Continuous optical scanning in polyacrylamide gel electrophoresis:estimation of the apparent diffusion coefficient of beta-lactoglobulin B.

The continuous scanning apparatus developed by Catsimpoolas was applied to an analysis of the concentration profiles of a protein, β-lactoglobulin B, while it was subjected to polyacrylamide gel electrophoresis (PAGE) in a multiphasic buffer system. Continuous optical scanning in PAGE permitted reliable estimation of the standard deviation of the concentration profile (σ), the relationship between σ² and time, and the apparent diffusion coefficient, D′, derived from σ², as the current density varied from 2 to 9 mA/cm², protein load varied from 250 to 900 μg/cm², and the ionic strength varied from 0.015 to 0.065 m. Under these conditions, D′ was linearly related to current density and protein load. Further, log (D′) was linearly related to gel concentration (%T) ranging from 6 to 14%. However, D′ was nonlinearly related to ionic strength. Due primarily to the ionic strength factor, the apparent diffusion coefficient of protein in gels appeared to be approximately 10-fold larger than under the conditions of high ionic strength conventionally used in sedimentation and diffusion studies. Extrapolation of D′ to 0% T, zero protein load, zero current density, and “infinite” ionic strength (assuming noninteraction of these factors), as well as correction for viscosity and temperature, yielded an estimated free-diffusion coefficient, D_20,w, of 3.1 × 10^?7 cm²/s, which is compatible with previously reported values. These studies indicate that the optimal resolution obtained by PAGE will be considerably lower than that predicted theoretically on the basis of free-diffusion coefficients, and suggest that electrostatic interaction between the proteins and/or deformation of voltage gradient and pH within the protein zones may contribute significantly to band spreading.     

Types of Amylases in Rice Grains

The subunit structure of phenoloxidase from the larvae of housefly, Musca domestica vicina Maquart, was investigated by urea treatment, SDS-polyacrylamide gel electrophoresis and electron microscopy. Phenoloxidase was dissociated into a single type of subunit (MW 6.5 × 10⁴) by 5 m urea treatment. A similar subunit (MW 6.1 × 10⁴) was also detected by SDS-polyacrylamide gel electrophoresis. Furthermore, four additional protein bands with molecular weights of 4.8 × 10⁴, 3.5 × 10⁴, 2.4 × 10⁴ and 1.2 × 10⁴ were detected by SDS-polyacrylamide gel electrophoresis by extensive incubation of phenoloxidase with SDS. A cylindrical molecular structure was deduced from the electron microscopic analysis. The outside and inside diameter and the height of phenoloxidase molecule were evaluated to be 100, 50 and 70 Å, respectively.     

Further studies of detergent-induced conformational transitions in proteins. Circular dichroism of ovalbumin, bacterial alpha-amylase, papain, and beta-lactoglobulin at various pH values.

The conformational transitions of ovalbumin, bacterial α-amylase, papain, and β-lactoglobulin were studied in the absence and presence of sodium dodecyl sulfate (SDS) between pH 2.75 and 12.0 by means of circular dichroism (CD) measurement. The weight ratios of SDS to protein in solutions were 14:1 in all experiments. The CD bands in the near-ultraviolet spectral region were strongly reduced by SDS, whereas those in the far-ultraviolet were enhanced. With the exception of the amylase, the mean residue ellipticities of the proteins at 222 nm were increased by SDS, especially in acidic solutions. At a pH of about 3.0, the [θ]₂₂₂ values approached ?17 (±2) · 10³ deg · cm² · dmol^?1. It is assumed that at a sufficiently low pH value the proteins which are complexed with SDS have a similar backbone conformation of moderate helical content. In alkaline solutions, the detergent effect was largely reduced due to electrostatic repulsion between the negatively charged protein and dodecyl ions. The near-ultraviolet spectra of ovalbumin, papain, and β-lactoglobulin at pH 6.4 were analyzed. Assignment of the resolved bands to the appropriate chromophores was also attempted.     

Purification and some properties of γ-conglycinin in soybean seeds

A 7S globulin (γ-conglycinin) which was one of four major antigenic components in soybean globulins was purified and found to be homogeneous on ultracentrifugation, disc electrophoresis, immunoelectrophoresis and disc electrofocusing by gel filtration, preparative-scale disc electrophoresis and two kinds of affinity chromatography. Subsequently, some physico-chemical properties of the protein were determined. The sedimentation coefficient, isoelectric point, MW and diffusion constant were 6·55S, pH 5·80, 104000 and 5·80 × 10^?7 cm²/sec, respectively. The protein was a glycoprotein which contained 5·49% total carbohydrate per protein. The protein did not aggregate and dissociate with a change of ionic strength from 0·1 to 0·5.     

Purine nucleoside phosphorylases purified from rat liver and Novikoff hepatoma cells.

Purine nucleoside phosphorylase (PNP) was purified from rat hepatoma cells and normal liver tissue utilizing the techniques of ammonium sulfate fractionation, heat treatment, ion-exchange and molecular exclusion chromatography, and polyacrylamide gel electrophoresis. Homogeneity was established by disc gel electrophoresis in the presence and absence of sodium dodecyl sulfate. Purified rat hepatoma and liver PNPs appeared to be identical with respect to subunit and native molecular weight, substrate specificity, heat stability, kinetics and antigenic identity. A native molecular weight of 84,000 was determined by gel filtration. A subunit molecular weight of 29,000 was determined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. A single isoelectric point was observed at pH 5.8, and the pH optimum was 7.5. Inosine, guanosine, xanthosine, and 6-mercaptopurine riboside were substrates for the enzymes. The apparent K_m for both inosine and guanosine was about 1.0 × 10^?4m and for phosphate was 4.2 × 10^?4m. Hepatoma and liver PNP showed complete cross-reactivity using antiserum prepared against the liver enzyme.     

Translational diffusion in the plasma membrane of sea urchin eggs

Translational diffusion in the plasma membrane of individual egg cells from the sea urchin species Paracentrotus lividus has been studied by fluorescence microphotolysis (FM). In order to probe the lipid phase of the membrane, procedures have been worked out by which the fluorescent analog 3,3′-dioctadecyl-oxatricarbocyanine (C₁₈diO) can be incorporated into the membrane. In the unfertilized egg a fraction R = 0.9 of C₁₈diO was mobile having an apparent diffusion coefficient of D = 6.0 × 10^?9 cm² sec^?1. Fifteen to twenty-five minutes after fertilization R and D were reduced to 0.8 and 2.7 × 10^?9 cm² sec^?1, respectively. In order to study diffusion of membrane proteins, procedures have been worked out by which the cell surface can be labeled with fluorescein-isothiocyanate (FITC). FITC binds to both the plasma membrane and the vitelline layer. Together with the vitelline layer two-thirds of the FITC-fluorescence could be removed from the egg surface. Gel electropherograms of isolated egg cortices showed various protein bands; however, only two of the protein bands were labeled with FITC. In the unfertilized egg a fraction R = 0.9 of the FITC-labeled membrane proteins was mobile having an apparent diffusion coefficient of D = 35 × 10^?11 cm² sem^?1. Fiteen to twenty-five minutes after fertilization R and D were reduced to 0.8 and 7.0 × 10^?11 cm² sec^?1, respectively. FITC-labeled proteins of the fertilization envelope were immobile. Our studies have shown (i) that the egg surface can be fluorescently labeled without blocking fertilization and early development, (ii) that the plasma membrane of unfertilized eggs is a fluid environment permitting a rapid movement of lipids and proteins, and (iii) that after fertilization a substantial degree of lipid and protein mobility is maintained.     

Purification and biochemical characterization of phytocystatin from Brassica alba

Phytocystatins belong to the family of cysteine proteinases inhibitors. They are ubiquitously found in plants and carry out various significant physiological functions. These plant derived inhibitors are gaining wide consideration as potential candidate in engineering transgenic crops and in drug designing. Hence it is crucial to identify these inhibitors from various plant sources. In the present study a phytocystatin has been isolated and purified by a simple two‐step procedure using ammonium sulfate saturation and gel filtration chromatography on Sephacryl S‐100HR from Brassica alba seeds (yellow mustard seeds).The protein was purified to homogeneity with 60.3% yield and 180‐fold of purification. The molecular mass of the mustard seed cystatin was estimated to be nearly 26 000 Da by sodium dodecyl sulfate polyacrylamide gel electrophoresis as well as by gel filtration chromatography. The stokes radius and diffusion coefficient of the mustard cystatin were found to be 23A° and 9.4 × 10^?7 cm²s^?1 respectively. The isolated phytocystatin was found to be stable in the pH range of 6–8 and is thermostable up to 60 °C. Kinetic analysis revealed that the phytocystatin exhibited non‐competitive type of inhibition and inhibited papain more efficiently (K_i = 3 × 10^?7 M) than ficin (K_i = 6.6 × 10^?7 M) and bromelain (Ki = 7.7 × 10^?7 M respectively). CD spectral analysis shows that it possesses 17.11% alpha helical content. Copyright © 2016 John Wiley & Sons, Ltd.     

Physicochemical and Enzymatic Properties of ATP: Nucleotide Pyrophosphotransferase

The molecular weight determined by the sedimentation equilibrium and SDS Polyacrylamide gel electrophoresis was 29,000 and 28,000, respectively. Isoelectric point of the enzyme was determined as pH 7.7. This enzyme contained large amounts of alanine, aspartic acid, glutamic acid and serine, and no cysteine residue was found. The enzyme was inhibited by SDS, KMnO₄, EDTA and tetracycline. GTP and GDP were the most active as pyrophosphate acceptor to the enzyme. The apparent Km for ATP was 2.2×10^?4 m and that for GTP was 2.1×10^?4m in the reaction of ATP+GTP→AMP+pppGpp. On the other hand, in the reaction of 2ATP→AMP+pppApp, the apparent Km for donor and acceptor ATP was 1.7×10^?3m. Effects of pH and metal ions on the enzymatic synthesis of pppGpp were also studied.     

Probing the fatty acid binding site of β-lactoglobulins

The interactions of fatty acids with porcine and bovine β-lactoglobulins were measured using tryptophan fluorescence enhancement. In the case of bovine β-lactoglobulin, the apparent binding constants for most of the saturated and unsaturated fatty acids were in the range of 10^?7 M at neutralpH. Bovine β-lactoglobulin displays only one high affinity binding site for palmitate with an apparent dissociation constant of 1·10^?7 M. The strength of the binding was decreasing in the following way: palmitate > stearate > myristate > arachidate > laurate. Caprylic and capric acids are not bound at all. The affinity of β-lactoglobulin for palmitate decreased as thepH of the incubation medium was lowered and BLG/palmitate complex was not observed atpH's lower than 4.5. Surprisingly, chemically modified bovine β-lactoglobulin and porcine β-lactoglobulin did not bind fatty acids in the applied conditions.     

Properties of a repressible alkaline phosphatase secreted by the wild-type strain 74a of neurospora crassa

A repressible extracellular alkaline phosphatase (with activity increasing steadily even up to pH 10.5) was purified from cultures of the wild-type strain 74A of Neurospora crassa, after growth on acetate and under limiting amounts of inorganic phosphate for 72 hr at 30°. The enzyme was homogeneous on polyacrylamide gel electrophoresis (PAGE) with or without sodium dodecyl sulphate (SDS). The MW was ca 172 000 and 82 000 as determined by Sephadex G-200 gel filtration and SDS-PAGE, respectively. The enzyme contained 23.6% neutral sugars, cations were not required for activity, and it was not inactivated by 5,5-dithiobis-(2-nitrobenzoic acid) (DTNB) at pH 8. Kinetic data showed Michaelian behaviour for the enzymatic hydrolysis of 4-nitrophenyl disodium orthophosphate (PNP-P) at pH 9 (the K_m value and Hill coefficient were 2.2 × 10^?4 M and 0.95, respectively). It was also shown that, at pH 9, the apparent number of Pi bound per dimer molecule equalled one, with a K_i value of 7.0 × 10^?4 M. The secreted enzyme showed half-lives of 23.5, 49.0 and 23.5 min at, pH 5.4, 7.4 and 9.0, respectively, after thermal inactivation at 60°. At pH 5.4, the half-life value was quite similar, while the others were respectively 2 and 4 times greater than those previously described for the repressible alkaline phosphatase retained by the mycelium at pH 5.6 or secreted by ‘slime’ cells.     

An aminopeptidase from Agave americana,isolation and physical characterization

A new aminopeptidase was isolated from Agave americana by fractionation, chromatography and gel filtration. The mw of the enzyme, determined by different procedures was 86000 ± 1500; the enzyme had a sedimentation coefficient of 4.96 S, a diffusion coefficient of 5.2 × 10^?7 cm²/sec, a Stokes radius of 3.8 nm, a partial specific volume of 0.733 cm³/g, a frictional ratio of 1.40, a molecular absorbancy index at 280 nm of 8.36 × 10⁴, an isoelectric point of 4.53 and contained 1.25% carbohydrate. The amino acid composition of the enzyme was determined and the aminoterminal residue was identified as lysine whilst the carboxylterminal residue was either leucine or isoleucine. No subunit structure was observed for the enzyme.     

The atypical RNA components of cytoplasmic ribosomes from Crithidia fasciculata

RNA extracted by cold phenol from the large cytoplasmic ribosomal subunit of the trypanosomatid flagellate Crithidia fasciculata and analyzed by polyacrylamide gel electrophoresis at 4 °C consisted of one species with a molecular weight of 1.3 × 10⁶ (relative to ribosomal RNA from E. coli MRE 600). When extracted with hot phenol (65 °C), the large ribosomal subunit gave rise to two components with molecular weights of 0.72 and 0.56 × 10⁶. On heating for 60 s, followed by rapid cooling, the single cold-phenol-extracted 1.30 × 10⁶-dalton species completely dissociated into two components of molecular weights 0.72 and 0.56 × 10⁶, present in equimolar amounts. When analyzed by polyacrylamide-agarose gel electrophoresis in the presence of SDS, RNA extracted by cold phenol from the large cytoplasmic ribosomal subunit consisted of three components of molecular weights 1.3, 0.72, and 0.56 × 10⁶, present in apparently equimolar amounts. RNA from the small cytoplasmic ribosomal subunit consisted of one species with a molecular weight of 0.84 × 10⁶, independent of extraction or analytical conditions. It is proposed that under high salt and low temperature conditions, the large ribosomal RNA molecule is held together by its secondary structure, and that denaturing extraction or analytical conditions reveal an otherwise “hidden” lesion present in the molecule in vivo.     

Physical properties of type i collagen in solution: Structure of α-Chains and β- and γ-components and two-component mixtures

The structure of thermally denatured Type I collagen has been studied using laser light scattering. The results indicate that the diffusion coefficients of α-chains and β- and γ-components are 1.550 ± 0.08 × 10^?7, 1.000 ± 0.05 × 10^?7, and 0.835 ± 0.04 × 10^?7 cm²/sec, respectively, at temperatures between 20 and 40°C. It is concluded from diffusion data that these species have hydrodynamic radii of about 13.8 nm (α-chain), 21.5 nm (β-component), and 25.7 nm (γ-component), consistent with previous studies of thermal denaturation by light scattering. It is also concluded, based on volume calculations, that a large volume increase occurs when the triple helix unfolds. Homodyne correlation functions for two component mixtures of α-chains and β-and γ-components appeared to decay exponentially. In all but one case discussed the correlation function could be fitted with a single component having a translational diffusion coefficient which was an intensity weighted average of the diffusion coefficient of each component present.     

Hydrodynamics,size, and shape of bacteriophage T4D tails and baseplates

We have used translational diffusion coefficient measurements and subunit hydrodynamic theory to determine the dimensions and shape of bacterioophage T4D baseplates and tails. The diffusion coefficient of the baseplate, measured by quasielastic laser light scattering (QLS), was determined previously by Wagenknecht and Bloomfield to be D = 8.56 × 10^?8 cm²/s. For the tail, we found D = 5.88 × 10^?8 cm²/s by QLS, and D = 6.02 × 10^?8 cm²/s by combining sedimentation coefficient and molecular weight in the Svedberg equation. These values, which have an uncertainty of ±2.7%, when combined with subunit hydrodynamic theory, enabled us to refine estimates of dimensions obtained by electron microscopy. For the hexagonal baseplate, the vertex-to-vertex distance is about 480 Å, the thickness is 160 Å, and there are six extended short fibers 320-Å long and 40 Å in diameter. When a baseplate of these dimensions is attached to a tail tube-sheath-connector complex 1050-Å long and 240 Å in diameter, the calculated D is 5.93 × 10^?8 cm²/s, within 1% of experiment. This combined use of electron microscopy and hydrodynamics, using the former to ascertain shape, and the latter to obtain solution dimensions, is a powerful approach to the structure of biomolecular complexes.     

The Binding of Asparagine,Glutamine and Homoserine to Human Erythrocytes Containing Hemoglobins S and CS and to Soluble Hemoglobins S and CS

Abstract

Tritium labeled asparagine binds to oxyhemoglobin S and to a mixture of hemoglobins C and S in the molar ratio of 3.38:1 and 8.2:1 respectively. From the dialysis equilibrium studies it appears that labeled asparagine does not bind to oxy- or deoxy- hemoglobin A nor to deoxyhemoglobin S. The constant for equilibrium association of asparagine for oxyhemoglobin S is 7.38 × 10⁷ M^?1 and for'oxyhemoglobin CS 4.8 × 10⁴ M^?1 at 23°C. Tritium labeled asparagine is bound to oxyhemoglobin S and CS sufficiently strongly to prevent dissociation under the conditions of gel electrophoresis at pH 9.50. The protein with and without bound asparagine, gluta-mine or homoserine, is indistinguishable in molecular net charge and size by the criteria of quantitative polyacrylamide gel electrophoresis (PAGE). Also there were no significant differences in mobility between hemoglobin S and hemoglobin C in the presence and absence of asparagine, glutamine and homoserine as detectable in agar coated cellulose acetate electrophoresis at pH 6.3. Erythrocytes containing hemoglobin S and CS, after incubation with tritium labeled asparagine and lysis under the conditions of gel electrophoresis at pH 9.5, release hemoglobin S and C with bound tritiated asparagine. No tritiated asparagine remains bound to the ghost.     

Raman studies of the crystalline, solution, and alkaline-denatured states of beta-lactoglobulin.

The Raman spectra of β-lactoglobulin in the crystalline, freeze-dried, and solution states are compared. The spectra of the freeze-dried and crystalline proteins were practically identical. The conformationally sensitive amide III line appearing at 1242 cm^?1 increased in intensity 30% upon dissolution of the protein in water which is interpreted as a conformational change in the disordered chains of the protein. This result appears to be a phenomenon for globular proteins containing a large disordered chain fraction. The alkaline denaturation of β-lactoglobulin was studied. When the pH was increased from 6.0 to 11.0, the amide III line shifted from 1242 to 1246 cm^?1, broadened, and decreased in intensity. This is consistent with the conversion of β-sheet regions in β-lactoglobulin to the disordered conformation, as has been proposed by other investigators. At pH 13.5 the amide III shifts to 1257 cm^?1 characteristic of a completely disordered protein, indicating that any remaining “core” of β-sheet has been randomized. Several changes in the intensities of the tyrosine and tryptophan vibrations accompany the denaturation. As the pH is increased from 6.0 (native state) to 11.0 (denatured state) the intensity ratio of two tyrosine ring vibrations, I₈₅₅ cm^?1/I₈₃₀ cm^?1, decreases from 1.0:0.9 to 1.0:1.3. The same ratio for a copolymer consisting of 95% glutamic acid and 5% tyrosine at pH 7.0, where the polymer forms a random coil exposing the tyrosine to the aqueous environment, is 1.0:0.62. This ratio more closely resembles that corresponding to β-lactoglobulin at pH 6.0 (native state) than pH 11.0 (denatured state) suggesting that the average tyrosine in the denatured state may be in a more hydrophobic environment than in the native state. A time-dependent polymerization of the denatured protein reported by other investigators and observed by us may account for the change in the tyrosine environment. A tryptophan vibration appearing at 833 cm^?1 in the spectrum of the native state becomes weak as the pH is increased to 11.0. The intensity of this line may also reflect the local environment of the tryptophan residue.     

Measurement of diffusion coefficient and electrophoretic mobility with a quasielastic light-scattering–band-electrophoresis apparatus

We have constructed an apparatus for the simultaneous measurement of electrophoretic mobility, μ, and diffusion coefficient, D, of macromolecules and cells. It combines band electrophoresis in a vertical, sucrose-gradient stabilized column, with quasielastic laser light-scattering determination of the diffusion coefficient of the species within the band. The entire electrophoresis cell is scanned through the laser beam of the quasielastic laser light-scattering apparatus by a vertical translation stage. Total intensity light-scattering measurement at each point in the cell gives the macromolecular concentration at that point. Solvent viscosity and electrical potential are measured at each point in the cell. Application of this apparatus to resealed red blood cell ghosts and to bovine hemoglobin indicates that measurements of field, viscosity, and migration distance are reliable, and that electroosmosis is insignificant. Application to T4D bacteriophage gives μ_20,w = (?1.05 ± 0.05) × 10^?4 cm²/V sec and D_20,w = (3.35 ± 0.10) × 10^?8 cm²/sec for fiberless particles, and μ_20,w = ?(0.59 ± 0.03) × 10^?4 cm²/V sec and D_20,w = (2.86 ± 0.09) × 10^?8 cm²/sec for whole phage with 6 fibers. Approximate analysis of these results with the Henry electrophoresis theory for spheres in dicates that each fiber contributes about 193 positive charges to the phage particle, compared with 327 from amino-acid analysis. The advantages and disadvantages of this apparatus, relative to conventional electrophoresis and to electrophoretic light scattering, are discussed.     

Histone-induced conformational changes in DNA as probed by quasi-elastic light scattering.

Quasi-elastic light scattering as measured by intensity fluctuation (self-beat) spectroscopy in the time domain can be profitably used to follow both the translational diffusion D and the dominant internal flexing mode τ_int of DNA and its complexes with various histones in aqueous salt solutions. Without histones, DNA is found to have D = 1.6 × 10^?8 cm²/sec and τ_int ? 5 × 10^?4 sec in 0.8 M NaCl, 2 M urea at 20°C. Total histone as well as fraction F2A induce supercoiling (D = 2.6 × 10^?8 cm²/sec, τ_int ? 2.8 × 10^?4 sec) whereas fraction F1 induces uncoiling (D = 1.0 × 10^?8 cm²/sec, τ_int ? 9.4 × 10^?4 sec). Upon increasing the salt concentration to 1.5 M the DNA–histone complex dissociates (D = 1.8 × 10^?8 cm²/sec). Upon decreasing the salt concentration to far below 0.8 M, the DNA–histone complex eventually precipitates as a chromatin gel.     

Biophysical and computational comparison on the binding affinity of three important nutrients to β-lactoglobulin: folic acid,ascorbic acid and vitamin K3

Small globular protein, β-lactoglobulin (βLG), which has significant affinity toward many drugs, is the most abundant whey protein in milk. In this study, the interaction of βLG with three important nutrients, ascorbic acid (ASC), folic acid (FOL), and vitamin K3 (VK3) was investigated by spectroscopic methods (UV–visible and fluorescence) along with molecular docking technique. The results of fluorescence measurements showed that studied nutrients strongly quenched βLG fluorescence in static (FOL and ACS) or static–dynamic combined quenching (VK3) mode. The values of binding constants (K_βLG-ASC ~ 4.34 × 10⁴ M^?1, K_βLG-FOL ~ 1.67 × 10⁴ M^?1and K_βLG-VK3 ~ 13.49 × 10⁴ M^?1 at 310 K) suggested that VK3 and FOL had stronger binding affinity toward βLG than ASC. Thermodynamic analysis indicated that hydrophobic interactions are the major forces in the stability of FOL–βLG complex with enthalpy- and entropy-driving mode while, hydrogen bonds and van der Waals interactions play a major role for βLG–ASC and βLG–VK3 associations. The results of 3D fluorescence FT-IR and UV–Visible measurements indicated that the binding of above nutrients to βLG may induce conformational and micro-environmental changes of protein. Also, there is a reciprocal complement between spectroscopic techniques and molecular docking modeling. The docking results indicate that the ASC, FOL, and VK3 bind to residues located in the subdomain B of βLG. Finally, this report suggests that βLG could be used as an effective carrier of above nutrients in functional foods.