Amyloid - WikiHQ

thumb|[[Micrograph showing amyloid deposits (pink) in 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 proteins characterised by a fibrillar morphology of typically 7–13 nm in diameter, a β-sheet secondary structure (known as cross-β) and ability to be stained by particular dyes, such as Congo red. In the human body, amyloids have been linked to the development of various diseases. human diseases, including amyloidosis, and may play a role in some neurodegenerative diseases. Some of these diseases are mainly sporadic and only a few cases are familial. Others are only familial. Some result from medical treatment. Prions are an infectious form of amyloids that can act as a template to convert other non-infectious forms. Amyloids may also have normal biological functions; for example, in the formation of fimbriae in some genera of bacteria, transmission of epigenetic traits in fungi, as well as pigment deposition and hormone release in humans. These polypeptide chains generally form β-sheet structures that aggregate into long fibers; however, identical polypeptides can fold into multiple distinct amyloid conformations.

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

thumb|upright=1.1|Amyloid of HET-s(218–289) prion pentamer, Podospora anserina ()

Definition

The name amyloid comes from the early mistaken identification by Rudolf Virchow of the substance as starch ( in Latin, from ), based on crude iodine-staining techniques. For a period, the scientific community debated whether or not amyloid deposits are fatty deposits or carbohydrate deposits until it was finally found (in 1859) that they are, in fact, deposits of albumin-like proteinaceous material.

The classical, histopathological definition of amyloid is an extracellular, proteinaceous fibrillar deposit exhibiting β-sheet 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. Recently this definition has come into question as some classic, amyloid species have been observed in distinctly intracellular locations.
A more recent, biophysical definition is broader, including any polypeptide that polymerizes to form a cross-β structure, in vivo or in vitro, inside or outside cells. Microbiologists, biochemists, biophysicists, chemists and physicists have largely adopted this definition, leading to some conflict in the biological community over an issue of language.

Proteins forming amyloids in diseases

To date, 37 human proteins have been found to form amyloid in pathology and be associated with well-defined diseases.

|Alzheimer's disease, Hereditary cerebral haemorrhage with amyloidosis

| Aβ

|α-synuclein

|Transmissible spongiform encephalopathy (e.g. Fatal familial insomnia, Gerstmann-Sträussler-Scheinker disease, Creutzfeldt–Jakob disease, New variant Creutzfeldt–Jakob disease)

|APrP

|Microtubule-associated protein tau

|Various forms of tauopathies (e.g. Pick's disease, Progressive supranuclear palsy, Corticobasal degeneration, Frontotemporal dementia with parkinsonism linked to chromosome 17, Argyrophilic grain disease)

|ATau

|Huntingtin exon 1

|Huntington's disease

|HTTex1

|ABri peptide

|Familial British dementia

|ABri

|ADan peptide

|Familial Danish dementia

|ADan

|Fragments of immunoglobulin light chains

|Diabetes mellitus type 2, Insulinoma

| AIAPP

|Calcitonin

|Medullary carcinoma of the thyroid

| ACal

|Atrial natriuretic factor

|Cardiac arrhythmias, Isolated atrial amyloidosis

|AANF

|Prolactin

|Pituitary prolactinoma

|APro

|Insulin

|Injection-localized amyloidosis

|AIns

|Lactadherin / 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

|Lichen amyloidosis, Macular amyloidosis

|AGal7

|Corneodesmosin

|Hypotrichosis simplex of the scalp

|ACor

|C-terminal fragments of TGFBI/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 human. These may be termed as functional or physiological or native amyloid.

Peptide/protein hormones stored as amyloids within endocrine secretory granules
Receptor-interacting serine/threonine-protein kinase 1/3 (RIP1/RIP3)
Fragments of prostatic acid phosphatase and semenogelins
Functional amyloid in other organisms:
Curli fibrils produced by E. coli, Salmonella, and a few other members of the Enterobacteriales (Csg). The genetic elements (operons) encoding the curli system are phylogenetic widespread and can be found in at least four bacterial phyla. 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
Fap fibrils in various species of Pseudomonas
Chaplins from Streptomyces coelicolor
Spidroin from Trichonephila edulis (spider) (Spider silk)
Hydrophobins from Neurospora crassa and other fungi
Fungal cell adhesion proteins forming cell surface amyloid regions with greatly increased binding strength
Environmental biofilms according to staining with amyloid specific dyes and antibodies.
Tubular sheaths encasing Methanosaeta thermophila filaments
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
Neuron-specific isoform of CPEB from Aplysia californica (marine snail)

Structure

thumb|Structure of a fibril, consisting of one single protofilament, of the amyloid β peptide viewed down the long axis of the fibril ()

Amyloids are formed of long unbranched fibers that are characterized by an extended β-sheet secondary structure in which individual β strands (β-strands) (coloured arrows in the adjacent figure) are arranged in an orientation perpendicular to the long axis of the fiber. Such a structure is known as cross-β structure. Each individual fiber may be 7–13 nanometres in width and a few micrometres in length. There are two characteristic scattering diffraction signals produced at 4.7 and 10 Å (0.47 nm and 1.0 nm), corresponding to the interstrand and stacking distances in β sheets.

X-ray diffraction studies of microcrystals revealed atomistic details of core region of amyloid, although only for simplified peptides having a length remarkably shorter than that of peptides or proteins involved in disease. The crystallographic structures show that short stretches from amyloid-prone regions of amyloidogenic proteins run perpendicular to the filament axis, consistent with the "cross-β" feature of amyloid structure. They also reveal a number of characteristics of amyloid structures – neighboring β-sheets are tightly packed together via an interface devoid of water (therefore referred to as dry interface), with the opposing β-strands slightly offset from each other such that their side-chains interdigitate. This compact dehydrated interface created was termed a steric-zipper interface. 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.

One complicating factor in studies of amyloidogenic polypeptides is that identical polypeptides can fold into multiple distinct amyloid conformations.

Formation

thumb|upright=1.35|Three phases of amyloid fibril formation: [[Incubation period|lag phase, exponential phase and plateau phase]]

Amyloid is formed through the polymerization of hundreds to thousands of monomeric peptides or proteins into long fibers. Amyloid formation involves a lag phase (also called nucleation phase), an exponential phase (also called growth phase) and a plateau phase (also called saturation phase), as shown in the figure. When the quantity of fibrils is plotted versus time, a sigmoidal 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 polypeptide chains (monomers) convert into a nucleus (monomer or oligomer) via a thermodynamically unfavourable process that occurs early in the lag phase. 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. In some cases, however, folded proteins can aggregate without crossing the major energy barrier for unfolding, by populating native-like conformations as a consequence of thermal fluctuations, ligand release or local unfolding occurring in particular circumstances. The rate constants of the various steps can be determined from a global fit of a number of time courses of aggregation (for example ThT fluorescence emission versus time) recorded at different protein concentrations. For example, humans produce amylin, an amyloidogenic peptide associated with type II diabetes, but in rats and mice prolines are substituted in critical locations and amyloidogenesis does not occur. Studies comparing synthetic to recombinant β amyloid peptide in assays measuring rate of fibrillation, fibril homogeneity, and cellular toxicity showed that recombinant β amyloid peptide has a faster fibrillation rate and greater toxicity than synthetic β amyloid peptide.

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.

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. 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.

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. 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

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. 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. 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.

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 aromatic dyes such as thioflavin T, congo red or NIAD-4. In general, this is attributed to the environmental change, as these dyes intercalate between β-strands to confine their structure.

Congo Red positivity remains the gold standard for diagnosis of amyloidosis. In general, binding of Congo Red to amyloid plaques produces a typical apple-green birefringence when viewed under cross-polarized light. Recently, significant enhancement of fluorescence quantum yield of NIAD-4 was exploited to super-resolution fluorescence imaging of amyloid fibrils and oligomers. To avoid nonspecific staining, other histology stains, such as the hematoxylin and eosin stain, are used to quench the dyes' activity in other places such as the nucleus, where the dye might bind. Modern antibody technology and immunohistochemistry 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.

References

External links

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