to PNU-99533, a hydroxamate-containing ligand that binds to the S1-S3 region (right side) of the stromelysin active site, and to PNU-107859 and PNU-142372, both thiadiazole-containing ligands that bind to the S1-S3 region (left side) of the stromelysin active site. 15N R1, R2 and NOE NMR relaxation measurements were recorded and analyzed for each complex. Different dynamic behaviors were observed for stromelysin complexed to the two classes of ligands, indicating that it may be possible to use protein dynamics to distinguish between different binding orientations. In the absence of bound ligand at the S1-S3 subsites, the S1-S3 residues were found to be relatively rigid. In contrast, the S1-S3 subsites were found to be flexible in the absence of interactions with ligand. The relative rigidness of the S1-S3 subsites may be responsible for MMP binding specificity by discriminating between ligands of different shapes. By contrast, the inherent flexibility of the S1-S3 subsites allows structural rearrangement to accommodate a broad range of incoming substrates or inhibitors. Similarities and differences in dynamics observed for each complex provide insights into the interactions responsible for protein–ligand recognition. The relevance of protein dynamics to structure-based drug design is discussed.  相似文献   

9.
Protein disulfide isomerase (PDI) is a multifunctional protein of the endoplasmic reticulum, which catalyzes the formation, breakage and rearrangement of disulfide bonds during protein folding. It consists of four domains designated a, b, b and a. Both a and a domains contain an active site with the sequence motif -Cys-Gly-His-Cys- involved directly in thiol-disulfide exchange reactions. As expected these domains have structures very similar to the ubiquitous redox protein thioredoxin. A low-resolution NMR structure of the b domain revealed that this domain adopts a fold similar to the PDI a domain and thioredoxin [Kemmink, J., Darby, N.J., Dijkstra, K., Nilges, M. and Creighton, T.E. (1997) Curr. Biol., 7, 239–245]. A refined ensemble of solution structures based on the input of 1865 structural restraints shows that the structure of PDI b is well defined throughout the complete protein except for about 10 residues at the C-terminus of the sequence. 15N relaxation data show that these residues are disordered and not part of this structural domain. Therefore the domain boundaries of PDI can now be fixed with reasonable precision. Structural comparison of the PDI b domain with thioredoxin and PDI a reveals several features important for thiol-disulfide exchange activity.  相似文献   

10.
Summary The 15N relaxation rates of the -aminoisobutyric acid (Aib)-rich peptide alamethicin dissolved in methanol at 27°C and 5°C, and dissolved in aqueous sodium dodecylsulfate (SDS) at 27°C, were measured using inverse-detected one-and two-dimensional 1H–15N NMR spectroscopy. Measurements of 15N longitudinal (RN(Nz)) and transverse (RN(Nx,y)) relaxation rates and the {1H} 15N nuclear Overhauser enhancement (NOE) at 11.7 Tesla were used to calculate (quasi-) spectral density values at 0, 50, and 450 MHz for the peptide in methanol and in SDS. Spectral density mapping at 0, 50, 450, 500, and 550 MHz was done using additional measurements of the 1H–15N lingitudinal two-spin order, RNH(2H infZ supN NZ), two-spin antiphase coherence, RNH(2H infN supZ Nx,y), and the proton longitudinal relaxation rate, RH(H infN supZ ), for the peptide dissolved in methanol only. The spectral density of motions was also modeled using the three-parameter Lipari-Szabo function. The overall rotational correlation times were determined to be 1.1, 2.5, and 5.7 ns for alamethicin in methanol at 27°C and 5°C, and in SDS at 27°C, respectively. From the rotational correlation time determined in SDS the number of detergent molecules associated with the peptide was estimated to be about 40. The average order parameter was about 0.7 and the internal correlation times were about 70 ps for the majority of backbone amide 15N sites of alamethicin in methanol and in SDS. The relaxation data, spectral densities, and order parameters suggest that the peptide N-H vectors of alamethicin are not as highly constrained as the core regions of folded globular proteins. However, the peptide backbone is clearly not as mobile as the most unconstrained regions of folded proteins, such as those found in the frayed C-and N-termini of some proteins, or in randomcoil peptides. The data also suggest significant mobility at both ends of the peptide dissolved in methanol. In SDS the mobility in the middle and at the ends of the peptide is reduced. The implications of the results with respect to the sterically hindered Aib residues and the biological activities of the peptide are discussed.To whom correspondence should be addressed.  相似文献   

11.
12.
15N R2 relaxation measurements are key for the elucidation of the dynamics of both folded and intrinsically disordered proteins (IDPs). Here we show, on the example of the intrinsically disordered protein α-synuclein and the folded domain PDZ2, that at physiological pH and near physiological temperatures amide—water exchange can severely skew Hahn-echo based 15N R2 relaxation measurements as well as low frequency data points in CPMG relaxation dispersion experiments. The nature thereof is the solvent exchange with deuterium in the sample buffer, which modulates the 15N chemical shift tensor via the deuterium isotope effect, adding to the apparent relaxation decay which leads to systematic errors in the relaxation data. This results in an artificial increase of the measured apparent 15N R2 rate constants—which should not be mistaken with protein inherent chemical exchange contributions, Rex, to 15N R2. For measurements of 15N R2 rate constants of IDPs and folded proteins at physiological temperatures and pH, we recommend therefore the use of a very low D2O molar fraction in the sample buffer, as low as 1%, or the use of an external D2O reference along with a modified 15N R2 Hahn-echo based experiment. This combination allows for the measurement of Rex contributions to 15N R2 originating from conformational exchange in a time window from µs to ms.  相似文献   

13.
Three methods were used to study N2 fixation and effects ofwater deficit on N2 fixation: C2H2 reduction assay (ARA), 15Ndilution technique and accumulated N content. In addition, 15Ndilution was calculated both in a traditional way and in a modifiedway, which takes into consideration N and 15N content for theplants before the experiment started. The three methods wereapplied on the following Rhizobium-symbioses: Acacia albidaDel (Faidherbia albida (Del) A. Chev.) and Leucaena leucocephala(Lam) de Wit., and the Frankia-symbiosis Casuarina equisetifoliaL. The plants wereabout 4-months-old when they were harvested. Nitrogen derived from N2 fixation in control plants of Acaciaalbida was 54·2 mg as measured with ARA, while it was28·5 mg as measured with the 15N dilution technique,compared to 30·7 mg calculated as accumulated N. In comparison,L. leucocephala fixed 41·6 mg N (ARA), 53·5 mgN(15N dilution technique) and 56·3 mg N (accumulatedN). The Frankia-symbiosis had fixed 27·4 mg N as measuredby ARA, 8·1 mg N as measured by 15N dilution techniqueand 12·3 mg N as accumulated N. There were no differencesbetween the estimates based ontraditional and modified waysof calculating 15N dilution. The immediate effect of water deficit treatment on N2 fixationwas continuously measured inall species with ARA, which startedto decrease approximately 10 d after the initiation of the treatment,and declined to less than 5% of the initial level after 21–28d. The decrease in the amount of N derived from N2 fixation wasstudied in L. leucocephala during the period of treatment. Therewas a 26% decrease in amount of N derived from N2 fixation asresult of water deficit (as measured with ARA), while the decreasewas 23% when measured withboth the 15N dilution method and asaccumulated N. The three different methods for measuring N2 fixation and effectsof water deficit on N2 fixation are discussed. Key words: Acacia albida, ARA, Casuarina equisetifolia, Leucaena leucocephala, 15N dilution, N2N fixation, water deficit  相似文献   

14.
(1) High-resolution 31P-NMR was used to study the environment of the phosphoserine residues of the phosphoproteins, αs1-casein B, β-casein A2 and β-casein C. For reference purposes 31P-NMR spectra of phosvitin and ovalbumin were also collected. (2) 31P resonances were assigned to specific phosphoserine residues as a result of comparisons of the high-resolution 31P-NMR spectra for αs1- and β-caseins and for peptide fragments of these proteins obtained by cyanogen bromide and trypsin cleavage. (3) Measurements of the enhancement of the relaxation rate for water protons (1H) on addition of Mn2+ to αs1-casein B and to a fragment αs1-CN3, obtained by cyanogen bromide cleavage, gave approximate pK values for the binding groups and suggest the possibility of a conformational change induced by varying the concentration of divalent cation.  相似文献   

15.
A combination of three heteronuclear three-dimensional NMR experiments tailored for sequential resonance assignments in uniformly 15N, 13C-labeled flexible polypeptide chains is described. The 3D (H)N(CO-TOCSY)NH, 3D (H)CA(CO-TOCSY)NH and 3D (H)CBCA(CO-TOCSY)NH schemes make use of the favorable 15N chemical shift dispersion in unfolded polypeptides, exploit the slow transverse 15N relaxation rates of unfolded polypeptides in high resolution constant-time [1H, 15N]-correlation experiments, and use carbonyl carbon homonuclear isotropic mixing to transfer magnetization sequentially along the amino acid sequence. Practical applications are demonstrated with the 100-residue flexible tail of the recombinant human prion protein, making use of spectral resolution up to 0.6 Hz in the 15N dimension, simultaneous correlation with the two adjacent amino acid residues to overcome problems associated with spectral overlap, and the potential of the presently described experiments to establish nearest-neighbor correlations across proline residues in the amino acid sequence.  相似文献   

16.
The role of glucocorticoids in regulating the rate of muscle protein breakdown was evaluated by measuring excretion of N(tau)-methylhistidine during administration of various doses of corticosterone to adrenalectomized rats. Groups of rats received daily subcutaneous injections of 0, 0.2, 0.5, 1.0, 5.0 or 10.0mg of corticosterone/day per 100g body wt. for 7 days, followed by 3 days without hormone treatment, after which they were killed. A group with intact adrenal glands served as an additional control. All animals were pair-fed with the untreated adrenalectomized group. No significant differences were noted in growth rate or N(tau)-methylhistidine excretion between the intact or adrenalectomized control groups, or those given 0.2, 0.5 and 1.0mg of corticosterone, whereas growth ceased and N(tau)-methylhistidine excretion rose markedly in the groups receiving 5 and 10mg of corticosterone. After these two high doses of corticosterone, but not after lower doses, there was a loss of weight of the gastrocnemius muscle per 100g of final body wt., but not of the soleus and extensor digitorum longus muscles. The two highest doses of corticosterone also resulted in an increase in liver weight per 100g of final body wt. Lower doses of corticosterone did not cause these changes. Plasma corticosterone concentrations, measured on the final day of injection and again at the time of killing, were decreased to near zero by adrenalectomy and were little raised by doses of 0.2 and 0.5mg daily, but were increased to within the normal range by the 1mg dose. At 5 and 10mg doses, plasma corticosterone concentrations were sustained at 2-3 times those of intact rats, and thus in the range reported for rats exposed to severe stress. Rats given 5 and 10mg doses of corticosterone had glycosuria, and showed considerably elevated concentrations of insulin in the plasma. It is concluded that plasma concentrations of glucocorticoids within the normal range do not regulate the rate of muscle protein breakdown, whereas excessive plasma concentrations of corticosteroids, equivalent to those observed in severe stress, can accelerate muscle protein breakdown.  相似文献   

17.
Summary The influence of the internal dynamics of two polypeptides comprising transmembrane -helix A or two -helices A and B of bacterioopsin on experimentally accessible 15N NMR relaxation rates was investigated by molecular dynamics (MD) simulations, combined with more simple mechanic considerations. Model-free order parameters and correlation times of internal motions [Lipari, G. and Szabo, A. (1982) J. Am. Chem. Soc., 104, 4546–4559] were calculated for these models. It was found that both peptides exhibit two types of internal motions of the amide bonds, on the pico- and nanosecond time scales, affecting 15N NMR relaxation. The fast fluctuations are local and correspond to the librational motions of the individual N–H vectors in an effective potential of atoms of the surrounding matrix. In contrast, the motions on the nanosecond time scale imply concerted collective vibrations of a large number of atoms and could be represented as bending oscillation of -helices, strongly overdamped by the ambient solvent. A few other molecular mechanisms of slow internal motion were found, such as local distortions of the -helices (e.g., -aneurysm), delocalized distortions of the -helical backbone, as well as oscillations of the tilt angle between the axes of the -helices A and B. The results are compared with 15N NMR relaxation data measured for the (1–36)bacterioopsin and (1–71)bacterioopsin polypeptides in chloroform-methanol (1:1) and in SDS micelles [Orekhov, V.Yu., Pervushin, K.V. and Arseniev, A.S. (1994) Eur. J. Biochem., 219, 887–896].Abbreviations C2 baeterioopsin-(7–63)-peptide - sA bacterioopsin-(7–32)-peptide - CPMG Carr-Purcell-Meiboom-Gill - MD molecular dynamics - rmsd root-mean-square deviation  相似文献   

18.
It is becoming increasingly apparent that proteins are not static entities and that their function often critically depends on accurate sampling of multiple conformational states in aqueous solution. Accordingly, the development of methods to study conformational states in proteins beyond their ground-state structure (“excited states”) has crucial biophysical importance. Here we investigate experimental schemes for optimally probing chemical exchange processes in proteins on the micro- to millisecond timescale by 15N R relaxation dispersion. The schemes use selective Hartmann–Hahn cross-polarization (CP) transfer for excitation, and derive peak integrals from 1D NMR spectra (Korzhnev et al. in J Am Chem Soc 127:713–721, 2005; Hansen et al. in J Am Chem Soc 131:3818–3819, 2009). Simulation and experiment collectively show that in such CP-based schemes care has to be taken to achieve accurate suppression of undesired off-resonance coherences, when using weak spin-lock fields. This then (i) ensures that relaxation dispersion profiles in the absence of chemical exchange are flat, and (ii) facilitates extraction of relaxation dispersion profiles in crowded regions of the spectrum. Further improvement in the quality of the experimental data is achieved by recording the free-induction decays in an interleaved manner and including a heating-compensation element. The reported considerations will particularly benefit the use of CP-based R relaxation dispersion to analyze conformational exchange processes in larger proteins, where resonance line overlap becomes the main limiting factor.  相似文献   

19.
A computational method, to predict the pKa values of the ionizable residues Asp, Glu, His, Tyr, and Lys of proteins, is presented here. Calculation of the electrostatic free-energy of the proteins is based on an efficient version of a continuum dielectric electrostatic model. The conformational flexibility of the protein is taken into account by carrying out molecular dynamics simulations of 10 ns in implicit water. The accuracy of the proposed method of calculation of pKa values is estimated from a test set of experimental pKa data for 297 ionizable residues from 34 proteins. The pKa-prediction test shows that, on average, 57, 86, and 95% of all predictions have an error lower than 0.5, 1.0, and 1.5 pKa units, respectively. This work contributes to our general understanding of the importance of protein flexibility for an accurate computation of pKa, providing critical insight about the significance of the multiple neutral states of acid and histidine residues for pKa-prediction, and may spur significant progress in our effort to develop a fast and accurate electrostatic-based method for pKa-predictions of proteins as a function of pH.  相似文献   

20.

Background and aims

The inoculation of cereal crops with plant growth-promoting bacteria (PGPB) is a potential strategy to improve fertilizer-N acquisition by crops in soils with low capacity to supply N. A study was conducted to assess the impact of three inoculants on grain yield, protein content, and urea-15 N recovery in maize (Zea mays L.) under Cerrado soil and climate conditions.

Methods

The main treatments included inoculants containing (i) Azospirillum brasilense strain Sp245, (ii) A. brasilense strains AbV5 + AbV6, (iii) Herbaspirillum seropedicae strain ZAE94, and (iv) a non-inoculated control. The subtreatments were (i) urea-N fertilization (100 kg N ha?1) at 30 days after sowing and (ii) no N addition at the stage. To determine fertilizer-N recovery, 15N–labelled urea was applied in microplots.

Results

Inoculants carrying A. brasilense improved urea-15 N acquisition efficiency in maize and also improved grain yield compared to the non-inoculated control, while urea-N fertilization enhanced grain quality by providing higher protein content.

Conclusion

Our results suggest that the inoculation of maize grains with PGPB represents a strategy to improve fertilizer-N recovery and maize yield in Cerrado soil with a low capacity to supply N.
  相似文献   

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