Self-assembly of the beta2-microglobulin NHVTLSQ peptide using a coarse-grained protein model reveals a beta-barrel species

Although a wide variety of proteins can assemble into amyloid fibrils, the structure of the early oligomeric species on the aggregation pathways remains unknown at an atomic level of detail. In this paper we report, using molecular dynamics simulations with the OPEP coarse-grained force field, the free energy landscape of a tetramer and a heptamer of the beta2-microglobulin NHVTLSQ peptide. On the basis of a total of more than 17 ns trajectories started from various states, we find that both species are in equilibrium between amorphous and well-ordered aggregates with cross-beta-structure, a perpendicular bilayer beta-sheet, and, for the heptamer, six- or seven-stranded closed and open beta-barrels. Moreover, analysis of the heptamer trajectories shows that the perpendicular bilayer beta-sheet is one possible precursor of the beta-barrel, but that this barrel can also be formed from a twisted monolayer beta-sheet with successive addition of chains. Comparison with previous aggregation simulations and the fact that nature constructs transmembrane beta-sheet proteins with pores open the possibility that beta-barrels with small inner diameters may represent a common intermediate during the early steps of aggregation.     

Analysis of minor flavonoids in Piper hostmannianum var. berbicense using liquid chromatography coupled with atmospheric pressure chemical ionization mass spectrometry

The fragmentations of hydroxylated flavanones, chalcones and dihydrochalcones were investigated by direct loop injection using an ion trap mass spectrometry equipped with atmospheric pressure chemical ionization (APCI) probe. Some of them have been isolated from the leaves of Piper hostmannianum var. berbicense and standards were used to confirm their fragmentation behaviour. In negative ion mode, fragmentations of these three types of flavonoids revealed specific diagnostic ions which allowed us to identify aglycones in a crude plant extract. The major fragment ion obtained in MS/MS experiment for methoxylated chalcones is the neutral loss of a methyl radical whereas a H(2)O molecule is lost in the case of methoxylated dihydrochalcones. Methoxylated chalcones and flavanones isomers could be differentiated by the relative intensity ratio of [M-H-CH(3)]*(-) and [M-H-C(2)H(2)O](-) ions. Based on UV and MS data, a decision tree that includes UV lambda(max) absorptions and MS/MS diagnostic ions was built in order to obtain structural information of unknown compounds present in the extract. This tree was used to identify flavonoids in the ethyl acetate extract of P. hostmannianum var. berbicense leaves after analysis by high-performance liquid chromatography-diode array detection-atmospheric pressure chemical ionization ion trap multistage mass spectrometry. A total of 11 flavonoids were tentatively characterized based on the MS fragmentations pattern observed in MS(n) experiments.     

Mass spectroscopic observation of shock-induced chemistry in liquid CS2

We have observed, via time-of-flight mass spectrometry, 13 chemical species more massive than CS2 produced by shocking liquid CS2 to very high pressure/temperature. The stoichiometry of three of these species is uniquely determined from the 12CS2 experiments; these species are C2S2, C3S2, and C4S2. The stoichiometry of the other 10 structures cannot be uniquely determined from 12CS2 experiments. However, by redoing the experiments using isotopically labeled CS2 (i.e., 13CS2), we determined the stoichiometry of nine of the remaining structures. The nine structures are Sn (n = 3-8) and CS3, C2S5, and C4S6. A structure with mass 297.1 amu was also observed in the 12CS2 experiments but was not detected in the 13CS2 experiments. This structure must be C6S7, C14S4, or C22S; given the low carbon content of the other observed carbon species, it is probably C6S7. The shockwaves to which the CS2 molecules were subjected were produced by the detonation of high mass-density solid explosives. The explosives used were either a plastic bonded form of cyclotetramethlylene tetranitramine or pure hexanitrostilbene. Numerical compressible fluid-mechanical simulations were done to estimate the pressures, temperatures, and time scales of the processes that occurred in the shocked CS2. The results obtained in the present experiments are related to earlier work on CS2's chemical reactivity that used both shockwave methods and static techniques to produce very high pressure.     

Synthesis, characterization and cytolytic activity of alpha-helical amphiphilic peptide nanostructures containing crown ethers

Many natural alpha-helical amphiphilic peptides are known to have lytic activity toward different cells. Herein, we describe the synthesis and the characterization of synthetic alpha-helical amphiphilic peptide nanostructures containing crown ethers, as well as the modulation of their cytolytic activity by adding different acidic dipeptide chains at the N- or C-terminus.     

Probing amyloid fibril formation of the NFGAIL peptide by computer simulations

Amyloid fibril formation, as observed in Alzheimer's disease and type II diabetes, is currently described by a nucleation-condensation mechanism, but the details of the process preceding the formation of the nucleus are still lacking. In this study, using an activation-relaxation technique coupled to a generic energy model, we explore the aggregation pathways of 12 chains of the hexapeptide NFGAIL. The simulations show, starting from a preformed parallel dimer and ten disordered chains, that the peptides form essentially amorphous oligomers or more rarely ordered beta-sheet structures where the peptides adopt a parallel orientation within the sheets. Comparison between the simulations indicates that a dimer is not a sufficient seed for avoiding amorphous aggregates and that there is a critical threshold in the number of connections between the chains above which exploration of amorphous aggregates is preferred.     

Albumin binding, relaxivity, and water exchange kinetics of the diastereoisomers of MS-325, a gadolinium(III)-based magnetic resonance angiography contrast agent

The amphiphilic gadolinium complex MS-325 ((trisodium-{(2-(R)-[(4,4-diphenylcyclohexyl) phosphonooxymethyl] diethylenetriaminepentaacetato) (aquo)gadolinium(III)}) is a contrast agent for magnetic resonance angiography (MRA). MS-325 consists of two slowly interconverting diastereoisomers, A and B (65:35 ratio), which can be isolated at pH > 8.5 (TyeklAr, Z.; Dunham, S. U.; Midelfort, K.; Scott, D. M.; Sajiki, H.; Ong, K.; Lauffer, R. B.; Caravan, P.; McMurry, T. J. Inorg. Chem. 2007, 46, 6621-6631). MS-325 binds to human serum albumin (HSA) in plasma resulting in an extended plasma half-life, retention of the agent within the blood compartment, and an increased relaxation rate of water protons in plasma. Under physiological conditions (37 degrees C, pH 7.4, phosphate buffered saline (PBS), 4.5% HSA, 0.05 mM complex), there is no statistical difference in HSA affinity or relaxivity between the two isomers (A 88.6 +/- 0.6% bound, r1 = 42.0 +/- 1.0 mM(-1) s(-1) at 20 MHz; B 90.2 +/- 0.6% bound, r1 = 38.3 +/- 1.0 mM(-1) s(-1) at 20 MHz; errors represent 1 standard deviation). At lower temperatures, isomer A has a higher relaxivity than isomer B. The water exchange rates in the absence of HSA at 298 K, kA298 = 5.9 +/- 2.8 x 10(6) s(-1), kB298 = 3.2 +/- 1.8 x 10(6) s(-1), and heats of activation, DeltaHA = 56 +/- 8 kJ/mol, DeltaHB = 59 +/- 11 kJ/mol, were determined by variable-temperature 17O NMR at 7.05 T. Proton nuclear magnetic relaxation dispersion (NMRD) profiles were recorded over the frequency range of 0.01-50 MHz at 5, 15, 25, and 35 degrees C in a 4.5% HSA in PBS solution for each isomer (0.1 mM). Differences in the relaxivity in HSA between the two isomers could be attributed to the differing water exchange rates.     

Comparison of two methods of measuring wood pyrolysis tar

Two methods for the sampling and analysis of tar produced from wood pyrolysis were compared. The first method used a conventional cold-trapping technique in solvent-filled impingers followed by liquid injection. The second one is a new application of multibed solid-phase adsorbent (SPA) tubes followed by thermal desorption (TD). Both methods are based on gas chromatography (GC) coupled with mass spectrometry (MS). Quantification was performed with a well reproducible GC-MS method with three internal deuterated standards. The SPA/TD method offers several advantages. No solvent is required, the detection levels are improved, and gas chromatography separation is easier. Moreover, sampling time is reduced from about 1h (for the conventional cold-trapping technique in impingers) to a few seconds. No discrimination was observed between the two sampling methods for the 10 quantified compounds (aromatic compounds from benzene to phenanthrene and phenols) except for benzene.