Angelo Accardo

Natural tri- to hexapeptides self-assemble in water to amyloid β-type fiber aggregates by unexpected α-helical intermediate structures

Many fatal neurodegenerative diseases such as Alzheimer’s, Parkinson, the prion-related diseases, and non-neurodegenerative disorders such as type II diabetes are characterized by abnormal amyloid fiber aggregates, suggesting a common mechanism of pathogenesis. We have discovered that a class of systematically designed natural tri- to hexapeptides with a characteristic sequential motif can simulate the process of fiber assembly and further condensation to amyloid fibrils, probably via unexpected dimeric α-helical intermediate structures. The characteristic sequence motif of the novel peptide class consists of an aliphatic amino acid tail of decreasing hydrophobicity capped by a polar head. To our knowledge, the investigated aliphatic tripeptides are the shortest ever reported naturally occurring amino acid sequence that can adopt α-helical structure and promote amyloid formation. We propose the stepwise assembly process to be associated with characteristic conformational changes from random coil to α-helical intermediates terminating in cross-β peptide structures. Circular dichroism and X-ray fiber diffraction analyses confirmed the concentration-dependent conformational changes of the peptides in water. Molecular dynamics simulating peptide behavior in water revealed monomer antiparallel pairing to dimer structures by complementary structural alignment that further aggregated and stably condensed into coiled fibers. The ultrasmall size and the dynamic facile assembly process make this novel peptide class an excellent model system for studying the mechanism of amyloidogenesis, its evolution and pathogenicity. The ability to modify the properties of the assembled structures under defined conditions will shed light on strategies to manipulate the pathogenic amyloid aggregates in order to prevent or control aggregate formation.

Aliphatic peptides show similar self-assembly to amyloid core sequences, challenging the importance of aromatic interactions in amyloidosis

The self-assembly of abnormally folded proteins into amyloid fibrils is a hallmark of many debilitating diseases, from Alzheimer’s and Parkinson diseases to prion-related disorders and diabetes type II. However, the fundamental mechanism of amyloid aggregation remains poorly understood. Core sequences of four to seven amino acids within natural amyloid proteins that form toxic fibrils have been used to study amyloidogenesis. We recently reported a class of systematically designed ultrasmall peptides that self-assemble in water into cross-β–type fibers. Here we compare the self-assembly of these peptides with natural core sequences. These include core segments from Alzheimer’s amyloid-β, human amylin, and calcitonin. We analyzed the self-assembly process using circular dichroism, electron microscopy, X-ray diffraction, rheology, and molecular dynamics simulations. We found that the designed aliphatic peptides exhibited a similar self-assembly mechanism to several natural sequences, with formation of α-helical intermediates being a common feature. Interestingly, the self-assembly of a second core sequence from amyloid-β, containing the diphenylalanine motif, was distinctly different from all other examined sequences. The diphenylalanine-containing sequence formed β-sheet aggregates without going through the α-helical intermediate step, giving a unique fiber-diffraction pattern and simulation structure. Based on these results, we propose a simplified aliphatic model system to study amyloidosis. Our results provide vital insight into the nature of early intermediates formed and suggest that aromatic interactions are not as important in amyloid formation as previously postulated. This information is necessary for developing therapeutic drugs that inhibit and control amyloid formation.

In Situ X-ray Scattering Studies of Protein Solution Droplets Drying on Micro- and Nanopatterned Superhydrophobic PMMA Surfaces

Superhydrophobic poly(methyl methacrylate) surfaces with contact angles of ∼170° and high optical and X-ray transparencies have been fabricated through the use of optical lithography and plasma etching. The surfaces contain either a microscale pattern of micropillars or a random nanofibrillar pattern. Nanoscale asperities on top of the micropillars closely resemble Nelumbo nucifera lotus leaves. The evolution of the contact angle of water and lysozyme solution droplets during evaporation was studied on the micro- and nanopatterned surfaces, showing in particular contact-line pinning for the protein solution droplet on the nanopatterned surface. The microstructural evolution of lysozyme solution droplets was studied on both types of surfaces in situ under nearly contact-free conditions by synchrotron radiation microbeam wide-angle and small-angle X-ray scattering revealing the increasing protein concentration and the onset of precipitation. The solid residuals show hollow sphere morphologies. Rastermicrodiffraction of the detached residuals suggests about a 1/3 volume fraction of ≥17 nm lysozyme nanocrystalline domains and about a 2/3 short-range-order volume fraction. About 5-fold larger nanocrystalline domains were observed at the attachment points of the sphere to the substrates, which is attributed to particle growth in a shear flow. Such surfaces represent nearly contact-free sample supports for studies of inorganic and organic solution droplets, which find applications in biochips.

Amyloid β peptide conformational changes in the presence of a lipid membrane system.

Here we are presenting a comparative analysis of conformational changes of two amyloid β peptides, Aβ(25-35) and Aβ(1-42), in the presence and absence of a phospholipid system, namely, POPC/POPS (1-palmitoyl-2-oleoylphospatidylcholine/palmitoyl-2-oleoylphospatidylserine), through Raman spectroscopy, synchrotron radiation micro Fourier-transform infrared spectroscopy, and micro X-ray diffraction. Ringlike samples were obtained from the evaporation of pure and mixed solutions of the proteins together with the POPC/POPS system on highly hydrophilic substrates. The results confirm the presence of a α-helical to β-sheet transition from the internal rim of the ringlike samples to the external one in the pure Aβ(25-35) residual, probably due to the convective flow inside the droplets sitting on highly hydrophilic substrates enhancing the local concentration of the peptide at the external edge of the dried drop. In contrast, the presence of POPC/POPS lipids in the peptide does not result in α-helical structures and introduces the presence of antiparallel β-sheet material together with parallel β-sheet structures and possible β-turns. As a control, Aβ(1-42) peptide was also tested and shows β-sheet conformations independently from the presence of the lipid system. The μXRD analysis further confirmed these conclusions, showing how the absence of the phospholipid system induces in the Aβ(25-35) a probable composite α/β material while its coexistence with the peptide leads to a not oriented β-sheet conformation. These results open interesting scenarios on the study of conformational changes of Aβ peptides and could help, with further investigations, to better clarify the role of enzymes and alternative lipid systems involved in the amyloidosis process of Aβ fragments.

Calcium Carbonate Mineralization: X-ray Microdiffraction Probing of the Interface of an Evaporating Drop on a Superhydrophobic Surface

The liquid/air interface of calcium bicarbonate solution drops was probed by synchrotron radiation microbeam scattering. The drops were deposited on a nanopatterned superhydrophobic poly(methyl methacrylate) surface and raster-scanned during evaporation by small-angle and wide-angle X-ray scattering. The appearance of about 200-nm-size calcite crystallites at the interface could be spatially resolved at the onset of crystallization. Diffuse scattering from the interface is attributed to a dense nanoscale amorphous calcium carbonate phase. Calcite was found to be the major phase in the solid residue with vaterite as minor phase.

Writing and Functionalisation of Suspended DNA Nanowires on Superhydrophobic Pillar Arrays

Nanowire arrays and networks with precisely controlled patterns are very interesting for innovative device concepts in mesoscopic physics. In particular, DNA templates have proven to be versatile for the fabrication of complex structures that obtained functionality via combinations with other materials, for example by functionalisation with molecules or nanoparticles, or by coating with metals. Here, the controlled motion of the a three-phase contact line (TCL) of DNA-loaded drops on superhydrophobic substrates is used to fabricate suspended nanowire arrays. In particular, the deposition of DNA wires is imaged in situ, and different patterns are obtained on hexagonal pillar arrays by controlling the TCL velocity and direction. Robust conductive wires and networks are achieved by coating the wires with a thin layer of gold, and as proof of concept conductivity measurements are performed on single suspended wires. The plastic material of the superhydrophobic pillars ensures electrical isolation from the substrate. The more general versatility of these suspended nanowire networks as functional templates is outlined by fabricating hybrid organic-metal-semiconductor nanowires by growing ZnO nanocrystals onto the metal-coated nanowires.

Fabrication of biocompatible free-standing nanopatterned films for primary neuronal cultures

Devising and constructing biocompatible devices for nervous system regeneration is an extremely challenging task. Besides tackling the issue of biocompatibility, biomaterials for neuroscience applications should mimic the complex environment of the extracellular matrix, which in vivo provides neurons with a series of cues and signals to guide cells towards their appropriate targets. In this work, a novel nanopatterned biocompatible poly-e-caprolactone (PCL) film is realized to assist the attachment and growth of primary hippocampal neurons. Costly and time-consuming processes can be avoided using plasma-surface nanotexturing obtained by a mixed gas SF6/Ar at −5 °C. The intrinsic composition and line topography of nanopatterned PCL ensure healthy development of the neuronal network, as shown by confocal microscopy, by analysing the expression of a range of neuronal markers typical of mature cultures, as well as by scanning electron microscopy. In addition, we show that surface nanopatterning improves differentiation of neurons compared to flat PCL films, while no neural growth was observed on either flat or nanopatterned substrates in the absence of a poly-D-lysine coating. Thus, we successfully optimized a nanofabrication protocol to obtain nanostructured PCL layers endowed with several mechanical and structural characteristics that make them a promising, versatile tool for future tissue engineering studies aimed at neural tissue regeneration.

Probing droplets on superhydrophobic surfaces by synchrotron radiation scattering techniques

A comprehensive review about the use of micro- and nanostructured superhydrophobic surfaces as a tool for in situ X-ray scattering investigations of soft matter and biological materials.

Superhydrophobic Surfaces Boost Fibril Self-Assembly of Amyloid β Peptides

Amyloid β (Aβ) peptides are the main constituents of Alzheimers amyloid plaques in the brain. Here we report how the unique microfluidic flows exerted by droplets sitting on superhydrophobic surfaces can influence the aggregation mechanisms of several Aβ fragments by boosting their fibril self-assembly. Aβ(25-35), Aβ(1-40), and Aβ(12-28) were dried both on flat hydrophilic surfaces (contact angle (CA) = 37.3°) and on nanostructured superhydrophobic ones (CA = 175.8°). By embedding nanoroughened surfaces on top of highly X-ray transparent Si3N4 membranes, it was possible to probe the solid residues by raster-scan synchrotron radiation X-ray microdiffraction (μXRD). As compared to residues obtained on flat Si3N4 membranes, a general enhancement of fibrillar material was detected for all Aβ fragments dried on superhydrophobic surfaces, with a particular emphasis on the shorter ones. Indeed, both Aβ(25-35) and Aβ(12-28) showed a marked crystalline cross-β phase with varying fiber textures. The homogeneous evaporation rate provided by these nanostructured supports, and the possibility to use transparent membranes, can open a wide range of in situ X-ray and spectroscopic characterizations of amyloidal peptides involved in neurodegenerative diseases and for the fabrication of amyloid-based nanodevices.

Lysozyme fibrillation induced by convective flow under quasi contact-free conditions

The evaporation of a lysozyme solution drop containing Ca2+ ions on a superhydrophobic poly(methyl methacrylate) surface was probed by X-ray microbeam raster-diffraction. We observe the rapid deposition of fibrillar lysozyme with amyloidic cross-β structure at the interface of the drop with the substrate under conditions of weak acidity, close to physiological.