Identification of amyloidogenic peptide sequences using a coarse-grained physicochemical model

Cross-beta amyloid is implicated in over 20 human diseases. Experiments suggest that specific sequence elements within amyloidogenic proteins play a major role in seeding amyloid formation. Identifying these seeding sequences is important for rationalizing the molecular mechanisms of amyloid formation and for elaborating therapeutic strategies that target amyloid. Theoretical techniques play an important role in facilitating the identification and structural characterization of putative seeding sequences; most amyloid species are not amenable to high resolution experimental structure techniques. In this study we have combined a coarse-grained physicochemical protein model with a highly efficient Monte Carlo sampling technique to identify amyloidogenic sequences in four proteins for which respective experimental peptide fragmentation data exist. Peptide sequences were defined as amyloidogenic if the ensemble structure predicted for three interacting peptides described a stable and regular three-stranded beta-sheet. For such peptides, free energies were calculated to provide a measure of amyloid propensity. The overall agreement between the experimental and predicted data is good, and we correctly identify several self-recognition motifs proposed to define the cross-beta amyloid fibril architectures of two of the proteins. Our results compare very favorably with those obtained using atomistic molecular dynamics methods, though our simulations are 30-40 times faster.     

Structure of a crystalline vapochromic platinum(II) salt

Square-planar cations of the orange form of [Pt(Me2bzimpy)Cl](PF6) x DMF [Me2bzimpy = 2,6-bis(N-methylbenzimidazol-2-yl)pyridine] stack along the b axis in a head-to-tail arrangement with short interplanar spacings (3.35 and 3.39 A). Long intermolecular Pt...Pt contacts [4.336(2) and 4.565(2) A] and comparatively short Me2bzimpy...Me2bzimpy distances are consistent with spectroscopic measurements for orange salts of Pt(Me2bzimpy)Cl+. The DMF solvent molecules line channels parallel to c, which may provide a conduit for vapor absorption. The crystals are vapochromic, changing from orange to violet upon exposure to acetonitrile vapor. The changes in spectroscopic properties accompanying vapor absorption are consistent with changes in intermolecular interactions between complexes.     

Structure and dynamics of alpha-lactalbumin adsorbed at a charged brush interface

We have studied the adsorption of alpha-lactalbumin at a planar poly(acrylic acid) (PAA) brush using neutron reflectometry (NR) and total internal reflection fluorescence (TIRF) spectroscopy. The PAA brush has been prepared by spin-coating silicon or quartz plates with a hydrophobic poly(styrene) film and by transferring the copolymer poly(styrene)-poly(acrylic acid) onto the modified surface. In the case of NR, the poly(styrene) film and the poly(styrene) chain ends of the copolymer were perdeuterated in order to generate a high contrast to the non-deuterated PAA brush. alpha-Lactalbumin was chosen as the model protein because it is a relatively small globular protein with a negative net charge at neutral pH-values, as chosen in the experiments. Thus, it is interacting with the PAA brush on the 'wrong' side of its isoelectric point. In addition, the effects of temperature on the volume fraction profile and the reorientational mobility of the protein within the PAA brush were determined. From the analysis of the NR data, it has been found that despite of its negative net charge, alpha-lactalbumin is penetrating into the PAA brush. Its volume fraction profile parallels that of the PAA brush, indicating an exclusive interaction between the protein and the PAA. No protein accumulation is found at the inner poly(styrene) or the outer solution interface of the PAA brush. When increasing the temperature from 20 to 40 degrees C, less protein is adsorbed, suggesting the presence of enthalpic interaction contributions. From the analysis of the TIRF data, a high degree of reorientational mobility of alpha-lactalbumin within a PAA brush can be inferred. The reorientational correlation time of alpha-lactalbumin labeled with the Alexa Fluor 488 dye was found to increase from 5.5 to 32 ns upon adsorption, which can well be explained by the higher viscosity inside the PAA brush. Overall, the results of this study quantify for the first time the molecular details of the unique interaction of a protein on the 'wrong' side of its isoelectric point with a planar charged brush interface. It is concluded that the high mobility of alpha-lactalbumin within a PAA brush can partially be understood by the presence of repulsive electrostatic interactions. There is no 'freezing' of the protein dynamics, which is a precondition for biological activity.     

Microwave-assisted three-component synthesis of 7-aryl-2-alkylthio-4,7-dihydro-1,2,4-triazolo[1,5-a]-pyrimidine-6-carboxamides and their selective reduction

Multicomponent reactions (MCRs) and microwave-assisted organic synthesis (MAOS) have been used as key methods for the synthesis of fused dihydropyrimidine derivatives. The three-component condensation of 3-amino-5-alkylthio-1,2,4-triazoles with aromatic aldehydes and acetoacetamides under microwave irradiation was developed as a rapid and efficient solution-phase method for the high-yielding preparation of 7-aryl-2-alkylthio-4,7-dihydro-1,2,4-triazolo[1,5-a]pyrimidine-6-carboxamide libraries. In addition, the selective reduction of the formed dihydrotriazolopyrimidines to trans-trans-2-alkylthio-7-aryl-4,5,6,7-tetrahydro-1,2,4-triazolo[1,5-a]pyrimidine-6-carboxamides was established. The described synthetic protocols provide rapid access to novel and diversely substituted dihydroazolopyrimidine libraries.     

The iromycins, a new family of pyridone metabolites from Streptomyces sp. I. Structure, NOS inhibitory activity, and biosynthesis

The iromycins A-D are members of a new family of rare alpha-pyridone metabolites. The isolation and structure elucidation of these microbial secondary metabolites from Streptomyces sp. Dra 17 revealed a N-heterocyclic core structure with two unusual side chains. Iromycins act as inhibitors of nitric oxide synthases (NOS), a protein family, which produces the crucial second messenger nitric oxide (NO). Importantly, these compounds inhibit selectively endothelial NOS rather than neuronal NOS and thus set prospects for both medical therapy and basic research. Feeding experiments with 13C- and 15N -labeled precursors indicated an uncommon type of polyketide biosynthesis and clearly ruled out an isoprenoid origin. A detoxification pathway of a particular secondary metabolite in the host strain is a rare observation and here we demonstrate it with the iromycin family.     

Integration of electron density and molecular orbital techniques to reveal questionable bonds: the test case of the direct Fe-Fe bond in Fe2(CO)9

The article illustrates the advantages of partitioning the total electron density rho(rb), its Laplacian (inverted Delta)2 rho(rb), and the energy density H(rb) in terms of orbital components. By calculating the contributions of the mathematically constructed molecular orbitals to the measurable electron density, it is possible to quantify the bonding or antibonding character of each MO. This strategy is exploited to review the controversial existence of direct Fe-Fe bonding in the triply bridged Fe2(CO)9 system. Although the bond is predicted by electron counting rules, the interaction between the two pseudo-octahedral metal centers can be repulsive because of their fully occupied t(2g) sets. Moreover, previous atoms in molecules (AIM) studies failed to show a Fe-Fe bond critical point (bcp). The present electron density orbital partitioning (EDOP) analysis shows that one sigma bonding combination of the t(2g) levels is not totally overcome by the corresponding sigma* MO, which is partially delocalized over the bridging carbonyls. This suggests the existence of some, albeit weak, direct Fe-Fe bonding.     

Magnetic molecular wheels and grids - the need for novel concepts in “zero-dimensional” magnetism

Supramolecular chemistry has allowed the production, by self-assembly, of inorganic complexes with a [N × N] square matrix-like configuration of N² metal centers. Interest in these systems is driven by the potential applications in information technology suggested by such a “two-dimensional” (2D), addressable arrangement of metal ions. From the magnetic perspective [N × N] grids constitute molecular model systems for magnets with extended interactions on a square lattice, which have gained enormous attention in the context of high-temperature superconductors. Numerous [2 × 2] grids as well as a few [3 × 3] grids with magnetic metal ions such as Cu(II), Ni(II), Co(II), Fe(II), and Mn(II) have been created. Magnetic studies unraveled a remarkable variety in their magnetic properties, which will be reviewed in this work with emphasis on the underlying physical concepts. An intriguing issue is the connection of [2 × 2] and [3 × 3] grids with “one-dimensional” (1D) rings, as experimentally realized in the molecular wheels. For a [2 × 2] square of spin centers the distinction between a 2D grid and a 1D ring is semantic, but also a [3 × 3] grid retains 1D character: it is best viewed as an octanuclear ring with an additional ion “doped” into its center. Challenging familiar concepts from conventional magnets, the current picture of elementary excitations in antiferromagnetic rings will be discussed, as a prerequisite to understand the complex [3 × 3] grids.     

Hydrogen Production by Water Dissociation in Surface‐Modified BaCoxFeyZr1−x−yO3−δ Hollow‐Fiber Membrane Reactor with Improved Oxygen Permeation

A porous perovskite BaCo_xFe_yZr_0.9?x?yPd_0.1O_3?δ (BCFZ‐Pd) coating was deposited onto the outer surface of a BaCo_xFe_yZr_1?x?yO_3?δ (BCFZ) perovskite hollow‐fiber membrane. The surface morphology of the modified BCFZ fiber was characterized by scanning electron microscopy (SEM), indicating the formation of a BCFZ‐Pd porous layer on the outer surface of a dense BCFZ hollow‐fiber membrane. The oxygen permeation flux of the BCFZ membrane with a BCFZ‐Pd porous layer increased 3.5 times more than that of the blank BCFZ membrane when feeding reactive CH₄ onto the permeation side of the membrane. The blank BCFZ membrane and surface‐modified BCFZ membrane were used as reactors to shift the equilibrium of thermal water dissociation for hydrogen production because they allow the selective removal of the produced oxygen from the water dissociation system. It was found that the hydrogen production rate increased from 0.7 to 2.1 mL H₂ min^?1 cm^?2 at 950 °C after depositing a BCFZ‐Pd porous layer onto the BCFZ membrane.     

Improved particle-packed HPLC/MS microchips for proteomic analysis

The influence of packing process parameters (packing pressure, application of ultrasound) and the stationary phase particle size (3.5 and 5 μm) on the chromatographic performance of HPLC/MS chips was systematically investigated for proteomic samples. First, reproducibility and detection limits of the separation were evaluated with a low‐complexity sample of tryptic BSA peptides. The influence of adsorbent packing quality on protein identification was then tested with a typical proteomics sample of high complexity, a human plasma protein fraction (Cohn fraction IV‐4). All HPLC/MS chips provided highly reproducible separations of these proteomic samples, but improved packing conditions and smaller particle sizes resulted in chromatograms with narrower peaks and correspondingly higher signal intensities. Improved separation performance increased the peak capacity, the number of identified peptides, and thus the sequence coverage in the proteomic samples, particularly for low sample amounts.     

Applying a dynamic method to the measurement of ion mobility

A dynamic method is applied to measure the mobility of gas-phase ions in the dual ion funnel interface of the electrospray source of a quadrupole orthogonal time-of-flight mass spectrometer. In a new operational mode, a potential barrier was formed in the second ion funnel of the mass spectrometer and then progressively increased. In this region, a flow of gas drags the ions into the mass spectrometer while the electric force applied by the potential barrier decelerates them. Ions with lower mobility can be carried by the gas flow more easily than those with high mobility. Thus, electrical forces can block the more mobile ions more easily. Hence, the electric barrier formed in the ion funnel permits only ions below a certain mobility threshold to enter the mass spectrometer. When the barrier voltage is increased, this threshold moves from high to low mobilities. Ions with mobilities above the threshold cannot enter the mass spectrometer, and their signal decreases to zero. Thus, in a barrier voltage scan, mass spectrometric signals of ions sequentially disappear. Differentiation of these decreasing ion signal curves produces peaks from which an ion mobility spectrum can be reconstructed. Blocking voltages, i.e., the positions of the peaks on the barrier voltage scale are directly related to the mobility of these ions. An internal calibration using ions with known mobility values helps determine the unknown ion mobilities and allows calculation of ionic cross sections.