Allostery in tRNA Synthetases Elucidated from MD Simulations and Protein Structure Networks

tRNA synthetases (aaRS) are enzymes crucial in the translation of genetic code. The enzyme accylates the acceptor stem of tRNA by the congnate amino acid bound at the active site, when the anti-codon is recognized by the anti-codon site of aaRS. In a typical aaRS, the distance between the anti-codon region and the amino accylation site is approximately 70 Å. We have investigated this allosteric phenomenon at molecular level by MD simulations followed by the analysis of protein structure networks (PSN) of non-covalent interactions. Specifically, we have generated conformational ensembles by performing MD simulations on different liganded states of methionyl tRNA synthetase (MetRS) from Escherichia coli and tryptophenyl tRNA synthetase (TrpRS) from Human. The correlated residues during the MD simulations are identified by cross correlation maps. We have identified the amino acids connecting the correlated residues by the shortest path between the two selected members of the PSN. The frequencies of paths have been evaluated from the MD snapshots[1]. The conformational populations in different liganded states of the protein have been beautifully captured in terms of network parameters such as hubs, cliques and communities[2]. These parameters have been associated with the rigidity and plasticity of the protein conformations and can be associated with free energy landscape. A comparison of allosteric communication in MetRS and TrpRS [3] elucidated in this study highlights diverse means adopted by different enzymes to perform a similar function. The computational method described for these two enzymes can be applied to the investigation of allostery in other systems.

Oxygen transfer in circular surface aeration tanks

Surface aeration systems employed in activated sludge plants are the most energy-intensive units of the plants and typically account for a higher percentage of the treatment facility's total energy use. The geometry of the aeration tank imparts a major effect on the system efficiency. It is said that at optimal geometric onditions, systems exhibits the maximum efficiency. Thus the quantification of the optimal geometric conditions in surface aeration tanks is needed. Optimal geometric conditions are also needed to scale up the laboratory result to the field installation. In the present work, experimental studies have been carried out on baffled and unbaffled circular surface aeration tanks to ascertain the optimal geometric conditions. It is found that no optimal geometric conditions exist for the liquid/water depth in circular surface aeration tanks; however, for design purposes, a standard value has been assumed. Based on the optimal geometric conditions, a scale-up equation has been developed for the baffled circular surface aeration tanks.

Coherence transfer via longitudinal spin order generalized pulse pair filtering for pure phase two-dimensional NMR spectroscopy

A generalized pulse pair has been suggested in which the longitudinal spin order is retained and the transverse components cancelled by random variation of the interval between pulses, in successive applications of the two-dimensional NMR algorithm. This method leads to pure phases and has been exploited to provide a simpler scheme for two-spin filtering and for pure phase spectroscopy in multiple-quantum-filtered two-dimensional NMR experiments.

Unsteady compressible 3-dimensional boundary-layer flow near an asymmetric stagnation point with mass transfer

The heat and mass transfer for unsteady laminar compressible boundary-layer flow, which is asymmetric with respect to a 3-dimensional stagnation point (i.e. for a jet incident at an angle on the body), have been studied. It is assumed that the free-stream velocity, wall temperature, and surface mass transfer vary arbitrarily with time and also that the gas has variable properties. The solution in the neighbourhood of the stagnation point has been obtained by series expansion in the longitudinal distance. The resulting partial differential equations have been solved numerically using an implicit finite-difference scheme. The results show that, in contrast with the symmetric flow, the maximum heat transfer does not occur at the stagnation point. The skin-friction and heat-transfer components due to asymmetric flow are only weakly affected by the mass transfer as compared to those components associated with symmetric flow. The variation of the wall temperature with time has a strong effect on the heat transfer component associated with the symmetric part of the flow. The skin friction and heat transfer are strongly affected by the variation of the density-viscosity product across the boundary layer. The skin friction responds more to the fluctuations of the free stream oscillating velocities than the heat transfer. The results have been compared with the available results and they are found to be in excellent agreement.

Ammonium ions prevent methylation of uridine to ribothymidine in Azotobacter vinelandii tRNA

It was shown that tRNA from Azotobacter vinelandii grown in the presence of ammonium chloride lacks ribothymidine while that grown in the absence of the ammonium salt contains this modified nucleoside. [32P]-Labelled tRNA from this organism grown in a medium containing the ammonium salt was digested with RNase T1 and the pseudouridinecontaining tetranucleotide, common to all tRNAs was isolated and analysed for the nucleoside replacing the ribothymidine. It was found to be uridine. Cells previously labelled with [32P]- phosphate in the ammonium salt medium were washed and incubated in the ammonium saltfree medium to test whether ribothymidine would be formed upon removal of the ammoniumions. Methylation of the uridine did not take place.

Heat-Transfer During Dropwise Condensation

A comprehensive model is developed for previous termheat transfernext term during previous termdropwise condensationnext term based on the assumption that previous termheat transfernext term takes place through the bare surface in between drops to form nuclei at nucleation sites during the waiting period required for nucleation. The dynamics of drop formation and surface renewal, and the presence of non-condensable gases in the vapour have been considered. The resulting equation expresses the dependence of the vapour-side previous termheat transfernext term coefficient on the previous termheatnext term flux, properties of the vapour, previous termcondensationnext term coefficient, mole fraction of non-condensable gases in the vapour, free area available for previous termcondensation,next term surface roughness and surface thermal properties. The equation is tested with the available data and the agreement is found to be satisfactory.

Influence of inclination angle of plate on friction, stick-slip and transfer layer-A study of magnesium pin sliding against steel plate

In this study, sliding experiments were conducted using pure magnesium pins against steel plates using an inclined pin-on-plate sliding tester. The inclination angle of the plate was varied in the tests and for each inclination angle, the pins were slid both perpendicular and parallel to the unidirectional grinding marks direction under both dry and lubricated conditions. SEM was used to study morphology of the transfer layer formed on the plates. Surface roughness of plates was measured using an optical profilometer. Results showed that the friction, amplitude of stick-slip motion and transfer layer formation significantly depend on both inclination angle and grinding marks direction of the plates. These variations could be attributed to the changes in the level of plowing friction taking place at the asperity level during sliding.

Studies on friction and formation of transfer layer when Al-4Mg alloy pins slid at various numbers of cycles on steel plates of different surface texture

In the present investigation, various kinds of textures, namely, unidirectional, 8-ground, and random were attained on the die surfaces. Roughness of the textures was varied using different grits of emery papers or polishing powders. Then pins made of Al-4Mg alloys were slid against steel plates at various numbers of cycles, namely 1, 2, 6, 10 and 20 under both dry and lubricated conditions using an inclined pin-on-plate sliding tester. The morphologies of the worn surfaces of the pins and the formation of transfer layer on the counter surfaces were observed using a scanning electron microscope. Surface roughness parameters of the plate were measured using an optical profilometer. It was observed that the coefficient of friction and formation of transfer layer during the first few cycles depend on the die surface textures under both dry and lubricated conditions. It was also observed that under lubricated condition, the coefficient of friction decreases with number of cycles for all kinds of textures. However, under dry condition, it ecreases for unidirectional and 8-ground surfaces while for random surfaces it increases with number of cycles

Influence of Solvent on Photoinduced Electron-Transfer Reaction: Time-Resolved Resonance Raman Study

Time-resolved resonance Raman spectroscopy (TR3) has been used to study the effect of solvent polarity on the mechanism and nature of intermediates formed in photoinduced electron-transfer reaction between triplet flouranil ((FL)-F-3) and tetramethylbenzene (TMB). Comparison of the TR3 spectra in polar, nonpolar, and medium polar media suggests that formation of radical anion due to electron-transfer reaction between (FL)-F-3 and TMB is favored in more polar solvents, whereas ketyl radical formation is more favored in less polar media. Compared to ketyl radical, the extent of radical anion formation is negligible in nonpolar solvents. Therefore, it is inferred that in nonpolar media ketyl radical is mainly generated by hydrogen-transfer reaction in the encounter complex between (FL)-F-3 and TMB. In solvents of medium polarity, the ion-pair decay leads to the formation of both ketyl radical and ketyl radical formed from the encounter between triplet state and the donor. Thus, competition between the formation of ketyl radical and ion pair is influenced by the solvent polarity. The nature of the ion pair in different solvent polarity has been investigated from the changes observed in the vibrational frequency of (fluoranil) FL part of the complex.

Heat transfer with solid liquid phase change initiating at a point in a semi infinite mold

Short-time analytical solutions of temperature and moving boundary in two-dimensional two-phase freezing due to a cold spot are presented in this paper. The melt occupies a semi-infinite region. Although the method of solution is valid for various other types of boundary conditions, the results in this paper are given only for the prescribed flux boundary conditions which could be space and time dependent. The freezing front propagations along the interior of the melt region exhibit well known behaviours but the propagations along the surface are of new type. The freezing front always depends on material parameters. Several interesting results can be obtained as particular cases of the general results.

Load Transfer from a Smooth Elastic Pin to a Large Sheet

The plane problem of load transfer from an elastic interference or clearance fit pin to a large elastic sheet with a perfectly smooth interface is solved. As the load on the pin is monotonically increased, the pin-hole interface is in partial contact above certain critical load in interference fit and throughout the loading range in clearance fit.Such situations result in mixed boundary-value problems with moving boundaries and the arc of contact varies nonlinearly with applied load. These problems are analyzed by an inverse technique in which the arcs of contact/separation are prescribed and the causative loads are evaluated. A direct method of analysis is adopted using biharmonic polar trigonometric stress functions and a simple collocation method for satisfying the boundary conditions. A unified analytical formulation is achieved for interference and clearance fits. The solutions for the linear problem of push fits are inherent in the unified analysis. Numerical results highlighting the effects of pin and sheet elasticity parameters are presented.

A rapid and sensitive method for the estimation of individual tRNA pools

A rapid and sensitive method is described to quantitatively compare tRNA pools for individual aminoacids in a single experiment. The procedure comprises of: (i) charging of total tRNA with a mixture of radiolabeled aminoacids, (ii) deacylation of the esterified tRNA with a volatile base and the recovery of the labeled aminoacid, (iii) derivatisation of the aminoacid with phenylisothiocyanate after mixing with excess of nonradioactive aminoacids, (iv) baseline separation of the phenylthiocarbamyl aminoacids by reverse phase high performance liquid chromatography monitored by A254nm and (v) quantitation of the radioactivity in individual aminoacid peaks. The radioactivity in the aminoacid peak corresponds to the quantity of the aminoacylated tRNA. The method has been successfully applied to quantitate the individual tRNA pools in the developing silk glands of Bombyx mori, a functionally adapted tissue which undergoes considerable variations in tRNA content. PSG, posterior silk gland; PITC, phenylisothiocyanate; DMAA, N,N-dimethyl-N-allylamine; APH, algal protein hydrolysate; ptc-, phenylthiocarbamyl; HPLC, high performance liquid chromatography.

Mass transfer effects on the generalised vortex flow over a stationary surface with or without magnetic field

The effect of injection and suction on the generalised vortex flow of a steady laminar incompressible fluid over a stationary infinite disc with or without magnetic field under boundary-layer approximations has been studied. The coupled nonlinear ordinary differential equations governing the self-similar flow have been numerically solved using the finite-difference scheme. The results indicate that the injection produces a deeper inflow layer and de-stabilises the motion while suction or magnetic field suppresses the inflow layer and produces stability. The effect of decreasingn, the parameter characterising the nature of vortex flow, is similar to that of increasing the injection rate.

Microprocessor Based Sinusoidal PWM Inverter by DMA Transfer

The implementation of three-phase sinusoidal pulse-width-modulated inverter control strategy using microprocessor is discussed in this paper. To save CPU time, the DMA technique is used for transferring the switching pattern from memory to the pulse amplifier and isolation circuits of individual thyristors in the inverter bridge. The method of controlling both voltage and frequency is discussed here.

5-Methyl-2-Thiouridine in the tRNA of Candida tropicalis and Its Localization in Lysine tRNA

35S incorporation studies showed that Candida tropicalis tRNA contained two thionucleosides, one of which was identified as 5-methyl-2-thiouridine. The other thionucleoside was alkali labile, and it appeared to be an ester. Pulse-chase experiments suggested that the two thionucleosides were structurally related. 5-Methyl-2-thiouridine was present in one of the lysine tRNAs. This is the first report of the presence of this nucleoside in a yeast tRNA.