The conserved protein kinase-A target motif in synapsin of Drosophila is effectively modified by pre-mRNA editing

Background  

Synapsins are abundant synaptic vesicle associated phosphoproteins that are involved in the fine regulation of neurotransmitter release. The Drosophila member of this protein family contains three conserved domains (A, C, and E) and is expressed in most or all synaptic terminals. Similar to mouse mutants, synapsin knock-out flies show no obvious structural defects but are disturbed in complex behaviour, notably learning and memory.     

Numerical simulation of the effect of grain fragmentation on the evolution of microstructure quantities

Meccanica - In this paper the effect of grain fragmentation of a cohesionless granular material on the change of microstructure quantities is investigated using a micropolar continuum model. To...     

Quantum-limited noise performance of a mode-locked laser diode

Low-noise operation of a 9-GHz hybridly mode-locked laser diode is demonstrated. The integrated timing jitter was 47 fs (10 Hz to 10 MHz) and 86 fs (10 Hz to 4.5 GHz), with a pulse width of 6.7 ps. The noise performance as a function of filter bandwidth and oscillator noise is also addressed.     

Unusual conformational preferences of 1,3‐dimethyl‐3‐isopropoxy‐3‐silapiperidine

The conformational analysis of the first representative of the Si‐alkoxy substituted six‐membered Si,N‐heterocycles, 1,3‐dimethyl‐3‐isopropoxy‐3‐silapiperidine, was performed by low‐temperature ¹H and ¹³C NMR spectroscopy and DFT theoretical calculations. In contrast to the expectations from the conformational energies of methyl and alkoxy substituents, the Me_axi‐PrO_eq conformer was found to predominate in the conformational equilibrium in the ratio Me_axi‐PrO_eq : Me_eqi‐PrO_ax of ca. 2 : 1 as from the ¹H and ¹³C NMR study. The thermodynamic parameters obtained by the complete line shape analysis showed that the main contribution to the barrier to ring inversion originates from the entropy term of the free energy of activation. Copyright © 2012 John Wiley & Sons, Ltd.     

Cyclobutadiene dianion derivatives – Planar 4c,6e or three-dimensional 6c,6e aromaticity?

The spatial magnetic properties (Through Space NMR Shieldings – TSNMRS) of two cyclobutadiene derivatives (2 and 5) and of a number of cyclobutadiene dianion derivatives (3, 4 and 6–8) have been calculated by the GIAO perturbation method employing the Nucleus-Independent Chemical Shift (NICS) concept of P. v. Ragué Schleyer, and visualized as Iso-Chemical-Shielding Surfaces (ICSS) of various size and direction. TSNMRS values can be successfully employed to quantify and visualize the (anti)aromaticity of the compounds studied and to discuss the influence of Li⁺ complexation to cyclobutadiene dianion (4a, 7 and 8) on planar 4c,6e or three-dimensional 6c,6e aromaticity.     

The structure of amorphous sulfur

The λ‐transition of elemental sulfur occurring at about 159°C has long been associated with the conversion of cyclic S₈ rings (c‐S₈) to amorphous polymer (a‐S) via a ring opening polymerization. Here we demonstrate, with the use of both density functional and Hartree‐Fock quantum mechanical calculations, the existence of an energetically accessible, locally stable, hypervalent state of S that can form branch sites in the polymer. The significance of this finding is that the λ‐transition is best described as a gelation transition. The geometry of the tetravalent S atom is trigonal bipyramidal, with a lone pair occupying one of the three equatorial sites; it lies in a local energy minimum about 31 kcal/mol above the normal divalent state, and so is accessible both thermally and photochemically. Because the branched structure is formed endothermically, Le Chatelier's principle confirms that a percolation network can form on heating the element. The reactions that form branched structures are reversible, implying that the gel is fluxional. It decomposes at higher temperatures as chain scission competes with branching. The hypervalent structure provides an essential insight into the chemistry of elemental sulfur.     

Intermolecular C-H bond activation promoted by a titanium alkylidyne

The transient titanium alkylidyne complex (PNP)TiCtBu (PNP = N-[2-P(CHMe2)2-4-methylphenyl]2-), prepared from alpha-hydrogen abstraction of the corresponding alkylidene-alkyl species (PNP)Ti=CHtBu(CH2tBu), can readily undergo intermolecular 1,2-addition of C-H bonds of benzene and SiMe4. Synthesis and reactivity, isotopic labeling, kinetics, and theoretical studies strongly favor an alkylidyne pathway and the alpha-H abstraction step to be the rate-determining step.     

Ab initio study of the substituent effects on the relative stability of the E and Z conformers of phenyl esters. Stereoelectronic effects on the reactivity of the carbonyl group

Equilibria between the Z (tau1= 0 degrees) and E (tau1= 180 degrees) conformers of p-substituted phenyl acetates 4 and trifluoroacetates 5 (X = OMe, Me, H, Cl, CN, NO2) were studied by ab initio calculations at the HF/6-31G* and MP2/6-31G* levels of theory. The preference for the Z conformer, DeltaE(HF), was calculated to be 5.36 kcal mol(-1) and 7.50 kcal mol(-1) for phenyl acetate and phenyl trifluoroacetate (i.e., with X = H), respectively. The increasing electron-withdrawing ability of the phenyl substituent X increases the preference of the Z conformer. An excellent correlation with a negative slope was observed for both series between DeltaE of the E-Z equilibrium and the Hammett sigma constant. By using an appropriate isodesmic reaction, it was shown that electron-withdrawing substituents decrease the stability of both conformers, but the effect is higher with the E conformer. Electron-withdrawing phenyl substituents decrease the delocalization of the lone pair of the ether oxygen to the C=O antibonding orbital (nO--> pi*C=O) in both the E and Z forms and in both series studied; this effect is higher in the E conformer than in the Z conformer. The nO --> pi*C=O electron donation has a minimum value with tau1= 90 degrees and a maximum value with tau1= 0 degrees (the Z conformer), the value with tau1= 180 degrees (the E conformer) being between these two values, obviously due to steric hindrance. The effects of the phenyl substituents on the reactivity of the esters studied are discussed in terms of molecular orbital interactions. ED/EW substituents adjust the availability of the pi*C=O antibonding orbital to interact with the lone pair orbital of the attacking nucleophile and therefore affect the reactivity: EW substituents increase and ED substituents decrease it. Excellent correlations were observed between the rate coefficients of nucleophilic acyl substitutions and pi*C=O occupancies of the ester series 4 and 5.     

Quantitative validation of different protein precipitation methods in proteome analysis of blood platelets

For the preparation of proteins for proteome analysis, precipitation is frequently used to concentrate proteins and to remove interfering compounds. Various methods for protein precipitation are applied, which rely on different chemical principles. This study compares the changes in the protein composition of human blood platelet extracts after precipitation with ethanol (EtOH) or trichloroacetic acid (TCA). Both methods yielded the same amount of proteins from the platelet preparations. However, the EtOH-precipitated samples had to be dialyzed because of the considerable salt content. To characterize single platelet proteins, samples were analyzed by two-dimensional fluorescence differential gel electrophoresis. More than 90% of all the spots were equally present in the EtOH- and TCA-precipitated samples. However, both precipitation methods showed a smaller correlation with nonprecipitated samples (EtOH 74.9%, TCA 79.2%). Several proteins were either reduced or relatively enriched in the precipitated samples. The proteins varied randomly in molecular weight and isoelectric point. This study shows that protein precipitation leads to specific changes in the protein composition of proteomics samples. This depends more on the specific structure of the protein than on the precipitating agent used in the experiment.