Assembly of Alzheimer's Aβ peptide into nanostructured amyloid fibrils

The self-assembly of β-amyloid (Aβ) peptide into highly ordered amyloid fibril structures represents one of the pathological hallmarks of Alzheimer's disease. This process leads to the transient stabilization of ordered or disordered intermediates, which are thought to act as the main pathogenic culprits in neurodegenerative amyloid disease. This review describes recent results from different biophysical techniques, ranging from structure determination to single-particle methods by which the outgrowth of individual fibrils can be followed, and it explains their contributions towards understanding the mechanism of assembly. Finally, we will outline emerging methods and molecules to specifically interfere with the assembly and pathogenic impact of Aβ peptide.     

Morphology and persistence length of amyloid fibrils are correlated to peptide molecular structure

The formation of amyloid fibrils is a self-assembly process of peptides or proteins. The superior mechanical properties of these fibrils make them interesting for materials science but constitute a problem in amyloid-related diseases. Amyloid structures tend to be polymorphic, and their structure depends on growth conditions. To understand and control the assembly process, insights into the relation between the mechanical properties and molecular structure are essential. We prepared long, straight as well as short, worm-like β-lactoglobulin amyloid fibrils and determined their morphology and persistence length by atomic force microscopy (AFM) and the molecular conformation using vibrational sum-frequency generation (VSFG) spectroscopy. We show that long fibrils with near-100% β-sheet content have a 40-times higher persistence length than short, worm-like fibrils with β-sheet contents below 80%.     

Cytochrome display on amyloid fibrils

Protein amyloid fibrils can be functionalized by coating the core protofilament with high concentrations of proteins and enzymes. This can be done elegantly by appending a functional domain to an amyloidogenic protein monomer, then assembling the monomers into a fibril. To display an array of biologically functional porphyrins on the surface of protein fibrils, we have fused the sequence of the small, soluble cytochrome b562 to an SH3 dimer sequence that can form classical amyloid fibrils rapidly under well-defined conditions. The resulting fusion protein also forms amyloid fibrils and, in addition, binds metalloporphyrins, at half of the porphyrin binding sites as shown by UV-vis and NMR spectroscopies. Once metalloporphyrins are bound to the fibrils, the resulting holo-cytochrome domains are spectroscopically identical to the wild type cytochrome. The concentration of metalloporphyrins on a saturated fibril is estimated to be of the order of approximately 20 mM, suggesting that they could be interesting systems for applications in nanotechnology.     

Light-triggered disassembly of amyloid fibrils

There is growing demand for novel methods that could render the controlled disassembly of higher-order structures formed, for example, by peptides. Herein, we demonstrate such a method based on the application of a photocaged variant of the amino acid lysine, namely, lys(Nvoc). Specifically, we introduce lys(Nvoc) into the primary sequence of the amyloidogenic peptide, Aβ(16-22), at a position where the native side chain is known to play a key role in fibril formation via hydrophobic interactions. Both AFM and infrared spectroscopic measurements indicate that the resultant Aβ(16-22) mutant is able to form fibrils whereas, more importantly, the fibrils thus formed can be completely disassembled upon irradiation with near-UV light, which cleaves the photolabile Nvoc moiety and triggers the restoration of the lysine side chain. These results suggest that the generation of a single charge in a highly hydrophobic region of the fibrils is sufficient to promote their dissociation. Thus, we envisage that the current approach will find useful applications wherein controlled structural disassembly or content release is required.     

Stabilization of peptide fibrils by hydrophobic interaction

Hydrophobic interactions play an important role in assembly processes in aqueous environments. In case of peptide amphiphiles, hydrophobicity is combined with hydrogen bonding to yield well-defined peptide-based aggregates. Here, we report a systematic study after the role of hydrophobic interactions on both stabilization and morphology of a peptide fibrillar assembly. For this purpose, alkyl tails were connected to a known beta-sheet forming peptide with the sequence KTVIIE. The introduction of n-alkyl groups induced thermal stability to the assemblies without affecting the morphology of the peptide aggregates.     

Mesoscopic properties of semiflexible amyloid fibrils

We have determined the contour length, persistence length, bending rigidity, and critical percolation concentration for semiflexible amyloid fibrils formed from the globular proteins beta-lactoglobulin, bovine serum albumin, and ovalbumin. The persistence length was estimated using an adjusted random contact model for highly charged semiflexible chains. We have found contour lengths in the range of 50 nm to 10 microm and persistence lengths in the range of 16 nm to 1.6 microm. This wide range of contour and persistence lengths and the ease of preparation of these amyloid fibrils make them ideal model systems for the study of semiflexible polymers.     

Probing small molecule binding to amyloid fibrils

Much effort has focussed in recent years on probing the interactions of small molecules with amyloid fibrils and other protein aggregates. Understanding and control of such interactions are important for the development of diagnostic and therapeutic strategies in situations where protein aggregation is associated with disease. In this perspective article we give an overview over the toolbox of biophysical methods for the study of such amyloid-small molecule interactions. We discuss in detail two recently developed techniques within this framework: linear dichroism, a promising extension of the more traditional spectroscopic techniques, and biosensing methods, where surface-bound amyloid fibrils are exposed to solutions of small molecules. Both techniques rely on the measurement of physical properties that are very directly linked to the binding of small molecules to amyloid aggregates and therefore provide an attractive route to probe these important interactions.     

Solid-state NMR study of amyloid nanocrystals and fibrils formed by the peptide GNNQQNY from yeast prion protein Sup35p

Sup35p is a prion protein found in yeast that contains a prion-forming domain characterized by a repetitive sequence rich in Gln, Asn, Tyr, and Gly amino acid residues. The peptide GNNQQNY7-13 is one of the shortest segments of this domain found to form amyloid fibrils, in a fashion similar to the protein itself. Upon dissolution in water, GNNQQNY displays a concentration-dependent polymorphism, forming monoclinic and orthorhombic crystals at low concentrations and amyloid fibrils at higher concentrations. We prepared nanocrystals of both space groups as well as fibril samples that reproducibly contain three (coexisting) structural forms and examined the specimens with magic angle spinning (MAS) solid-state nuclear magnetic resonance. 13C and 15N MAS spectra of both nanocrystals and fibrils reveal narrow resonances indicative of a high level of microscopic sample homogeneity that permitted resonance assignments of all five species. We observed variations in chemical shift among the three dominant forms of the fibrils which were indicated by the presence of three distinct, self-consistent sets of correlated NMR signals. Similarly, the monoclinic and orthorhombic crystals exhibit chemical shifts that differ from one another and from the fibrils. Collectively, the chemical shift data suggest that the peptide assumes five conformations in the crystals and fibrils that differ from one another in subtle but distinct ways. This includes variations in the mobility of the aromatic Tyr ring. The data also suggest that various structures assumed by the peptide may be correlated to the "steric zipper" observed in the monoclinic crystals.     

Study of amyloid fibrils via atomic force microscopy

Protein fibrils are a crucial subject of study in various research fields and disciplines. Amyloid fibrils are highly ordered fibrillar structures assembled from either peptides or unfolded proteins, which have a great importance in biology, medicine and recently have started to find an important role in many nanotechnology applications. Understanding the mechanisms of fibrillation, the structural features, and the physical and mechanical properties of these fibrils is an essential step to both unraveling their biological role and also their successful applications in nanotechnology and material science. Atomic force microscopy (AFM) is one of the most widely used single-molecule techniques to study the properties of amyloid fibrils. In this review we will discuss how the application of AFM during last few years has allowed moving considerably forward in the research of amyloid fibrils. We will review how AFM has rapidly evolved from a purely microscopic technique, providing important information about fibril structure and fibrillation processes, to a tool capable to probe also intrinsic properties of amyloid fibrils such as their strength and Young's moduli.     

Pyrroloquinoxaline hydrazones as fluorescent probes for amyloid fibrils

Here we describe the identification and preliminary characterization of a new class of pyrrolo(imidazo)quinoxaline hydrazones as florescent probes for Aβ(1-42) fibrils. All the newly developed compounds were able to bind amyloid fibrils formed in vitro and some of them displayed an increase of their fluorescence upon binding. When tested on brain tissue preparations presenting Aβ deposits, the described hydrazones selectively stained amyloid structures and did not display aspecific binding. The hydrazones did not show antifibrillogenic activity and electron microscopy analysis revealed that they do not interfere with fibrils structure. The described pyrrolo(imidazo)quinoxalines could be useful for studying amyloid structures in vitro. Moreover, their experimentally proven ability to cross the blood-brain barrier in mouse opens the possibility of developing these compounds as potential amyloid imaging agents for in vivo applications.     

New biocompatible thermo-reversible hydrogels from PNiPAM-decorated amyloid fibrils

New biocompatible temperature-responsive hydrogels have been obtained by using unprecedented low concentration of amyloid fibril-PNiPAM hybrids. The viscoelasticity of the hydrogels can be finely controlled by tuning the PNiPAM layers without changing the structure or concentration of the amyloid fibrils.     

The formation of nematic liquid crystal phases by hen lysozyme amyloid fibrils

Amyloid fibrils are a polymeric aggregate of protein. The fibrils are typically on the order of micrometers long, with widths of 10-20 nm. They are generally regarded as stiff, and nonbranching. It is well-known that similar synthetic polymers and biopolymers such as DNA and polysaccharides, have a tendency to form liquid crystalline phases when incubated under appropriate conditions. Here we show that amyloid fibrils from the protein hen lysozyme can similarly form liquid crystal phases. The most common phase observed is the nematic. Alignment can persist for several centimeters. When the fibrils are freeze-thawed to shorten them, similar phases form but at higher concentrations, confirming the importance of the aspect ratio of the fibrils. Freeze-thawed fibrils are also seen to form "tactoids", discrete liquid crystalline structures. The addition of NaCl to the solutions appears to only have a minor effect, while the effect of pH appears much more significant. We propose that the consideration of amyloid fibrils as polymer analogues should open new routes to explore in the burgeoning field of biomaterials.     

The aggregation-enhancing huntingtin N-terminus is helical in amyloid fibrils

The 17-residue N-terminus (htt(NT)) directly flanking the polyQ sequence in huntingtin (htt) N-terminal fragments plays a crucial role in initiating and accelerating the aggregation process that is associated with Huntington's disease pathogenesis. Here we report on magic-angle-spinning solid-state NMR studies of the amyloid-like aggregates of an htt N-terminal fragment. We find that the polyQ portion of this peptide exists in a rigid, dehydrated amyloid core that is structurally similar to simpler polyQ fibrils and may contain antiparallel β-sheets. In contrast, the htt(NT) sequence in the aggregates is composed in part of a well-defined helix, which likely also exists in early oligomeric aggregates. Further NMR experiments demonstrate that the N-terminal helical segment displays increased dynamics and water exposure. Given its specific contribution to the initiation, rate, and mechanism of fibril formation, the helical nature of htt(NT) and its apparent lack of effect on the polyQ fibril core structure seem surprising. The results provide new details about these disease-associated aggregates and also provide a clear example of an amino acid sequence that greatly enhances the rate of amyloid formation while itself not taking part in the amyloid structure. There is an interesting mechanistic analogy to recent reports pointing out the early-stage contributions of transient intermolecular helix-helix interactions in the aggregation behavior of various other amyloid fibrils.     

Self-assembled nanochaperones enable the disaggregation of amyloid insulin fibrils

The deposition of highly ordered amyloid fibrils is recognized as a hallmark of amyloidosis diseases such as Alzheimer’s disease and Parkinson’s disease.Disaggregating the amyloid fibrils is considered as one of the effective strategies for the control and treatment of amyloidosis diseases.In this article,by simulating the function of natural molecular chaperones,co-assembled block copolymer micelles with coordination groups of nitrilotriacetic acid(NTA)and hydrophobic microdomains of poly(Nisopropylacrylamide)(PNIPAM)on the surface were used as nanochaperones(n Chaps)to disaggregate amyloid insulin fibrils.Zinc ions chelated by NTA can bind the histidine imidazole residues while the PNIPAM microdomains can interact with the exposed hydrophobic sites on the amyloid insulin fibrils,which synergistically perturb the stability of amyloid insulin fibrils,loosen their structure,and finally promote their disaggregation.A combination of characterizations with fluorescence spectroscopy,transmission electron microscopy(TEM),dynamic hight scattering(DLS),and quartz crystal microbalance(QCM)demonstrated that mature amyloid insulin fibrils were completely disaggregated after incubating with n Chaps for 90 h.This study may provide a promising strategy for the development of n Chaps for the treatment of amyloidosis diseases.     

Spider silk and amyloid fibrils: a structural comparison

Although spider silks have been studied for decades, the assembly properties of the underlying silk proteins have still not been unravelled. Previously, the detection of amyloid-like nanofibrils in the spider's silk gland suggested their involvement in the assembly process.Recombinantly produced spider silk also self-assembles into nanofibrils. In order to investigate the structural properties of such silk nanofibrils in more detail, they have been compared to amyloid-like fibrils to highlight structural similarities.     

New insight into the IR-spectra/structure relationship in amyloid fibrils: a theoretical study on a prion peptide

Molecular-level structural information on amyloid aggregates is of great importance for the understanding of protein-misfolding-related deseases. Nevertheless, this kind of information is experimentally difficult to obtain. In this work, we used molecular dynamics (MD) simulations combined with a mixed quantum mechanics/molecular mechanics theoretical methodology, the perturbed matrix method (PMM), in order to study the amide I' IR spectrum of fibrils formed by a short peptide, the H1 peptide, derived from residues 109 through 122 of the Syrian hamster prion protein. The PMM/MD approach allows isolation of the amide I' signal arising from any desired peptide group of the polypeptide chain and quantification of the effect of the excitonic coupling on the frequency position. The calculated single-residue signals were found to be in good agreement with the experimental site-specific spectra obtained by means of isotope-labeled IR spectroscopy, providing a means for their interpretation at the molecular level. In particular, our results confirm the experimental hypothesis that residues ala117 are aligned in all strands and that the alignment gives rise to a red shift of the corresponding site-specific amide I' mode due to strong excitonic coupling among the ala117 peptide groups. In addition, our data show that a red shift of the amide I' band due to strong excitonic coupling can also occur for amino acids adjacent in sequence to the aligned ones. Thus, a red shift of the signal of a given isotope-labeled amino acid does not necessarily imply that the peptide groups under consideration are aligned in the β-sheet.