Molecular dynamics study of water channels in natural and synthetic amyloid-ß fibrils.

We compared all-atom explicit solvent molecular dynamics simulations of three types of Aß(1-40) fibrils: brain-seeded fibrils (2M4J, with a threefold axial symmetry) and the other two, all-synthetic fibril polymorphs (2LMN and 2LMP, made under different fibrillization conditions). Fibril models were constructed using either a finite or an infinite number of layers made using periodic images. These studies yielded four conclusions. First, finite fibrils tend to unravel in a manner reminiscent of fibril dissolution, while infinite fibrils were more stable during simulations. Second, salt bridges in these fibrils remained stable in those fibrils that contained them initially, and those without salt bridges did not develop them over the time course of the simulations. Third, all fibrils tended to develop a "stagger" or register shift of ß-strands along the fibril axis. Fourth and most importantly, the brain-seeded, 2M4J, infinite fibrils allowed bidirectional transport of water in and out of the central longitudinal core of the fibril by rapidly developing gaps at the fibril vertices. 2LMP fibrils also showed this behavior, although to a lesser extent. The diffusion of water molecules in the fibril core region involved two dynamical states: a localized state and directed diffusion in the presence of obstacles. These observations provided support for the hypothesis that Aß fibrils could act as nanotubes. At least some Aß oligomers resembled fibrils structurally in having parallel, in-register ß-sheets and a sheet-turn-sheet motif. Thus, our findings could have implications for Aß cytotoxicity, which may occur through the ability of oligomers to form abnormal water and ion channels in cell membranes.

Multidimensional dipolar exchange-assisted recoupling measurements in solid-state NMR.

Aseries of uni- and multidimensional variants of the dipolar exchange-assisted recoupling (DEAR) NMR experiment is described and applied to determinations of (13)C-(14)N dipolar local field spectra in amino acids and dipeptides. The DEAR protocol recouples nearby nuclei by relying on differences in their relative rates of longitudinal relaxation, and has the potential to give quantitative geometric results without requiring radiofrequency pulsing on both members of a coupled spin pair. One- and two-dimensional variants of this recoupling strategy on generic I-S pairs are discussed, and measurements of (13)C-(14)N distances and 2D local field experiments sensitive to the relative orientation of CN vectors with respect to the (13)C shielding tensor are presented. Since these measurements did not involve pulsing on the broad nitrogen resonance, their results were independent of the quadrupolar parameters of this nucleus. High-resolution 3D NMR versions of the 2D experiments were also implemented in order to separate their resulting local field patterns according to the isotropic shifts of inequivalent (13)C sites. These high-resolution 3D acquisitions involved collecting a series of 2D DEAR NMR data sets on rotating samples as a function of spinning angle, and then subjecting the resulting data to a processing akin to that involved in variable-angle correlation NMR. Once successfully tested on l-alanine this experiment was applied to the analysis of a series of dipeptides, allowing us to extract separate local field (13)C-(14)N spectra from this type of multisite systems.

Enhanced sensitivity in RIACT/MQ-MAS NMR experiments using rotor assisted population transfer.

The rotor assisted population transfer (RAPT) sequence is used to enhance the sensitivity of the RIACT(II) experiment for spin-3/2 quadrupolar nuclei. A detailed theoretical analysis of the polarizations that contribute to different types of MQ-MAS experiments is provided. In particular, two polarization pathways are distinguished for the creation of triple-quantum coherence. The existence of these pathways is experimentally demonstrated by comparing the sensitivities of different sequences with and without RAPT preparation.

Orientational alignment in solids from bidimensional isotropic-anisotropic nuclear magnetic resonance spectroscopy: applications to the analysis of aramide fibers.

The use of two-dimensional isotropic-anisotropic correlation spectroscopy for the analysis of orientational alignment in solids is presented. The theoretical background and advantages of this natural-abundance 13C NMR method of measurement are discussed, and demonstrated with a series of powder and single-crystal variable-angle correlation spectroscopy (VACSY) experiments on model systems. The technique is subsequently employed to analyze the orientational distributions of three polymer fibers: Kevlar 29, Kevlar 49 and Kevlar 149. Using complementary two-dimensional NMR data recorded on synthetic samples of poly(p-phenyleneterephthalamide), the precursor of Kevlar, it was found that these commercial fibers possess molecules distributed over a very narrow orientational range with respect to the macroscopic director. The widths measured for these director distribution arrangements were (12 +/- 1.5) degrees for Kevlar 29, (15 +/- 1.5) degrees for Kevlar 49, and (8 +/- 1.5) degrees for Kevlar 149. These figures compare well with previous results obtained for non-commercial fiber samples derived from the same polymer.