Chain conformation of water-insoluble hyperbranched polysaccharide from fungus

Water-insoluble polysaccharide (TM3a), extracted from sclerotia of Pleurotus tuber-regium, was identified as a hyperbranched beta-d-glucan from the results of one- and two-dimensional NMR and GC-MS analysis. The degree of branching of TM3a is 65.5%. TM3a was fractionated by using a non-solvent addition method into 14 fractions, and its solution properties in 0.25 M LiCl/dimethylsulfoxide (DMSO) solution were studied systematically by using static laser light scattering, dynamic light scattering, and viscometry at 25 degrees C. The dependences among the values of intrinsic viscosity ([eta]), radius of gyration (z 1/2), and hydradynamic radius (Rh) on weight-average molecular weight (Mw) were found as the following: [eta] = 0.46Mw0.30+/-0.01, z 1/2 = 4.79 x 10-2Mw0.43+/-0.04, and Rh = 5.01 x 10-2Mw0.41+/-0.02 in the Mw range from 1.94 x 105 to 2.06 x 107 for TM3a in a 0.25 M LiCl/DMSO solution at 25 degrees C. The current theory of polymer solution was applied to explain the relationship among the fractal dimension, ratio of geometric to hydrodynamic radius (rho = z 1/2/Rh), and MwA2/[eta] of TM3a. The results indicated that TM3a existed as a compact chain conformation with a sphere-like structure in LiCl/DMSO solution. Furthermore, by using transmission electron microscopy, we observed directly the spherical molecules with an average diameter of 23.0 +/- 1.8 nm.     

Molecular characterisation of soybean polysaccharides: an approach by size exclusion chromatography, dynamic and static light scattering methods

Water soluble polysaccharides from soybean (SSPS) have a pectin-like structure and are used as stabilisers in acidified beverages. Physicochemical properties such as structure, molecular weight and shape or conformation are primary factors controlling their functional properties. Two soybean polysaccharides, a native SSPS and a modified SSPS treated with beta-(1-->4)-D-galactosidase (GPase/SSPS) were studied by dynamic and static light scattering (DLS, SLS) and size exclusion chromatography (SEC). Consecutive filtrations using a range of membrane pore size removed a small fraction of macromolecular aggregates from dilute polysaccharide solutions with relatively little effect on the major component molecules as monitored by DLS and SEC measurements. Access to aggregate-free dilute solutions of SSPS and GPase/SSPS allowed the direct measurement of molecular characteristics. SLS results showed that SSPS had a weight average molecular weight of (645+/-11)x 10(3)g/mol and a radius of gyration, Rg, of (23.5+/-2.8)nm. By comparing R(g) with the hydrodynamic radius, Rh (21.1+/-0.5 nm) obtained from DLS, the structural parameter rho (Rg/Rh) was found to be 1.1, suggesting that SSPS has an overall globular shape due to a highly branched structure. The modified SSPS had a significantly lower molecular weight (287+/-18)x 10(3)g/mol but a similar radius of gyration (23.2+/-1.7 nm). The structure parameter rho of GPase/SSPS was higher (rho=1.3) because of a smaller hydrodynamic radius (17.7+/-1.8 nm). This suggests that GPase/SSPS has a much less branched structure yet still differs significantly from a linear random coil conformation (rho=1.7-2.0). The results derived from SLS and DLS are in agreement with the conclusions obtained from a chemical analysis where the reduction of molecular weight of GPase/SSPS was caused by the cleavage of galactan side chains.     

Structure and RNA content of the prosomes.

Duck erythroblasts prosomes were analysed by small angle neutron scattering (SANS), dynamic light scattering and (cryo-)electron microscopy. A molecular weight of approximately 720,000 +/- 50,000, a radius of gyration of 64 +/- 2 A and a hydrodynamic radius of approximately 86 A were obtained. Electron micrographs show a hollow cylinder-like particle with a diameter of 120 A, a height of 170 A and a diameter of 40 A for the cavity, built of four discs, the two outer ones being more pronounced than those in the center. Results from SANS indicate less then 5% of RNA in the purified prosomes, but nuclease protection assays confirm its presence.     

Rheological and light scattering properties of flaxseed polysaccharide aqueous solutions

Polysaccharides isolated from flaxseed meals using ethanol consisted of a soluble ( approximately 7.5% w/w) and an insoluble fraction (2% w/w). The soluble fraction was dialyzed in various salt concentrations and characterized using viscometry and light scattering techniques. Observations using a size-exclusion column coupled to a multiangle laser light scattering (SEC-MALLS) revealed three molecular weight fractions consisting of a small amount ( approximately 17%) of large molecular weight species (1.0 x 10(6)) and a large amount ( approximately 69%) of small molecular weight species (3.1 x 10(5) Da). Dynamic light scattering measurements indicated the presence of very small molecules (hydrodynamic radius approximately 10 nm) and a very large molecular species (hydrodynamic radius in excess of 100 nm); the latter were probably aggregates. The intrinsic viscosity, [eta], of the polysaccharide in Milli-Q water was 1030 +/- 20 mL/g. The viscosity was due largely to the large molecular weight species since viscosity is influenced by the hydrodynamic volume of molecules in solution. The Smidsrod parameter B obtained was approximately 0.018, indicating that the molecules adopted a semi-flexible conformation. This was also indicated by the slope ( approximately 0.56) from the plot of root-mean-square (RMS) radius versus molar mass (M(w)).     

Persistence length of titin from rabbit skeletal muscles measured with scattering and microrheology techniques

The persistence length of titin from rabbit skeletal muscles was measured using a combination of static and dynamic light scattering, and neutron small angle scattering. Values of persistence length in the range 9-16 nm were found for titin-II, which corresponds to mainly physiologically inelastic A-band part of the protein, and for a proteolytic fragment with 100-nm contour length from the physiologically elastic I-band part. The ratio of the hydrodynamic radius to the static radius of gyration indicates that the proteins obey Gaussian statistics typical of a flexible polymer in a -solvent. Furthermore, measurements of the flexibility as a function of temperature demonstrate that titin-II and the I-band titin fragment experience a similar denaturation process; unfolding begins at 318 K and proceeds in two stages: an initial gradual 50% change in persistence length is followed by a sharp unwinding transition at 338 K. Complementary microrheology (video particle tracking) measurements indicate that the viscoelasticity in dilute solution behaves according to the Flory/Fox model, providing a value of the radius of gyration for titin-II (63 +/- 1 nm) in agreement with static light scattering and small angle neutron scattering results.     

Chain conformation of sulfated derivatives of beta-glucan from sclerotia of Pleurotus tuber-regium

Six water-insoluble (1-->3)-beta-D-glucan fractions TM8-1 to TM8-6 with weight-average molecular mass Mw ranging from 5.76 to 77.4x10(4) obtained from the sclerotia of Pleurotus tuber-regium were sulfated to produce the water-soluble fractions S-TM8-1 to S-TM8-6 with Mw from 6.0 to 64.8x10(4). The degree of substitution (DS) of S-TM8 fractions was analyzed by elemental analysis (EA) to be 1.14-1.74. The 13C NMR results indicated that the C-6 was fully substituted, and C-2, C-4 were partially substituted by the sulfo-groups. The Mw and the intrinsic viscosity [eta] of the S-TM8 fractions were measured, respectively, by size-exclusion chromatography combined with laser light scattering (SEC-LLS), LLS and viscometry in phosphate buffer solution (PBS) at 37 degrees C. The dependences of [eta] and radius of gyration z(1/2) on Mw for the S-TM8 samples were found to be [eta]=1.89x10(-2) Mw(0.70) (cm3/g) and z(1/2)=1.12x10(-4) Mw(0.81) (nm) in the Mw range tested. Based on current theories for a wormlike chain model, the molar mass per unit contour length ML and persistence length q of the S-TM8 were calculated to be 990 nm(-1) and 8.5 nm, respectively. The relatively higher q value suggested a more expanded flexible chain of S-TM8 in PBS. The water-solubility and relatively expanded chain conformation of the STM8 fractions were considered to be significant to their antiviral activity.     

Solution properties of chitin in alkali

The solution properties of alpha-chitin dissolved in 2.77 M NaOH are discussed. Chitin samples in the weight-average molecular weight range 0.1 x 10(6) g/mol to 1.2 x 10(6) g/mol were prepared by heterogeneous acid hydrolysis of chitin. Dilute solution properties were measured by viscometry and light scattering. From dynamic light scattering data, relative similar size distributions of the chitin samples were obtained, except for the most degraded sample, which contained aggregates. Second virial coefficients in the range 1 to 2 x 10(-3) mL.mol.g(-2) indicated that 2.77 M NaOH is a good solvent to chitin. The Mark-Houwink-Sakurada equation and the relationship between the z-average radius of gyration (Rg) and the weight-average molecular weight (Mw) were determined to be [eta] = 0.10Mw0.68 (mL.g(-1)) and Rg = 0.17Mw0.46 (nm), respectively, suggesting a random-coil structure for the chitin molecules in alkali conditions. These random-coil structures have Kuhn lengths in the range 23-26 nm.     

Shape and quaternary structure of alpha-globulin from sesame (Sesamum indicum L.) seed as revealed by small angle x-ray scattering and quasi-elastic light scattering

The alpha-globulin from sesame seed has a molar mass of 2.7 X 10(5) g mol-1, determined by x-ray scattering, and (2.8 +/- 0.3) 10(5) g mol-1, determined by quasi-elastic light scattering. The radius of gyration RG amounts to (4.1 +/- 0.1) nm and (3.9 +/- 0.2) nm as determined by Guinier approximation and from the distribution function D(x), respectively. The molecule has a Stokes radius Rs of (5.4 +/- 0.15) nm and a maximum dimension L of (11 less than L less than 15) nm. The translational diffusion coefficient D0(20),w and the ratio of fractional coefficients f/fmin amount to (3.95 +/- 0.12) X 10(-7) cm2 s-1 and 1.25, respectively. The quaternary structure of the protein molecule is approximated by a model consisting of six spherical subunits situated at the vertices of an octahedron having the symmetry 32.     

Solution properties of conventional gum arabic and a matured gum arabic (Acacia (sen) SUPER GUM)

Dilute solution properties of two specially matured gum arabic samples (EM1 and EM2) were compared to the conventional gum (EM0) using static light scattering. The apparent molar mass (M(w,app) and radius of gyration (R(g,app)) for the three samples showed unusual concentration dependence. These data were satisfactorily interpreted by a simple association model that takes into account the repulsive interaction among clusters, which allowed us to obtain the true molar mass (Mw(0)) and radius of gyration (Rg(0)). A common power law relation was observed between Mw(0) and Rg(0) , giving a somewhat higher exponent than expected for linear and branched polymers in a good solvent. Mw(0) and Rg(0) obtained for the three gums do not differ significantly from each other. However, the data showed clearly a constant increase of the association from EM0 to EM2 with increasing concentration. This is in accordance with the previously observed improved functional properties for the matured products.     

Size, shape and secondary structure of calponin

The overall size and shape of the chicken gizzard calponin (CaP) h1 molecule was investigated by dynamic light scattering (DLS) measurements. From the DLS experiments, a z-averaged translational diffusion coefficient is derived (5.75 +/- 0.3) x 10(-7) cm(2) s(-1), which corresponds to a hydrodynamic radius of 3.72 nm for calponin. The frictional ratio (1.8 for the unhydrated molecule and 1.5 for the hydrated one) suggests a pronounced anisotropic structure for the molecule. An ellipsoidal model in length 19.4 nm and with a diameter of 2.6 nm used for hydrodynamic calculations was found to reproduce the DLS experimental data. The evaluation of the secondary structure of CaP h1 from the CD spectra by two independent methods has revealed that it contains, on average, 23% helix, 19% beta-strand, 18% beta-turns and loops, and 40% of remainder structures. These values are in good agreement with those predicted from the amino-acid sequence. Predictions used for CaP h1 were applied to other isoforms of known sequences and revealed that all calponins share a common secondary structure. Moreover, the predicted structure of the calponin CH domain is identical to that found by X-ray studies of the spectrin, fimbrin and utrophin CH domains.     

Statistical conformation of human plasma fibronectin

Fibronectin is a multifunctional glycoprotein (molecular mass, M = 530 kg/mol) of the extra cellular matrix (ECM) having a major role in cell adhesion. In physiological conditions, the conformation of this protein still remains debated and controversial. Here, we present a set of results obtained by scattering experiments. In "native" conditions, the radius of gyration (R(g) = 15.3 +/- 0.3 nm) was determined by static light scattering as well as small-angle neutron scattering. The hydrodynamic radius (R(H) = 11.5 +/- 0.1 nm) was deduced from quasi-elastic light scattering measurements. These results imply a low internal concentration compared to that of usual globular proteins. This is also confirmed by the ratio R(H)/R(g) = 0. 75 +/- 0.02 consistent with a Gaussian chain, whereas R(H)/R(g) = 1. 3 for spherical shaped molecules. However, adding a denaturing agent (urea 8 M) increases R(g) by a factor 2. This means that fibronectin "native" chain is not either completely unfolded. The average shape of fibronectin conformation was also probed by small-angle neutron scattering performed for reverse scattering vector q(-)(1) smaller than R(g) (0.2 < q(-)(1) < 15 nm). The measured form factor is in complete agreement with the form factor of a random string of 56 beads of 5 nm diameter. It rules out the possibility of unfolded chain as well as globular structures. These results have structural and biological implications as far as ECM organization is concerned.     

Light scattering studies of bovine skin proteodermatan sulfate

The proteodermatan sulfate (PDS) of bovine skin is a low molecular weight proteoglycan with a molecular structure consisting of a protein chain and a sulfated polysaccharide chain covalently linked at the 4-serine of the protein. Static and dynamic laser light scattering methods have been used to determine the weight-average molecular weight, Mw, zeta-average radius of gyration, Rg zeta, and zeta-average translational diffusion coefficient, Dto, zeta, of bovine skin PDS. We have also characterized the two components of PDS, i.e., the protein core and the dermatan sulfate (DS) chain. (The latter contained an N-terminal-linked penta- or tetrapeptide.) Interpretation of the PDS data is complicated by the block copolymer nature of its structure. When appropriate corrections are made, our results indicate that Mw for PDS monomer is 62,000 when dissolved in 4M guanidine hydrochloride (GdnHCl), and increases to 610,000 in 0.15M NaCl. Mw for the core protein in 4M GdnHCl is 39,000, and this also increases substantially to 650,000 in 0.15M NaCl. In contrast, Mw for the DS chain is 24,000 in 0.15M NaCl, indicating that there is minimal self-association of DS in 0.15M NaCl. Thus we conclude that the self-association of PDS involves the protein core. Comparison of Rg zeta and Rh, the average hydrodynamic radius, suggests that trace amounts of aggregation persist for the PDS and its core protein even in 4M GdnHCl. This conclusion is supported by evaluation of the second moments of the dynamic light scattering correlation function. Comparisons of the observed Dto, zeta for PDS with predicted values using hydrodynamic theory are consistent with a "lollipop" conformation for the molecule.     

The tetrameric form of ribosomal protein L7/L12 from Escherichia coli

A tetrameric form of the ribosomal protein L7/L12 has been prepared and its structure studied by using hydrodynamic methods, photon correlation spectroscopy, and small angle x-ray scattering. The tetrameric nature of the protein preparation is confirmed by three independent determinations of its molecular weight, with analysis of accurate sedimentation equilibrium data giving the most reliable estimate. The species has a Stokes radius of 4.0 +/- 0.1 nm and an absolute frictional ratio of 1.7. Taken together, the hydrodynamic measurements suggest the possibility of a flat structure, and this is consistent with the x-ray scattering results. The molecule has a radius of gyration of 3.6 +/- 0.05 nm and a maximum dimension of 11-12 nm. A geometric model consisting of four elongated monomers, arranged in a plane, is proposed.     

Characterization of Chlorobium tepidum chlorosomes: a calculation of bacteriochlorophyll c per chlorosome and oligomer modeling

The bacteriochlorophyll (Bchl) c content and organization was determined for Chlorobium (Cb.) tepidum chlorosomes, the light-harvesting complexes from green photosynthetic bacteria, using fluorescence correlation spectroscopy and atomic force microscopy. Single-chlorosome fluorescence data was analyzed in terms of the correlation of the fluorescence intensity with time. Using this technique, known as fluorescence correlation spectroscopy, chlorosomes were shown to have a hydrodynamic radius (Rh) of 25 +/- 3.2 nm. This technique was also used to determine the concentration of chlorosomes in a sample, and pigment extraction and quantitation was used to determine the molar concentration of Bchl c present. From these data, a number of approximately 215,000 +/- 80,000 Bchl c per chlorosome was determined. Homogeneity of the sample was further characterized by dynamic light scattering, giving a single population of particles with a hydrodynamic radius of 26.8 +/- 3.7 nm in the sample. Tapping-mode atomic force microscopy (TMAFM) was used to determine the x,y,z dimensions of chlorosomes present in the sample. The results of the TMAFM studies indicated that the average chlorosome dimensions for Cb. tepidum was 174 +/- 8.3 x 91.4 +/- 7.7 x 10.9 +/- 2.71 nm and an overall average volume 90,800 nm(3) for the chlorosomes was determined. The data collected from these experiments as well as a model for Bchl c aggregate dimensions was used to determine possible arrangements of Bchl c oligomers in the chlorosomes. The results obtained in this study have significant implications on chlorosome structure and architecture, and will allow a more thorough investigation of the energetics of photosynthetic light harvesting in green bacteria.     

Small-angle X-ray studies of the human immunoglobulin molecule Kol.

The conformation of the human immunoglobulin molecul Kol [IgG I, kappa2 gamma2, Gm(f)+] was studied by small-angle X-ray scattering in 0.15 M NaCl solution. The radius of gyration was found to be 5.84 +/- 0.04 nm, the volume 329 +/- 15 nm3 and the molecular weight 150 000 +/- 10 000. Information on the overall shape was obtained by comparing the experimental scattering curve with the calculated curves for various models. The models were obtained by arranging the models found for the Fab and Fc fragments of the same immunoglobulin molecule in a different manner. A model which fits all the date and the form of the experimental scattering curve is presented.     

Structure and chain conformation of beta-glucan isolated from Auricularia auricula-judae

From Auricularia auricula-judae, a water soluble beta-D-glucan, named as AAG, was isolated by extraction with 70% ethanol/water solution. Its chemical structure was analyzed by gas chromatography (GC), gas chromatography-mass spectrometry (GC-MS), matrix-assisted laser desorption /ionization (MALDI)-time of flight (TOF), and 1D, 2D NMR. AAG was detected, for the first time, to be composed of a main chain of (1-->4)-linked D-glucopyranosyl with glucopyranosyl side groups at O6. With the help of MALDI-TOF-MS, the sequence and the distribution of glucuronic acid were determined and the content of glucuronic acid is about 19%. Five fractions were prepared from the AAG sample in water by ultrasonic degradation method. Their molecular weight, size, and shape (chain conformation) were studied by dynamics light scattering (DLS), static laser light scattering (LLS), size exclusion chromatography combined LLS (SEC-LLS) and viscometry in 0.1M NaCl aqueous solution at 25 degrees C. The dependence of intrinsic viscosity ([eta]) on Mw for this polysaccharide was established to be [eta] = 1.22 x10(-3)Mw (1.00) (cm3 g(-1)) in the range of Mw from 3.40 x 10(4) to 2.88 x 10(5). The conformational parameters of the AAG polysaccharide were found to be 820 nm(-1) for molar mass per unit contour length (ML), 12.3 nm for persistence length (q) and 2.1 for rho (s2(1/2)/Rh). The results suggested that the polysaccharide exists as extended chains in 0.1M NaCl aqueous solution. The chemical structure of AAG containing glucuronic acid and side groups led to steric hindrance, resulting in the increased stiffness of the chains.     

Shape, symmetry, hydration and secondary structure of the legumin from Vicia faba in solution

The following physical parameters of the legumin from Vicia faba were determined by means of small-angle X-ray scattering, quasi-elastic light scattering and circular dichroism: molar mass, M = 3.5 X 10(5) g/mol; radius of gyration, Rg = 4.45 nm; maximum dimension, L = 13 nm; translational diffusion coefficient, D0(20),w = 3.38 X 10(-7) cm2 X s-1; alpha-helix content about 15%; content of beta-sheets 10%; dihedral point group symmetry of the molecule 32.     

An elongated model of the Xenopus laevis transcription factor IIIA-5S ribosomal RNA complex derived from neutron scattering and hydrodynamic measurements.

The precise molecular composition of the Xenopus laevis TFIIIA-5S ribosomal RNA complex (7S particle) has been established from small angle neutron and dynamic light scattering. The molecular weight of the particle was found to be 95,700 +/- 10,000 and 86,700 +/- 9000 daltons from these two methods respectively. The observed match point of 54.4% D2O obtained from contrast variation experiments indicates a 1:1 molar ratio. It is concluded that only a single molecule of TFIIIA, a zinc-finger protein, and of 5S RNA are present in this complex. At high neutron scattering contrast radius of gyration of 42.3 +/- 2 A was found for the 7S particle. In addition a diffusion coefficient of 4.4 x 10(-11) [m2 s-1] and a sedimentation coefficient of 6.2S were determined. The hydrodynamic radius obtained for the 7S particle is 48 +/- 5 A. A simple elongated cylindrical model with dimensions of 140 A length and 59 A diameter is compatible with the neutron results. A globular model can be excluded by the shallow nature of the neutron scattering curves. It is proposed that the observed difference of 15 A in length between the 7S particle and isolated 5S RNA most likely indicates that part(s) of the protein protrudes from the end(s) of the RNA molecule. There is no biochemical evidence for any gross alteration in 5S RNA conformation upon binding to TFIIIA.     

The thermal depolymerization of porcine submaxillary mucin

The time dependence of the molecular weight, radius of gyration, and hydrodynamic size distribution for porcine submaxillary mucin (PSM) in solution have been studied using static and dynamic light scattering. The weight average molecular weight (Mw) of PSM in 6 M guanidine HCl, pH 7, is initially 3 X 10(6) and decreases with time in three phases: rapidly from 3-2 X 10(6), less rapidly from 2-0.9 X 10(6), and slowly below 0.9 X 10(6). The rates of decrease are much greater at pH 2. The energy of activation associated with each phase is 20 kcal/mol, which is similar to that reported for peptide bond cleavage at an aspartic acid residue. Addition of mercaptoethanol to PSM in 6 M guanidine HCl leads to a rapid decrease in Mw to 0.9 X 10(6), followed by a very slow further decrease. These results suggest that native PSM consists of subunits (Mw = 0.9 X 10(6] that are linked by disulfide bonds to form dimers (Mw = 2 X 10(6] and then higher aggregates. This cross-linking appears to occur at unglycosylated regions of the protein core, which are believed to be richer in aspartic acid than the rest of the molecule.