Single-molecule studies of amyloid proteins: from biophysical properties to diagnostic perspectives.

In neurodegenerative diseases, a wide range of amyloid proteins or peptides such as amyloid-beta and α-synuclein fail to keep native functional conformations, followed by misfolding and self-assembling into a diverse array of aggregates. The aggregates further exert toxicity leading to the dysfunction, degeneration and loss of cells in the affected organs. Due to the disordered structure of the amyloid proteins, endogenous molecules, such as lipids, are prone to interact with amyloid proteins at a low concentration and influence amyloid cytotoxicity. The heterogeneity of amyloid proteinscomplicates the understanding of the amyloid cytotoxicity when relying only on conventional bulk and ensemble techniques. As complementary tools, single-molecule techniques (SMTs) provide novel insights into the different subpopulations of a heterogeneous amyloid mixture as well as the cytotoxicity, in particular as involved in lipid membranes. This review focuses on the recent advances of a series of SMTs, including single-molecule fluorescence imaging, single-molecule force spectroscopy and single-nanopore electrical recording, for the understanding of the amyloid molecular mechanism. The working principles, benefits and limitations of each technique are discussed and compared in amyloid protein related studies.. We also discuss why SMTs show great potential and are worthy of further investigation with feasibility studies as diagnostic tools of neurodegenerative diseases and which limitations are to be addressed.

Characterization of megahertz X-ray laser beams by multishot desorption imprints in PMMA.

Proper diagnostics of intense free-electron laser (FEL) X-ray pulses is indisputably important for experimental data analysis as well as for the protection of beamline optical elements. New challenges for beam diagnostic methods are introduced by modern FEL facilities capable of delivering powerful pulses at megahertz (MHz) repetition rates. In this paper, we report the first characterization of a defocused MHz 13.5-nm beam generated by the free-electron laser in Hamburg (FLASH) using the method of multi-pulse desorption imprints in poly(methyl methacrylate)(PMMA). The beam fluence profile is reconstructed in a novel and highly accurate way that takes into account the nonlinear response of material removal to total dose delivered by multiple pulses. The algorithm is applied to experimental data of single-shot ablation imprints and multi-shot desorption imprints at both low (10 Hz) and high (1 MHz) repetition rates. Reconstructed response functions show a great agreement with the theoretical desorption response function model.

Experimental study of EUV mirror radiation damage resistance under long-term free-electron laser exposures below the single-shot damage threshold.

The durability of grazing- and normal-incidence optical coatings has been experimentally assessed under free-electron laser irradiation at various numbers of pulses up to 16 million shots and various fluence levels below 10% of the single-shot damage threshold. The experiment was performed at FLASH, the Free-electron LASer in Hamburg, using 13.5 nm extreme UV (EUV) radiation with 100 fs pulse duration. Polycrystalline ruthenium and amorphous carbon 50 nm thin films on silicon substrates were tested at total external reflection angles of 20° and 10° grazing incidence, respectively. Mo/Si periodical multilayer structures were tested in the Bragg reflection condition at 16° off-normal angle of incidence. The exposed areas were analysed post-mortem using differential contrast visible light microscopy, EUV reflectivity mapping and scanning X-ray photoelectron spectroscopy. The analysis revealed that Ru and Mo/Si coatings exposed to the highest dose and fluence level show a few per cent drop in their EUV reflectivity, which is explained by EUV-induced oxidation of the surface.

Mechanism of single-shot damage of Ru thin films irradiated by femtosecond extreme UV free-electron laser.

Ruthenium is a perspective material to be used for XUV mirrors at free-electron laser facilities. Yet, it is still poorly studied in the context of ultrafast laser-matter interaction. In this work, we present single-shot damage studies of thin Ru films irradiated by femtosecond XUV free-electron laser pulses at FLASH. Ex-situ analysis of the damaged spots, performed by different types of microscopy, shows that the weakest detected damage is surface roughening. For higher fluences we observe ablation of Ru. Combined simulations using Monte-Carlo code XCASCADE(3D) and the two-temperature model reveal that the damage mechanism is photomechanical spallation, similar to the case of irradiating the target with optical lasers. The analogy with the optical damage studies enables us to explain the observed damage morphologies.

Role of heat accumulation in the multi-shot damage of silicon irradiated with femtosecond XUV pulses at a 1 MHz repetition rate.

The role played by heat accumulation in multi-shot damage of silicon was studied. Bulk silicon samples were exposed to intense XUV monochromatic radiation of a 13.5 nm wavelength in a series of 400 femtosecond pulses, repeated with a 1 MHz rate (pulse trains) at the FLASH facility in Hamburg. The observed surface morphological and structural modifications are formed as a result of sample surface melting. Modifications are threshold dependent on the mean fluence of the incident pulse train, with all threshold values in the range of approximately 36-40 mJ/cm2. Experimental data is supported by a theoretical model described by the heat diffusion equation. The threshold for reaching the melting temperature (45 mJ/cm2) and liquid state (54 mJ/cm2), estimated from this model, is in accordance with experimental values within measurement error. The model indicates a significant role of heat accumulation in surface modification processes.

Mo/Si multilayer-coated amplitude-division beam splitters for XUV radiation sources.

Amplitude-division beam splitters for XUV radiation sources have been developed and extensively characterized. Mo/Si multilayer coatings were deposited on 50 nm-thick SiN membranes. By changing the multilayer structure (periodicity, number of bilayers, etc.) the intensity of the reflected and transmitted beams were optimized for selected incident radiation parameters (wavelength, incident angle). The developed optical elements were characterized by means of XUV reflectometry and transmission measurements, atomic force microscopy and optical interferometry. Special attention was paid to the spatial homogeneity of the optical response and reflected beam wavefront distortions. Here the results of the characterization are presented and improvements required for advanced applications at XUV free-electron lasers are identified. A flatness as low as 4 nm r.m.s. on 3 × 3 mm beam splitters and 22 nm r.m.s. on 10 × 10 mm beam splitters has been obtained. The high-spatial-frequency surface roughness was about 0.7-1 nm r.m.s. The middle-spatial-frequency roughness was in the range 0.2-0.8 nm r.m.s. The reflection and transmission of the beam splitters were found to be very homogeneous, with a deviation of less than 2% across the full optical element.

Cross interactions between Apolipoprotein E and amyloid proteins in neurodegenerative diseases.

Three common Apolipoprotein E isoforms, ApoE2, ApoE3, and ApoE4, are key regulators of lipid homeostasis, among other functions. Apolipoprotein E can interact with amyloid proteins. The isoforms differ by one or two residues at positions 112 and 158, and possess distinct structural conformations and functions, leading to isoform-specific roles in amyloid-based neurodegenerative diseases. Over 30 different amyloid proteins have been found to share similar characteristics of structure and toxicity, suggesting a common interactome. The molecular and genetic interactions of ApoE with amyloid proteins have been extensively studied in neurodegenerative diseases, but have not yet been well connected and clarified. Here we summarize essential features of the interactions between ApoE and different amyloid proteins, identify gaps in the understanding of the interactome and propose the general interaction mechanism between ApoE isoforms and amyloid proteins. Perhaps more importantly, this review outlines what we can learn from the interactome of ApoE and amyloid proteins; that is the need to see both ApoE and amyloid proteins as a basis to understand neurodegenerative diseases.

Investigating the interaction of x-ray free electron laser radiation with grating structure.

The interaction of free electron laser pulses with grating structure is investigated using 4.6±0.1 nm radiation at the FLASH facility in Hamburg. For fluences above 63.7±8.7 mJ/cm2, the interaction triggers a damage process starting at the edge of the grating structure as evidenced by optical and atomic force microscopy. Simulations based on solution of the Helmholtz equation demonstrate an enhancement of the electric field intensity distribution at the edge of the grating structure. A procedure is finally deduced to evaluate damage threshold.

ATP Impedes the Inhibitory Effect of Hsp90 on Aß40 Fibrillation.

Heat shock protein 90 (Hsp90) is a molecular chaperone that assists protein folding in an Adenosine triphosphate (ATP)-dependent way. Hsp90 has been reported to interact with Alzheimers disease associated amyloid-ß (Aß) peptides and to suppress toxic oligomer- and fibril formation. However, the mechanism remains largely unclear. Here we use a combination of atomic force microscopy (AFM) imaging, circular dichroism (CD) spectroscopy and biochemical analysis to quantify this interaction and put forward a microscopic picture including rate constants for the different transitions towards fibrillation. We show that Hsp90 binds to Aß40 monomers weakly but inhibits Aß40 from growing into fibrils at substoichiometric concentrations. ATP impedes this interaction, presumably by modulating Hsp90's conformational dynamics and reducing its hydrophobic surface. Altogether, these results might indicate alternative ways to prevent Aß40 fibrillation by manipulating chaperones that are already abundant in the brain.

High Reflectance Nanoscale V/Sc Multilayer for Soft X-ray Water Window Region.

V/Sc multilayer is experimentally demonstrated for the first time as a high reflectance mirror for the soft X-ray water window region. It primarily works at above the Sc-L edge (λ = 3.11 nm) under near normal incidence while a second peak appears at above the V-L edge (λ = 2.42 nm) under grazing incidence. The V/Sc multilayer fabricated with a d-spacing of 1.59 nm and 30 bilayers has a smaller interface width (σ = 0.27 and 0.32 nm) than the conventional used Cr/Sc (σ = 0.28 and 0.47 nm). For V/Sc multilayer with 30 bilayers, the introduction of B4C barrier layers has little improvement on the interface structure. As the number of bilayers increasing to 400, the growth morphology and microstructure of the V/Sc layers evolves with slightly increased crystallization. Nevertheless, the surface roughness remains to be 0.25 nm. A maximum soft X-ray reflectance of 18.4% is measured at λ = 3.129 nm at 9° off-normal incidence using the 400-bilayers V/Sc multilayer. According to the fitted model, an s-polarization reflectance of 5.2% can also be expected at λ = 2.425 nm under 40° incidence. Based on the promising experimental results, further improvement of the reflectance can be achieved by using a more stable deposition system, exploring different interface engineering methods and so on.

Fixed target combined with spectral mapping: approaching 100% hit rates for serial crystallography.

The advent of ultrafast highly brilliant coherent X-ray free-electron laser sources has driven the development of novel structure-determination approaches for proteins, and promises visualization of protein dynamics on sub-picosecond timescales with full atomic resolution. Significant efforts are being applied to the development of sample-delivery systems that allow these unique sources to be most efficiently exploited for high-throughput serial femtosecond crystallography. Here, the next iteration of a fixed-target crystallography chip designed for rapid and reliable delivery of up to 11 259 protein crystals with high spatial precision is presented. An experimental scheme for predetermining the positions of crystals in the chip by means of in situ spectroscopy using a fiducial system for rapid, precise alignment and registration of the crystal positions is presented. This delivers unprecedented performance in serial crystallography experiments at room temperature under atmospheric pressure, giving a raw hit rate approaching 100% with an effective indexing rate of approximately 50%, increasing the efficiency of beam usage and allowing the method to be applied to systems where the number of crystals is limited.

Mapping atomic motions with ultrabright electrons: towards fundamental limits in space-time resolution.

The long held objective of directly observing atomic motions during the defining moments of chemistry has been achieved based on ultrabright electron sources that have given rise to a new field of atomically resolved structural dynamics. This class of experiments requires not only simultaneous sub-atomic spatial resolution with temporal resolution on the 100 femtosecond time scale but also has brightness requirements approaching single shot atomic resolution conditions. The brightness condition is in recognition that chemistry leads generally to irreversible changes in structure during the experimental conditions and that the nanoscale thin samples needed for electron structural probes pose upper limits to the available sample or "film" for atomic movies. Even in the case of reversible systems, the degree of excitation and thermal effects require the brightest sources possible for a given space-time resolution to observe the structural changes above background. Further progress in the field, particularly to the study of biological systems and solution reaction chemistry, requires increased brightness and spatial coherence, as well as an ability to tune the electron scattering cross-section to meet sample constraints. The electron bunch density or intensity depends directly on the magnitude of the extraction field for photoemitted electron sources and electron energy distribution in the transverse and longitudinal planes of electron propagation. This work examines the fundamental limits to optimizing these parameters based on relativistic electron sources using re-bunching cavity concepts that are now capable of achieving 10 femtosecond time scale resolution to capture the fastest nuclear motions. This analysis is given for both diffraction and real space imaging of structural dynamics in which there are several orders of magnitude higher space-time resolution with diffraction methods. The first experimental results from the Relativistic Electron Gun for Atomic Exploration (REGAE) are given that show the significantly reduced multiple electron scattering problem in this regime, which opens up micron scale systems, notably solution phase chemistry, to atomically resolved structural dynamics.