Amyloid

small bowel

. Duodenum with amyloid deposition in lamina propria. Amyloid shows up as homogeneous pink material in lamina propria and around blood vessels. 20× magnification.

Amyloids are aggregates of

) and form fibrous deposits within and around cells. These protein misfolding and deposition processes disrupt the healthy function of tissues and organs.

Such amyloids have been associated with (but not necessarily as the cause of) more than 50

Amyloids have been known to arise from many different proteins.[2]^[7] These polypeptide chains generally form β-sheet structures that aggregate into long fibers; however, identical polypeptides can fold into multiple distinct amyloid conformations.^[8] The diversity of the conformations may have led to different forms of the prion diseases.^[6]

An unusual secondary structure named α sheet has been proposed as the toxic constituent of amyloid precursor proteins,^[9] but this idea is not widely accepted at present.

Definition

The name amyloid comes from the early mistaken identification by

• The classical,
  secondary structure and identified by apple-green birefringence when stained with congo red under polarized light. These deposits often recruit various sugars and other components such as serum amyloid P component, resulting in complex, and sometimes inhomogeneous structures.^[11] Recently this definition has come into question as some classic, amyloid species have been observed in distinctly intracellular locations.^[12]
• A more recent,
  physicists have largely adopted this definition,^[13][14] leading to some conflict in the biological community over an issue of language
  .

Proteins forming amyloids in diseases

To date, 37 human

A table is included below.

Protein	Diseases	Official abbreviation
Amyloid precursor protein[15][16][17][18]	Alzheimer's disease, Hereditary cerebral haemorrhage with amyloidosis	Aβ
α-synuclein[16]	Parkinson's disease, Parkinson's disease dementia, Dementia with Lewy bodies, Multiple system atrophy	AαSyn
PrPSc[19]	New variant Creutzfeldt-Jacob disease )	APrP
Microtubule-associated protein tau	Various forms of Argyrophilic grain disease )	ATau
Huntingtin exon 1[20][21]	Huntington's disease	HTTex1
ABri peptide	Familial British dementia	ABri
ADan peptide	Familial Danish dementia	ADan
Fragments of immunoglobulin light chains[22]	Light chain amyloidosis	AL
Fragments of immunoglobulin heavy chains[22]	Heavy chain amyloidosis	AH
full length of N-terminal fragments of Serum amyloid A protein	AA amyloidosis	AA
Transthyretin	Leptomeningeal amyloidosis	ATTR
β-2 microglobulin	Hereditary visceral amyloidosis (familial)	Aβ2M
N-terminal fragments of Apolipoprotein AI	ApoAI amyloidosis	AApoAI
C-terminally extended Apolipoprotein AII	ApoAII amyloidosis	AApoAII
N-terminal fragments of Apolipoprotein AIV	ApoAIV amyloidosis	AApoAIV
Apolipoprotein C-II	ApoCII amyloidosis	AApoCII
Apolipoprotein C-III	ApoCIII amyloidosis	AApoCIII
fragments of Gelsolin	Familial amyloidosis, Finnish type	AGel
Lysozyme	Hereditary non-neuropathic systemic amyloidosis	ALys
fragments of Fibrinogen α chain	Fibrinogen amyloidosis	AFib
N-terminally truncated Cystatin C	Hereditary cerebral hemorrhage with amyloidosis, Icelandic type	ACys
IAPP (Amylin)[23][24]	Diabetes mellitus type 2 , Insulinoma	AIAPP
Calcitonin[22]	Medullary carcinoma of the thyroid	ACal
Atrial natriuretic factor	Cardiac arrhythmias, Isolated atrial amyloidosis	AANF
Prolactin	Pituitary prolactinoma	APro
Insulin	Injection-localized amyloidosis	AIns
Medin	Aortic medial amyloidosis	AMed
Lactotransferrin / Lactoferrin	Gelatinous drop-like corneal dystrophy	ALac
Odontogenic ameloblast-associated protein	Calcifying epithelial odontogenic tumors	AOAAP
Pulmonary surfactant-associated protein C (SP-C)	Pulmonary alveolar proteinosis	ASPC
Leukocyte cell-derived chemotaxin-2 (LECT-2)	Renal LECT2 amyloidosis	ALECT2
Galectin-7	Macular amyloidosis	AGal7
Corneodesmosin	Hypotrichosis simplex of the scalp	ACor
C-terminal fragments of Keratoepithelin	Lattice corneal dystrophy type I , Lattice corneal dystrophy type 3A, Lattice corneal dystrophy Avellino type	AKer
Semenogelin-1 (SGI)	Seminal vesicle amyloidosis	ASem1
Proteins S100A8/A9	Prostate cancer	none
Enfuvirtide	Injection-localized amyloidosis	AEnf

Non-disease and functional amyloids

Many examples of non-pathological amyloid with a well-defined physiological role have been identified in various organisms, including

• Functional amyloid in
  Homo sapiens
  :
  • Intralumenal domain of melanocyte protein PMEL^[27]
  • Peptide/protein hormones stored as amyloids within endocrine secretory granules^[28]
  • Receptor-interacting serine/threonine-protein kinase 1/3 (RIP1/RIP3)^[29]
  • Fragments of prostatic acid phosphatase and semenogelins^[30]

• Functional amyloid in other organisms:
  • operons) encoding the curli system are phylogenetic widespread and can be found in at least four bacterial phyla.^[31]
    This suggest that many more bacteria may express curli fibrils.
  • GvpA, forming the walls of particular Gas vesicles, i.e. the buoyancy organelles of aquatic archaea and eubacteria^[32]
  • Fap fibrils in various species of Pseudomonas^[33][34]
  • Chaplins from
    Streptomyces coelicolor^[35]
  • Spidroin from Trichonephila edulis (spider) (Spider silk)^[36]
  • Hydrophobins from Neurospora crassa and other fungi^[37]
  • Fungal cell adhesion proteins forming cell surface amyloid regions with greatly increased binding strength^[38][39]
  • Environmental biofilms according to staining with amyloid specific dyes and antibodies.^[40]
  • Tubular sheaths encasing Methanosaeta thermophila filaments^[41]

• Functional amyloid acting as prions
  • Several
    yeast prions are based on an infectious amyloid, e.g. [PSI+] (Sup35p); [URE3] (Ure2p
    ); [PIN+] or [RNQ+] (Rnq1p); [SWI1+] (Swi1p) and [OCT8+] (Cyc8p)
  • Prion HET-s from Podospora anserina^[42]
  • Neuron-specific isoform of CPEB from
    Aplysia californica (marine snail)^[43]

Structure

Amyloids are formed of long unbranched fibers that are characterized by an extended

The term "cross-β" was based on the observation of two sets of diffraction lines, one longitudinal and one transverse, that form a characteristic "cross" pattern.

Amyloid fibrils are generally composed of 1–8 protofilaments (one protofilament also corresponding to a fibril is shown in the figure), each 2–7 nm in diameter, that interact laterally as flat ribbons that maintain the height of 2–7 nm (that of a single protofilament) and are up to 30 nm wide; more often protofilaments twist around each other to form the typically 7–13 nm wide fibrils.[2] Each protofilament possesses the typical cross-β structure and may be formed by 1–6 β-sheets (six are shown in the figure) stacked on each other. Each individual protein molecule can contribute one to several β-strands in each protofilament and the strands can be arranged in antiparallel β-sheets, but more often in parallel β-sheets. Only a fraction of the polypeptide chain is in a β-strand conformation in the fibrils, the remainder forms structured or unstructured loops or tails.

For a long time our knowledge of the atomic-level structure of amyloid fibrils was limited by the fact that they are unsuitable for the most traditional methods for studying protein structures. Recent years have seen progress in experimental methods, including

There are eight theoretical classes of steric-zipper interfaces, dictated by the directionality of the β-sheets (parallel and anti-parallel) and symmetry between adjacent β-sheets. A limitation of X-ray crystallography for solving amyloid structure is represented by the need to form microcrystals, which can be achieved only with peptides shorter than those associated with disease.

Although bona fide amyloid structures always are based on intermolecular β-sheets, different types of "higher order" tertiary folds have been observed or proposed. The β-sheets may form a β-sandwich, or a β-solenoid which may be either β-helix or β-roll. Native-like amyloid fibrils in which native β-sheet containing proteins maintain their native-like structure in the fibrils have also been proposed.^[50] There are few developed ideas on how the complex backbone topologies of disulfide-constrained proteins, which are prone to form amyloid fibrils (such as insulin and lysozyme), adopt the amyloid β-sheet motif. The presence of multiple constraints significantly reduces the accessible conformational space, making computational simulations of amyloid structures more feasible. ^[51]

One complicating factor in studies of amyloidogenic polypeptides is that identical polypeptides can fold into multiple distinct amyloid conformations.^[6] This phenomenon is typically described as amyloid polymorphism.^{[8][52] [53]} It has notable biological consequences given that it is thought to explain the prion strain phenomenon.

Formation

Amyloid is formed through the

time course is observed reflecting the three distinct phases.

In the simplest model of 'nucleated polymerization' (marked by red arrows in the figure below), individual unfolded or partially unfolded

A different model, called 'nucleated conformational conversion' and marked by blue arrows in the figure below, was introduced later on to fit some experimental observations: monomers have often been found to convert rapidly into misfolded and highly disorganized oligomers distinct from nuclei.[58] Only later on, will these aggregates reorganise structurally into nuclei, on which other disorganised oligomers will add and reorganise through a templating or induced-fit mechanism (this 'nucleated conformational conversion' model), eventually forming fibrils.^[58]

Normally

In these native-like conformations, segments that are normally buried or structured in the fully folded and possessing a high propensity to aggregate become exposed to the solvent or flexible, allowing the formation of native-like aggregates, which convert subsequently into nuclei and fibrils. This process is called 'native-like aggregation' (green arrows in the figure) and is similar to the 'nucleated conformational conversion' model.

A more recent, modern and thorough model of amyloid fibril formation involves the intervention of secondary events, such as 'fragmentation', in which a fibril breaks into two or more shorter fibrils, and 'secondary nucleation', in which fibril surfaces (not fibril ends) catalyze the formation of new nuclei.[57] Both secondary events increase the number of fibril ends able to recruit new monomers or oligomers, therefore accelerating fibril formation through a positive feedback mechanism. These events add to the well recognised steps of primary nucleation (formation of the nucleus from the monomers through one of models described above), fibril elongation (addition of monomers or oligomers to growing fibril ends) and dissociation (opposite process).

Such a new model is described in the figure on the right and involves the utilization of a

, Cohen, Michaels and coworkers and considers the time evolution of the concentration ${\displaystyle f(t,j)}$ of fibrils of length ${\displaystyle j}$ (here ${\displaystyle j}$ represents the number of monomers in an aggregate).[60] where ${\displaystyle \delta _{i,j}}$ denotes the Kronecker delta. The physical interpretation of the various terms in the above master equation is straight forward: the terms on the first line describe the growth of fibrils via monomer addition with rate constant ${\displaystyle k_{+}}$ (elongation). The terms on the second line describe monomer dissociation, i.e. the inverse process of elongation. ${\displaystyle k_{\rm {off}}}$ is the rate constant of monomer dissociation. The terms on the third line describe the effect of fragmentation, which is assumed to occur homogeneously along fibrils with rate constant ${\displaystyle k_{-}}$. Finally, the terms on the last line describe primary and secondary nucleation respectively. Note that the rate of secondary nucleation is proportional to the mass of aggregates, defined as ${\displaystyle M(t)=\sum _{j=n_{1}}^{\infty }jf(t,j)}$.

Following this analytical approach, it has become apparent that the lag phase does not correspond necessarily to only nucleus formation, but rather results from a combination of various steps. Similarly, the exponential phase is not only fibril elongation, but results from a combination of various steps, involving primary nucleation, fibril elongation, but also secondary events. A significant quantity of fibrils resulting from primary nucleation and fibril elongation may be formed during the lag phase and secondary steps, rather than only fibril elongation, can be the dominant processes contributing to fibril growth during the exponential phase. With this new model, any perturbing agents of amyloid fibril formation, such as putative

, etc., can be assigned to a specific step of fibril formation.

Amino acid sequence and amyloid formation

In general, amyloid

There are multiple classes of amyloid-forming polypeptide sequences.

Other polypeptides and proteins such as amylin and the β amyloid peptide do not have a simple consensus sequence and are thought to aggregate through the sequence segments enriched with hydrophobic residues, or residues with high propensity to form β-sheet structure.^[61] Among the hydrophobic residues, aromatic amino-acids are found to have the highest amyloidogenic propensity.^[65][66]

Cross-polymerization (fibrils of one polypeptide sequence causing other fibrils of another sequence to form) is observed in vitro and possibly in vivo. This phenomenon is important, since it would explain interspecies prion propagation and differential rates of prion propagation, as well as a statistical link between Alzheimer's and type 2 diabetes.^[67] In general, the more similar the peptide sequence the more efficient cross-polymerization is, though entirely dissimilar sequences can cross-polymerize and highly similar sequences can even be "blockers" that prevent polymerization.^{[citation needed]}

Amyloid toxicity

The reasons why amyloid cause diseases are unclear. In some cases, the deposits physically disrupt tissue architecture, suggesting disruption of function by some bulk process. An emerging consensus implicates prefibrillar intermediates, rather than mature amyloid fibers, in causing cell death, particularly in neurodegenerative diseases.^[17][68] The fibrils are, however, far from innocuous, as they keep the protein homeostasis network engaged, release oligomers, cause the formation of toxic oligomers via secondary nucleation, grow indefinitely spreading from district to district^[2] and, in some cases, may be toxic themselves.^[69]

Calcium dysregulation has been observed to occur early in cells exposed to protein oligomers. These small aggregates can form ion channels through lipid bilayer membranes and activate NMDA and AMPA receptors. Channel formation has been hypothesized to account for calcium dysregulation and mitochondrial dysfunction by allowing indiscriminate leakage of ions across cell membranes.^[70] Studies have shown that amyloid deposition is associated with mitochondrial dysfunction and a resulting generation of reactive oxygen species (ROS), which can initiate a signalling pathway leading to apoptosis.^[71] There are reports that indicate amyloid polymers (such as those of huntingtin, associated with Huntington's disease) can induce the polymerization of essential amyloidogenic proteins, which should be deleterious to cells. Also, interaction partners of these essential proteins can also be sequestered.^[72]

All these mechanisms of toxicity are likely to play a role. In fact, the aggregation of a protein generates a variety of aggregates, all of which are likely to be toxic to some degree. A wide variety of biochemical, physiological and cytological perturbations has been identified following the exposure of cells and animals to such species, independently of their identity. The oligomers have also been reported to interact with a variety of molecular targets. Hence, it is unlikely that there is a unique mechanism of toxicity or a unique cascade of cellular events. The misfolded nature of protein aggregates causes a multitude of aberrant interactions with a multitude of cellular components, including membranes, protein receptors, soluble proteins, RNAs, small metabolites, etc.

Histological staining

In the clinical setting, amyloid diseases are typically identified by a change in the spectroscopic properties of planar

Congo Red positivity remains the gold standard for diagnosis of

has made specific staining easier, but often this can cause trouble because epitopes can be concealed in the amyloid fold; in general, an amyloid protein structure is a different conformation from the one that the antibody recognizes.

See also

• JUNQ and IPOD
• Proteopathy
• Protein aggregation predictors

References

External links

Wikimedia Commons has media related to Amyloid.

• Bacterial Inclusion Bodies Contain Amyloid-Like Structure at SciVee
• Amyloid Cascade Hypothesis
• Amyloid: Journal of Protein Folding Disorders web page
• Role of anesthetics in Alzheimer's disease: Molecular details revealed