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1.
Water suppression by selective preirradiation is increasingly difficult to achieve on probeheads with high quality factor because of the opposing forces of radiation damping. Here we show that a simple modification to the WET scheme provides reliable water suppression in aqueous solutions of proteins and peptides with minimal saturation of the Hα protons. The scheme is shown to work also with dilute peptide solutions. It is recommended to maintain the water suppression during the evolution time of COSY experiments by weak selective irradiation that causes only minimal Bloch-Siegert shifts. The new water-suppression scheme suppresses the water magnetization by spatial scrambling. Traditional water suppression by preirradiation is similarly based more on water scrambling due to the radiofrequency inhomogeneity than on relaxation effects.Electronic Supplementary Material Electronic Supplementary material is available for this article at and accessible for authorised users.  相似文献   

2.
This paper considers stages of the search (initiated by V. P. Skulachev) for a receptor protein for fatty acids that is involved in their uncoupling effect. Based on these studies, mechanism of the ADP/ATP antiporter involvement in the uncoupling induced by fatty acids was proposed (Skulachev, V. P. (1991) FEBS Lett., 294, 158– 162). New data (suppression by carboxyatractylate of the SDS-induced uncoupling, pH-dependence of the ADP/ATP and the glutamate/aspartate antiporter contributions to the uncoupling, etc.) led to modification of this hypothesis. During discussion of the uncoupling effect of fatty acids caused by opening of the Ca2+-dependent pore, special attention is given to the effects of carboxyatractylate added in the presence of ADP. The functioning of the uncoupling protein UCP2 in kidney mitochondria is considered, as well as the diversity observed by us in effects of 200 µM GDP on decrease in under the influence of oleic acid added after H2O2 (in the presence of succinate, oligomycin, malonate). A speculative explanation of the findings is as follows: 1) products of lipid and/or fatty acid peroxidation (PPO)modify the ADP/ATP antiporter in such a way that its involvement in the fatty acid-induced uncoupling is suppressed by GDP; 2) GDP increases the PPO concentration in the matrix by suppression of efflux of fatty acid hydroperoxide anions through the UCP (Goglia, F., and Skulachev, V. P. (2003) FASEB, 17, 1585–1591)and/or of efflux of PPO anions with involvement of the GDP-sensitive ADP/ATP antiporter; 3) PPO can potentiate the oleate-induced decrease in due to inhibition of succinate oxidation.Translated from Biokhimiya, Vol. 70, No. 2, 2005, pp. 197–202.Original Russian Text Copyright © 2005 by Mokhova, Khailova.This revised version was published online in April 2005 with corrections to the post codes.  相似文献   

3.
Summary Gradient-enhanced versions of the homonuclear TOCSY experiment are described, with solvent suppression and sensitivity superior to that of a conventional TOCSY experiment. The pulse sequences are constructed by appending a WATERGATE module to a z-filtered TOCSY experiment. Pulsed-field gradients and appropriately phased selective rf pulses are used to maintain precise control of the water magnetization vector. Problems associated with radiation damping and spin-locking of the water magnetization are thus alleviated. The water magnetization is returned to equilibrium prior to each acquisition, which improves water suppression and minimizes signal losses due to saturation transfer.  相似文献   

4.
Summary The backbone dynamics of free ribonuclease T1 and its complex with the competitive inhibitor 2GMP have been studied by 15N longitudinal and transverse relaxation experiments, combined with {1H, 15H} NOE measurements. The intensity decay of individual amide cross peaks in a series of (1H, 15N)-HSQC spectra with appropriate relaxation periods (Kay, L.E. et al. (1989) Biochemistry, 28, 8972–8979; Kay, L.E. et al. (1992) J. Magn. Reson., 97, 359–375) was fitted to a single exponential by using a simplex algorithm in order to obtain 15N T1 and T2 relaxation times. These experimentally obtained values were analysed in terms of the model-free approach introduced by Lipari and Szabo (Lipari, G. and Szabo, A. (1982) J. Am. Chem. Soc., 104, 4546–4559; 4559–4570). The microdyramical parameters accessible by this approach clearly indicate a correlation between the structural flexibility and the tertiary structure of ribonuclease T1, as well as restricted mobility of certain regions of the protein backbone upon binding of the inhibitor. The results obtained by NMR are compared to X-ray crystallographic data and to observations made in molecular dynamics simulations.  相似文献   

5.
The field metabolic rates (FMR) and rates of water flux were measured in two species of varanid lizards over five periods of the year in tropical Australia. The energetics of these species were further investigated by directly measuring activity (locomotion) and body temperatures of free-ranging animals by radiotelemetry, and by measuring standard metabolic rate (over a range of body temperatures) and activity metabolism in the laboratory. Seasonal differences in the activity and energetics were found in these goannas despite similar, high daytime temperatures throughout the year in tropical Australia. Periods of inactivity were associated with the dry times of the year, but the onset of this period of inactivity differed with respect to habitat even within the same species. Varanus gouldii, which inhabit woodlands only, were inactive during the dry and late dry seasons. V. panoptes that live in the woodland had a similar seasonal pattern of activity, but V. panoptes living near the floodplain of the South Alligator River had their highest levels of activity during the dry season when they walked long distances to forage at the receding edge of the floodplain. However, during the late dry season, after the floodplain had dried completely, they too became inactive. For V. gouldii, the rates of energy expenditure were 196 kJ kg–1 day–1 for active animals and 66 kJ kg–1 day–1 for inactive animals. The rates of water influx for these groups were respectively 50.7 and 19.5 ml kg–1 day–1. For V. panoptes, the rates of energy expenditure were 143 kJ kg–1 day–1 for active animals and 56 kJ kg–1 day–1 for inactive animals. The rates of water influx for these two groups were respectively 41.4 and 21.0 ml kg–1 day–1. We divided the daily energy expenditure into the proportion of energy that lizards used when in burrows, out of burrows but inactive, and in locomotion for the two species during the different seasons. The time spent in locomotion by V. panoptes during the dry season is extremely high for a reptile (mean of 3.5 h/day spent walking), and these results provide an ecological correlate to the high aerobic capacity found in laboratory measurements of some species of varanids.  相似文献   

6.
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   

7.
An 15N off-resonance R 1 spin relaxation study of an L99A point mutant of T4 lysozyme is presented. Previous CPMG-based relaxation dispersion studies of exchange in this protein have established that the molecule interconverts between a populated ground state and an excited state (3.4%) with an exchange rate constant of 1450 s–1 at 25°C. It is shown that for the majority of residues in this protein the offset dependence of the R 1 relaxation rates cannot be well fit using models which are only valid in the fast exchange regime. In contrast, a recently derived expression by Trott and Palmer (J. Magn. Reson., 154, 157–160, 2002) which is valid over a wider window of exchange than other relations, is shown to fit the data well. Values of (signed) chemical shift differences between exchanging sites have been extracted and are in reasonable agreement with shift differences measured using CPMG methods. A set of simulations is presented which help establish the exchange regimes that are best suited to analysis by off-resonance R 1 techniques.  相似文献   

8.
We describe solid state NMR measurements on frozen solutions of the complex of the 24-residue HIV-1 gp120 V3 loop peptide RP135 with the Fab fragment of the anti-gp120 antibody 0.5, using rotational echo double resonance (REDOR). In order to probe possible hydrogen bonding between arginine side chains and glycine backbone carbonyls in the region of the conserved Gly-Pro-Gly-Arg (GPGR) motif of the V3 loop, RP135 samples were prepared with 15N labels at the nitrogen positions of arginine side chains and 13C labels at glycine carbonyl positions and 13C-detected 13C-15N REDOR measurements were performed on peptide/antibody complexes of these labeled samples. Such hydrogen bonding was previously observed in a crystal structure of the V3 loop peptide/antibody complex RP142/59.1 [Ghiara et al. (1994) Science, 264, 82–85], but is shown by the REDOR measurements to be absent in the RP135/0.5 complex. These results confirm the antibody-dependent conformational differences in the GPGR motif suggested by previously reported solid state NMR measurements of and backbone dihedral angles in the RP135/0.5 complex. In addition, we describe REDOR measurements on the helical synthetic peptide MB(i+4)EK in frozen solution that establish our ability to detect 13C-15N dipole–dipole couplings in the distance range appropriate to these hydrogen bonding studies. We also report the results of molecular modeling calculations on the central portion RP135, using a combination of the solid state NMR restraints of Weliky et al. [Nat. Struct. Biol., 6, 141–145, 1999] and the liquid state NMR restraints of Tugarinov et al. (Nat. Struct. Biol., 6, 331–335, 1999]. The dynamics calculations demonstrate the mutual compatibility of the two sets of experimental structural restraints and reduce ambiguities in the solid state NMR restraints that result from symmetry and signal-to-noise considerations.  相似文献   

9.
10.
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   

11.
Measurement of exchange rates between water and NH protons by magnetization transfer methods is often complicated by artifacts, such as intramolecular NOEs, and/or TOCSY transfer from C protons coincident with the water frequency, or exchange-relayed NOEs from fast exchanging hydroxyl or amine protons. By applying the Phase-Modulated CLEAN chemical EXchange (CLEANEX-PM) spin-locking sequence, 135°(x) 120°(-x) 110°(x) 110°(-x) 120°(x) 135°(-x) during the mixing period, these artifacts can be eliminated, revealing an unambiguous water-NH exchange spectrum. In this paper, the CLEANEX-PM mixing scheme is combined with Fast-HSQC (FHSQC) detection and used to obtain accurate chemical exchange rates from the initial slope analysis for a sample of 15N labeled staphylococcal nuclease. The results are compared to rates obtained using Water EXchange filter (WEX) II-FHSQC, and spin-echo-filtered WEX II-FHSQC measurements, and clearly identify the spurious NOE contributions in the exchange system.  相似文献   

12.
Constant-time 3D heteronuclear relayed E.COSY [Schmidt et al. (1996) J. Biomol. NMR, 7, 142–152], as based on generic 2D small-flip-angle HMQC-COSY [Schmidt et al. (1995) J. Biomol. NMR, 6, 95–105], has been modified to allow for quantitative determination of heteronuclear three-bond 3 J(H,C) couplings. The method is applicable to amino acid spin topologies with carbons in the position which lack attached protons, i.e. to asparagine, aspartate, and aromatic residues in uniformly 13C-enriched proteins. The pulse sequence critically exploits heteronuclear triple-quantum coherence (HTQC) of CH2 moieties involving geminal H proton pairs, taking advantage of improved multiple-quantum relaxation properties, at the same time avoiding scalar couplings between those spins involved in multiple-quantum coherence, thus yielding E.COSY-type multiplets with a splitting structure that is simpler than with the original scheme. Numerical least-squares 2D line-shape simulation is used to extract 3 J(H,C) coupling constants which are of relevance to side-chain 1 dihedral-angle conformations in polypeptides. Methods are demonstrated with recombinant 15N,13C-enriched ribonuclease T1 and Desulfovibrio vulgaris flavodoxin with bound oxidized FMN.  相似文献   

13.
Two independent relaxation kinetics methods were used to study samples of α-hemocyanin kindly furnished to us by members of the Biochemical Laboratory of the University of Groningen. A Durrum-Gibson stopped-flow apparatus was used to obtain concentration-jump data in the light-scattering mode. A recently developed pressurejump light-scattering apparatus was used to obtain completely independent data. The studies were made in 0.1 m acetate buffer at pH 5.7 containing 0.4 m NaCl, conditions under which equilibrium light-scattering studies had been reported by Engelborghs and Lontie (1973, J. Mol. Biol., 77, 577–587). In the companion paper (Kegeles, 1977, Arch. Biochem. Biophys., 180, 530–536), a model is proposed, consisting of a system containing a mixture of reactive and unreactive whole molecules, from which data are derived for the formation constant of whole molecules from halves and the fraction of material which is capable of undergoing reaction. The present study uses this estimate of this fraction of reactive material to permit the evaluation of overall rate constants and equilibrium constants. When the estimate of 65% of reactive material derived without making nonideality corrections is applied to the kinetics data, very satisfactory agreement is obtained between the equilibrium constant acquired from equilibrium data and the equilibrium constants derived from the kinetics data.  相似文献   

14.
Effects of water-stress treatment of Zea mays L. plants on protoplast volume and photosynthesis in leaf slices exposed to solutions of different osmotic potential ( s) were studied. Decreased photosynthetic capacity in the leaf slices at low tissue w was associated with dehydration-induced protoplast-volume reduction. Leaf slices from plants exposed to in-situ water deficits exhibited greater photosynthetic capacity and relative protoplast volume at low water potential ( w) invitro than tissue from control plants.In-situ water stress induced osmotic adjustment of the leaf tissue as determined by pressure/volume analysis. It is concluded that plant acclimation to low leaf w may involve a reduced degree of cell shrinkage at a given w. This acclimation would allow for the maintenance of relatively higher photosynthetic capacity at low water protentials.Symbols s Osmotic potential - w water potential New Jersey Agricultural Experiment Station Publication No. 12149-6-87  相似文献   

15.
Molecular mechanics calculations have been employed to obtain models of the complexes between Saccharomyces cerevisiae phosphoenolpyruvate (PEP) kinase and the ATP analogs pyridoxal 5-diphosphoadenosine (PLP-AMP) and pyridoxal 5-triphosphoadenosine (PLP-ADP), using the crystalline coordinates of the ATP-pyruvate-Mn2+-Mg2+ complex of Escherichia coli PEP carboxykinase [Tari et al. (1997), Nature Struct. Biol. 4, 990–994]. In these models, the preferred conformation of the pyridoxyl moiety of PLP-ADP and PLP-AMP was established through rotational barrier and simulated annealing procedures. Distances from the carbonyl-C of each analog to -N of active-site lysyl residues were calculated for the most stable enzyme-analog complex conformation, and it was found that the closest -N is that from Lys290, thus predicting Schiff base formation between the corresponding carbonyl and amino groups. This prediction was experimentally verified through chemical modification of S. cerevisiae PEP carboxykinase with PLP-ADP and PLP-AMP. The results here described demonstrate the use of molecular modeling procedures when planning chemical modification of enzyme-active sites.  相似文献   

16.
Summary The peptide hormone motilin was synthesised with a 13C-enriched -carbon in the leucine at position 10. In aqueous solution, six different relaxation rates were measured for the 13C–H fragment as a function of temperature and with and without the addition of 30% (v/v) of the cosolvent d 2-1,1,1,3,3,3-hexafluoro-2-propanol (HFP). The relaxation rates were analysed employing the spectral density mapping technique introduced by Peng and Wagner [(1992) J. Magn. Reson., 98, 308–322] and using the model-free approach by Lipari and Szabo [(1982) J. Am. Chem. Soc., 104, 4546–4570]. The fit to various models of dynamics was also considered. Different procedures to evaluate the overall rotational correlation time were compared. A single exponential time correlation function was found to give a good fit to the measured spectral densities only for motilin in 30% (v/v) HFP at low temperatures, whereas at high temperatures in this solvent, and in D2O at all temperatures, none of the considered models gave an acceptable fit. A new empirical spectral density function was tested and found to accurately fit the experimental spectral density mapping points. The application of spectral density mapping based on NMR relaxation data for specific 13C–1H vector is shown to be a highly useful method to study biomolecular dynamics. Advantages are high sensitivity, high precision and uniform sampling of the spectral density function over the frequency range.Abbreviations CD circular dichroism - NOE nuclear Overhauser enhancement - NOESY two-dimensional NOE spectroscopy - INEPT insensitive nuclei enhanced by polarisation transfer - DANTE delays alternating with nutations for tailored excitation - WALTZ-16 wideband, alternating phase, low-power technique for zero residual splitting - FID Free induction decay - ppm parts per million - TSPA 3-trimethylsilyl-(3,3,2,2-d)-propionic acid - HFP d 2-1,1,1,3,3,3-hexafluoro-2-propanol - CPMG Carr-Purcell-Meiboom-Gill - TFD time-resolved fluorescence depolarisation - CSA chemical shift anisotropy Partly presented at the symposium Dynamics and Function of Biomolecules, Szeged, Hungary, July 31–August 2, 1993.  相似文献   

17.
Summary Plant water relations and shoot growth rate of shrubs resprouting after fire or unburnt were measured in a semi-arid poplar box (Eucalyptus populnea) shrub woodland of eastern Australia. In vegetation unburnt for about 60 years, the dawn xylem water potential (x) of the dominant shrub species was about-1.0 MPa when the soil was wet and-8.0 MPa when the soil was very dry. At any one time, the dominant shrub species,Eremophila mitchellii, E. sturtii, Geijera parviflora andCassia nemophila, were similar in x butAcacia aneura andDodonaea viscosa were consistently higher in x than this group when the soil was moist and lower when the soil was dry. The dominant tree species,Eucalyptus populnea andE. intertexta, appeared to have access to additional water beneath the hardpan which is located 60–80 cm below the surface. When shrubs were under extreme water stress (x of-8 MPa), the trees had a x of-3 to-3.6 MPa. Following a fire, both x and leaf stomatal conductance (g s) of resprouting shrubs were higher for about 5 years than comparable-aged unburnt vegetation, with relative differences in x increasing with drought stress. Elongation rate of resprouts was positively linked to prefire shrub height in 3 of 4 species. However, shrubs resprouting after high intensity fires had substantially higher rates of shoot elongation than after low intensity fires which were in turn higher than for foliar expansion of unburnt shrubs. It is concluded that the growth rate of resprouting shrubs is primarily determined by physiological/ morphological factors associated with plant size but is also assisted by greater availability of water and possibly nutrients for a period after fire.  相似文献   

18.
The turgor pressure and water relation parameters were determined in single photoautotrophically grown suspension cells and in individual cells of intact leaves of Chenopodium rubrum using the miniaturized pressure probe. The stationary turgor pressure in suspension-cultured cells was in the range of betwen 3 and 5 bar. From the turgor pressure relaxation process, induced either hydrostatically (by means of the pressure probe) or osmotically, the halftime of water exchange was estimated to be 20±10 s. No polarity was observed for both ex- and endosmotic water flow. The volumetric elastic modulus, , determined from measurements of turgor pressure changes, and the corresponding changes in the fractional cell volume was determined to be in the range of between 20 and 50 bar. increases with increasing turgor pressure as observed for other higher plant and algal cells. The hydraulic conductivity, Lp, is calculated to be about 0,5–2·10–6 cm s–1 bar–1. Similar results were obtained for individual leaf cells of Ch. rubrum. Suspension cells immobilized in a cross-linked matrix of alginate (6 to 8% w/w) revealed the same values for the half-time of water exchange and for the hydraulic conductivity, Lp, provided that the turgor pressure relaxation process was generated hydrostatically by means of the pressure probe. Thus, it can be concluded that the unstirred layer from the immobilized matrix has no effect on the calculation of Lp from the turgor pressure relaxation process, using the water transport equation derived for a single cell surrounded by a large external volume. By analogy, this also holds true for Lp-values derived from turgor pressure changes generated by the pressure probe in a single cell within the leaf tissue. The fair similarity between the Lp-values measured in mesophyll cells in situ and mesophyll-like suspension cells suggests that the water transport relations of a cell within a leaf are not fundamentally different from those measured in a single cell.  相似文献   

19.
Proton two‐dimensional time domain nmr involving T1, T, T1D, and T2 measurements was applied to hydrated polyglycine powders. The results were analyzed for magnetization exchange and found to be consistent with a general three‐site (glycine–water–glycine) exchange model. The intrinsic glycine and water proton relaxation parameters as well as the three exchange rates were obtained. Estimates of correlation times for water molecule motion at hydration sites are presented. © 1999 John Wiley & Sons, Inc. Biopoly 50: 630–640, 1999  相似文献   

20.
The water relations of leaves of Tradescantia virginiana were studied using the miniaturized pressure probe (Hüsken, E. Steudle, Zimmermann, 1978 Plant Physiol. 61, 158–163). Under well-watered conditions cell turgor pressures, P o, ranged from 2 to 8 bar in epidermal cells. In subsidiary cells P o was about 1.5 to 4.5 bar and in mesophyll cells about 2 to 3.5 bar. From the turgor pressure, relaxation induced in individual cells by changing the turgor pressure directly by means of the pressure probe, the half-time of water exchange was measured to be between 3 and 100 s for the epidermal, subsidiary, and mesophyll cells. The volumetric elastic modulus, , of individual cells was determined by changing the cell volume by a defined amount and simultaneously measuring the corresponding change in cell turgor pressure. The values for the elastic modulus for epidermal, subsidiary, and mesophyll cells are in the range of 40 to 240 bar, 30 to 200 bar, and 6 to 14 bar, respectively. Using these values, the hydraulic conductivity, L p, for the epidermal, subsidiary, and mesophyll cells is calculated from the turgor pressure relaxation process (on the basis of the thermodynamics of irreversible processes) to be between 1 and 55·10-7 cm s-1 bar-1. The data for the volumetric elastic modulus of epidermal and subsidiary cells indicate that the corresponding elastic modulus for the guard cells should be considerably lower due to the large volume changes of these cells during opening or closing. Recalculation of experimental data obtained by K. Raschke (1979, Encycl. Plant Physiol. N.S., vol. 7, pp 383–441) on epidermal strips of Vicia faba indicates that the elastic modulus of guard cells of V. faba is in the order of 40–80 bar for closed stomata. However, with increasing stomatal opening, i.e., increasing guard cell volume, decreases. Therefore, in our opinion Raschke's results would indicate a relationship between guard cell volume and which would be inverse to that for plant cells known in the literature. assumes values between 20–40 bar when the guard cell colume is soubled.  相似文献   

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