||This article may be too technical for most readers to understand. (February 2013)|
Amyloids are insoluble fibrous protein aggregates sharing specific structural traits. They arise from at least 18 inappropriately folded versions of proteins and polypeptides present naturally in the body. These misfolded structures alter their proper configuration such that they erroneously interact with one another or other cell components forming insoluble fibrils. They have been associated with the pathology of more than 20 serious human diseases in that abnormal accumulation of amyloid fibrils in organs may lead to amyloidosis, and may play a role in various neurodegenerative disorders.
The name amyloid comes from the early mistaken identification by Rudolf Virchow of the substance as starch (amylum in Latin), 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 albumoid proteinaceous material.
- The classical, histopathological definition of amyloid is an extracellular, proteinaceous deposit exhibiting beta sheet structure. Common to most cross-beta-type structures, in general, they are identified by apple-green birefringence when stained with congo red and seen 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-beta structure, in vivo or in vitro. Some of these, although demonstrably cross-beta sheet, do not show some classic histopathological characteristics such as the Congo-red birefringence. Microbiologists and biophysicists have largely adopted this definition, leading to some conflict in the biological community over an issue of language.
The remainder of this article will use the biophysical context.
Diseases featuring amyloids
The International Society of Amyloidosis classifies amyloid fibrils based upon associated proteins.
Non-disease and functional amyloids
- Native amyloids in 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.
- Functional amyloids in Pseudomonas (Fap)
- Chaplins from Streptomyces coelicolor
- Podospora Anserina Prion Het-s
- Malarial coat protein
- Spider silk (some but not all spiders)
- Mammalian melanosomes (pMel)
- Tissue-type plasminogen activator (tPA), a hemodynamic factor
- ApCPEB protein and its homologues with a glutamine-rich domain
- Pmel17 derived amyloid within the melanosomal matrix
- Peptide/protein hormones stored as amyloids within endocrine secretory granules
- Proteins and peptides engineered to make amyloid that display specific properties, such as ligands that target cell surface receptors
- Several yeast prions are based on an infectious amyloid, e.g. [PSI+] (Sup35p); [URE3] (Ure2p); [PIN+] (Rnq1p); [SWI1+] (Swi1p) and [OCT8+] (Cyc8p)
- Functional amyloids are abundant in most environmental biofilms according to staining with amyloid specific dyes and antibodies
Amyloid is characterized by a cross-beta sheet quaternary structure. While amyloid is usually identified using fluorescent dyes, stain polarimetry, circular dichroism, or FTIR (all indirect measurements), the "gold-standard" test to see whether a structure contains cross-beta fibres is by placing a sample in an X-ray diffraction beam. The term "cross-beta" was based on the observation of two sets of diffraction lines, one longitudinal and one transverse, that form a characteristic "cross" pattern. There are two characteristic scattering diffraction signals produced at 4.7 and 10 Ångstroms (0.47 nm and 1.0 nm), corresponding to the interstrand and stacking distances in beta sheets. The "stacks" of beta sheet are short and traverse the breadth of the amyloid fibril; the length of the amyloid fibril is built by aligned strands.
Recent X-ray diffraction studies of microcrystals revealed atomistic details of core region of amyloid. In the crystallographic structure, short stretches from amyloid-prone region of amyloidogenic proteins run perpendicular to the filament axis, confirming the "cross-beta" model. In addition, two layers of beta-sheet interdigitate to create compact dehydrated interface termed as steric-zipper interface. There are eight classes of steric-zipper interfaces, depending on types of beta-sheet (parallel and anti-parallel) and symmetry between two adjacent beta-sheets.
In general, amyloid polymerization (aggregation or non-covalent polymerization) is sequence-sensitive, that is, causing mutations in the sequence can prevent self-assembly, especially if the mutation is a beta-sheet breaker, such as proline or non-coded alpha-aminoisobutyric acid. 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 Amyloid beta 1-42 in assays measuring rate of fibrillation, fibril homogeneity, and cellular toxicity showed that recombinant Amyloid beta 1-42 has a faster fibrillation rate and greater toxicity than synthetic Amyloid beta 1-42 peptide. This observation combined with the irreproducibility of certain Amyloid beta 1-42 experimental studies has been suggested to be responsible for the lack of progress in Alzheimer’s research. Consequently, there has been renewed efforts to manufacture Amyloid beta 1-42 and other amyloid peptides at unprecedented (>99%) purity.
There are two broad classes of amyloid-forming polypeptide sequences. Glutamine-rich polypeptides are important in the amyloidogenesis of Yeast and mammalian prions, as well as Trinucleotide repeat disorders including Huntington's disease. When peptides are in a beta-sheet conformation, including arrangements in which the beta-strands are parallel and in-register (causing alignment of residues), glutamines can brace the structure by forming inter-strand hydrogen bonding between its amide carbonyls and nitrogens. In general, for this class of diseases, toxicity correlates with glutamine content. This has been observed in studies of onset age for Huntington's disease (the longer the polyglutamine sequence the sooner the symptoms appear), and has been confirmed in a C. elegans model system with engineered polyglutamine peptides.
Other polypeptides and proteins such as amylin and the Alzheimer's beta protein do not have a simple consensus sequence and are thought to operate by hydrophobic association. Among the hydrophobic residues, aromatic amino-acids are found to have the highest amyloidogenic propensity.
For these peptides, 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. Polypeptides will not cross-polymerize their mirror-image counterparts, indicating that the phenomenon involves specific binding and recognition events.
The fast aggregation process, rapid conformational changes as well as solvent effects provide challenges in measuring monomeric and oligomeric amyloid peptide structures in solution. Theoretical and computational studies complement experiments and provide insights that are otherwise difficult to obtain using conventional experimental tools. Several groups have successfully studied the disordered structures of amyloid and reported random coil structures with specific structuring for monomeric and oligomeric amyloid as well as how genetics and oxidative stress impact the flexible structures amyloid in solution.
The reasons for amyloid association disease 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. 
Calcium dysregulation has been observed in cells exposed to amyloid oligomers. These small aggregates can form ion channels in planar lipid bilayer membranes. 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 
In the clinical setting, amyloid diseases are typically identified by a change in the fluorescence intensity of planar aromatic dyes such as thioflavin T or congo red. Congo-red positivity remains the gold standard for diagnosis of amyloidosis. In general, this is attributed to the environmental change, as these dyes intercalate between beta-strands. In general, congophilic amyloid plaques cause apple-green birefringence when viewed through crossed polarimetric filters. 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.
- Marina Rami´rez-Alvarado, Jane S. Merkel, and Lynne Regan (2000). "A systematic exploration of the influence of the protein stability on amyloid fibril formation in vitro". PNAS 97 (16): 8979–8984. doi:10.1073/pnas.150091797. PMC 16807. PMID 10908649.
- Kyle R.A. (2001). "Amyloidosis: a convoluted story". Brit. J. Haem. 114 (3): 529–538. doi:10.1046/j.1365-2141.2001.02999.x. PMID 11552976.
- Sipe J. D., Cohen A.S. (2000). "Review: History of the Amyloid Fibril". J. Struct. Biol. 130 (2–3): 88–98. doi:10.1006/jsbi.2000.4221. PMID 10940217.
- Lin CY, Gurlo T, Kayed R, et al. (May 2007). "Toxic human islet amyloid polypeptide (h-IAPP) oligomers are intracellular, and vaccination to induce anti-toxic oligomer antibodies does not prevent h-IAPP-induced beta-cell apoptosis in h-IAPP transgenic mice". Diabetes 56 (5): 1324–32. doi:10.2337/db06-1579. PMID 17353506.
- Nilsson MR (September 2004). "Techniques to study amyloid fibril formation in vitro". Methods (San Diego, Calif.) 34 (1): 151–60. doi:10.1016/j.ymeth.2004.03.012. PMID 15283924.
- Fändrich M (August 2007). "On the structural definition of amyloid fibrils and other polypeptide aggregates". Cellular and molecular life sciences : CMLS 64 (16): 2066–78. doi:10.1007/s00018-007-7110-2. PMID 17530168.
- Chiang PK, Lam MA, Luo Y (September 2008). "The many faces of amyloid beta in Alzheimer's disease". Current molecular medicine 8 (6): 580–4. doi:10.2174/156652408785747951. PMID 18781964.
- Irvine GB, El-Agnaf OM, Shankar GM, Walsh DM (2008). "Protein aggregation in the brain: the molecular basis for Alzheimer's and Parkinson's diseases". Molecular medicine (Cambridge, Mass.) 14 (7–8): 451–64. doi:10.2119/2007-00100.Irvine. PMC 2274891. PMID 18368143.
- Ferreira ST, Vieira MN, De Felice FG (2007). "Soluble protein oligomers as emerging toxins in Alzheimer's and other amyloid diseases". IUBMB life 59 (4–5): 332–45. doi:10.1080/15216540701283882. PMID 17505973.
- Haataja L, Gurlo T, Huang CJ, Butler PC (May 2008). "Islet amyloid in type 2 diabetes, and the toxic oligomer hypothesis". Endocrine Reviews 29 (3): 303–16. doi:10.1210/er.2007-0037. PMC 2528855. PMID 18314421.
- Höppener JW, Ahrén B, Lips CJ (August 2000). "Islet amyloid and type 2 diabetes mellitus". The New England Journal of Medicine 343 (6): 411–9. doi:10.1056/NEJM200008103430607. PMID 10933741.
- "More than just mad cow disease", Nature Structural Biology 8, 281 (2001) doi:10.1038/86132
- Truant R, Atwal RS, Desmond C, Munsie L, Tran T (September 2008). "Huntington's disease: revisiting the aggregation hypothesis in polyglutamine neurodegenerative diseases". The FEBS journal 275 (17): 4252–62. doi:10.1111/j.1742-4658.2008.06561.x. PMID 18637947.
- Weydt P, La Spada AR (August 2006). "Targeting protein aggregation in neurodegeneration--lessons from polyglutamine disorders". Expert opinion on therapeutic targets 10 (4): 505–13. doi:10.1517/1472818.104.22.1685. PMID 16848688.
- "Amyloidosis, Overview" by Bruce A Baethge and Daniel R Jacobson
- Dotti CG, De Strooper B (February 2009). "Alzheimer's dementia by circulation disorders: when trees hide the forest". Nat. Cell Biol. 11 (2): 114–6. doi:10.1038/ncb0209-114. PMID 19188916.
- Sipe JD, Benson MD, Buxbaum JN, et al. (September 2010). "Amyloid fibril protein nomenclature: 2010 recommendations from the nomenclature committee of the International Society of Amyloidosis". Amyloid 17 (3–4): 101–104. doi:10.3109/13506129.2010.526812. PMID 21039326.
- Hammer ND, Wang X, McGuffie BA, Chapman MR (May 2008). "Amyloids: friend or foe?". Journal of Alzheimer's disease : JAD 13 (4): 407–19. PMC 2674399. PMID 18487849.
- Dueholm M. S., Albertsen M., Otzen D., Nielsen P. H. (2012). "Curli functional amyloid systems are phylogenetically widespread and display large diversity in operon and protein structure". In Webber, Mark Alexander. PLoS ONE 7 (12): e51274. doi:10.1371/journal.pone.0051274. PMC 3521004. PMID 23251478.
- Dueholm M. S., Petersen S. V., Sønderkaer M., Larsen P., Christiansen G., Hein K. L., Enghild J. J., Nielsen J. L., Nielsen K. L., Nielsen P. H. (2010). "Functional amyloid in Pseudomonas". Mol Microbiol 77 (4): 1009–1020. doi:10.1111/j.1365-2958.2010.07269.x. PMID 20572935.
- Dueholm M. S., Søndergaard M. T., Nilsson M., Christiansen G., Stensballe A., Overgaard M. T., Givskov M., Tolker-Nielsen T., Otzen D. E., Nielsen P. H. (2013). "Expression of Fap amyloids in Pseudomonas aeruginosa, P. fluorescens, and P. putida results in aggregation and increased biofilm formation". Microbiologyopen 2 (3): 365–382. doi:10.1002/mbo3.81. PMC 3684753. PMID 23504942.
- Maji, S.K.; et al. (2009). "Functional Amyloids As Natural Storage of Peptide Hormones in Pituitary Secretory Granules". Sceince 325 (5938): 328–332. doi:10.1126/science.1173155. PMID 19541956.
- Bongiovanni, M.N.; et al. (2011). "Functional fibrils derived from the peptide TTR1-cycloRGDfK that target cell adhesion and spreading". Biomaterials 26 (26): 6099–110. doi:10.1016/j.biomaterials.2011.05.021. PMID 21636126.
- Larsen P., Nielsen J. L., Dueholm M. S., Wetzel R., Otzen D., Nielsen P. H. (2007). "Amyloid adhesins are abundant in natural biofilms". Environ Microbiol 9 (12): 3077–3090. doi:10.1111/j.1462-2920.2007.01418.x. PMID 17991035.
- Wormell RL. New fibres from proteins. Academic Press, 1954, pg 106.
- Sunde M., Serpell L. C. et al. (1997). "Common core structure of amyloid fibrils by synchrotron X-ray diffraction". J Mol Biol 273 (3): 729–39. doi:10.1006/jmbi.1997.1348. PMID 9356260.
- Rebecca, Nelson; M. Sawaya; M. Balbirnie; A. Madsen; C. Riekel; R. Grothe; D. Eisenberg (9 Jun 2005). "Structure of the cross-beta spine of amyloid-like fibrils". Nature 435 (7043): 773–778. doi:10.1038/nature03680. PMC 1479801. PMID 15944695.
- Sawaya, Michael; Sambashivan S, Nelson R, Ivanova MI, Sievers SA, Apostol MI, Thompson MJ, Balbirnie M, Wiltzius JJ, McFarlane HT, Madsen AØ, Riekel C, Eisenberg D. (24 May 2007). "Atomic structures of amyloid cross-beta spines reveal varied steric zippers". Nature 447 (7143): 453–457. doi:10.1038/nature05695. PMID 17468747.
- Gilead S, Gazit E (August 2004). "Inhibition of amyloid fibril formation by peptide analogues modified with alpha-aminoisobutyric acid". Angew. Chem. Int. Ed. Engl. 43 (31): 4041–4. doi:10.1002/anie.200353565. PMID 15300690.
- finder, v; glockshuber (2009). "The Recombinant Amyloid-β Peptide Aβ1–42 Aggregates Faster and Is More Neurotoxic than Synthetic Aβ1–42". Journal of Molecular Biology 396 (1): 9–18. doi:10.1016/j.jmb.2009.12.016. PMID 20026079.
- Editor (2011). "State of Aggregation". Nature Neuroscience 14 (4): 399. doi:10.1038/nn0411-399. PMID 21445061.
- "BioPure Amyloid Peptides".
- Morley JF, Brignull HR, Weyers JJ, Morimoto RI. The threshold for polyglutamine-expansion protein aggregation and cellular toxicity is dynamic and influenced by aging in Caenorhabditis elegans. Proc Natl Acad Sci U S A. 2002 Aug 6;99(16):10417-22. Epub 2002 Jul 16.
- Gazit E (January 2002). "A possible role for pi-stacking in the self-assembly of amyloid fibrils". FASEB J. 16 (1): 77–83. doi:10.1096/fj.01-0442hyp. PMID 11772939.
- Pawar A. P., Dubay K. F. et al. (2005). "Prediction of "Aggregation-prone" and "Aggregation-susceptible" Regions in Proteins Associated with Neurodegenerative Diseases". J Mol Biol 350 (2): 379–92. doi:10.1016/j.jmb.2005.04.016. PMID 15925383.
- Jackson, K., Barisone, G. A., Diaz, E., Jin, L.-w., DeCarli, C. and Despa,F. (2013). "Amylin deposition in the brain: A second amyloid in Alzheimer disease?". Annals of Neurology: n/a. doi:10.1002/ana.23956.
- Wise-Scira O, Xu L, Kitahara T, Coskuner O, (October 2011). "Amyloid-β peptide structure in aqueous solution varies with fragment size". Journal of Chemical Physics 135 (1): 205101–11. doi:10.1063/1.3662490.
- Demuro A, Mina E, Kayed R, Milton SC, Parker I, Glabe CG (April 2005). "Calcium dysregulation and membrane disruption as a ubiquitous neurotoxic mechanism of soluble amyloid oligomers". The Journal of Biological Chemistry 280 (17): 17294–300. doi:10.1074/jbc.M500997200. PMID 15722360.
- Kagan BL,Azimov R,Azimova R (2004-11-01). "Amyloid Peptide Channels". J Membrane Biol 202 (1): 1=10.
- Kadowaki H. et al. (2005). "Amyloid beta induces neuronal cell death through ROS-mediated ASK1 activation". Cell Death Differ 12 (1): 19–24. doi:10.1038/sj.cdd.4401528. PMID 15592360.
- Kochneva-Pervukhova, NV; Alexandrov, AI, Ter-Avanesyan, MD (2012). "Amyloid-mediated sequestration of essential proteins contributes to mutant huntingtin toxicity in yeast". In Tuite, Mick F. PLoS ONE 7 (1): e29832. doi:10.1371/journal.pone.0029832. PMC 3256205. PMID 22253794.
- Dutch forum
-  Amyloidosis Foundation
- Bacterial Inclusion Bodies Contain Amyloid-Like Structure at SciVee
- Amyloid Cascade Hypothesis
- Stanford University Amyloid Center
- Amyloid Treatment and Research Program at Boston University
- Amyloid: Journal of Protein Folding Disorders web page at InformaWorld
- Information, support and advice to anyone with Amyloidosis, particularly in Australia (www.amyloidosisaustralia.org)
- UK National Amyloidosis Centre - one of the largest amyloid diagnosis and research centres at ucl.ac.uk
- Engineering Amyloid for material at University of California, Berkeley
- National Kidney and Urologic Diseases Information Clearinghouse at National Institute of Health
- Role of anesthetics in Alzheimer's disease: Molecular details revealed
- Mini Review Amyloidosis Covering structure, mechanisms of action and kinetics of amyloid fibrils.
- Video of amyloid formation.