**2.1 Morphological differences in amyloid aggregates**

*Amyloid Diseases*

discussed.

dementia caused due to improper aggregation of amyloidogenic proteins-amyloid-β (Aβ), which is a cleavage product of amyloid precursor protein (APP) and tau, stabilizes microtubules in neurons [3]. Prognosis is also closely associated with aggregation of α-Synuclein (αS) protein into Lewy bodies usually concentrated in presynaptic terminals [4]. Human islet amyloid polypeptide (IAPP), also known as amylin, is secreted along with insulin from pancreatic β-islet cells. IAPP rich amyloid plaques, facilitated by insulin resistance, are hallmarks of T2D [5]. β-sheeted infectious isoform of cellular prion protein (PrP) causes transmissible spongiform

In this chapter, we review various structures and conformations attained by Aβ peptides during the process of aggregation. We begin with introducing different morphologies and conformations attained by amyloids during this process. We outline mechanisms of amyloid pathology, either directly mediated by aggregates or indirectly through generation of oxidative stress. We have briefly alluded to chaperone functions of Heat shock protein (Hsp) family and their interactions to different amyloid structures as well as intracellular protease mechanisms. It is important to note that such intracellular proteases are almost entirely inefficient in dealing with large insoluble plaques. Here we emphasize on additional endogenous proteins which show potential as chaperones, albeit through different mechanisms. Towards the end, we discuss the role of oxidative stress in accelerating AD pathology and the effect of Aβ interactions with metal species. Mechanisms to alleviate oxidative stress and their possible protective role in AD have been

encephalopathy (TSE), broadly known as prion disease [2].

**2. Structural and biophysical basis of amyloid aggregation**

Aβ(1–42) seeds precludes aggregation of Aβ(1–40) [8].

Membrane glycoprotein APP is cleaved by β-secretase and γ-secretase enzymes generating 36–49 residue long peptides, among which amyloidogenic Aβ(1–40) and Aβ(1–42) are well-known culprits in AD [6]. Unstructured monomeric amyloids polymerize to form fibrillar structures with characteristic cross-β morphology formed by in-register β-sheets which align parallel to the fibrillar axis whereas perpendicularly extended side-chains pack closely to form tight steric zippers [2]. Nuclear magnetic resonance (NMR) spectroscopy studies on amyloid monomers or fibrillar structures to identify characteristic dynamic structural features. X-ray crystallographic studies have helped in identifying structural motifs through fiber diffraction and mass-per-length studies through EM provide information regarding specific symmetries identified in filaments. NMR models of Aβ monomeric peptides show predominantly α-helices with propensity to convert into β-sheets [6]. The α-helical conformation is also observed among on-pathway transient intermediates, possibly mediated by interactions of hydrophilic N-terminal residues [7]. These intermediates then give way to β-sheet conformation in higher oligomeric species which eventually transition into mature fibrils. *In vitro* aggregation of Aβ monomers into fibrils can be carefully curated to obtained different fibril morphology. In solid state nuclear magnetic resonance (ssNMR) spectra, cross-peaks originating from hydrophobic core and C-terminal regions within amyloid fibrils, prepared without seeding indicate presence of polymorphs. Formation of homogenous fibrils from

αS binds to neuronal membranes in a highly α-helical state as opposed to the unfolded monomeric conformation [7]. The antipathic N-terminal sequence has tendency to form α-helical conformation, central region from aa 61–95 is highly hydrophobic and amyloidogenic, and the C-terminal domain provides flexibility to the protein without attaining any specific structure [7]. Prefibrillar αS shows

**190**

Disordered or misfolded monomers can convert into a range of amyloid species, e.g., spherical oligomers, amorphous aggregates, annular oligomers, protofibrils, inclusion bodies or insoluble fibrils, based on the pathological pathways (**Table 1**). Dynamic intermediate oligomers form transient structures facilitating on-pathway conversion from misfolded monomers to fibrils. The spherical and annular aggregates get generated off-pathway and contribute highly to amyloid mediated neurotoxicity [2, 9]. The Lewy bodies formed by αS are example of intracellular amyloid inclusions [10]. Formation of a specific aggregated form is usually controlled by process of nucleation. In primary nucleation, seeds are formed by spontaneous aggregation of monomers followed by fibril elongation, whereas fragments from mature fibrils recruit monomers to facilitate the polymerization in secondary nucleation process. However, this process is specific to monomeric species; seeding with Aβ(1–42) fibrils does not contribute to aggregation of Aβ(1–40) [8]. Comparison between kinetic profiles of seeded and non-seeded Aβ(1–40) suggest that aggregation follows the seeded fibrils template [8]. Monomeric Aβ(1–40) samples form striated ribbons under constant agitation, and twisted fibrils under undisturbed conditions [11]. NMR can also be used to study kinetics of oligomer interactions by utilizing the constant exchange of detectable monomers with other invisible oligomeric species, through saturation transfer difference (STD) experiments [12]. Amyloid fibrils show protease resistance and are insoluble in detergents. However, their affinity to small lipophilic molecules is amenable for detection through biophysical assays using Congo red and thioflavin dyes [13]. These fluorescent dyes can be used to quantify β-sheet rich amyloid fibrils under laboratory conditions where fluorescent intensity linearly correlates with fibril formation [14]. Morphology of amyloid fibrils can be studied using transmission electron microscopy (TEM) by observing diffraction patterns. Whether fibrils form a ribbon-like or a striated pattern, can be calculated by mass-per-length constraints [15]. Different amyloid structures can be categorized


#### **Table 1.**

*Summary of amyloid structures observed in AD.*

based on symmetry and periodicity with these methods [16]. Aβ40 fibrils structure have either 2-fold (2A) or 3-fold (3Q ) rotational symmetry with a twisted morphology with periodicity of 120 ± 20 nm, and roughly 8 nm width [2, 11]. IAPP fibrils also lead to formation of striated and twisted ribbons [11].
