Separation of intramolecular NOE and exchange peaks in water exchange spectroscopy using spin-echo filters

Summary A technique for separating intramolecular NOE and solvent-proton exchange peaks in exchange spectroscopy is demonstrated. This method utilizes the large differences in relaxation and coupling properties of water and macromolecules to separate the two effects. The spin-echo filter consists of a water-frequency selective 90° pulse followed by a spin-echo sequence. If the echo time is sufficiently long, protein resonances (e.g. CH protons) excited by the selective pulse are removed due to their much shorter T₂ values and J-coupling evolution. By combining the filter with exchange spectroscopy (EXSY) or water exchange (WEX) filter experiments, exchange peaks can be selectively observed. In this paper the filter is combined with a modified version of the WEX filter (WEX II filter) with 1D and 2D detection and applied to a zinc finger peptide and to staphylococcal nuclease, allowing estimation of the contribution of intramolecular NOEs to the exchange spectra.To whom correspondence should be addressed.     

The productivity of mesocyclops leuckrarti (Claus) in Lake Kinneret (Israel)

Specific rates of growth (Cw) of Mesocyclops leuckarti, young male and female instars varied between 0.03–0.26 and 0.03–0.17 g_(w.w.)/g_(w.w.)/day respectively at 15° and 22°C, whilst at IV–V copepodid stages females showed a higher Cw values. During 1969–1975 the averages of productivity and monthly P/B ratios were 44 (±23) g_(w.w.) (= 5g_(w.w.)/m²/month) and 3.1 respectively. P/B ratios were highly correlated (r(sup2)=0.98) with temperature changes. Metabolic parameters and P/B ratios were found to be similar to other water bodies in the world indicating an adaptation of M. leuckarti to different conditions.     

Determination of sugar conformations by NMR in larger DNA duplexes using both dipolar and scalar data: Application to d(CATGTGACGTCACATG)2

Summary Different methods for determining sugar conformations in large oligonucleotides have been evaluated using both J-coupling and NOE data. In order to simulate COSY spectra, reliable estimates of line widths are required. We have measured T_1p (=T₂) values for a large number of protons of the hexadecamer d(CATGTGACGTCACATG)₂ using a new two-dimensional NMR experiment (T1RHOSY) to provide baseline information for the simulations. Both DQF-COSY and P.E.COSY cross-peaks have been systematically simulated as a function of line width, digitisation and signal-to-noise ratio. We find that for longer correlation times (5 ns), where line widths are comparable to or larger than active couplings, only {ie190-1} is reasonably accurately determined (within ±1 Hz). Under these conditions, additional information is needed to determine the sugar conformation. We have used apparent distances H1-2-H4 and H2-H4, which provide a range of P_s over an interval of ca. 20°. Complete analysis of time courses for intraresidue NOEs, with and without coupling constants, has also been evaluated for determining nucleotide conformations. Whereas P_s is poorly determined in the absence of both intrasugar NOEs and coupling constants, the range of solutions is decreased when intrasugar NOEs and {ie190-2} are also available. DQF-COSY, P.E.COSY and NOESY spectra at different mixing times of the hexadecamer d(CATGTGACGTCACATG)₂ were recorded at three temperatures. A detailed analysis of the NOEs and coupling constants provided estimates of the sugar conformations in the hexadecamer. At 50 °C, the sugar conformations are well determined by the scalar and dipolar data, with pseudorotation phase angles of 126–162° and mole fractions of the S conformation (f_s) of 0.86±0.05. There was no statistically significant difference between f_s for the purines and the pyrimidines, although there was a small tendency for P_s of the purines to be larger than those of the pyrimidines. At 25 °C, the sugar conformations were much less well determined, although the estimates of f_s were the same within experimental error as at 50 °C. The experimental and theoretical results provide guidelines for the limits of conformational analysis of nucleic acids based on homonuclear NMR methods.     

Amino acid-specific isotopic labeling and active site NMR studies of iron(II)- and iron(III)-superoxide dismutase from Escherichia coli

We have developed and employed multiple amino acid-specific isotopic labeling schemes to obtain definitive assignments for active site ¹H NMR resonances of iron(II)- and iron(III)-superoxide dismutase (Fe(II)SOD and Fe(III)SOD) from Escherichia coli. Despite the severe relaxivity of high-spin Fe(III), we have been able to assign resonances to ligand His 1 protons near 100 ppm, and and protons collectively between 20 and 50 ppm, in Fe(III)SOD. In the reduced state, we have assigned all but 7 ligand protons, in most cases residue-specifically. A pair of previously unreported broad resonances at 25.9 and 22.1 ppm has been conclusively assigned to the protons of Asp 156, superseding earlier assignments (Ming et al. (1994) Inorg. Chem., 33, 83–87). We have exploited higher temperatures to resolve previously unobserved ortho-like ligand His proton resonances, and specific isotopic labeling to distinguish between the possibilities of 2 and 1 protons. These are the closest protein protons to Fe(II) and therefore they have the broadest (4000 Hz) and most difficult to detect resonances. Our assignments permit interpretation of temperature dependences of chemical shifts, pH dependences and H/D exchange rates in terms of a hydrogen bond network and the Fe(II) electronic state. Interestingly, Fe(II)SOD's axial His ligand chemical shifts are similar to those of the axial His ligand of Rhodopseudomonas palustris cytochrome c (Bertini et al. (1988) Inorg. Chem., 37, 4814–4821) suggesting that Fe(II)SOD's equatorial His₂Asp^– ligation is able to reproduce some of the electronic, and thus possibly chemical, properties of heme coordination for Fe²⁺.     

NMR and X-ray characterization of a platinum(II) complex with (−)sparteine

A platinum(II) complex containing the diamine (−)sparteine has been synthesized for the first time and fully characterized by ¹H and ¹³C NMR spectroscopy and X-ray crystallography. (−)Sparteine is an alkaloid containing four fused rings and four asymmetric centers of configurations 6R, 7S, 9S, and 11S at the four tertiary carbon atoms. In the cis conformation it can act as a chelating N-donor ligand toward a metal ion. The steric bulkiness of this ligand is such that the Pt-N bond lengths are greater than normal and the angle between the cis-chlorido ligands is well below the theoretical value of 90°. This sparteine complex of platinum appears to be an ideal substrate for investigating the stereochemistry of adducts with nucleotides and DNA. For instance the orientation of a coordinated nucleobase can be determined with precision by monitoring the strength of NOE cross peaks between the sparteine protons pointing toward the metal center and key protons of the coordinated nucleobase(s) (e.g. H8 protons of guanine or adenine).     

The effect of selective deuteration on magnetization transfer in larger proteins

Summary The effects of selective deuteration on calculated NOESY intensities have been analyzed for the structure of theE. coli trp aporepressor, a 25 kDa protein. It is shown that selectively deuteratedtrp aporepressor proteins display larger calculated NOESY intensities than those for the same interproton distances in the natural abundance protein. The relatively larger magnetization transfer is demonstrated by a comparison of the NOE build-up curves for specific proton pairs, and for the calculated NOE intensities of short-range NOEs to backbone amide protons. This increase in intensity is especially pronounced for the NH¹–NH¹⁺¹ cross peaks in the -helical regions, and particularly for amide protons of two sequential deuterated residues. The effect is shown to be further intensified for longer mixing times. It is also shown that in all cases, each amide proton exhibits stronger NOEs to its own side chain, with an enhanced effect for deuterated derivatives. This theoretical analysis demonstrates that an evaluation of the relative NOE intensities for different selectively deuterated analogs may be an important tool in assigning NMR spectra of large proteins. These results also serve as a guide for the interpretation of NOEs in terms of distances for structure calculations based on data using selectively deuterated proteins.     

The solution conformation of sialyl-α(2→6)-lactose studied by modern NMR techniques and Monte Carlo simulations

Summary We present a comprehensive strategy for detailed characterization of the solution conformations of oligosaccharides by NMR spectroscopy and force-field calculations. Our experimental strategy generates a number of interglycosidic spatial constraints that is sufficiently large to allow us to determine glycosidic linkage conformations with a precision heretofore unachievable. In addition to the commonly used {¹H,¹H} NOE contacts between aliphatic protons, our constraints are: (a) homonuclear NOEs of hydroxyl protons in H₂O to other protons in the oligosaccharide, (b) heteronuclear {¹H,¹³C} NOEs, (c) isotope effects of O¹H/O²H hydroxyl groups on¹³C chemical shifts, and (d) long-range heteronuclear scalar coupling across glycosidic bonds.We have used this approach to study the trisaccharide sialyl-(26)-lactose in aqueous solution. The experimentally determined geometrical constraints were compared to results obtained from force-field calculations based on Metropolis Monte Carlo simulations. The molecule was found to exist in 2 families of conformers. The preferred conformations of the (26)-linkage of the trisaccharide are best described by an equilibrium of 2 conformers with angles at –60° or 180° and of the 3 staggered rotamers of the angle with a predominantgt conformer. Three intramolecular hydrogen bonds, involving the hydroxyl protons on C8 and C7 of the sialic acid residue and on C3 of the reducing-end glucose residue, contribute significantly to the conformational stability of the trisaccharide in aqueous solution. Supplementary material available from the corresponding author: Table containing values for the dihedral angles , , , , and for bond angles , for the six lowest-energy conformations of sialyl-(26)-lactose (1 page).     

Resonance assignments, secondary structure and topology of leukaemia inhibitory factor in solution

The chemical shift assignments and secondary structure of a murine–human chimera,MH35, of leukaemia inhibitory factor (LIF), a 180-residue protein of molecular mass 20 kDa,have been determined from multidimensional heteronuclear NMR spectra acquired on auniformly 13C,15N-labelled sample. Secondary structure elements were defined on the basisof chemical shifts, NH-CH coupling constants, medium-range NOEs and the location ofslowly exchanging amide protons. The protein contains four -helices, the relativeorientations of which were determined on the basis of long-range, interhelical NOEs. The fourhelices are arranged in an up-up-down-down orientation, as found in other four-helical bundlecytokines. The overall topology of MH35-LIF is similar to that of the X-ray crystallographicstructure for murine LIF [Robinson et al. (1994) Cell, 77, 1101–1116]. Differencesbetween the X-ray structure and the solution structure are evident in the N-terminal tail, wherethe solution structure has a trans-Pro17 compared with the cis-Pro17 found in the crystalstructure and the small antiparallel -sheet encompassing residues in the N-terminus andCD loop in the crystal structure is less stable.     

Copper(II) complexes of the beta-blocker pindolol: properties, structure, biological activity

The complex formation between copper(II) and the antihypertensive drug pindolol (HPin) was studied both in aqueous and methanolic media. Two complexes are formed at different metal-to-ligand molar ratios. The mononuclear complex Cu(Pin)₂(HPin)₂ contains two ligands in an anionic bidentate form and two - in a neutral form bound monodentately. The second complex Cu₂Pin₂Cl₂ is dinuclear and its structure was determined by X-ray diffraction. The compound crystallizes in the monoclinic group C2/c with cell components a = 14.4998(13)Å, b = 18.511(2)Å, c = 14.2982(13)Å, =90 °, =109.556(2)°, =90 ° and Z = 12 at 293K. A pharmacological study on the influence of pindolol and its mononuclear complex on the heart rate of rats was performed. The complex is more active and has a longer effect in comparison with the pure non-coordinated pindolol in equitoxic doses.     

Optimization of eicosapentaenoic acid production byPhaeodactylum tricornutumin the flat panel airlift (FPA) reactor

Biomass and eicosapentaenoic acid (EPA) productivities were investigated in a flat panel airlift loop reactor ideally mixed by static mixers. Growth with ammonium, urea and nitrate as nitrogen source were performed at different aeration rates. Cultures grew on ammonium but the decay of pH strongly inhibited biomass increase. On urea biomass productivity reached 2.35 g L^–1d^–1at an aeration rate of 0.66 vvm (24 h light per day, 1000 mol photon m^–2s^–1). Aeration rates between 0.33 vvm and 0.66 vvm and maximal productivities on urea were linearly dependent. Productivity on nitrate never exceeded 1.37 g L^–1d^–1. In the range of maximum productivity photosynthesis efficiency of 10.6% was reached at low irradiance (250 mol photon m^–2s^–1). Photosynthesis efficiency decreased to 4.8% at 1000 mol photon m^–2s^–1. At these high irradiances the flat panel airlift reactor showed a 35% higher volume productivity than the bubble column. At continuous culture conditions the influence of CO₂concentration in the supply air was tested. Highest productivities were reached at 1.25% (v/v) CO₂where the continuous culture yielded 1.04 g L^–1d^–1(16 h light per day, 1000 mol photon m^–2s^–1). The average EPA content amounted to 5.0% of cell dry weight, that resulted in EPA productivities of 52 mg L^–1d^–1(continuous culture, 16 h light per day) or 118 mg L^–1d^–1(batch culture, 24 h light per day).     

Zur filtrationsleistung von Dreissena,Sphaerium und Pisidium (Eulamellibranchiata)

Zusammenfassung Mit einer indirekten Methode (Messung der Konzentrations-abnahme einer kolloidalen Graphitlösung) wurden die Filtrationsraten von 4 Kleinmuschelarten (Dreissena polymorpha, Sphaerium corneum, Pisidium amnicum und Pisidium casertanum) bei hoher (14°, 15° bzw. 20°C) und bei niedriger (5° bzw. 6°C) Temperatur bestimmt. Die Unterschiede der Filtrationsraten beim Vergleich der Werte hoher mit denen niedriger Temperatur sind bei allen Größenklassen weitgehend signifikant. Die Filtrationsleistung großer Individuen ist stärker temperaturabhängig als die kleiner. Die Filtrationsraten ml/g Lebendgewicht und Stunde der jeweils größten Tiere der untersuchten Arten lassen eine Abhängigkeit von der Mobilität erkennen: Das im Vergleich zu den beiden übrigen Arten ziemlich mobile P. amnicum zeigt die niedrigsten, die vollsessile Dreissena die höchsten Werte. Die Bedeutung der Kleinmuscheln für die Selbstreinigung der Gewässer wird an einigen Beispielen näherungsweise berechneter Filtrationskapazitäten pro m² Bodengrund aufgezeigt.

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Summary The filtration rates of four species of eulamellibranchs (Dreissena polymorpha, Sphaerium corneum, Pisidium amnicum and Pisidium casertanum) are measured at high (14°, 15° respectively 20°C) and low (5° respectively 6°C) temperatures by an indirect method. The differences of filtration rates at high and low temperatures are significant in all classes of size. The filtration efficiency of large individuals is more dependent on temperature than that of small ones. The filtration rate ml/g live weight and hour of the largest animals of the species tested depend on mobility: P. amnicum, which is rather mobile compared with the other species, shows the lowest, the completely sessile Dreissena the highest values. The importance of small bivalves for the self-cleaning of waters is shown by some examples of filtration capacities per m² of bottom approximately calculated.

     

A note on the nutrition of Stylaria lacustris (Oligochaeta: Naididae)

Stylaria lacustris (L.) was offered ¹⁴C-labelled algae. The ingestion rate of diatoms was 0.79 g carbon/hour at 19°C. Diatoms (Nitzschia actinastroides) were well assimilated, green algae (Scenedesmus acuminatus) were practically not assimilated. The less assimilable algae are ingested at higher rates, indicating a regulation mechanism. Biomass doubling time was estimated to be about 3.6 days at 19°C.     

A 3D NOESY-(HCACO)NH experiment for the measurement of NOEs involving 1Hα in 13C-/15N-labeled proteins dissolved in H2O

Summary A 3D NOESY-(HCACO)NH experiment is described that transfers NOEs from ¹H to the backbone ¹H^N in the succeeding residue for detection. Using this strategy, NOEs involving ¹H protons that resonate exactly at the water frequency can be detected. NOEs from an overlapping ¹H proton that is attached to degenerate ¹³C can also be resolved. The performance of this approach is demonstrated for the ¹³C-/¹⁵N-labeled Hck/SH2 dissolved in H₂O.     

Coordination versatility of 1,3-bis[3-(2-pyridyl)pyrazol-1-yl]propane: Co(II) and Ni(II) complexes

The ligand 1,3-bis[3-(2-pyridyl)pyrazol-1-yl]propane (L⁸) has afforded six-coordinate monomeric and dimeric complexes [(L⁸)Co^II(H₂O)₂][ClO₄]₂ (1), [(L⁸)Ni^II(MeCN)₂][BPh₄]₂ (2), [(L⁸)Ni^II(O₂CMe)][BPh₄] (3), and . The crystal structures of 1, 2 · MeCN, 3, and 4 revealed that the ligand L⁸ is flexible enough to expand its coordinating ability by fine-tuning the angle between the chelating fragments and hence folds around cobalt(II)/nickel(II) centers to act as a tetradentate chelate, allowing additional coordination by two trans-H₂O, cis-MeCN, and a bidentate acetate affording examples of distorted octahedral , , and coordination. The angles between the two CoN₂/NiN₂ planes span a wide range 23.539(1)° (1), 76.934(8)° (2), and 69.874(14)° (3). In contrast, complex 4 is a bis-μ-1,3-acetato-bridged (syn-anti coordination mode) dicobalt(II) complex [Co?Co separation: 4.797(8) Å] in which L⁸ provides terminal bidentate pyridylpyrazole coordination to each cobalt(II) center. To our knowledge, this report provides first examples of such a coordination versatility of L⁸. Absorption spectral studies (MeCN solution) have been done for all the complexes. Complexes 1-3 are uniformly high-spin. Temperature-dependent (2-300 K) magnetic studies on 4 reveal weak ferromagnetic exchange coupling between two cobalt(II) (S = 3/2) ions. The best-fit parameters obtained are: Δ (axial splitting parameter) = −765(5) cm⁻¹, λ (spin-orbit coupling) = −120(3) cm⁻¹, k (orbital reduction factor) = 0.93, and J (magnetic exchange coupling constant) = +1.60(2) m⁻¹.     

Spectroscopic and electrochemical properties of heteroleptic cationic copper complexes bis-(diphenylphosphino)alkane-(2,2′-biquinoline)copper(I). Crystal structure of bis(diphenylphosphino)ethane-(2,2′-biquinoline)copper(I) perchlorate

A series of [Cu^(I)(2,2′-biquinoline)(L)](ClO₄) complexes (L = bis(diphenylphosphino)methane (bppm), 1,2-bis(diphenylphosphino)ethane (bppe), 1,4-bis(diphenylphosphino)butane (bppb)) have been synthesized and characterized by elemental analysis, conductivity, ESI-mass, NMR and UV-Vis spectroscopies, cyclic voltammetry, X-ray diffraction ([Cu^(I)(2,2′-biquinoline)(bppe)](ClO₄)) and DFT calculations. These compounds are monometallic species in a distorted tetrahedral arrangement, in contrast with related compounds found as dinuclear according to diffraction studies. The spectroscopic properties are not directly correlated with the length of alkyl chain bridge between the bis-diphenylphosphine groups. In this way, the chemical shift of some 2,2′-biquinoline protons and the metal to ligand charge transfer (Cu to 2,2′-biquinoline) follows the order [Cu(2,2′-biquinoline)(bppm)](ClO₄), [Cu(2,2′-biquinoline)(bppb)](ClO₄), [Cu(2,2′-biquinoline)(bppe)](ClO₄). The same dependence is followed by the potentials to Cu(II)/Cu(I) couple. These results are discussed in terms of inter-phosphorus alkane chain length and tetrahedral distortions on copper.     

Sequence-specific 1H and 15N resonance assignments and secondary structure of GDP-bound human c-Ha-Ras protein in solution

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.     

Process parameters and reusability of the free cell mass of Torulaspora delbrueckii for the production of L-phenylacetylcarbinol (L-PAC)

The effect of process parameters on the biotransformation of benzaldehyde to L-phenylacetylcarbinol (L-PAC) using a yeast isolate identified as Torulaspora delbrueckii was studied. The maximum yield of L-PAC obtained was (331 mg) per 100 ml biotransformation medium (glucose 3%, peptone 0.6% and at pH 4.5) from 600 mg of benzaldehyde with 8 h of reaction at 30 ± 2 °C. Growing the organism in presence of 3% glucose reduced the biotransformation time to 120 min. Addition of 0.6% acetaldehyde (30–35%) lead to an increase in L-PAC yield to 450 mg%. Semi-continuous feeding of benzaldehyde (200 mg) and acetaldehyde (200 l) four times at 30 min intervals could produce 683 mg of L-PAC/100 ml biotransformation medium. Chiral HPLC analysis of purified L-PAC and PAC-diol showed 99% enantiomeric purity. The cell mass was found to be reusable for biotransformation up to nine times when benzaldehyde and acetaldehyde levels were maintained at (350 mg and 350 l)–(400 mg and 400 l). At concentrations from 450 mg and 450 l to 600 mg and 600 l, however the cell mass could give efficient biotransformation only during one use.     

Formation and molecular structure of novel Ru(III) dimers of a symmetric antitumor drug analogue

The symmetrical anionic and neutral dimers [H(TMSO)₂]₂trans-[{RuCl₄(TMSO)}₂](μ-pyz) (1), and mer-[{RuCl₃(TMSO)₂}₂](μ-pyz) (2) were isolated by the reaction of [H(TMSO)] trans-[RuCl₄(TMSO)₂] and mer-[RuCl₃(TMSO)₃] with heterocyclic nitrogen donor ligand pyrazine (pyz) at room temperature. These complexes can be regarded as unprecedented examples in the general Creutz-Taube family of ruthenium dimers. Each ruthenium center in 1 and 2 has a coordination environment akin to that of known anionic and neutral monomeric Ru(III) complexes. Crystals of 1 · acetone are orange, needle like, space group , a=10.419(3) Å, b=10.539(3) Å, c=12.595(5) Å, α=69.837(16)°, β=69.968(15)°, γ=74.330(15)° and crystals of 2 · 4TMSO are orange prisms, trigonal, space group , a=33.971(5) Å, b=33.971(5) Å, c=12.210(2) Å, α=90°, β=90° and γ=120°.     

Dimethylsulphoniopropionate (DMSP) accumulation in green macioalgae from polar to temperate regions: interactive effects of light versus salinity and light versus temperature

Summary The effect of photon fluence rate on the ß-dimethylsulphoniopropionate (DMSP) content of salt-stressed eulittoral green macroalgae from different geographic regions was determined. At 55 mol photons m^–2s^–1 DMSP increased continuously with increasing salinities up to 68 in Ulothrix implexa, Ulothrix subflaccida, Enteromorpha bulbosa and Acrosiphonia arcta from Antarctica, while the Subantarctic/cold-temperate Ulva rigida and the temperate Blidingia minima showed a large rise in intracellular DMSP concentration only under gentle hypersaline treatment (51). At the highest salinity tested the DMSP content of the latter species declined. In contrast, the capacity to form DMSP in the dark under hypersaline conditions was very low in all species. In addition, the DMSP content of the Antarctic species was determined after one year cultivation at 0°C under photon fluence rates of 2, 30 and 55 mol m^–2s^–1. All isolates increased their DMSP concentration with increasing irradiance. In contrast to previous experiments done at 10°C, these species exhibited up to 5 fold higher DMSP values at 0°C under most photon fluence rates. The data support the idea of a light-dependent DMSP biosynthesis, and also demonstrate the stimulating effect of low water temperatures on the DMSP content of Antarctic green macroalgae. Apparently, in these plants DMSP may function as a cryoprotectant.Contribution No. 547 of the Institute for Polar and Marine Research, Bremerhaven