Levans. II. Light-scattering and sedimentation data of Streptococcus salivarius Levan in water.

The molecular weights and radii of gyration of Streptococcus salivarius levan fractions were obtained from light-scattering measurements in water. Sedimentation coefficients and partial specific volumes of the fractions were also obtained. Double logarithmic plots of [η] versus M?_w and S⁰ versus M?_w yielded slopes having values of 0.17 and 0.62, respectively. The data and various calculated parameters show that levan from Streptococcus salivarius is highly branched and behaves hydrodynamically as a compact particle of spherical symmetry.     

Very low-angle light scattering. A characterization method for high-molecular-weight DNA

A very low-angle light-scattering photometer is described with respect to optical features, scattering cell, correction factors, and absolute calibration in the angular range 2°–35°. An improved microfiltration apparatus was used to obtain essentially dust-free aqueous solutions for very low-angle light scattering. The instrument was calibrated with silicotungstic acid, an absolute molecular-weight standard, and the calibration was confirmed with the use of several secondary standards. Very low-angle light-scattering measurements were made to determine the weight-average molecular weight M?_r and z-average radius of gyration R_g,z of a commerical preparation of calf-thymus DNA. Microfiltration of the solutions allowed measurements down to 6°. The value M?_r = 20.0 × 10⁶ obtained by extrapolating 6°–9° data to 0° is more than three times that from 30°–75° data (6.38 × 10⁶) but ～20% smaller than that from 10–35° data (23.7 × 10⁶). The experimental errors in M?_r and R_g,z are estimated to be ±8% and ±14%, respectively. Combined 6°–75° data from two photometers fit well a theoretical scattering curve for a model wormlike coil of the same M?_r as the DNA sample.     

Physicochemical parameters of partially hydrolyzed S. salivarius levan fractions

The fractions obtained from the partially hydrolyzed branched Streptococcus salivarius levan were examined in solution. Sedimentation coefficients, S⁰, intrinsic viscosities, [η], weight-average molecular weights, M _w, and radii of gyration were obtained from sedimentation velocity, viscosity, and light-scattering measurements. Double logarithmic plots of [η] vs M _w and S⁰ vs M _w each yielded two linear segments intersecting at M _w ≈ 10⁵. Hydrodynamic data suggest that fractions of M _w > 10⁵ behave as compact spheres, whereas for M _w < 10⁵, the particles are best characterized as linear random coils. Calculations based on theories of random coils and spheres support the above observations.     

Some dilute-solution parameters of the levan of streptococcus salivarius in various solvents

The intrinsic viscosities, weight-average molecular weights (M?_w), and radii of gyration [($\text{R}{}^2{}_{\mathrm{g}}$)^{$\text{1}\text{2}$}≈] of Streptococcus salivarius levan in various solvents were respectively obtained from viscosity and light-scattering measurements. The data showed that the levan in water is not aggregated by hydrogen bonds, and that the values of both the refractive index and ($\text{R}{}^2{}_{\mathrm{g}}$)^{$\text{1}\text{2}$} are lower in water than in aqueous solutions of urea. Urea may break intramolecular hydrogen-bonds, e.g., between branches, allowing the molecule to expand.     

Light scattering and viscosity study of heat aggregation of insulin

Aggregation behavior and hydrodynamic parameters of insulin have been determined from static and dynamic light scattering experiments and intrinsic viscosity measurements carried out at pH 4.0, 7.5, and 9.0 in the temperature range 20–40°C in aqueous solutions. The protein aggregated extensively at elevated temperatures in the acidic solutions. Intermolecular interactions were found to be attractive and to increase with temperature. The measured intrinsic viscosity [η], diffusion coefficient D₀, molecular weight M, and radius of gyration R_g exhibited the universal behavior: M[η] = (2.4 ± 02) × 10⁻²⁷ (R_e,η/R_e,D)³(D_0η/T)⁻³ and (D₀√n)₋₁ ≃ (√6 πη₀ζβ/k_BT) [1 + 0.201)(v/β³)√n], where n is the number of segments in the polypeptide. The effective hydrodynamic radii deduced from [η], (R_e, η) and the same deduced from D₀, (R_e,D) showed a constant ratio, (R_e,η/R_e,D = 1.1 ± 0.1). R_e,D/R_g = ξ was found to be (0.76 ± 0.07). From the known solvent viscosity η₀, the segment length β was deduced to be (10 ± 1) Å. The excluded volume was deduced to be (5 Å)³ regardless of pH. The Flory-Huggins interaction parameter was found to be χ = 0.45 ± 0.04, independent of pH and temperature. © 1998 John Wiley & Sons, Inc. Biopoly 45: 1–8, 1998     

The molecular structure and solution conformation of an acidic heteropolysaccharide from Auricularia auricula-judae

A water soluble acidic heteropolysaccharide named WAF was isolated from Auricularia auricula‐judae by extracting with 0.9% NaCl solution. By using gas chromatography, gas chromatography‐mass spectrometry, and NMR, its chemical structure was determined to be composed of a backbone of α‐(1→3)‐linked D ‐mannopyranose residues with pendant side groups of β‐D ‐xylose, β‐D ‐glucose, or β‐D ‐glucuronic acid at position O6 or O2. Six fractions prepared from WAF with a weight‐average molecular mass (M_w) between 5.9 × 10⁴ and 64.7 × 10⁴ g/mol were characterized with laser light scattering and viscometry in 0.1M NaCl at 25°C. The dependence of intrinsic viscosity ([η]) and radius of gyration (R_g) on M_w for this polysaccharide were found to be [η] = 1.79 × 10^?3M_w^0.96 cm³ g^?1 and R_g = 6.99 × 10^?2 M_w^0.54 nm. The molar mass per unit contour length (M_L) and the persistence length (L_p) were estimated to be 1124 nm^?1 and 11 nm, respectively. The WAF exhibited a semirigid character typical of linear polysaccharides. Molecular modeling was then used to predict the ordered and disordered states of WAF; the simulated M_L and L_p were however much smaller than the experimental values. Taken altogether, the results suggested that WAF formed a duplex in solution. © 2010 Wiley Periodicals, Inc. Biopolymers 95: 217–227, 2011.     

Ionic polysaccharides. IV. Free-rotation dimensions for disaccharide polymers. Comparison with experiment for hyaluronic acid

The root-mean-square end-to-end distance has been calculated for a model allowing free rotation about glycoside bonds for the general case of polysaccharides having a disaccharide repeating unit. Numerical estimates are given for several naturally occurring structures based on an idealized pyranose unit in the C1 chair conformation. Extrapolation procedures which make use of the intrinsic viscosity [η] in good solvents to obtain unperturbed dimensions do not represent, data for hyaluronic acid very well, especially at low molecular weights. However, order-of-magnitude estimates suggest that this polymer behaves similarly to other polysaccharides, and probably has stiffer local structure than typical non-ionic synthetic polymers. A double logarithmic plot of the product of [η] and M?_w, the weight-average molecular weight, against the degree of polymerization in the range for M?_w of 10⁴ to 2 × 10⁴ permits a straight-line fit of available data for all the glycosaminoglycans, including heparin and the chondroitin sulfates, as well as sodium carboxymethyl cellulose. This result suggests similarity of short-chain hydrodynamic behavior of these polymers.     

Effects of the water-miscible organic solvents on lactoperoxidase purified from creek-water buffalo milk

Water buffalo lactoperoxidase (WBLPO) was purified with Amberlite CG-50 (NH₄ ⁺ form) resin, CM-Sephadex C-50 ion-exchange chromatography, and Sephadex G-100 gel-filtration chromatography from skimmed buffalo milk. The purity of the WBLPO was shown with SDS-PAGE. The R_z(A ₄₁₂/A ₂₈₀) value for the WBLPO was 0.9. The optimum pH for the WBLPO was at 6.0. The K _m value at optimum pH and 25°C was 0.13 mM. The V _max value at optimum pH and 25°C was 5.3 mol/min per ml. The K _i values for methanol, ethanol, dimethyl sulfoxide (DMSO), acetonitrile, isopropanol, tetrahydrofuran (THF), N,N"-dimethylformamide (DMF), and ethylene glycol were 1.087, 0.364, 0.302, 0.459, 0.330, 0.126, 0.093, and 2.125 M, respectively. All the solvents showed competitive inhibition. The I ₅₀ values of methanol, ethanol, dimethyl sulfoxide, acetonitrile, isopropanol, tetrahydrofuran, N,N"-dimethylformamide, and ethylene glycol were 2.910, 0.942, 0.537, 1.320, 0.875, 0.470, 0.405, and 3.920 M, respectively. Ethylene glycol, methanol, acetonitrile, and ethanol have been found to be very promising solvents for performing biocatalytic reactions with LPO in organic media.     

Specific non-histone protein fractions associated with ‘active’ chromatin in immunized rats

Summary Non-histone proteins of normal, non-immunized rats and rats immunized with mouse spleen cells were labelled with three different amino acids: [³H]tryptophan, [³H]methionine and [³H]leucine. Chromatin was fractionated at increasing salt concentrations into three fractions: 0.35 M NaCl-soluble, 2 M NaCl-soluble and residual. Non-histone protein fractions F (M_r 12 000) and H (M_r 3 000) highly labelled with [³H]tryptophan, lower with [³H]methionine but not with [³H]leucine, were present mainly in the residual fraction. After DNAse II treatment non-histone protein fractions F and H disappeared in chromatin fractions and were present in Mg^2– soluble fractions which suggests that, similar to the fractions I (M_r below 3 000) and B (M_r 120 000) described previously (5), these fractions may be associated with active transcribed genes.     

The small-scale production of [U-C]acetylene from BaCO3: Application to labeling of ammonia monooxygenase in autotrophic nitrifying bacteria

A small-scale method has been adapted from an established procedure for the generation of [U-¹⁴C]acetylene from inexpensive and commonly available precursors. The method involves the fusing of Ba¹⁴CO₃ with excess barium metal to produce Ba¹⁴C₂. The BaC₂ is reacted with water to generate acetylene which is then selectively dissolved into dimethyl sulfoxide (DMSO). The results presented demonstrate the effect of Ba:BaCO₃ ratio on the concentrations of various gases released during the hydrolysis reaction and quantify the selectivity of the DMSO-trapping process for each gas. [U-¹⁴C]-Acetylene generated by this method has been used to inactivate ammonia monooxygenase in three species of autotrophic nitrifying bacteria: Nitrosomonas europaea, Nitrosococcus oceanus, and Nitrosolobus multiformis. Our results demonstrate that acetylene inactivation of this enzyme in all three species results in the covalent incorporation of radioactive label into a polypeptide of apparent M_r of 25,000–27,000, as determined by sodium dodecylsulfate-polyacrylamide gel electrophoresis and fluorography.     

Delineating the conformational dynamics of intermediate structures on the unfolding pathway of β-lactoglobulin in aqueous urea and dimethyl sulfoxide

Abstract

The funnel shaped energy landscape model of the protein folding suggests that progression of folding proceeds through multiple pathways, having the multiple intermediates which leads to multidimensional free-energy surface. Herein, we applied all-atom MD simulation to conduct a comparative study on the structure of β-lactoglobulin (β-LgA) in aqueous mixture of 8?M urea and 8?M dimethyl sulfoxide (DMSO), at different temperatures. The cumulative results of multiple simulations suggest a common unfolding pathway of β-LgA, occurred through the stable and meta-stable intermediates (I), in both urea and DMSO. However, the free-energy landscape (FEL) analyses show that the structural transitions of I-states are energetically different. In urea, FEL shows distinct ensemble of intermediates, I1 and I2, separated by the energy barrier of ～3.0?kcal mol^?1. Similarly, we find the population of two distinct I1 and I2 states in DMSO, however, the I1 appeared transiently around ～30–35?ns and is short-lived. But, the I2 ensemble is observed structurally compact and long-lived (～50–150?ns) as compared to unfolding in urea. Furthermore, the I1 and I2 are separated through a high energy barrier of ～6.0?kcal mol^?1. Thus, our results provide the structural insights of intermediates which essentially bear the signature of a different unfolding pathway of β-LgA in urea and DMSO.

Abbreviations β-LgA β-lactoglobulin

DMSO dimethyl sulfoxide

FEL free-energy landscape

GdmCl guanidinium chloride

I intermediate state

MG molten globule state

PME particle mesh Ewald

Q fraction of native contacts

RMSD root mean square deviation

RMSF root mean square fluctuation

R_g radius of gyration

SASA solvent Accessible Surface Area

scSASA the side chain SASA

Trp tryptophan

Communicated by Ramaswamy H. Sarma     

Diurnal and seasonal variations in stomatal conductance of rice at elevated atmospheric CO2 under fully open‐air conditions

Understanding of leaf stomatal responses to the atmospheric CO₂ concentration, [CO₂], is essential for accurate prediction of plant water use under future climates. However, limited information is available for the diurnal and seasonal changes in stomatal conductance (g_s) under elevated [CO₂]. We examined the factors responsible for variations in g_s under elevated [CO₂] with three rice cultivars grown in an open‐field environment under flooded conditions during two growing seasons (a total of 2140 individual measurements). Conductance of all cultivars was generally higher in the morning and around noon than in the afternoon, and elevated [CO₂] decreased g_s by up to 64% over the 2 years (significantly on 26 out of 38 measurement days), with a mean g_s decrease of 23%. We plotted the g_s variations against three parameters from the Ball‐Berry model and two revised versions of the model, and all parameters explained the g_s variations well at each [CO₂] in the morning and around noon (R² > 0.68), but could not explain these variations in the afternoon (R² < 0.33). The present results provide an important basis for modelling future water use in rice production.     

Small-angle x-ray scattering of bovine nasal cartilage proteoglycan in solution

The proteoglycan subunit (PGS) from bovine nasal cartilage was examined in water and in 0.15 N LiCl by small-angle x-ray scattering (SAXS). The molecular weight of 2.5 × 10⁶ and the radius of gyration, R_g = 493 Å, in 0.15 N LiCl, obtained by SAXS, are in good agreement with values reported by others for similar preparations. Values of the radius of gyration of the cross section, mass per unit length, and persistence length of the PGS are also reported. The low value of intrinsic viscosity ([η]) found in 0.15 N LiCl, and a comparison of the experimental distance distribution function to that of the theoretical distance distribution function for sphere, suggest that the PGS in salt solution approaches spherical symmetry. The much higher value of [η] in water suggests a prolate ellipsoid of low axial ratio.     

Characterization of group C meningococcal polysaccharide by light-scattering spectroscopy. III. Determination of molecular weight, radius of gyration, and translational diffusional coefficient.

Group-specific polysaccharides isolated by means of a cetavlon procedure are immunogenic in man and induce protective immunity against meningococcal meningitis. Minute quantities of the polymers in solution can act as vaccines. We now report the first characterization of a fractionated (C-1) group C polysaccharide in 0.4KM KCl and 0.05M sodium acetate by means of light-scattering spectroscopy. Independent measurements of refractive index increments, absolute scattered intensities, angular scattering intensities and line widths as a function of scattering angles and delay times at different concentrations using incident wavelengths of 632.8 nm from a He–Ne laser and of 488 nm from an argon–ion laser yield information on aggregation properties, molecular weight (M_r), radius of gyration 〈r⁰_g〉^1/2_z, translational diffusion coefficient 〈D〉⁰_z, and second virial coefficients A₂ and B₂ of C-1 polysaccharide. At relatively high ionic strength (0.04M KCl + 0.05M sodium acetate), we obtain for the C-1 polysaccharide in solution M_r = 5.15 × 10⁵, 〈r²_g〉^1/2_z = 345 Å, A₂ = 1.25 × 10^?4 ml/g, 〈D〉 = 1.16 × 10^?7 cm²/sec with a corresponding Stokes radius of 240 Å and B₂ = 4.4 ml/g. A₂ and B₂ are the second virial coefficients from intensity- and diffusion-coefficient measurements. The C-1 polysaccharide aggregates in solution and behaves hydrodynamically like random coils. Viscosity and sedimentation studies further confirm our conclusions that the fractioned C-1 polysaccharide aggregates in solution and EDTA can partially break up those aggregates. However, the system remains polydisperse even after adding an excess amount of EDTA. The weight-average molecular weight of the C-1 polysaccharide in solution depends upon ionic strength and exhibits a minimum at ～0.2M KCl. Finally, viscosity, light-scattering, and sedimentation results all show that the aggregated macromolecular system behaves like random-coiled polymers with no measurable shape factors.     

Infinite dilution viscoelastic properties of poly(gamma-benzyl-L-glutamate) in m-cresol.

The real and imaginary parts of complex viscosity, η′ and η″, are measured for dilute solutions of poly(γ-benzyl-L -glutamate) in m-cresol, a helicogenic solvent. The frequency range is 2.2–525 kHz; the concentration range 0.2–5 g/dl; the temperature 30°C, and the molecular weights M_r are 6.4 × 10⁴–17 × 10⁴. The dispersion curve of extrapolated intrinsic dynamic viscosity [η′] of samples with M_r > 10⁵ is interpreted in terms of three mechanisms appearing from low to high frequencies: end-over-end rotation, flexural deformation, and side-chain motion. For a sample with M_r < 10⁵, the flexural relaxation disappears and a plateau of [η′] is distinctly observed between rotational and side-chain relaxations. Rotational relaxation times of all the samples obey the Kirkwood–Auer theory. The strong concentration dependence of rotational relaxation time is explained by collisions of molecules rather than association. Flexural relaxation times calculated from a theory by assuming the persistence length as 1200 Å are consistent with observed dispersion curves of [η′].     

Chain conformation and bioactivity of water‐soluble polysaccharide extracted from Rhizoma Panacis Japonici

A water‐soluble α‐(1→4)‐D ‐glucan heteropolysaccharide with 37% degree of branch extracted by base from Rhizoma Panacis Japonici, coded as RPS3, was fractionated into six fractions by the method of nonsolvent addition. Their weight‐average molecular mass (M_w), polydispersity index (M_w/M_n), and radius of gyration (〈s²〉_z^1/2) were determined with laser light scattering (LLS) and size exclusion chromatography combined with LLS. The structure of the fraction was determined by methylation analyses and ¹³C NMR. The dependences of intrinsic viscosity ([η]) and 〈s²〉_z^1/2 on M_w were established as [η] = 0.71 M_w^{0.27 ± 0.01} (cm³/g) and 〈s²〉_z^1/2 = 1.53 M_w^{0.27 ± 0.02} (nm) in the M_w range from 5.62 × 10⁴ to 3.05 × 10⁶ (g/mol) for RPS3 in 0.15M NaCl aqueous solution at 25°C. On the basis of the current theory of the polymer solution, the fractal dimension (d_f), unperturbed chain dimension (A), and characteristic ratio (C_∞) were calculated to be 3.0, 1.48 Å, and 15.1, respectively. The results revealed that the RPS3 chains existed as spherical conformation in the aqueous solution. Transmission electron microscope further provided the evidence of the sphere shape of the RPS3 and its fractionated molecules in water. In vitro cytotoxicity assay indicated that the fractions could inhibit the tumor cells and showed no harm to normal cells at low dose. The bioactivity was relative with molecular mass of the samples. © 2010 Wiley Periodicals, Inc. Biopolymers 93: 383–390, 2010. This article was originally published online as an acceptedpreprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office atbiopolymers@wiley.com     

How to compare fluctuating asymmetry of different traits

Comparing fluctuating asymmetry (FA) between different traits can be difficult because traits vary at different scales. FA is generally quantified either as the variance of the difference between left and right (σ²_L?R) or the mean of the absolute value of this difference (μ_|R?L|). Corrections for scale differences are obtained by dividing by trait size mean. We show that a third index, one minus the correlation coefficient between left and right (1 ? r_L,R), is equivalent to σ²_L?R standardized by trait size variance. The indices are compared with Monte‐Carlo simulations. All achieve the expected correction for scale differences. High type I error rates (false indication of differences) occur only for σ²_L?R and μ_|R?L| if trait sizes close to or below 0 occur. 1 ? r_L,R with a bootstrap test has always low error rates. Recommendation of the index to be used should be based on whether standardization of FA by trait size mean or trait size variance is preferred. A survey of 36 traits in the Speckled Wood Butterfly (Pararge aegeria) indicated that σ²_L?R is slightly higher correlated to trait size variance than to trait size mean. Thus 1 ? r_L,R seems to be the superior index and should be reported when FA of different traits is compared.     

Effects of Acidification, Sodium Chloride, and Moisture Levels on Wheat Dough: II. Modeling of Bread Texture and Staling Kinetics

The effect of three experimental factors pH (addition of lactic acid and sodium hydroxide), water, and sodium chloride (NaCl) addition on wheat bread making performance (volume, baking loss, crumb firmness, crumb grain features) and the crumb staling during storage was studied. The staling behavior was modeled with the Avrami equation and with linear regressions. All bread quality parameters were reliably modeled using response surface methodology (up to R ² ?=?0.97). The crumb staling behavior was better described by a linear regression than by the rate constant k of the Avrami equation (R ² ?=?0.87 / R ² ?=?0.36). The highest volume can be achieved with the experimental values pH 5.39, 0.41?g NaCl 100?g^?1 flour and 68.7?g water 100?g^?1 flour. Correlation analysis revealed significant linear dependency of dough rheology (complex shear modulus) on the firmness of the bread crumb (r?=?0.73) and staling attributes (r????0.73). Dough microstructural properties showed significant but low correlation with bread making performance attributes.