Hydroxyl radical probe of the calmodulin-melittin complex interface by electrospray ionization mass spectrometry

The calcium-dependent interaction of calmodulin and melittin is studied through the application of a radical probe approach in which solutions of the protein and peptide and protein alone are subjected to high fluxes of hydroxyl and other oxygen radicals on millisecond timescales. These radicals are generated by an electrical discharge within an electrospray ion source of a mass spectrometer. Condensation of the electrosprayed droplets followed by proteolytic digestion of both calmodulin and melittin has identified residues in both which participate in the interaction and/or are shielded from solvent within the protein complex. Consistent with other theoretical models and available experimental data, the tryptophan residue of melittin at position 19 is shown to be critical to the formation of the complex with the C-terminal domain of peptide enveloped by and protected from oxidation upon binding to the protein. Furthermore, the N-terminal domain (to residue 36) and tyrosine at position 99 in calmodulin are significantly protected from limited oxidation upon the binding of melittin while exposing the phenylalanine residue at position 92 of the flexible loop domain. The N-terminus (through residue 36) of calmodulin is shown to lie in closer proximity to the melittin helix than its C-terminal counterpart (residues 127-148) based upon the protection levels measured at reactive residues within these segments of the protein.     

Computer experiments on crystalline nylons: structural analysis of nylons with large aliphatic segments

A theoretical study based on force-field calculations has been performed to investigate the structural preferences of crystalline even nylons n with large and very large aliphatic segments. Atomistic energy calculations and Monte Carlo simulations were carried out considering the conventional and forms of nylons 10, 12, 18, 24, and 32. Results indicated that the form is the most favored for nylons 10, 12, 18, and 24. However, the structure was unstable for nylon 32, a polymer in which the density of hydrogen bonds is almost negligible. In this case, the arrangement is energetically more favored than the one.     

Simultaneous multichannel mass-specific detection for high-performance liquid chromatography using an array detector sector-field mass spectrometer

The use of a separation step, such as liquid chromatography, prior to inductively coupled plasma mass spectrometry (ICP–MS) has become a common tool for highly selective and sensitive analyses. This type of coupling has several benefits including the ability to perform speciation analysis or to remove isobaric interferences. Several limitations of conventional instruments result from the necessity to scan or pulse the mass spectrometer to obtain a complete mass spectrum. When the instrument is operated in such a non-continuous manner, duty cycle is reduced, resulting in poorer absolute limits of detection. Additionally, with scanning instruments, spectral skew can be introduced into the measurement, limiting quantitation accuracy. To address these shortcomings, a high-performance liquid chromatograph has been coupled to an ICP–MS capable of continuous sample introduction and simultaneous multimass detection. These features have been realized with a novel detector array, the focal plane camera. Instrument performance has been tested for both speciation analysis and for the elimination of isobaric interferences. Absolute limits of detection in the sub picogram to tens of picograms regime are obtainable, while the added mass dimension introduced by simultaneous detection dramatically increases chromatographic peak capacity.     

The Saunders-Bell Analysis of Tunnel Effects in Reactions with Kinetic Isotope Effects

The primary kinetic isotope effects of deuterium were investigated in 22 hydrogen and deuterium transfer reactions, including enzymatic and nonenzymatic hydride transfer reactions, elimination reactions, and reactions catalyzed by enzymes lipooxygenase, amine dehydrogenase, and methylmalonyl-CoA mutase. In each case, the Saunders-Bell analysis was applied to calculate the tunnel effects and the corresponding thermodynamic parameters. The Saunders-Bell analysis was effective in 14 cases out of 22. A high degree of correlation was found between the barrier factor, the tunnel factor, and the entropy factor among all reactions studied. From this, a general relationship between the three factors was derived, based on the Saunders-Bell analysis of the Bell equation; the Saunders-Bell analysis is valid within certain limits of the barrier factor. This general relationship is universally valid for all hydrogen/deuterium transfer reactions in nature with moderate tunneling, when the Saunders-Bell analysis applies.     

Phase morphology of iPP/aPS/SEP blends

Supermolecular structure and phase morphology of the ternary isotactic polypropylene/atactic polystyrene/poly(styrene-b-ethylene-co-propylene) (iPP/aPS/SEP) compression molded blends with 100/0, 90/10, 70/30, and 50/50 iPP/aPS weight ratios and with different amounts of added SEP compatibilizer were studied by optical microscopy (OM), scanning electron microscopy (SEM), transmission electron microscopy (TEM), small-angle X-ray scattering (SAXS) and wide-angle X-ray diffraction (WAXD). SEP significantly reduced the size of dispersed aPS particles that enabled better spherulitization in the iPP matrix. Furthermore, iPP spherulites in ternary blends with 90/10 iPP/aPS weight ratio became larger in comparison with the pure iPP. TEM revealed that the SEP formed continuous interface layer around the dispersed aPS particles even when only 2.5 wt.% of SEP was added. Particle size distribution was distinctly bimodal. When the SEP content was increased to 10 wt.%, joining together smaller and bigger aPS and SEP particles formed dispersed aggregates. Additionally, both amorphous components (aPS and SEP) influenced crystallization process of iPP matrix and so modified, to some extent, its final supermolecular structure. SEP compatibilizer did not significantly affect crystallite orientation. The increase of crystallite sizes, which was more affected by the addition of aPS than by the addition of SEP, seemed to be influenced by the solidification effect rather than by the phase morphology of the blends.     

Phosphorylation of phospholipase D1 and the modulation of its interaction with RhoA by cAMP-dependent protein kinase

Agents that elevate cellular cAMP are known to inhibit the activation of phospholipase D (PLD). We investigated whether PLD can be phosphorylated by cAMP-dependent protein kinase (PKA) and PKA-mediated phosphorylation affects the interaction between PLD and RhoA, a membrane regulator of PLD. PLD1, but not PLD2 was found to be phosphorylated in vivo by the treatment of dibutyryl cAMP (dbcAMP) and in vitro by PKA. PKA inhibitor (KT5720) abolished the dbcAMP-induced phosphorylation of PLD1, but dibutyryl cGMP (dbcGMP) failed to phosphorylate PLD1. The association between PLD1 and Val14RhoA in an immunoprecipitation assay was abolished by both dbcAMP and dbcGMP. Moreover, RhoA but not PLD1 was dissociated from the membrane to the cytosolic fraction in dbcAMP-treated cells. These results suggest that both PLD1 and RhoA are phosphorylated by PKA and the interaction between PLD1 and RhoA is inhibited by the phosphorylation of RhoA rather than by the phosphorylation of PLD1.     

The de novo methylation activity of Dnmt3a is distinctly different than that of Dnmt1

Background  

Though Dnmt1 is considered the primary maintenance methyltransferase and Dnmt3a and Dnmt3b are considered de novo methyltransferases in mammals, these three enzymes may work together in maintaining as well as establishing DNA methylation patterns. It has been proposed that Dnmt1 may carry out de novo methylation at sites in the genome with transient single-stranded regions, such as replication origins, and then spread methylation from these nucleation sites in vivo, even though such activity has not been reported.     

Tagless extraction-retentate chromatography: a new global protein digestion strategy for monitoring differential protein expression

A new global protein digestion and selective peptide extraction strategy for the purpose of monitoring differential protein expression, coined as tagless extraction-retentate chromatography, is introduced. Target protein populations are firstly digested under reduced and alkylated conditions, and resultant peptides selectively extracted via covalent attachment to methionine residues by bromoacetyl reactive groups tethered to the surface of glass beads packed in small reaction vessels. After conjugation, reactive beads are stringently washed to remove nonspecifically bound peptides and then later treated with beta-mercaptoethanol to release captured methionine peptides in their nascent state, without complicating affinity tags. Recovered methionine containing peptides are profiled using the surface-enhanced laser desorption/ionization (SELDI) retentate chromatography mass spectrometry (RCMS) method. Selected peptides are further studied employing ProteinChip tandem mass spectrometry (MS/MS) analysis to identify their parent proteins. This approach has been applied to an Escherichia coli lysate model system and has demonstrated facility in reducing global digest complexity, sensitivity to low protein expression levels, and significant quantitative capability. It is envisioned that tagless extraction-RCMS will evolve to be a valuable approach for both basic research and clinical proteomics endeavors.     

Synthesis of stable analogues of thiamine di- and triphosphate as tools for probing a new phosphorylation pathway

Thiamine (vitamin B1) is an essential nutritional factor metabolized inside the body in its mono-, di-, and triphosphate forms. Although the action of thiamine and thiamine diphosphate have been intensely investigated, many questions remain unanswered and the role of thiamine triphosphate is still especially unknown. To probe recent hypotheses on the implication of thiamine triphosphate in a new phosphorylation pathway involving synaptic proteins, we synthesized a series of thiamine di- and triphosphate analogues that are resistant to both enzymatic and chemical hydrolyses. The key step in the preparation of the title compounds is the coupling of thiamine propyl disulfide with adequately protected methylenebis-phosphonic acid, the corresponding triphosphate analogue, and difluoromethylenebisphosphonic acid.