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1.
Protein hydration studied with homonuclear 3D1H NMR experiments   总被引:3,自引:0,他引:3  
Summary Homonuclear 3D1H NOESY-TOCSY and 3D1H ROESY-TOCSY experiments were used to resolve and assign nuclear Overhauser effect (NOE) cross peaks between the water signal and individual polypeptide proton resonances in H2O solutions of the basic pancreatic trypsin inhibitor. Combined with a novel, robust water-suppression technique, positive and negative intermolecular NOEs were detected at 4°C. The observation of positive NOEs between water protons and protein protons enables more precise estimates of the very short residence times of the water molecules in the hydration sites on the protein surface.  相似文献   

2.
Summary Nuclear Overhauser effect (NOE) measurements on molecules in solution provide information about only the ensemble-averaged properties of these molecules. An algorithm is presented that uses a list of NOEs to produce an ensemble of molecules that on average agrees with these NOEs, taking into account the effect of surrounding spins on the buildup of each NOE (spin diffusion). A simplified molecular dynamics simulation on several copies of the molecule in parallel is restrained by forces that are derived directly from differences between calculated and measured NOEs. The algorithm is tested on experimental NOE data of a helical peptide derived from bovine pancreatic trypsin inhibitor.  相似文献   

3.
Virtually complete sequence specific 1H and 15N resonance assignments are presented for acid denatured reduced E. coli glutaredoxin 3. The sequential resonance assignments of the backbone rely on the combined use of 3D F1-decoupled ROESY-15N-HSQC and 3D 15N-HSQC-(TOCSY-NOESY)-15N-HSQC using a single uniformly 15N labelled protein sample. The sidechain resonances were assigned from a 3D TOCSY-15N-HSQC and a homonouclear TOCSY spectrum. The presented assignment strategy works in the absence of chemical exchange peaks with signals from the native conformation and without 13C/15N double labelling. Chemical shifts, 3J(H, NH) coupling constants and NOEs indicate extensive conformational averaging of both backbone and side chains in agreement with a random coil conformation. The only secondary structure element persisting at pH 3.5 appears to be a short helical segment comprising residues 37 to 40.Abbreviations HSQC heteronuclear single quantum coherence - NMR nuclear magnetic resonance - NOE nuclear Overhauser effect - NOESY two-dimensional NOE spectroscopy - ROE nuclear Overhauser effect in the rotating frame - ROESY two-dimensional ROE spectroscopy - TOCSY total correlation spectroscopy - TPPI time proportional phase incrementation Correspondence to: G. Otting  相似文献   

4.
Conformations of dibucaine and tetracaine in small unilamellar phosphatidylcholine vesicles have been investigated by nuclear Overhauser effects (NOEs) in 1H nuclear magnetic resonance spectroscopy. Two-dimensional NOE and chemical exchange correlated spectroscopy (NOESY) and rotating frame NOE spectroscopy (ROESY) methods have been applied for obtaining the NOEs. In the NOESY spectra, NOEs between protons within the drug were overwhelmed by spin diffusion even at a short mixing time. This observation reduced the usefulness of the NOESY method on the one hand, however, on the other hand it facilitated remarkably in revealing signals due to the drug, hidden in the broad resonances of the membranes. In the ROESY spectra, the spin diffusion phenomena were less effective; accordingly the conformations of the drugs interacting with membranes were determined by the ROESY method. The observed NOE data showed that dibucaine takes more than two conformations and that both dibucaine and tetracaine are present as a dimer in the membranes. Molecular dynamics calculations supported these findings.  相似文献   

5.
The residence times of individual hydration water molecules in the major and minor grooves of DNA were measured by nuclear magnetic resonance (NMR) spectroscopy in aqueous solutions of d-(CGCGAATTCGCG)2 and d-(AAAAATTTTT)2. The experimental observations were nuclear Overhauser effects (NOE) between water protons and the protons of the DNA. The positive sign of NOEs with the thymine methyl groups shows that the residence times of the hydration water molecules near these protons in the major groove of the DNA must be shorter than about 500 ps, which coincides with the behavior of surface hydration water in peptides and proteins. Negative NOEs were observed with the hydrogen atoms in position 2 of adenine in both duplexes studied. This indicates that a 'spine of hydration' in the minor groove, as observed by X-ray diffraction in DNA crystals, is present also in solution, with residence times significantly longer than 1 ns. Such residence times are reminiscent of 'interior' hydration water molecules in globular proteins, which are an integral part of the molecular architecture both in solution and in crystals.  相似文献   

6.
Nuclear Overhauser effect (NOE) studies of the symmetrical cystine peptides (Formula: see text) (n = 1-3) in dimethylsulfoxide, have resulted in the simultaneous observation of both positive and negative NOEs. Positive NOEs are observed on the Trp C2H and C4H protons of the indole ring upon irradiation of Trp C alpha H and C beta H2 resonances in the peptides where n = 1 and 2. Negative NOEs are observed between backbone NH and C alpha H protons. The magnitudes of the observed NOEs are sensitive to changes in molecular size and solvent viscosity. The results demonstrate that NOEs may be a useful probe of sidechain segmental motion in oligopeptides.  相似文献   

7.
We report the complete assignment of the 1H-nmr spectrum of beta-casomorphin-5 in DMSO-d6 solution. With a combination of one-dimensional, double quantum filtered correlated spectroscopy, homonuclear Hartmann-Hahn, and rotating frame nuclear Overhauser enhancement spectroscopy (ROESY) spectra, we were able to differentiate the four conformers originating from two Xxx-Pro bonds present in the sequence. Exchange peaks in the ROESY spectra confirmed the presence of four interchanging conformational isomers. Based on integrations, the relative populations of the four species were estimated, while characteristic sequential nuclear Overhauser enhancements (NOEs) were used to determine the orientation of the Xxx-Pro bonds. This orientation was also shown to correlate with the chemical shift changes for the alpha protons of both the Xxx and Pro residues. Finally, interresidue NOEs indicate conformational preferences for the aromatic side chains, especially in the all-trans conformer.  相似文献   

8.
The growth yield of Chlorella vulgaris, Y kJ defined as g cells harvested per kJ of light energy absorbed by the cells, was assessed in a turbidostat culture by varying CO2 and O2 partial pressures ( and ). The value of Y kJ ranged from 3.1×10-3 to 5.0×10-3 g cells/kJ under light-limited conditions [ = 1.02.4%, = 065%; total pressure of gas (composed of CO2, O2 and N2)=1 atm]. In the light-limited environment, the algal specific growth rate deteriorated appreciably with the increase of . The deterioration accounts for the above range of Y kJ observed. The growth inhibition due to oxygen that was defined by subtracting from 1.0 the ratio of at given values of to that at = 0% extended from 0.07–0.30 (7–30%). However, glycolate could not be detected in the turbidostat culture. Isotopic experiments on the specific rate of 14CO2 uptake also revealed that the inhibition due to oxygen was from 22–38% when was varied from 0 to nearly 100%. These effects of oxygen were discussed, referring to the activity of ribulose-1,5-bisphosphate carboxylase that is inhibited competitively by oxygen.Non-Standard Abbreviations INH isonicotinic acid hydrazide - PPO 2,5-diphenyloxazole - DCMU 3-(-3,4-dichlorophenyl)-1,1-dimetylurea - CA carbonic anhydrase - RuP2 ribulose-1,5-bisphosphate  相似文献   

9.
Summary In seawater (SW)-adaptedMugil andFundulus, gill effluxes of Na+ and of Cl and the simultaneously recorded transgill potential (P.D.) differ according to whether they are measured in stressed or rested animals.In rested animals of the two species, transfer to Ringer's solution considerably reduces the P.D. but not . InFundulus, is also decreased. Transfer of the two species from SW to fresh water (FW) reduces and by 75 to 85% and leads to a large inversion of P.D. When K+ is added to FW, a gill depolarization occurs, as well as a large increase of and .These results suggest that: 1) the P.D. originates primarily from the diffusion of cations, the gill permeability to Na+ ( ) being greater than that to Cl ( ), 2) a Cl/Cl exchange independent of P.D. is associated with the Cl pump; 3) Cl pump activity is linked to Na+/K+ exchange which in turn is associated to a Na+/Na+ exchange diffusion mechanism.In stressed individuals of the two species, the P.D. in SW, as well as the P.D. changes observed during transfer experiments, are considerably reduced. The decrease of and observed after transfer from SW to FW are also minimised. Changes are smaller inFundulus. The decrease of P.D. characterizing stressed animals may be at least in part due to a 3 to 4 fold increase of which becomes equal to in both species.As a result of stress, the K+-activated Na+ and Cl excretion mechanisms are totally inhibited inFundulus and partially so inMugil.Stress response seems more intense inFundulus and recovery from stress faster inMugil.  相似文献   

10.
P Cagas  C A Bush 《Biopolymers》1992,32(3):277-292
To probe differences in conformation of the type 1 and type 2 linkages in blood group oligosaccharides, two-dimensional nuclear Overhauser effect spectroscopy (2D-NOESY) and 1H T1 data were obtained for two blood group A oligosaccharide alditols containing the type 1 and type 2 linkage. The NOE data were interpreted using a complete relaxation matrix approach. Simulations of NOE and T1 values were made using disaccharide and tetrasaccharide model conformations generated by a systemic variation of the glycosidic dihedral angles phi and psi. NOEs from the amide protons of GlcNAc and GalNAc in the type 1 pentasaccharide alditol were obtained, and simulated in a manner similar to those from carbon-bound protons. In addition to providing data for determining the conformation of the type 1 linkage from amide proton NOEs of GlcNAc and GalNAc to neighboring residues, amide proton NOEs also yield information on the orientation of the acetamido side chains. The amide NOE data indicated subtle differences in the orientation of the amide side chain of GlcNAc among the A type 1 pentasaccharide alditol and two previously studied blood group oligosaccharides, lacto-N-difucohexaose 1 and lacto-N-fucopentaose 1. From the NOE and 1H T1 data, and from simple rigid geometry energy calculations, it is concluded that the type 1 and type 2 linkages in the oligosaccharides studied have different conformations and that these conformations are relatively rigid in solution.  相似文献   

11.
The conformational properties of the pentapeptide Ser-Phe-Leu-Leu-Arg (P5), a human thrombin receptor-derived sequence forming part of a tethered ligand which activates the thrombin receptor, and its more active amide derivative Ser-Phe-Leu-Leu-Arg-NH2 (P5-NH2), have been studied by proton NMR spectroscopy in dimethylsulfoxide. Measurements of nuclear Overhauser effects, performed using two-dimensional rotating frame nuclear Overhauser (ROESY) and one-dimensional nuclear Overhauser enhancement (NOE) spectroscopy, revealed that P5 exists mainly in an extended conformation. However, proton–proton 1D-NOEs between Phe CH and Ser CH, Leu3 CH and Leu3 NH, and Leu4 CH and Leu4 NH, as well as between the Ser and Arg sidechains, also implicated a minor conformer for P5 having a curved backbone and a near-cyclic structure. In contrast to P5, measurements of NOEs and ROEs for P5-NH2 revealed a more stabilized cyclic structure which may account for its higher biological potency. Thus strong interresidue sequential NH (i)–NH (i + 1) interactions, as well as C-terminal carboxamide to N-terminal side-chain interactions, i.e., Arg CONH2 to Phe ring and Arg CONH2 to Ser , observed at lower levels of the ROESY spectrum, supported a curved backbone structure for SFLLR-NH2. Since the higher potaency P5-NH2 analogue adopts predominantly a cyclic structure, a cyclic bioactive conformation for thrombin receptor agonist peptides is suggested.  相似文献   

12.
Maximum submergence time of Canada geese was 18% of that of similarly sized Pekin ducks. Due to a smaller respiratory system volume the oxygen store of Canada geese was 82% of that of Pekin ducks, accounting for approximately 33% of the difference in underwater survival times. The respiratory properties and volume of the blood were similar in both species. Both species utilised approximately 79% of the respiratory oxygen store and 90% of the blood oxygen store. Therefore, most of the species difference in survival times was due to a less effective oxygen-conserving cardiovascular response (bradycardia, peripheral vasoconstriction) in Canada geese. Duck cardiac chronotropic sensitivity to hypoxia during submergence was twice that observed in geese. Furthermore, a lower hypoxic ventilatory response was observed in geese than in ducks. Density of monoamine varicosities in hindlimb artery walls was lower in geese than ducks. However, electrical stimulation of the hindlimb muscles did not cause ascending vasodilation during submergence in either species, perhaps due to higher levels of catecholamines in submerged geese. We conclude that the major difference between species is higher oxygen chemosensitivity in ducks which effects a much more rapid and efficacious oxygen-conserving response during forced submergence.Abbreviations ATPS · BTPS · STPD CNS central nervous system - EEG electroencephalogram - ECG electrocardiogram - EDTA ethylenediaminetetra-acetic acid - HPLC high performance liquid chromatography - fractional oxygen concentration of inspired air - pre-immersion fractional concentration of oxygen in the respiratory system - pre-emersion fractional concentration of oxygen in the respiratory system - [Hb] haemoglobin concentration - Hct haematocrit - HR heart rate - M B body mass - M b brain mass - M h heart mass - partial pressure of carbon dioxide in arterial blood - partial pressure of oxygen in arterial blood - SPG sucrose-potassium phosphate-glyoxylic acid - t d maximum underwater survival time - respiratory minute volume - V pl plasma volume - V rs respiratory system volume - accessible respiratory system oxygen store - total non-myoglobin-bound oxygen store - V tb blood volume - blood oxygen store  相似文献   

13.
Summary The energy requirements of Adélie penguin (Pygoscelis adeliae) chicks were analysed with respect to body mass (W, 0.145–3.35 kg, n=36) and various forms of activity (lying, standing, minor activity, locomotion, walking on a treadmill). Direct respirometry was used to measure O2 consumption ( ) and CO2 production. Heart rate (HR, bpm) was recorded from the ECG obtained by both externally attached electrodes and implantable HR-transmitters. The parameters measured were not affected by hand-rearing of the chicks or by implanting transmitters. HR measured in the laboratory and in the field were comparable. Oxygen uptake ranged from in lying chicks to at maximal activity, RQ=0.76. Metabolic rate in small wild chicks (0.14–0.38 kg) was not affected by time of day, nor was their feeding frequency in the colony (Dec 20–21). Regressions of HR on were highly significant (p< 0.0001) in transmitter implanted chicks (n=4), and two relationships are proposed for the pooled data, one for minor activities ( ), and one for walking ( ). Oxygen consumption, mass of the chick (2–3 kg), and duration of walking (T, s) were related as , whereas mass-specific O2 consumption was related to walking speed (S, m·s-1) as .Abbreviations bpm beats per minute - D distance walked (m) - ECG electrocardiogram - HR heart rate (bpm) - ns number of steps - RQ respiratory quotient - S walking speed (m·s-1) - T time walked (s) - W body mass (kg)  相似文献   

14.
Summary Adelie penguins (Pygoscelis adeliae) experience a wide range of ambient temperatures (T a) in their natural habitat. We examined body temperature (T b), oxygen consumption ( ), carbon dioxide production ( ), evaporative water loss ( ), and ventilation atT a from –20 to 30 °C. Body temperature did not change significantly between –20 and 20°C (meanT b=39.3°C).T b increased slightly to 40.1 °C atT a=30°C. Both and were constant and minimal atT a between –10 and 20°C, with only minor increases at –20 and 30°C. The minimal of adult penguins (mean mass 4.007 kg) was 0.0112 ml/[g·min], equivalent to a metabolic heat production (MHP) of 14.9 Watt. The respiratory exchange ratio was approximately 0.7 at allT a. Values of were low at lowT a, but increased to 0.21 g/min at 30°C, equivalent to 0.3% of body mass/h. Dry conductance increased 3.5-fold between –20 and 30°C. Evaporative heat loss (EHL) comprised about 5% of MHP at lowT a, rising to 47% of MHP atT a=30°C. The means of ventilation parameters (tidal volume [VT], respiration frequency [f], minute volume [I], and oxygen extraction [ ]) were fairly stable between –20 and 10°C (VT did not change significantly over the entireT a range). However, there was considerable inter- and intra-individual variation in ventilation patterns. AtT a=20–30°C,f increased 7-fold over the minimal value of 7.6 breaths/min, and I showed a similar change. fell from 28–35% at lowT a to 6% atT a=30°C.Abbreviations C thermal conductance - EHL evaporative heat loss - oxygen extraction - f respiratory frequency - MHP metabolic heat production - evaporative water loss - LCT lower critical temperature - RE respiratory exchange ratio - T a ambient temperature - T b body temperature - rate of oxygen consumption - rate of carbon dioxide production - I inspiratory minute volume - VT tidal volume  相似文献   

15.
A long-term field experiment was initiated to simulate chronic atmospheric N deposition, a widespread phenomenon in industrial regions of the world. Eight years of experimental nitrate ( ) additions (3 g -N m–2 per year) to four different northern hardwood forests located along a 500 km geographic gradient dramatically increased leaching losses of -N, dissolved organic carbon (DOC), and dissolved organic nitrogen (DON). During the last two water years, the average increase in solution -N and DON leaching from the -amended plots was 2.2 g N m–2, equivalent to 72% of the annual experimental N addition. Results indicate that atmospheric N deposition may rapidly saturate some northern hardwood ecosystems across an entire biome in the upper Great Lakes Region of the USA. Changes in soil C and N cycling induced by chronic N deposition have the potential in this landscape to significantly alter the flux of DOC and DON from upland to aquatic ecosystems. Michigan Gradient study site characteristics are similar to those of European forests most susceptible to N saturation.  相似文献   

16.
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   

17.
Summary All the backbone 1H and 15N magnetic resonances (except for Pro residues) of the GDP-bound form of a truncated human c-Ha-ras proto-oncogene product (171 amino acid residues, the Ras protein) were assigned by 15N-edited two-dimensional NMR experiments on selectively 15N-labeled Ras proteins in combination with three-dimensional NMR experiments on the uniformly 15N-labeled protein. The sequence-specific assignments were made on the basis of the nuclear Overhauser effect (NOE) connectivities of amide protons with preceding amide and/or Cprotons. In addition to sequential NOEs, vicinal spin coupling constants for amide protons and C protons and deuterium exchange rates of amide protons were used to characterize the secondary structure of the GDP-bound Ras protein; six strands and five helices were identified and the topology of these elements was determined. The secondary structure of the Ras protein in solution was mainly consistent with that in crystal as determined by X-ray analyses. The deuterium exchange rates of amide protons were examined to elucidate the dynamic properties of the secondary structure elements of the Ras protein in solution. In solution, the -sheet structure in the Ras protein is rigid, while the second helix (A66-R73) is much more flexible, and the first and fifth helices (S17-124 and V152-L171) are more rigid than other helices. Secondary structure elements at or near the ends of the effector-region loop were found to be much more flexible in solution than in the crystalline state.  相似文献   

18.
The dynamics of amino acid side chains of uniformly 13C/15N-enriched ribonuclease T1 (RNase T1) have been investigated. Heteronuclear longitudinal relaxation rates, 1H/13C NOEs, and transverse cross-correlated cross-relaxation rates between the Sx and the SxIz1Iz2 operators (SIIS cross relaxation) [Ernst and Ernst (1994) J. Magn. Reson., A110, 202-213] have been determined in this study. New pulse sequences for measuring the longitudinal relaxation time and the heteronuclear NOE of aliphatic side chain carbon nuclei were developed using the CCONH type of magnetization transfer and 1HN detection. In addition, an improved pulse sequence for the determination of the SIIS cross relaxation is presented. For the analysis of the relaxation rates, the model of restricted rotational diffusion around the 1 dihedral angle has been applied [London and Avitabile (1978) J. Am. Chem. Soc., 100, 7159-7165]. These techniques were used in order to describe the side chain dynamics of the small globular protein RNase T1 (104 amino acids, MW about 11 kDa). Qualitative values of microdynamical parameters were obtained for 73 out of 85 amino acid side chains (glycine and alanine residues excepted) whereas more quantitative values were derived for 67 -CH and -CH2 groups.  相似文献   

19.
Summary The brush turkey (Alectura lathami) and mallee fowl (Leipoa ocellata) are megapode birds that incubate their eggs by burying them in mounds. Respiratory gas exchange between the buried eggs and the atmosphere occurs mainly by diffusion through about 60 cm of decomposing forest litter (brush turkey) or sand (mallee fowl).Gas fluxes in the brush turkey mound are greatly influenced by the respiration of thermophilic microorganisms which consume O2 at rates over eight times that of all of the eggs. The respiratory exchange ratio ( ) of the microorganisms is 0.75 and theQ 10 for metabolism is 2.56. Fermentation and nitrogen fixation do not occur in the mounds.If the mound becomes too wet, gas tensions near the eggs can become critical because water increases rates of microbial respiration and impedes gas diffusion. However, field mounds are relatively dry, possibly because the adult bird modifies the shape of the mound and affects the entry of rain water. At egg level in field mounds, and are about 132 and 21 Torr, respectively, in both species. Embryonic respiration decreases and increases about 5 Torr in the immediate environment of individual eggs in late development. Due to a high eggshell gas conductance, which increases during incubation, the gas tensions within the shell of late embryos ( ca. 108 Torr, ca. 47 Torr) are not far from the mean values found in species that nest above ground.  相似文献   

20.
Intermolecular nuclear Overhauser effects (NOEs) were measured between the protons of various small solvent or gas molecules and the non-specific lipid transfer protein (ns-LTP) from wheat. Intermolecular NOEs were observed with the hydrophobic pocket in the interior of wheat ns-LTP, which grew in intensity in the order cyclopropane (saturated solution) < methane (140 bar) < ethane (40 bar) < acetonitrile (5% in water) < cyclohexane (saturated solution) < benzene (saturated solution). No intermolecular NOEs were observed with dioxane (5% in water). The intermolecular NOEs were negative for all of the organic molecules tested. Intermolecular NOEs between wheat ns-LTP and water were weak or could not be distinguished from exchange-relayed NOEs. As illustrated by the NOEs with cyclohexane versus dioxane, the hydrophobic pocket in wheat ns-LTP preferably binds non-polar molecules. Yet, polar molecules like acetonitrile can also be accommodated. The pressure dependence of the NOEs between methane and wheat ns-LTP indicated incomplete occupancy, even at 190 bar methane pressure. In general, NOE intensities increased with the size of the ligand molecule and its vapor pressure. NMR of the vapor phase showed excellent resolution between the signals from the gas phase and those from the liquid phase. The vapor concentration of cyclohexane was fivefold higher than that of the dioxane solution, supporting the binding of cyclohexane versus uptake of dioxane.  相似文献   

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