Kyle L. Morris

Exploring the sequence determinants of amyloid structure using position-specific scoring matrices

Protein aggregation results in β-sheet–like assemblies that adopt either a variety of amorphous morphologies or ordered amyloid-like structures. These differences in structure also reflect biological differences; amyloid and amorphous β-sheet aggregates have different chaperone affinities, accumulate in different cellular locations and are degraded by different mechanisms. Further, amyloid function depends entirely on a high intrinsic degree of order. Here we experimentally explored the sequence space of amyloid hexapeptides and used the derived data to build Waltz, a web-based tool that uses a position-specific scoring matrix to determine amyloid-forming sequences. Waltz allows users to identify and better distinguish between amyloid sequences and amorphous β-sheet aggregates and allowed us to identify amyloid-forming regions in functional amyloids.

The Common Architecture of Cross-β Amyloid

Amyloid fibril deposition is central to the pathology of more than 30 unrelated diseases including Alzheimers disease and Type 2 diabetes. It is generally accepted that amyloid fibrils share common structural features despite each disease being characterised by the deposition of an unrelated protein or peptide. The structure of amyloid fibrils has been studied using X-ray fibre diffraction and crystallography, solid-state NMR and electron paramagnetic resonance, and many different, sometimes opposing, models have been suggested. Many of these models are based on the original interpretation of the cross-beta diffraction pattern for cross-beta silk in which beta-strands run perpendicular to the fibre axis, although alternative models include beta-helices and natively structured proteins. Here, we have analysed opposing model structures and examined the necessary structural elements within the amyloid core structure, as well as producing idealised models to test the limits of the core conformation. Our work supports the view that amyloid fibrils share a number of common structural features, resulting in characteristic diffraction patterns. This pattern may be satisfied by structures in which the strands align close to perpendicular to the fibre axis and are regularly arranged to form beta-sheet ribbons. Furthermore, the fibril structure contains several beta-sheets that associate via side-chain packing to form the final protofilament structure.

Structural Basis for Increased Toxicity of Pathological Aβ42:Aβ40 Ratios in Alzheimer Disease

Background: Amyloid β peptide plays a role in Alzheimer disease. Results: Interaction of amyloid β peptides with 40 and 42 amino acids has consequences for oligomer formation. Conclusion: Increased production of amyloid β peptide with 42 amino acids affects the behavior of the entire amyloid β peptide pool. Significance: This might explain the synaptotoxic effect observed with a shift in amyloid β peptide production. The β-amyloid peptide (Aβ) is directly related to neurotoxicity in Alzheimer disease (AD). The two most abundant alloforms of the peptide co-exist under normal physiological conditions in the brain in an Aβ42:Aβ40 ratio of ∼1:9. This ratio is often shifted to a higher percentage of Aβ42 in brains of patients with familial AD and this has recently been shown to lead to increased synaptotoxicity. The molecular basis for this phenomenon is unclear. Although the aggregation characteristics of Aβ40 and Aβ42 individually are well established, little is known about the properties of mixtures. We have explored the biophysical and structural properties of physiologically relevant Aβ42:Aβ40 ratios by several techniques. We show that Aβ40 and Aβ42 directly interact as well as modify the behavior of the other. The structures of monomeric and fibrillar assemblies formed from Aβ40 and Aβ42 mixtures do not differ from those formed from either of these peptides alone. Instead, the co-assembly of Aβ40 and Aβ42 influences the aggregation kinetics by altering the pattern of oligomer formation as evidenced by a unique combination of solution nuclear magnetic resonance spectroscopy, high molecular weight mass spectrometry, and cross-seeding experiments. We relate these observations to the observed enhanced toxicity of relevant ratios of Aβ42:Aβ40 in synaptotoxicity assays and in AD patients.

Hydrophobic, aromatic, and electrostatic interactions play a central role in amyloid fibril formation and stability

Amyloid-like fibrous crystals formed by the peptide KFFEAAAKKFFE have been previously characterized and provide an ideal model system to examine the importance of specific interactions by introducing specific substitutions. We find that the removal of any phenylalanine residue completely abrogates assembly ability, while charged residues modulate interactions within the structure resulting in alternative fibrillar morphologies. X-ray fiber diffraction analysis reveals that the essential backbone packing of the peptide molecules is maintained, while small changes accommodate differences in side chain size in the variants. We conclude that even very short peptides are adaptable and add to the growing knowledge regarding amyloid polymorphisms. Additionally, this work impacts on our understanding of the importance of residue composition for amyloidogenic peptides, in particular the roles of electrostatic, aromatic, and hydrophobic interactions in amyloid assembly.

Effect of Molecular Structure on the Properties of Naphthalene−Dipeptide Hydrogelators

Dipeptide-conjugates can be efficient low molecular weight hydrogelators. However, the effective design of a gelator for a specific application is compromised by the lack of a clear understanding of the design rules that govern assembly and hence gelation. Here, we report a library of naphthalene-dipeptides, their physical chemical properties, and gelation ability. We have varied both the amino acids in the dipeptides and the substitution on the naphthalene ring to allow variation of the structure throughout the molecule. We have examined the effects of these permutations on the critical micelle concentration and air-water partition coefficient at high pH and the apparent pK(a). We show that there is a clear link between these properties and the predicted hydrophobicity of the overall conjugates, rather than the properties varying with, for example, the dipeptide sequence. The majority of these dipeptide-conjugates are effective hydrogelators, although there is no apparent link between the solution properties and whether or not a conjugate is a hydrogelator. Nevertheless, where gelation occurs, the link between hydrophobicity and apparent pK(a) allows the prediction of the pH at which a gel will be formed and hence informed choice of gelator for specific applications.

Iron promotes the toxicity of amyloid beta peptide by impeding its ordered aggregation

We have previously shown that overexpressing subunits of the iron-binding protein ferritin can rescue the toxicity of the amyloid β (Aβ) peptide in our Drosophila model system. These data point to an important pathogenic role for iron in Alzheimer disease. In this study, we have used an iron-selective chelating compound and RNAi-mediated knockdown of endogenous ferritin to further manipulate iron in the brain. We confirm that chelation of iron protects the fly from the harmful effects of Aβ. To understand the pathogenic mechanisms, we have used biophysical techniques to see how iron affects Aβ aggregation. We find that iron slows the progression of the Aβ peptide from an unstructured conformation to the ordered cross-β fibrils that are characteristic of amyloid. Finally, using mammalian cell culture systems, we have shown that iron specifically enhances Aβ toxicity but only if the metal is present throughout the aggregation process. These data support the hypothesis that iron delays the formation of well ordered aggregates of Aβ and so promotes its toxicity in Alzheimer disease.

On crystal versus fiber Formation in dipeptide hydrogelator systems

Naphthalene dipeptides have been shown to be useful low-molecular-weight gelators. Here we have used a library to explore the relationship between the dipeptide sequence and the hydrogelation efficiency. A number of the naphthalene dipeptides are crystallizable from water, enabling us to investigate the comparison between the gel/fiber phase and the crystal phase. We succeeded in crystallizing one example directly from the gel phase. Using X-ray crystallography, molecular modeling, and X-ray fiber diffraction, we show that the molecular packing of this crystal structure differs from the structure of the gel/fiber phase. Although the crystal structures may provide important insights into stabilizing interactions, our analysis indicates a rearrangement of structural packing within the fibers. These observations are consistent with the fibrillar interactions and interatomic separations promoting 1D assembly whereas in the crystals the peptides are aligned along multiple axes, allowing 3D growth. This observation has an impact on the use of crystal structures to determine supramolecular synthons for gelators.

The delicate balance between gelation and crystallisation: structural and computational investigations

Predicting the ability of low molecular weight molecules to form hydrogels is difficult. Here, we have examined the self-assembly behavior of two chemically and structurally similar functionalized dipeptides, one of which is found to form a meta-stable hydrogel (1) and the other forming a crystalline solid (2). To investigate the reasons for these differences, we have employed computational methods to explore the crystal energy landscapes of the two molecules and examined differences in their preferred packing arrangements. We show that this method accurately predicts the packing for the crystalline solid, 2. Furthermore, the predictions for the gel-former 1 suggest that one-dimensional hydrogen-bonding arranged into tightly coiled molecular columns is a preferred mode of packing for this system, but is unfavorable for 2. The different tendencies of forming these columns could provide an explanation for the different behavior of the two molecules and demonstrate that this approach could be useful for the future predictable design of low molecular weight gelators.

A central role for dityrosine crosslinking of Amyloid-β in Alzheimer's disease.

BackgroundAlzheimer’s disease (AD) is characterized by the deposition of insoluble amyloid plaques in the neuropil composed of highly stable, self-assembled Amyloid-beta (Aβ) fibrils. Copper has been implicated to play a role in Alzheimer’s disease. Dimers of Aβ have been isolated from AD brain and have been shown to be neurotoxic.ResultsWe have investigated the formation of dityrosine cross-links in Aβ42 formed by covalent ortho-ortho coupling of two tyrosine residues under conditions of oxidative stress with elevated copper and shown that dityrosine can be formed in vitro in Aβ oligomers and fibrils and that these links further stabilize the fibrils. Dityrosine crosslinking was present in internalized Aβ in cell cultures treated with oligomeric Aβ42 using a specific antibody for dityrosine by immunogold labeling transmission electron microscopy. Results also revealed the prevalence of dityrosine crosslinks in amyloid plaques in brain tissue and in cerebrospinal fluid from AD patients.ConclusionsAβ dimers may be stabilized by dityrosine crosslinking. These results indicate that dityrosine cross-links may play an important role in the pathogenesis of Alzheimer’s disease and can be generated by reactive oxygen species catalyzed by Cu2+ ions. The observation of increased Aβ and dityrosine in CSF from AD patients suggests that this could be used as a potential biomarker of oxidative stress in AD.

Rational Design of Helical Nanotubes from Self-assembly of Coiled-coil Lock Washers

Design of a structurally defined helical assembly is described that involves recoding of the amino acid sequence of peptide GCN4-pAA. In solution and the crystalline state, GCN4-pAA adopts a 7-helix bundle structure that resembles a supramolecular lock washer. Structurally informed mutagenesis of the sequence of GCN4-pAA afforded peptide 7HSAP1, which undergoes self-association into a nanotube via noncovalent interactions between complementary interfaces of the coiled-coil lock-washer structures. Biophysical measurements conducted in solution and the solid state over multiple length scales of structural hierarchy are consistent with self-assembly of nanotube structures derived from 7-helix bundle subunits. The dimensions of the supramolecular assemblies are similar to those observed in the crystal structure of GCN4-pAA. Fluorescence studies of the interaction of 7HSAP1 with the solvatochromic fluorophore PRODAN indicated that the nanotubes could encapsulate shape-appropriate small molecules with high binding affinity.