Structural Studies Providing Insights into Production and Conformational Behavior of Amyloid-β Peptide Associated with Alzheimer's Disease Development

Abstract

Alzheimer's disease is the most common type of neurodegenerative disease in the world. Genetic evidence strongly suggests that aberrant generation, aggregation, and/or clearance of neurotoxic amyloid-β peptides (Aβ) triggers the disease. Aβ accumulates at the points of contact of neurons in ordered cords and fibrils, forming the so-called senile plaques. Aβ isoforms of different lengths are found in healthy human brains regardless of age and appear to play a role in signaling pathways in the brain and to have neuroprotective properties at low concentrations. In recent years, different substances have been developed targeting Aβ production, aggregation, interaction with other molecules, and clearance, including peptide-based drugs. Aβ is a product of sequential cleavage of the membrane glycoprotein APP (amyloid precursor protein) by β- and γ-secretases. A number of familial mutations causing an early onset of the disease have been identified in the APP, especially in its transmembrane domain. The mutations are reported to influence the production, oligomerization, and conformational behavior of Aβ peptides. This review highlights the results of structural studies of the main proteins involved in Alzheimer's disease pathogenesis and the molecular mechanisms by which perspective therapeutic substances can affect Aβ production and nucleation.

Keywords: Alzheimer’s disease; amyloid precursor protein; amyloid-β peptide; bioactive peptides for therapy and diagnosis; molecular mechanism; neuronal membrane; protein–protein and protein–lipid interactions; structural–dynamical properties; toxic oligomerization.

Figure 1

Schematic representation of structures of amyloid precursor protein and α-, β-, and γ-secretases responsible for Aβ production. PDB accession number is indicated for each molecule throughout the figure. (a) Molecular surfaces of the structural elements of α-, β-, and γ-secretases. Single-span transmembrane (TM) domains of α- and β-secretases are shown as bars where high-resolution structure is unavailable. (b) Full-length APP structure based on individually resolved structures of its parts: flexible intracellular C-terminal domain (AICD), TM domain, connected through a flexible extracellular juxtamembrane (JM) region (containing Aβ metal-binding domain) to an ectodomain consisting of (i) E1 subunit including a cysteine-rich growth factor-like domain (HBD1/GFLD) and a copper/zinc-binding domain (CuBD), an acidic region (Ac), a Kunitz-type protease inhibitor domain (KPI), and (ii) E2 subunit with a second heparin-binding domain (HBD2). Resolved domain structures are shown as ribbon diagrams, and unstructured flexible connecting loops are shown as solid lines. The familial mutations attributed to increased risk or earlier age of AD development are shown in black on the TM and JM segments. A673T mutation decreasing APP proteolysis by β-secretases is highlighted in cyan. Sites of cleavage by α-, β-, and γ-secretases are indicated by arrows color-coded to distinguish between two alternative cleavage cascades generating Aβ_1–42 and Aβ_1–40 peptides (48 > 45 > 42 vs. 49 > 46 > 43 > 40). Cholesterol molecule interacting with the N-terminal part of APP TM helix is shown. The inset demonstrating the helical APP TM domain (in green) with a C-terminal turn (3 a.a. residues) unfolded into a β-strand is shown in the γ-secretase active center.

Figure 2

Structural diversity of Aβ aggregation states, aggregation pathways, and examples of biologically relevant interaction targets. Corresponding PDB accession numbers are indicated alongside the diagrams. (a) Free and cation-bound monomeric Aβ peptides (the structure combined from solution NMR structures of folded Aβ_1–16 metal-binding domain and Aβ_17–42 fragment) are capable of dimerizing via different dimerization interfaces situated in the TM, JM, and metal-binding site regions using protein–protein and protein–cation interactions involving α-helix, β-strand, and random coil structures. (b) Alternative dimers nucleate aggregation into neurotoxic intermediate oligomers that can interact with different target proteins and lipid membranes of neurons. (c) Two known configurations of predominantly β-structured minor oligomers capable of forming pore-like proteolipid aggregates and prone to further aggregation into protofibrillar structures. (d) Diverse structural motifs that can constitute amyloid fibril core structures capable of further aggregating into filaments and fibrillary deposits. (e) Two possible alternative fibril structures with biaxial and triaxial symmetry depositing to form macroscopic aggregates (f) constituting senile plaques, a known hallmark of AD. All the diverse Aβ aggregation forms appear to interact with multiple alternative targets, thus mediating normal physiological functions or pathological processes. The interactions are known to occur in multiple morphological units and organelles, including plasma and synaptic membranes and inter- and intracellular components.

Figure 3

Schematic representation of the generic strategy for search of peptide-based therapeutic agents affecting Aβ production pathways and/or suppressing neurotoxic effects of Aβ oligomers. The therapeutic agent (shown in red) can (1) act at the stage of APP processing through interaction with Aβ precursors (in green) processed by γ-secretase complex (PDB: 6IYC), modifying production of mature Aβ isoforms; (2) bind soluble Aβ aggregates, suppressing their toxicity; (3) interfere with interactions of toxic Aβ aggregates with membrane surface, inhibiting their conversion into β-structured membrane-bound oligomers; (4) modify toxic properties of membrane-incorporated Aβ oligomers associated with membrane permeabilization [140]; (5) target pore-like transmembrane structures formed by Aβ oligomers (PDB: 6RHY), e.g., inhibiting transmembrane transport of cations; and (6) prevent Aβ from inducing abnormal functioning of soluble and membrane-associated proteins, e.g., nicotinic acetylcholine receptor (PDB: 2BG9), which can be inhibited by diverse Aβ oligomers in different manners.