Amino-acid Type Identification in 15N-HSQC Spectra by Combinatorial Selective 15N-labelling

The efficiency of cell-free protein synthesis combined with combinatorial selective ¹⁵N-labelling provides a method for the rapid assignment of ¹⁵N-HSQC cross-peaks to the 19 different non-proline amino-acid types from five ¹⁵N-HSQC spectra. This strategy was explored with two different constructs of the C-terminal domain V of the τ subunit of the Escherichia coli DNA polymerase III holoenzyme, τ_C16 and τ_C14. Since each of the five ¹⁵N-HSQC spectra contained only about one third of the cross-peaks present in uniformly labelled samples, spectral overlap was much reduced. All ¹⁵N-HSQC cross-peaks of the backbone amides could be assigned to the correct amino-acid type. Availability of the residue-type information greatly assisted the evaluation of the changes in chemical shifts observed for corresponding residues in τ_C16 vs. those in τ_C14, and the analysis of the structure and mobility of the C-terminal residues present in τ_C16 but not in τ_C14.     

Prominent collagen type VI expression in juvenile angiofibromas

The extracellular matrix component collagen type VI demonstrates potent growth-stimulatory effects and has been associated with aggressive tumour growth. Although, juvenile angiofibromas (JAs) often exhibit an aggressive growth pattern, the collagen type VI expression of this fibrovascular tumour has not been addressed so far. RT-PCR, Western blot analysis and immunohistochemistry were used in this study to analyse collagen type VI, type VI collagen receptor subunits (integrin α1, α2, α10, α11 and β1) and the type VI collagen receptor NG2 in JAs (N = 15) and nasal mucosa (NM, N = 8) samples. The mRNA expression of all three collagen type VI chains was found to be up-regulated significantly (P < 10⁻³–10⁻⁵, adjusted) in JAs compared to NM tissues. The Western blot analysis proved highly prominent collagen-type VI expression in JAs. The ApoTome technique revealed strong collagen-type VI signals in tumour endothelium. NG2 (P < 10⁻³, adjusted) and α11-integrin (P = 0.04, adjusted) showed a significantly higher mRNA expression levels in JAs than in NM samples. NG2, α1-, α2- and β1-intergin were located to tumour vessels, and additional stromal signals were observed for NG2 and α1-integrin in JAs. This study demonstrates a prominent collagen-type VI expression in JAs. The collagen-type VI may exert an important growth stimulus in this tumour.     

The internal rotational barriers about NCα and CαC backbone bonds of polypeptides

In many studies on the protein folding problem it is assumed that the internal rotational barriers about NC^α and C^αC backbone bonds in unfolded polypeptides are quite small, around 0.7 kcal/mol, of an order comparable to the energy of kT at normal temperature (where k is Boltzmann’s constant and T is the temperature in K) and hence that rotations about these bonds occur almost freely. Here it is highlighted that such consideration is an unfortunate mistake. Approximate values for the rotational barriers of NC^α and C^αC bonds are suggested from computations of U(f \phi , ψ) potential energy surface (PES) maps of a number of oligopeptides by a semiempirical method for conformational analysis. The proposed values are about 16 kcal/mol for NC^α bonds and 6 kcal/mol for C^αC bonds. The values of the same barriers estimated from some ab initio quantum-mechanical PES maps for several dipeptides available in literature are also highlighted.     

Single-channel properties of a stretch-sensitive chloride channel in the human mast cell line HMC-1

A stretch-activated (SA) Cl⁻ channel in the plasma membrane of the human mast cell line HMC-1 was identified in outside-out patch-clamp experiments. SA currents, induced by pressure applied to the pipette, exhibited voltage dependence with strong outward rectification (55.1 pS at +100 mV and an about tenfold lower conductance at −100 mV). The probability of the SA channel being open (P _o) also showed steep outward rectification and pressure dependence. The open-time distribution was fitted with three components with time constants of τ_1o = 755.1 ms, τ_2o = 166.4 ms, and τ_3o = 16.5 ms at +60 mV. The closed-time distribution also required three components with time constants of τ_1c = 661.6 ms, τ_2c = 253.2 ms, and τ_3c = 5.6 ms at +60 mV. Lowering extracellular Cl⁻ concentration reduced the conductance, shifted the reversal potential toward chloride reversal potential, and decreased the P _o at positive potentials. The SA Cl⁻ currents were reversibly blocked by the chloride channel blocker 4,4′-diisothiocyanatostilbene-2,2′-disulfonic acid (DIDS) but not by (Z)-1-(p-dimethylaminoethoxyphenyl)-1,2-diphenyl-1-butene (tamoxifen). Furthermore, in HMC-1 cells swelling due to osmotic stress, DIDS could inhibit the increase in intracellular [Ca²⁺] and degranulation. We conclude that in the HMC-1 cell line, the SA outward currents are mediated by Cl⁻ influx. The SA Cl⁻ channel might contribute to mast cell degranulation caused by mechanical stimuli or accelerate membrane fusion during the degranulation process.     

Improved accuracy of <Superscript>15</Superscript>N–<Superscript>1</Superscript>H scalar and residual dipolar couplings from gradient-enhanced IPAP-HSQC experiments on protonated proteins

The presence of dipole-dipole cross-correlated relaxation as well as unresolved E.COSY effects adversely impacts the accuracy of ¹ J _NH splittings measured from gradient-enhanced IPAP-HSQC spectra. For isotropic samples, the size of the systematic errors caused by these effects depends on the values of ² J _NHα , ³ J _NHβ and ³ J _HNHα . Insertion of band-selective ¹H decoupling pulses in the IPAP-HSQC experiment eliminates these systematic errors and for the protein GB3 yields ¹ J _NH splittings that agree to within a root-mean-square difference of 0.04 Hz with values measured for perdeuterated GB3. Accuracy of the method is also highlighted by a good fit to the GB3 structure of the ¹H-¹⁵N RDCs extracted from the minute differences in ¹J_NH splitting measured at 500 and 750 MHz ¹H frequencies, resulting from magnetic susceptibility anisotropy. A nearly complete set of ² J _NHα couplings was measured in GB3 in order to evaluate whether the impact of cross-correlated relaxation is dominated by the ¹⁵N–¹H ^α or ¹⁵N–¹H ^β dipolar interaction. As expected, we find that ² J _NHα  ≤ 2 Hz, with values in the α-helix (0.86 ± 0.52 Hz) slightly larger than in β-sheet (0.66 ± 0.26 Hz). Results indicate that under isotropic conditions, N–H^N/N–H ^β cross-correlated relaxation often dominates. Unresolved E.COSY effects under isotropic conditions involve ³ J _HNHα and J _NHα , but when weakly aligned any aliphatic proton proximate to both N and H^N can contribute. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

First results from plasma density measurements in the FTU tokamak by means of a two-frequency pulsed time-of-flight refractometer

A pulsed time-of-flight refractometer was developed and tested to determine the mean plasma density in the T-11M tokamak by measuring the propagation time of nanosecond microwave pulses in plasma. Later, it was also proposed to use such an instrument to measure and control the mean plasma density in the ITER tokamak by probing the plasma with an extraordinary wave, the electric field of which is perpendicular to the magnetic field in plasma, in the transparency window at frequencies of 50–100 GHz. To avoid the effect of the density profile shape on the measurement results in the nonlinear mode of refractometer operation (near the cutoff), a system operating at two different probing frequencies was developed and tested. Such a system provides two values of the time delay, which can be used to estimate the peaking factor of the density distribution α and correctly determine the linear density 〈Nl〉, regardless of the density profile (assuming a smooth density profile of the form of N(ρ) = N(0)(1 − ρ²)^α, where N(0) is the central plasma density and ρ = r/a is the normalized plasma radius). The first experiments on density measurements in the FTU tokamak performed with this refractometer are described, and results from these experiments are presented. The formation of a thin dense plasma layer in the zone of a strong magnetic field (the so-called MARFE layer) at a relatively low (for FTU) plasma density of ∼6 × 10¹⁹ m⁻³ was detected. The thickness of this layer, determined from the refractometry data, agrees well with the data obtained using a digital camera.     

Linking conformation change to hemoglobin activation via chain-selective time-resolved resonance Raman spectroscopy of protoheme/mesoheme hybrids

Time-resolved resonance Raman (RR) spectra are reported for hemoglobin (Hb) tetramers, in which the α and β chains are selectively substituted with mesoheme. The Soret absorption band shift in mesoheme relative to protoheme permits chain-selective recording of heme RR spectra. The evolution of these spectra following HbCO photolysis shows that the geminate recombination rates and the yields are the same for the two chains, consistent with recent results on ¹⁵N-heme isotopomer hybrids. The spectra also reveal systematic shifts in the deoxyheme ν ₄ and ν _Fe–His RR bands, which are anticorrelated. These shifts are resolved for the successive intermediates in the protein structure, which have previously been determined from time-resolved UV RR spectra. Both chains show Fe–His bond compression in the immediate photoproduct, which relaxes during the formation of the first intermediate, R_deoxy (0.07 μs), in which the proximal F-helix is proposed to move away from the heme. Subsequently, the Fe–His bond weakens, more so for the α chains than for the β chains. The weakening is gradual for the β chains, but is abrupt for the α chains, coinciding with completion of the R–T quaternary transition, at 20 μs. Since the transition from fast- to slow-rebinding Hb also occurs at 20 μs, the drop in the α chain ν _Fe–His supports the localization of ligation restraint to tension in the Fe–His bond, at least in the α chains. The mechanism is more complex in the β chains.     

CACA-TOCSY with alternate <Superscript>13</Superscript>C–<Superscript>12</Superscript>C labeling: a <Superscript>13</Superscript>C<Superscript>α</Superscript> direct detection experiment for mainchain resonance assignment,dihedral angle information,and amino acid type identification

We present a ¹³C direct detection CACA-TOCSY experiment for samples with alternate ¹³C–¹²C labeling. It provides inter-residue correlations between ¹³C^α resonances of residue i and adjacent C^αs at positions i − 1 and i + 1. Furthermore, longer mixing times yield correlations to C^α nuclei separated by more than one residue. The experiment also provides C^α-to-sidechain correlations, some amino acid type identifications and estimates for ψ dihedral angles. The power of the experiment derives from the alternate ¹³C–¹²C labeling with [1,3-¹³C] glycerol or [2-¹³C] glycerol, which allows utilizing the small scalar ³J_CC couplings that are masked by strong ¹J_CC couplings in uniformly ¹³C labeled samples.     

Understanding UV-driven metabolism in the hypersaline ciliate Fabrea salina

By using NMR spectroscopy, a non-invasive investigation technique, we performed in vivo experiments aimed at uncovering the metabolic pathways involved in the early response of Fabrea salina cells to ultraviolet (UV) radiation. This hypersaline ciliate was chosen as a model organism because of its well-known high resistance to UV radiation. Identical cell samples were exposed to visible radiation only (control samples, CS) and to UV-B + UV-A + visible radiation (treated samples, TS), and NMR spectra of in vivo cells were collected at different exposure times. Resonances were identified through one- and two-dimensional experiments. To compare experiments performed at variable irradiation times on different culture batches, metabolite signals affected by the UV exposure were normalized to corresponding intensity at τ = 0, the zero exposure time. The most affected metabolites are all osmoprotectants, namely, choline, glycine-betaine, betaines, ectoine, proline, α-trehalose and sucrose. The time course of these signals presents qualitative differences between CS and TS, and most of these osmoprotectants tend to accumulate significantly in TS in a UV dose-dependent manner. A picture of the immediate stress response of F. salina against UV radiation in terms of osmoprotection, water retention and salting-out prevention is described.     

A thermostable α-galactosidase from Lenzites elegans (Spreng.) ex Pat. MB445947: purification and properties

An α-galactosidase was isolated from a culture filtrate of Lenzites elegans (Spreng.) ex Pat. MB445947 grown on citric pectin as carbon source. It was purified to electrophoretic homogeneity by ammonium sulfate precipitation, gel filtration chromatography and anion-exchange chromatography. The relative molecular mass of the native purified enzyme was 158 kDa determined by gel filtration and it is a homodimer (Mr subunits = 61 kDa). The optimal temperature for enzyme activity was in the range 60–80 °C. This α-galactosidase showed a high thermostability, retaining 94 % of its activity after preincubation at 60 °C for 2 h. The optimal pH for the enzyme was 4.5 and it was stable from pH 3 to 7.5 when the preincubation took place at 60 °C for 2 h. It was active against several α-galactosides such as p-nitrophenyl-α-d-galactopyranoside, α-d-melibiose, raffinose and stachyose. The α-galactosidase is a glycoprotein with 26 % of structural sugars. Galactose was a non-competitive inhibitor with a Ki = 22 mM versus p-nitrophenyl-α-d-galactoside and 12 mM versus α-d-melibiose as substrates. Glucose was a simple competitive inhibitor with a Ki = 10 mM. Cations such as Hg²⁺ and p-chloromercuribenzoate were also inhibitors of this activity, suggesting the presence of –SH groups in the active site of the enzyme. On the basis of the sequence of the N-terminus (SPDTIVLDGTNFALN) the studied α-galactosidase would be a member of glycosyl hydrolase family 36 (GH 36). Given the high optimum temperature and heat stability of L. elegans α-galactosidase, this fungus may become a useful source of α-galactosidase production for multiple applications.     

Physico-chemical characterization of a new heteropolysaccharide produced by a native isolate of heterofermentative <Emphasis Type="Italic">Lactobacillus</Emphasis> sp. CFR-2182

A heterofermentative Lactobacillus sp. CFR-2182 was isolated from dahi samples and it was found to produce 8.0 and 20.5 g/L heteropolysaccharide (HePS) in EPS medium (a simplified synthetic medium) and modified MRS broth, respectively, after 72 h at 30°C. The total carbohydrate, reducing sugar and moisture contents of the purified HePS were 74, 10.6 and 2 g, respectively, per 100 g on dry weight basis. The HePS produced in EPS medium had glucose and mannose in 17:1 ratio. The HePS was non-gelling and non-film forming type. It was completely soluble in water and 1 N sodium hydroxide solution. Gel permeation chromatography and HPLC analysis indicated considerable heterogeneity of the HePS, having three fractions with molecular weights ranging from 3.3 × 10⁴ to 1.32 × 10⁶ Da. The enzymatic hydrolysis of the HePS with pullulanase and α-amylase [with α(1→4) linkage] indicated the presence of α(1→6) and traces of α(1→4) linkages, respectively. NMR analysis of the EPS revealed unique chemical shifts.     

Electrostatic determinants of the ion channel control of the nicotinic acetylcholine receptor of Torpedo californica

The patch clamp K⁺-conductance G of the nicotinic acetylcholine receptor (AcChoR) dimer (M_r≈ 590 000) of Torpedo californica, reconstituted in lipid vesicles, which decreases with increasing Ca²⁺-concentration in the range 0.1≤[Ca²⁺]/mM≤2, can be quantitatively rationalized by Ca²⁺-binding to negatively charged sites, causing charge reversal reducing the normal K⁺-accumulation in the channel vestibules. Cleavage of the sialic acid residues (up to 20±2 per dimer) reduces the K⁺-accumulation factor α = G₀/G_∞ from α = 3±0.8 of the normal AcChoR to α = 2±0.7 for the desialyated AcChoR. Desialysation also decreases the Ca²⁺-sensitivity of the conductance from G₀ = 96.6±6 pS at [Ca²⁺]→0 of the normal AcChoR to G₀ = 84.2±6 pS. Endogenous hyperphosphorylation (to up to 28±4 phosphates per dimer) enhances the vestibular K⁺-accumulation to α = 3.6±0.7, without affecting the Ca²⁺-dissociation equilibrium constant K_Ca = 0.34± 0.05 mM at 295 K (22 °C). Most interestingly, even in the absence of AcCho, the hyperphosphorylated AcChoR dimer exhibits spontaneously long-lasting open channel events (τ = 200±50 ms). At [AcCho] = 2 μM there are two open states (τ ₁ = 20±10 ms, τ ₂ = 140±60 ms) whereas the normal AcChoR dimer has only one open state (τ = 6±4 ms). – Physiologically important is that (i) the sialic acid and phosphate residues render the AcChoR conductance sensitive to control by divalent ions and (ii) the channel behavior of the hyperphosphorylated AcChoR without AcCho appears to indicate pathophysiologically high phosphorylation activity of the cell leading, among others, to myasthenic syndromes. Received: 10 November 1997 / Revised version: 12 January 1998 / Accepted: 7 March 1998     

Scaling and organization of electroencephalographic background activity and alpha rhythm in healthy young adults

The coexistence of the broad-band fluctuation and α rhythm of the brain dynamics is studied based on the zero-crossing property of the local electroencephalographic (EEG) recording in eyes closed and eyes open. A two-component zero-crossing scenario, consisting of a broad-band fractal and narrow-band rhythm components, is assumed. Scaling is found in the power law distribution p(τ) ~ τ ^−ν of the crossing time interval τ of the broad-band fluctuation. In α dominant brain state, the α rhythm interval L also exhibits scaling in the form of power law distribution: . Our main result is the relationship that characterizes the organization of these two prominent features of the brain dynamics. The possible role of self-organized criticality of punctuated equilibrium in this organization is discussed.     

Spectral characterization of the recombinant mouse tumor suppressor 101F6 protein

Tumor suppressor protein 101F6, a gene product of the 3p21.3 (human) and 9F1 (mouse) chromosomal region, has recently been identified as a member of the cytochrome b561 (Cyt-b561) protein family by sequence homology. The His₆-tagged recombinant mouse tumor suppressor Cyt-b561 protein (TSCytb) was recently expressed in yeast and purified, and the ascorbate reducibility was determined. TSCytb is auto-oxidizable and has two distinct heme b centers with redox potentials of ~40 and ~140 mV. Its split α-band in the dithionite-reduced spectrum at both 295 and 77 K is well resolved, and the separation between the two α-peaks is ~7 nm (~222 cm⁻¹). Singular value decomposition analysis of the split α-band in the ascorbate-reduced spectra revealed the presence of two major spectral components, each of them with split α-band but with different peak separations (6 and 8 nm). Similar minor differences in peak separation were obtained when the split α-bands in ascorbate-reduced difference spectra at low (<1 mM) and high (>10 mM) ascorbate concentrations were analysed. According to low-temperature electron paramagnetic resonance (EPR) spectroscopy, the two heme b centers are in the low-spin ferric state with maximum principal g values of 3.61 and 2.96, respectively. These values differ from the ones observed for other members of the Cyt-b561 family. According to resonance Raman spectroscopy, the porphyrin rings are in a relaxed state. The spectroscopic results are only partially in agreement with those obtained earlier for the native chromaffin granule Cyt-b561.     

Force–velocity relationship for multiple kinesin motors pulling a magnetic bead

Although the velocity of single kinesin motors against an opposing force F of 0–10 pN is well known, the behavior of multiple kinesin motors working to overcome a larger load is still poorly understood. We have carried out gliding assays in which 3–7 Drosophila kinesin-1 motors moved a microtubule at 200–700 μm/s against a 0–31 pN load at saturating [ATP]. The load F was generated by applying a spatially uniform magnetic field gradient to a superparamagnetic bead attached to the (+) end of the microtubule. When F was scaled by the average number of motors 〈n〉, the force–velocity relationship for multiple motors was similar to the force–velocity relationship for a single motor, supporting a minimal load-sharing model. The velocity distribution at low load has a single mode consistent with rapid fluctuations of n. However, against a load of 2.5–4.7 pN/motor, additional modes appeared at lower velocity. These observations support the Klumpp–Lipowsky model of multimotor transport [Proc Natl Acad Sci USA 102. 17284–17289 (2005)].     

In vitro somatic embryogenesis and plant regeneration in Zantedeschia hybrids

A method for regeneration of plants from tuber explants of a Zantedeschia hybrid via somatic embryogenesis was developed. In vitro cultures were initiated starting from both anthers and tubers. Somatic embryogenesis was only achieved from tuber explants. 6-Benzyladenine (BA) at 0.6 or 2 mg l⁻¹ in combination with 2 mg l⁻¹ α-naphthaleneacetic acid (NAA) yielded the highest number of embryos per explant. The somatic embryos converted into plantlets on Murashige and Skoog basal medium supplemented with vitamins, micro- and macronutrients, 1 mg l⁻¹ 6-τ-τ-(dimethylallylamino)-purine (2iP), 3% sucrose and 0.7% agar. This is the first report on induction of somatic embryogenesis in Zantedeschia.     

Presteady-State Currents of the Rabbit Na+/Glucose Cotransporter (SGLT1)

The rabbit Na⁺/glucose cotransporter (SGLT1) exhibits a presteady-state current after step changes in membrane voltage in the absence of sugar. These currents reflect voltage-dependent processes involved in cotransport, and provide insight on the partial reactions of the transport cycle. SGLT1 presteady-state currents were studied as a function of external Na⁺, membrane voltage V _m , phlorizin and temperature. Step changes in membrane voltage—from the holding V _h to test values, elicited transient currents that rose rapidly to a peak (at 3–4 msec), before decaying to the steady state, with time constants τ≈4–20 msec, and were blocked by phlorizin (K _i ≈30 μm). The total charge Q was equal for the application of the voltage pulse and the subsequent removal, and was a function of V _m . The Q-V curves obeyed the Boltzmann relation: the maximal charge Q _max was 4–120 nC; V _0.5, the voltage for 50% Q _max was −5 to +30 mV; and z, the apparent valence of the moveable charge, was 1. Q _max and z were independent of V _h (between 0 and −100 mV) and temperature (20–30°C), while increasing temperature shifted V _0.5 towards more negative values. Decreasing [Na⁺] _o decreased Q _max, and shifted V _0.5 to more negative voltages 9by −100 mV per 10-fold decrease in [Na⁺] _o ). The time constant τ was voltage dependent: the τ-V relations were bell-shaped, with maximal τ_max 8–20 msec. Decreasing [Na⁺] _o decreased τ_max, and shifted the τ-V curves towards more negative voltages. Increasing temperature also shifted the τ-V curves, but did not affect τ_max. The maximum temperature coefficient Q ₁₀ for τ was 3–4, and corresponds to an activation energy of 25 kcal/mole. Simulations of a 6-state ordered kinetic model for rabbit Na⁺/glucose cotransport indicate that charge-movements are due to Na⁺-binding/dissociation and a conformational change of the empty transporter. The model predicts that (i) transient currents rise to a peak before decay to steady-state; (ii) the τ-V relations are bell-shaped, and shift towards more negative voltages as [Na⁺] _o is reduced; (iii) τ_max is decreased with decreasing [Na⁺] _o ; and (iv) the Q-V relations are shifted towards negative voltages as [Na⁺] _o is reduced. In general, the kinetic properties of the presteady-state currents are qualitatively predicted by the model. Received: 12 August 1996/Revised: 30 September 1996     

Small scale vertical gradients of Arctic ice algal photophysiological properties

Photosynthetic parameters of phytoplankton and sea ice algae from landfast sea ice of the Chukchi Sea off Point Barrow, Alaska, were assessed in spring 2005 and winter through spring 2006 using Pulse Amplitude Modulated (PAM) fluorometry including estimates of maximum quantum efficiency (F _v/F _m), maximum relative electron transport rate (rETR_max), photosynthetic efficiency (α), and the photoadaptive index (E _k). The use of centrifuged brine samples allowed to document vertical gradients in ice algal acclimation with 5 cm vertical resolution for the first time. Bottom ice algae (0–5 cm from ice–water interface) expressed low F _v/F _m (0.331–0.426) and low α (0.098–0.130 (μmol photons m⁻²s⁻¹)⁻¹) in December. F _v/F _m and α increased in March and May (0.468–0.588 and 0.141–0.438 (μmol photons m⁻²s⁻¹)⁻¹, respectively) indicating increased photosynthetic activity. In addition, increases in rETR_max (3.3–16.4 a.u.) and E _k (20–88 μmol photons m⁻² s⁻¹) from December to May illustrates a higher potential for primary productivity as communities become better acclimated to under-ice light conditions. In conclusion, photosynthetic performance by ice algae (as assessed by PAM fluorometry) was tightly linked to sea ice salinity, temperature, and inorganic nutrient concentrations (mainly nitrogen).