Structural Biochemistry/Proteins/Recent Progress in Understanding Alzheimer's β-Amyloid structures

Introduction
The formation of amyloid fibrils, protofibrils, and oligomers from β-amyloid peptides have been very crucial for the research of the disease, Alzheimers. However, determining the structures of these peptides has been a struggle. In the past five years, there has been new data obtained about these structures through electron cryo-microscopy and NMR which has enhanced scientists' understanding of a certain mechanism, Aβ aggregation and has paved new pathways of relevance of specific conformers in terms of neurodegenerative pathologies.

Structural diversity of β-amyloid aggregates
The β-amyloid (Aβ) peptide resides inside the human brain as a proteolytic fragment of the amyloid precursor protein, with an amphiphilic structure, possessing a hydrophilic N- and hydrophobic C terminus. The two most studied Aβ alloforms are Aβ(1-40) and aβ(1-42), where they contain 40 and 42 residues, respectively. More than 10 single-site sequence variants have been connected to similar forms of Alzheimer's disease. These alloforms are important because since Aβ amyloid fibrils form the center of amyloid plaques inside the brain parenchyma, they are correlated to Alzheimer's disease. Scientists have been trying to determine the structure of these alloforms, but they cannot be isolated or easily purified within the laboratories. Thus, there is no reliable structural information of Aβ amyloid fibrils. This provides a challenge for scientists who need this structural information to understand their biological properties.

Cross-β structure of Aβ amyloid fibrils
Amyloid fibrils are fibrillar polypetide aggregates with a cross-β structure. In cross-β structures, the β-sheet plane ad the backbone hydrogen bonds connecting the β-strands are positioned parallel to the axis while the β-strands run perpendicular to the axis. Further study of these structures showed that these peptides hve things called steric zippers. Steric zipper are composed of a pair of two cross-β sheets with interlacing side chains. They're formed by many short peptide chins, like Aβ residues 37-42 or 35-40. Also, steric zipper's structure is similar to that of the spine of amyloid fibrils.

General topology and polymorphism of mature amyloid fibrils
TEM (transmission electron microscopy) and atomic force microscopy have observed that mature amyloid fibrils have a length greater than 1 um, whereas previously analyzed fibrils were thought to have a length of about 25 nm. Mature Aβ amyloid fibrils have one or more protogilaments. Amyloid protofilaments create the substructures of mature fibrils, found by TEM to show that these fibrils are twisted left-handed with polarity. Studying thes structures shows that there's a structural feature of structural polymorphism of amyloid fibrils. Structural polymorphism is the variability in peptide conformation of fibrils3D reconstructions of polymorphic amyloid fibrils have revealed that fibrils differ in:
 * (i) number of protofilaments
 * (ii) different internal protofilament substructures
 * (iii) relative protofilament orientation

In addition to structural polymorphism (or inter-sample polymorphism), study of Aβ fibril samples with single particle techniques has shown that there is a lot of intra-sample polymorphism. Such as, an analysis of Aβ(1-40) fibrils created in 50mM sodium borate with a pH of 9 has revealed variations in the fibril width (13 to 29 nm); however, most fibrils demonstrate crossover distances of 100 to 200 nm. Thus, there is a wide range of morphologies, especially when fibrils are grown under sodium or potassium chloride (buffer systems).

Structural deformations report on the nanoscale flexibility properties of amyloid fibrils
Structural deformation is another cause for heterogeneity of amyloid samples besides polymorphism. These deformations bend and twist themselves and although these can create more potential problems for structural analysis, they can be used to understand anoscale mechanical properties of amyloid fibrils.

Structural methods for studying amyloid fibrils
Atomic structures of full-length Aβ fibrils have not been found because:
 * There has not been any fibril that creates a crystal suitable for X-ray crystallography
 * The fibrils are too large for NMR techniques.

However, solid-state NMR and cryo-EM have been found to possibly determine the structure of Aβ amyloid fibrils at atomic resolution.

Solid-state NMR can determine structural constraints like chemical shift values, bond angles, and/or specific interatomic distances, and thus, identify residues of Aβ amyloids interconnecting with the β-sheet structure of fibrils.

Cryo-EM can visualize the structure of the fibrils and can calculate their 3D density. Thus, the observation of individual fibrils can determine specific fibril morphologies.

Protofilament structure of mature Aβ fibrils
The protofilament substructure of an Aβ fibril has been found by cryo-EM. The protofilaments have cross-sectional dimensions of 4 x 11 nm and a cross-sectional subdivision of quasi twofold symmetry (4 x 5 nm) with two peripheral regions. Aβ(1-40) fibril contains two protofilaments and Aβ(1-42) fibril contains only one protofilament. The single-protofilament in Aβ(1-42) fibril has two equally shaped peripheral regions, fully solvent-exposed and structurally disordered. In contrast, the two-rotofilament Aβ(1040) fibril has an arch-shaped peripheral region at the protofilament-protofilament interface. The other peripheral region is the one that is solvent-exposed and structurally disordered.

Structural comparison of Aβ(1-40) and Aβ(1-42)
The Aβ(1-42) peptide is more pathogenic than the Aβ(1-40) peptide. For example, when it is expressed in Drosophila melanogaster, the Aβ(1-40) peptide is very toxic and halves the life-span of the animal; however, Aβ(1-40) don't present a discernible phenotype. Although of this difference, their chemical properties are pretty similar (the first 40 residues are identical) which leads to similarities in their conformation proerpties. Some of the differences include the Aβ(1-42) peptide having additional two C-terminal residues and the higher aggregation propensity of Aβ(1-40). Also, Aβ(1-42) can affect aggregation mechanisms of Aβ(1-40) and thus prevents formation of matue Aβ(1-40) fibrils.

According to cryo-EM of these two peptides, it shows differences in their protofilament packing. Aβ(1-40) fibrils have either a single-protofilament arrangement or a two-protofilament arrangement with a hollow core. But, all in all, the protofilaments of these two fibrils are pretty similar. For example, they can both produce the same mPL values, cross-sectional areas and shapes, and the cross-sections of the protofilaments  have a similar division at the one central and two peripheral regions. Thus, they have similar peptide folding. Also, according to IR and NMR data, they both have concluded that both fibrils have a parallel β-sheet structure.

Reference
Fandrich, Marcus, and Matthias Schmidt, and Nikolaus Grigorieff. "Recent Progress in understanding Alzheimer's β-amyloid structures ." Trends in Biochemical Sciences 36.6 (2011) 338-345. Academic Search Complete. Web. 21 Nov. 2012.