Stochastic kinetics of ribosomes: Single motor properties and collective behavior

Syntheses of protein molecules in a cell are carried out by ribosomes.A ribosome can be regarded as a molecular motor which utilizes the input chemical energy to move on a messenger RNA (mRNA) track that also serves as a template for the polymerization of the corresponding protein. The forward movement, however, is characterized by an alternating sequence of translocation and pause. Using a quantitative model, which captures the mechanochemical cycle of an individual ribosome, we derive an exact analytical expression for the distribution of its dwell times at the successive positions on the mRNA track. Inverse of the average dwell time satisfies a Michaelis-Menten-type'' equation and is consistent with the general formula for the average velocity of a molecular motor with an unbranched mechanochemical cycle. Extending this formula appropriately, we also derive the exact force-velocity relation for a ribosome. Often many ribosomes each synthesizes a copy of the same protein. We extend the model of a single ribosome by incorporating steric exclusion of different individuals on the same track. We draw the phase diagram of this model of ribosome traffic in three-dimensional spaces spanned by experimentally controllable parameters. We suggest new experimental tests of our theoretical predictions.

Hormonal induction of riboflavin carrier protein in the chicken oviduct and liver: a comparison of kinetics and modulation

Estrogen (E) induction of riboflavin carrier protein (RCP) in the chicken oviduct and liver was investigated to compare and contrast the kinetics, hormonal specificity and modulation of its elaboration in the 2 steroid-responsive tissues. During primary stimulation, continued daily E administration to immature female chicks elicited, after an initial lag, rapid growth and RCP content of the oviduct; neither progesterone (P) nor testosterone (T) could substitute for E in this respect. Furthermore, P given along with E curtailed tissue growth and its RCP content, whereas E + T had a synergistic effect on tissue growth only. During secondary stimulation, E administration steeply enhanced both tissue weight and RCP content without any lag. Interestingly, P (but not T) could substitute for E in augmenting magnum RCP concentration to a comparable extent while a concomitant effect on tissue growth was less marked. In contrast, hepatic induction of RCP was absolutely E-specific during both primary and secondary stimulations. Secondary stimulation with either E or P of E-primed birds enhanced the rates of RCP synthesis in the oviduct relative to that of total protein, whereas in the liver only E was effective in this regard. The absolute rate of E-induced RCP synthesis in both the steroid-stimulated tissues was significantly higher than that of general protein elaboration.

Role of conformational dynamics in kinetics of an enzymatic cycle in a nonequilibrium steady state

Enzyme is a dynamic entity with diverse time scales, ranging from picoseconds to seconds or even longer. Here we develop a rate theory for enzyme catalysis that includes conformational dynamics as cycling on a two-dimensional (2D) reaction free energy surface involving an intrinsic reaction coordinate (X) and an enzyme conformational coordinate (Q). The validity of Michaelis-Menten (MM) equation, i.e., substrate concentration dependence of enzymatic velocity, is examined under a nonequilibrium steady state. Under certain conditions, the classic MM equation holds but with generalized microscopic interpretations of kinetic parameters. However, under other conditions, our rate theory predicts either positive (sigmoidal-like) or negative (biphasic-like) kinetic cooperativity due to the modified effective 2D reaction pathway on X-Q surface, which can explain non-MM dependence previously observed on many monomeric enzymes that involve slow or hysteretic conformational transitions. Furthermore, we find that a slow conformational relaxation during product release could retain the enzyme in a favorable configuration, such that enzymatic turnover is dynamically accelerated at high substrate concentrations. The effect of such conformation retainment in a nonequilibrium steady state is evaluated.

Kinetics of thermal decomposition of barium zirconyl oxalate

Kinetics of the thermal decomposition of anhydrous barium zirconyl oxalate and a carbonate intermediate have been studied. Decomposition of the anhydrous oxalate, though it could be explained based on a contracting-cube model, is quite complex. Kinetics of decomposition of the intermediate carbonate Ba2Zr2O5CO3 is greatly influenced by thermal effects during its formation. (agr-t) curves are sigmoidal and obey a power law equation followed by first order decay. Presence of carbon in the vacuum-prepared carbonate has a strong deactivating effect. Decomposition of the carbonate is accompanied by growth in particle size of the product barium zirconate.

Structure, energetics and diffusion properties of isomers of trimethyl benzene in beta zeolite: Uptake and Monte Carlo simulation study

A Monte Carlo study along with experimental uptake measurements of 1,2,3-trimethyl benzene, 1,2,4-trimethyl benzene and 1,3,5-trimethyl benzene (TMB) in beta zeolite is reported. The TraPPE potential has been employed for hydrocarbon interaction and harmonic potential of Demontis for modeling framework of the zeolite. Structure, energetics and dynamics of TMB in zeolite beta from Monte Carlo runs reveal interesting information about the diameter, properties of these isomers on confinement. Of the three isomers, 135TMB is supposed to have the largest diameter. It is seen TraPPE with Demontis potential predicts a restricted motion of 135TMB in the channels of zeolite beta.Experimentally, 135TMB has the highest transport diffusivity whereas MID results suggest this has the lowest self diffusivity. (C) 2009 Elsevier Inc. Ail rights reserved.

Liquid phase oxidation of propionaldehyde: Kinetics of initiation step

A method of determining the rate of the initiation reaction in the liquid phase oxidation of propionaldehyde is described.

Kinetics and Mechanism of the Transformation of Vaterite to Calcite

The transformation of vaterite to calcite was investigated systematically. The transition temperature and the energetics of the transformation were determined from differential thermal curves. The variations of lattice constants and crystallite size, accompanying the transformation were studied by X-ray diffractometry. The kinetics of transformation were investigated in the temperature range 460–490°C. The kinetic data were analysed with the help of three separate solid-state models.

Crystallization Kinetics and Electrical Relaxation of BaO-0.5Li(2)O-4.5B(2)O(3) Glasses

Transparent glasses in the composition BaO-0.5Li(2)O-4.5B(2)O(3) (BLBO) were fabricated via the conventional melt-quenching technique. X-ray powder diffraction combined with differential scanning calorimetric (DSC) studies carried out on the as-quenched samples confirmed their amorphous and glassy nature, respectively. The crystallization behavior of these glasses has been studied by isothermal and nonisothermal methods using DSC. Crystallization kinetic parameters were evaluated from the Johnson-Mehl-Avrami equation. The value of the Avrami exponent (n) was found to be 3.6 +/- 0.1, suggesting that the process involves three-dimensional bulk crystallization. The average value of activation energy associated with the crystallization of BLBO glasses was 317 +/- 10 kJ/mol. Transparent glass-ceramics were fabricated by controlled heat-treatment of the as-quenched glasses at 845 K/40 min. The dielectric constants for BLBO glasses and glass-ceramics in the 100 Hz-10 MHz frequency range were measured as a function of the temperature (300-925 K). The electrical relaxation and dc conductivity characteristics were rationalized using electric modulus formalism. The imaginary part of the electric modulus spectra was modeled using an approximate solution of the Kohlrausch-Williams-Watts relation. The temperature-dependent behavior of stretched exponent (beta) was discussed for the as-quenched and heat-treated BLBO glasses.

Kinetics of vapour phase oxidation of furfural on vanadium catalyst

Vapour phase oxidation of furfural over vanadium pentoxide catalyst was studied using an isothermal flow reactor in the temperature range of 220–280°C. Maleic anhydride and carbon dioxide are found to be formed from furfural by a parallel reaction scheme. The following rate equation based on the two-stage redox mechanism—the substance to be oxidized reduces the catalyst which in turn is reoxidized by oxygen from the feed—is found to explain the data satisfactorily.The reoxidation of the reduced catalyst was found to be the rate controlling step.

Mechanism of adsorption effects on electrode kinetics: Part I: Selection rules in the case of low coverage by molecular surfactants

It is shown that the effect of adsorption of inert molecules on electrode reaction rates is completely accounted for, by introducing into the rate equation, adsorption-induced changes in both the effective electrode area as well as in the electrostatic potential at the reaction site with an additional term for the noncoulombic interaction between the reactant and the adsorbate. The electrostatic potential at the reaction site due to the adsorbed layer is calculated using a model of discretely-distributed molecules in parallel orientation when adsorbed on the electrode with an allowance for thermal agitation. The resulting expression, which is valid for the limiting case of low coverages, is used to predict the types of molecular surfactants that are most likely to be useful for acceleration and inhibition of electrode reactions.

Resistivity noise in crystalline magnetic nanowires and its implications to domain formation and kinetics

We have investigated the time-dependent fluctuations in electrical resistance, or noise, in high quality crystalline magnetic nanowires within nanoporous templates. The noise increases exponentially with increasing temperature and magnetic field, and has been analyzed in terms of domain wall depinning within the Neel-Brown framework. The frequency-dependence of noise also indicates a crossover from nondiffusive kinetics to long-range diffusion at higher temperatures, as well as a strong collective depinning, which need to be considered when implementing these nanowires in magnetoelectronic devices.

Mechanism of aminoacylation of tRNA : Influence of spermine on the kinetics of aminoacyl-tRNA synthesis by isoleucyl- and valyl-tRNA synthetases from Mycobacterium smegmatis

Isoleucyl-tRNA synthetase has been purified to homogeneity from Mycobacterium smegmatis. The influence of spermine on the kinetics of valyl-tRNA and isoleucyl-tRNA formation has been investigated by Cleland's method (Cleland, W.W. (1963) Biochim. Biophys. Acta 67, 104–137, 173–187, 188–196). The results suggest that in the presence of spermine and suboptimal concentration of Mg2+, the formation of valyl-tRNA and isoleucyl-tRNA follows a sequential* mechanism. In the presence of an optimal concentration of Mg2+, both valyl-tRNA and isoleucyl-tRNA formation proceeds by a ping-pong mechanism. However, in the presence of spermine and optimal concentrations of Mg2+, valyl-tRNA formation follows the ping-pong mechanism while isoleucyl-tRNA formation follows the sequential mechanism.

Intrinsic kinetics of trickle bed reactors

Abstract is not available.

Prediction of Intrinsic kinetics in diffusion disguised immobilized enzyme systems

When immobilized enzyme kinetics are disguised by inter- and intraparticle diffusion effects, an approximate mathematical procedure is indicated whereby experimental data obtained in the limiting ranges of first- and zeroth-order Michaelis-Menten kinetics could be used for the prediction of the kinetic constants.