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Biomedical subjects

A P Sokolov

Publications and source records attributed to A P Sokolov.

At least 19 recordsLinked to original sources

Influence of hydration on the dynamics of lysozyme.

Quasielastic neutron and light-scattering techniques along with molecular dynamics simulations were employed to study the influence of hydration on the internal dynamics of lysozyme. We identified three major relaxation processes that contribute to the observed dynamics in the picosecond to nanosecond time range: 1), fluctuations of methyl groups; 2), fast picosecond relaxation; and 3), a slow relaxation process. A low-temperature onset of anharmonicity at T approximately 100 K is ascribed to methyl-group dynamics that is not sensitive to hydration level. The increase of hydration level seems to first increase the fast relaxation process and then activate the slow relaxation process at h approximately 0.2. The quasielastic scattering intensity associated with the slow process increases sharply with an increase of hydration to above h approximately 0.2. Activation of the slow process is responsible for the dynamical transition at T approximately 200 K. The dependence of the slow process on hydration correlates with the hydration dependence of the enzymatic activity of lysozyme, whereas the dependence of the fast process seems to correlate with the hydration dependence of hydrogen exchange of lysozyme.

Animals↗

Onsets of anharmonicity in protein dynamics.

Two onsets of anharmonicity are observed in the dynamics of the protein lysozyme. One at T approximately 100 K appears in all samples regardless of hydration level and is consistent with methyl group rotation. The second, the well-known dynamical transition at T approximately 200-230 K, is only observed at a hydration level h greater than approximately 0.2 and is ascribed to the activation of an additional relaxation process. Its variation with hydration correlates well with variations of catalytic activity suggesting that the relaxation process is directly related to the activation of modes required for protein function.

Cold Temperature↗

Correlation of fragility of supercooled liquids with elastic properties of glasses.

We present a detailed analysis of correlations between fragility and other parameters of glass-forming systems. The analysis shows the importance of the ratio between the instantaneous bulk and shear modulus of glass-forming systems, or their Poisson ratio, for structural alpha relaxation and fast dynamics. In particular, for simple glass formers, the bulk to shear modulus ratio in the glassy state correlates with fragility in the liquid state and is inversely proportional to the intensity of the boson peak. A simple relationship between the temperature dependence of the viscosity of liquids at high temperatures and near the glass transition is used to rationalize these correlations. We argue that the ratio of the moduli controls the high-temperature activation energy of the structural relaxation and in this way affects the fragility. The ratio also defines the amplitude of the structural relaxation (i.e., the nonergodicity parameter) and the latter influences the strength of the boson peak. These observations might explain the puzzling correlation observed between the fragility and fast dynamics in glass-forming systems.

Journal Article↗

Poisson's ratio and the fragility of glass-forming liquids.

The nature of the transformation by which a supercooled liquid 'freezes' to a glass--the glass transition--is a central issue in condensed matter physics but also affects many other fields, including biology. Substantial progress has been made in understanding this phenomenon over the past two decades, yet many key questions remain. In particular, the factors that control the temperature-dependent relaxation and viscous properties of the liquid phase as the glass transition is approached (that is, whether the glass-forming liquid is 'fragile' or 'strong') remain unclear. Here we show that the fragility of a glass-forming liquid is intimately linked to a very basic property of the corresponding glass phase: the relative strength of shear and bulk moduli, or Poisson's ratio.

Journal Article↗

Protein and solvent dynamics: how strongly are they coupled?

Analysis of Raman and neutron scattering spectra of lysozyme demonstrates that the protein dynamics follow the dynamics of the solvents glycerol and trehalose over the entire temperature range measured 100-350 K. The protein's fast conformational fluctuations and low-frequency vibrations and their temperature variations are very sensitive to behavior of the solvents. Our results give insight into previous counterintuitive observations that protein relaxation is stronger in solid trehalose than in liquid glycerol. They also provide insight into the effectiveness of glycerol as a biological cryopreservant.

Glycerol↗

Biosynthesis of citric and isocitric acids from ethanol by mutant Yarrowia lipolytica N 1 under continuous cultivation.

The effect of ethanol, zinc, and iron (Fe(2+) and Fe(3+)) concentration and of oxygen supply on cell growth and the production of citric acid (CA) and isocitric acid (ICA) from ethanol by mutant Yarrowia lipolytica N 1 was studied under continuous cultivation. The following peculiarities of Y. lipolytica metabolism were found: (1) intensive CA production occurred under yeast growth limitation by nitrogen; (2) inhibition of yeast growth by ethanol was accompanied by significant alterations in fatty acid composition of lipids; (3) the production of CA and ICA from ethanol required high concentrations of zinc and iron ions; (4) the intracellular iron concentration determined whether CA or ICA was predominantly formed; (5) the cell's requirement for oxygen depended on the intracellular iron concentration. The events taking place in the production of CA and ICA were evaluated through the activities of enzyme systems involved in the metabolism of ethanol and CA in this strain.

Citric Acid↗

Brillouin and Umklapp scattering in polybutadiene: comparison of neutron and x-ray scattering.

We report a comparison of high resolution inelastic x-ray Brillouin scattering to coherent inelastic neutron scattering for amorphous deuterated polybutadiene, done for one temperature in the glass phase and another one in the melt. The x-ray scattering proves to be by far the better technique for such a polymer within its present resolution bounds. The neutron scattering allows one to extend these measurements to a much better resolution, showing an additional quasielastic signal in the melt. The results suggest x-ray measurements at higher momentum transfer, to see whether they are complementary to neutrons.

Journal Article↗

Methylobacterium extorquens strain P14, a new methylotrophic bacteria producing poly-beta-hydroxybutyrate (PHB).

Strain P14 of facultative methylotrophic bacteria that synthetisizes poly-beta-hydroxybutyrate has been isolated. The cells are gram-negative motile rods with a polar flagellum. They do not form spores or capsules, but do have a caretenoid pigment. Predominant in the fatty acid composition of the cells is cis-vaccenic acid (cis 18:1: omega 7)--72%. In the phospholipid composition phosphatidylcholine predominates (45%), along with phosphatidylenthanoloamine (27%) and phosphatidylglycerol (17%). The main biquinone is Q-10; other ubiquinones (Q-8, Q-9, Q-11) are present in minor quantities. The cells accomplish the icl-variant of serine pathway. The GC content of DNA (Tm) is 65 mole%. A high level DNA-DNA homology with representatives of the genus Methylobacterium was observed. The strain has been identified as Methylobacterium extorquens strain P14.

Culture Media↗

Purification and characterization of citrate synthase from Methylobacterium extorquens--a methylotrophic producer of polyhydroxybutyrate.

Citrate synthase (citrate oxaloacetate-lyase, CoA-acetylating; EC 4.1.3.7, CS) was isolated and purified to homogeneity from a methylotrophic producer of polyhydroxybutyrate (PHB), Methylobacterium extorquens 15. The purification procedure includes streptomycin sulfate treatment of cell-free extract, ammonium sulfate fractionation, two steps of hydrophobic chromatography, and ion-exchange chromatography. The specific activity of the final enzyme preparation was 24 U/mg protein. The enzyme has apparent molecular weight 260 kD and consists of four 66-kD subunits. The enzyme shows a sigmoid saturation curve with CoASA (h = 1.3). Kinetic parameters are: K(m) = 84 microM for CoASA; K(m) = 12 microM for oxaloacetate; Vmax = 29.7 mumoles/min per mg protein. KCl at concentrations up to 80 mM activates the CS. ATP exerts a significant inhibitory effect on the enzyme activity, whereas NAD(P)H, isocitrate, alpha-ketoglutarate, ADP, acetoacetyl-CoA, glyoxylate, and glutamate have no influence. A possible role of the CS in coordinated control of CoASA transformation through the tricarboxylic acid cycle and PHB biosynthesis in this methylotroph is discussed.

Chromatography, Liquid↗

[Properties of pyruvate carboxylase of the facultative methylotrope Pseudomonas oleovorans].

Pyruvate carboxylase of the facultative methylotroph Pseudomonas oleovorans was purified 40-fold by ammonium sulfate fractionation, gel filtration on Ultrogel AcA 34, ion-exchange chromatography on DEAE-Biogel A and concentration on DEAE-Sepharose CL-6B. The enzyme exerts its maximal activity in the presence of Mg2+ (pH 7.5, 40 degrees), is unstable and completely inactivated within 6 hrs at 25 degrees. In the presence of Mg2+ monovalent cations stimulate the enzyme activity. The molecular weight of pyruvate carboxylase as determined by gel filtration of Sepharose CL-6B is 300,000. The enzyme molecule contains biotin. The apparent Km values for pyruvate, ATP and HCO3- are 1.77, 0.19 and 0.23 mM, respectively. CoASAc, alpha-ketoglutarate and glutamate have no effect on the enzyme activity. The enzyme is inhibited by aspartate, malate, oxaloacetate and is activated by citrate, isocitrate and phosphosugars. The role of pyruvate carboxylase in methylotrophic metabolism of Ps. oleovorans is discussed.

Enzyme Activation↗

[Dihydroxyacetone synthase from the methanol-utilizing yeast Candida boidinii].

A procedure for purification of dihydroxyacetone synthase catalyzing the formation of dihydroxyacetone and glyceraldehyde 3-phosphate from formaldehyde and xylulose 5-phosphate has been developed. Using ion-exchangers with increasing affinity for dihydroxyacetone synthase, a homogenous preparation of the enzyme with specific activity of 2 u./mg has been obtained. The enzyme is made up of 2 subunits with m. w. of 76,000, contains thiamine pyrophosphate, requires Mg2+ for its activity and differs from yeast transketolase by substrate specificity and some other properties. The role of dihydroxyacetone synthase in metabolism of methanol-utilizing yeasts is discussed.

Aldehyde-Ketone Transferases↗

[Purification and properties of glucose-6-phosphate and 6-phosphogluconate dehydrogenases from Pseudomonas oleovorans].

The glucose-6-phosphate and 6-phosphogluconate dehydrogenases i. e. enzymes of dissimilatory hexulose phosphate cycle, were isolated from the cells of the facultative methylotrophic bacterium Pseudomonas oleovorans. The purification procedure included protein fractionation by ammonium sulfate, gel-filtration through Sephacryl S-200 and chromatography on DEAE Bio-Gel A and phosphocellulose, resulting in a 400-fold purification of the enzyme. During analytical disc-electrophoresis in polyacrylamide gel the glucose-6-phosphate dehydrogenase preparation produced a single band; 6-phosphogluconate dehydrogenase was found to contain small contaminations. The molecular weights of the dehydrogenases are 100000 and 110000, respectively. Both enzymes have two subunits. The Km values for glucose-6-phosphate dehydrogenase are 65 mkM for glucose-6-phosphate and 28 mkM for NADP; those for 6-phosphogluconate dehydrogenase are 152 mkM for 6-phosphogluconate and 55 mkM for NADP. Nucleotides are found to be the most active inhibitors of glucose-6-phosphate dehydrogenase. 6-Phosphogluconate dehydrogenase is inhibited by ribose-5-phosphate and fructose-1,6-diphosphate.

Glucosephosphate Dehydrogenase↗

Kinetic properties of the purified 3-hexulosephosphate synthase from Pseudomonas oleovorans.

The kinetic characteristics of the purified 3-hexulosephosphate synthase from the facultative methylotroph Pseudomonas oleovorans were investigated. It could be demonstrated that the dependence of the reaction rate on the rib(ul)ose-5-phosphate as well as the formaldehyde concentration has a complex shape with the appearence of plateau and trough regions. The shape of the curve is changed in dependence on the fixed level of the second substrate. Multiple forms of the 3-hexulosephosphate synthase were found to be responsible for the generation of the complex kinetic characteristics. By means of ion exchange chromatography it was possible to separate four active enzyme forms with different kinetic characteristics. These forms were also found to be interconvertible. This behaviour of the 3-hexulosephosphate synthase is assumed to have the main regulatory function of the enzyme.

Aldehyde-Lyases↗

[Purification and properties of 3-hexulosephosphate synthase from facultative methylotroph Pseudomonas oleovorans].

3-Hexulosephosphate synthase (HPS), the key enzyme of the hexulosephosphate cycle of formaldehyde fixation, was isolated from facultative methylotroph Pseudomonas oleovorans. Enzyme was purified 100-fold. The purification procedure involved fractionation with ammonium sulfate, gel-filtration on Sephadex G-150 and chromatography on DEAE-Sephadex A-50. The purified enzyme gave single band on analytical polyacrylamide gel electrophoresis. Optimal conditions for activity of HPS are: pH 7,0, temperature 50 degrees C. The molecular weight was calculated to be 45 000 from gel-filtration experiments. HPS is active only in the presence of Mg2+ or Mn2+. Ribulose-5-phosphate is the sole acceptor of formaldehyde. Activity of the enzyme is inhibited by NADH and NADPH.

Aldehyde-Lyases↗

[The isolation, purification, and some properties of NAD-dependent isocitrate dehydrogenase from the organic acid-producing yeast Yarrowia lipolytica].

The NAD+-dependent isocitrate dehydrogenase of the organic acid-producing yeast Yarrowia lipolytica was isolated, purified, and partially characterized. The purification procedure included four steps: ammonium sulfate precipitation, acid precipitation, hydrophobic chromatography, and gel-filtration chromatography. The enzyme was purified 129-fold with a yield of 31% and had a specific activity of 22 U/mg protein. The molecular mass of the enzyme was found to be 412 kDa. The enzyme consists of eight identical subunits with a molecular mass of about 52 kDa. The Km for NAD+ is 136 microM, and that for isocitrate is 581 microM. The effect of some intermediates of the citric acid cycle and nucleotides on the enzyme activity was studied. The role of isocitrate dehydrogenase (NAD+) in the overproduction of citric and keto acids is discussed.

Ammonium Sulfate↗