The amylome is the universe of proteins that are capable of forming amyloid-like fibrils. Here we investigate the factors that enable a protein to belong to the amylome. A major factor is the presence in the protein of a segment that can form a tightly complementary interface with an identical segment, which permits the formation of a steric zipper-two self-complementary beta sheets that form the spine of an amyloid fibril. Another factor is sufficient conformational freedom of the self-complementary segment to interact with other molecules. Using RNase A as a model system, we validate our fibrillogenic predictions by the 3D profile method based on the crystal structure of NNQQNY and demonstrate that a specific residue order is required for fiber formation. Our genome-wide analysis revealed that self-complementary segments are found in almost all proteins, yet not all proteins form amyloids. The implication is that chaperoning effects have evolved to constrain selfcomplementary segments from interaction with each other.3D profile | ribonuclease A | Rosetta energy | steric zipper S eventy-five years ago, the pioneering biophysicist William Astbury speculated that every protein might have a fibrous state as well as a globular state (1). Astbury was the first to describe the cross-beta fibril diffraction pattern, now accepted as the definitive signature of the amyloid state of proteins. Astbury's observation was on a denatured protein, albumin in poached egg white. Today it is established that amyloid diseases, including Alzheimer's and prion diseases, are associated with elongated, unbranched protein fibrils (2, 3). However, functional proteins are also found in the amyloid state. These include the egg stalk of the green lace-wing fly (4), the Pmel17 protein associated with skin pigmentation (5), and a large number of secretory hormones (6). Conversely, in the past decade, Pertinhez et al. (7) and others (8-10) have shown that many globular proteins can be converted to the amyloid state by a variety of denaturing processes, suggesting that conversion may be generally applicable to all proteins. So the question arises, to what extent is this conjecture true? That is, how large is the amylome?Computer algorithms have been proposed to answer a somewhat broader question: What is the aggregation propensity of a given protein sequence? Aggregates, in general, include amyloidlike fibrils but also other types of fibrils and nonfibrillar aggregates. TANGO (11) identifies beta-aggregating regions of proteins by using a statistical mechanics algorithm based on the physico-chemical principles of beta-sheet formation. For each residue, it calculates the energy of structural states derived from statistical and empirical considerations and then computes the occupancy of the beta-aggregation conformational state. Although beta-aggregation propensity by itself is not necessarily indicative of amyloid formation, it plays a major role in determining the tendency to ultimately form organized structures such as amyloid fibrils. Howeve...

Amyloid diseases, including Alzheimer's, Parkinson's, and the prion conditions, are each associated with a particular protein in fibrillar form. These amyloid fibrils were long suspected to be the disease agents, but evidence suggests that smaller, often transient and polymorphic oligomers are the toxic entities. Here we identify a segment of the amyloid-forming protein, alphaB crystallin, which forms an oligomeric complex exhibiting properties of other amyloid oligomers: beta-sheet-rich structure, cytotoxicity, and recognition by an anti-oligomer antibody. The X-ray-derived atomic structure of the oligomer reveals a cylindrical barrel, formed from six anti-parallel, protein strands, which we term a cylindrin. The cylindrin structure is compatible with a sequence segment from the Abeta protein of Alzheimer's disease. Cylindrins offer models for the hitherto elusive structures of amyloid oligomers.

Although amyloid fibers are found in neurodegenerative diseases, evidence points to soluble oligomers of amyloid-forming proteins as the cytotoxic species. Here, we establish that our preparation of toxic amyloid-β 1-42 (Abeta42) fibrillar oligomers (TABFOs) shares with mature amyloid fibrils the cross-β structure, in which adjacent β-sheets adhere by interpenetration of protein side chains. We study the structure and properties of TABFOs by powder X-ray diffraction, EM, circular dichroism, FTIR spectroscopy, chromatography, conformational antibodies, and celluar toxicity. In TABFOs, Abeta42 molecules stack into short protofilaments consisting of pairs of helical β-sheets that wrap around each other to form a superhelix. Wrapping results in a hole along the superhelix axis, providing insight into how Abeta may form pathogenic amyloid pores. Our model is consistent with numerous properties of Abeta42 fibrillar oligomers, including heterogenous size, ability to seed new populations of fibrillar oligomers, and fiber-like morphology.Abeta oligomers | toxic oligomers | Alzheimer's disease | domain swapping | protein aggregation S everal neurodegenerative diseases are correlated with amyloid fibrillar deposits (1). For a number of these diseases, it has been postulated that amyloid fibers may not play the primary causative role (2). Rather, soluble aggregates of the amyloidogenic proteins are likely the relevant etiological agents (2, 3). The most prevalent of these neurodegenerative diseases, Alzheimer's disease (4), is strongly linked to the presence of soluble aggregates of amyloid-β (Abeta) (5). Abeta aggregates have been shown to impair neurite function (6), synaptic morphology (7), cognitive function (8), and cell viability (9). In the prion conditions, also classed as amyloid diseases (10), small oligomers have also been identified as the toxic species (11). Recently, the availability of structure-specific antibodies has provided a means to group oligomers into two broad antigenic categories known as prefibrillar and fibrillar oligomers (12). Fibrillar oligomers are recognized by the OC antibody isolated from rabbits immunized with Abeta fibers (13), suggesting that Abeta fibrillar oligomers share surface features with Abeta fibers. In addition to fiber-like morphology, fibrillar oligomers are similar to fibers in that fibrillar oligomers can seed new populations of fibrillar oligomers (14). The ability to seed suggests that, like fibers, fibrillar oligomers are organized into a repeating array or lattice of monomers, wherein the monomers have identical structures. Fibrillar oligomers likely have a distinct lattice from fibers, because Abeta fibrillar oligomers do not seed Abeta fiber formation (14). Here, we characterize a particular preparation of fibrillar oligomers that we term toxic Abeta 1-42 (Abeta42) fibrillar oligomers (TABFOs).The structure of amyloid fibers may provide insight into the structure of fibrillar oligomers. Fiber diffraction studies of chemically pure amyloid display a cross-β diffraction...