Functional amyloids can be found in bacteria, unicellular eukaryotes, fungi, plants, insects and vertebrates, playing roles as diverse as surface protection and modification, mediation of pathogen-host interactions, pigment biosynthesis, homeostasis control, hormone storage and release, signal transduction, among others. The aggregation of a polypeptide chain into amyloid fibrils and their accumulation and deposition into insoluble plaques and intracellular inclusions is the hallmark of several misfolding diseases known as amyloidoses. Alzheimer′s, Parkinson′s and Huntington’s diseases are some of the approximately 50 amyloid diseases described to date.
|Disease||Precursor Protein||Polypeptide Length (n° of Residues)||Structural Organization of Precursor|
|Alzheimer’s disease||Amyloid-β variants||37–44||IDP|
|Spongiform encephalopathies||Prion protein or its fragments||208||IDP and α-helical|
|Frontotemporal dementia with Parkinsonism||Tau||352–441||IDP|
|Amyotrophic lateral sclerosis||Superoxide dismutase 1||153||β-sheet|
|Huntington’s disease||Huntingtin with polyQ expansion||3144||Mostly IDP|
|Neuroferritinopathy||Ferritin||175 or 183||α-helical|
|Familial British dementia||ABri||34||IDP|
|Familial Danish dementia||ADan||34||IDP|
|Familial amyloid polyneuropathy||Transthyretin variants||127||β-sheet|
|Non-Neuropathic Systemic Amyloidosis|
|Amyloid light chain amyloidosis||Immunoglobulin light chains or its fragments||~90||β-sheet|
|Amyloid heavy chain amyloidosis||Immunoglobulin heavy chains or its fragments||~220||β-sheet|
|Amyloid A amyloidosis||Serum amyloid A protein fragments||45–104||α-helical and unknown fold|
|Familial Mediterranean fever||Serum amyloid A protein fragments||45–104||α-helical and unknown fold|
|Apolipoprotein A1 amyloidosis||Apo A-1 fragments||80–93||IDP|
|Senile systemic amyloidosis||Wild-type transthyretin||127||β-sheet|
|Familial amyloid cardiomyopathy||Transthyretin variants||127||β-sheet|
|Lysozyme amyloidosis||Lysozyme variants||130||α-helical and β-sheet|
|Finnish hereditary amyloidosis||Fragments of gelsolin variants||53 or 71||IDP|
|Non-Neuropathic Localized Amyloidosis|
|Type II diabetes||Islet amyloid polypeptide||37||IDP|
|Injection-localized amyloidosis||Insulin||21 and 30||α-helical|
|Gelatinous drop-like corneal dystrophy||Lactoferrin||691||α-helical and β-sheet|
|Medullary carcinoma of the thyroid||Calcitonin||32||IDP|
|Localized cutaneous amyloidosis||Galectin 7||136||β-sheet|
|Atrial amyloidosis||Atrial natriuretic factor||28||IDP|
|X-ray and electron diffraction||1. Discovery of short protein segments that can themselves form amyloid fibrils and closely related crystals;
2. Development of synchrotron X-ray microbeams sufficiently focused and intense to determine a structure from a single crystal.
|1. May yield atomic resolution;
2. Is not limited by the molecular weight of the specimen.
|1. Well-ordered microcrystals needed;
2. The fibrils formed by some segments may represent the spines of polymorphs of full fibrils, but others may not;
3. The crystallized segment is only a few residues in length, thus nothing is revealed about the fibril structure outside the spine;
4. The steric zippers structures only show homo-steric zippers.
|ssNMR||1. Innovations in high-field magnets, pulse sequences, high-resolution multi-channel magic-angle spinning (MAS) probes, ultrafast MAS, isotopic labeling schemes, use of quadrupolar nuclei as spectroscopic probes and solid-state dynamic nuclear polarization (DNP).||1. No need for crystals;
2. Structural information obtained on: identity of residues, recognition of parallel versus antiparallel β-sheets, register of strands within a sheet, and inter-residue contacts of amino acid side chains;
3. ssNMR-determined models show the overall conformation of the well-ordered portion of the chain around the protofilament spine;
4. Can be used to determine dihedral angles and inter-atom distances in the fibril subunits.
|1. Amyloid-forming proteins are expressed recombinantly from media containing isotopically labeled amino acids;
2. Reliability of molecular models is highly dependent on the number of experimental constraints that have been collected;
3. The relative positions of atoms are not as accurately determined as in an atomic-resolution crystal structure;
4. The sensitivity of the experiments and spectral resolution decrease with the increase in molecular weight.
|cryo-EM||1. Introduction of high-field microscopes;
2. New generation of direct detectors record the incident electrons in a thin, sensitive layer so that the signal is not scattered into surrounding pixels resulting in an improvement in image processing.
|1. Near atomic-resolution structures of large molecular complexes without the need for crystals;
2. May yield the overall fibril structure: the number of protofilaments; the degree of twist; and, depending on the number of well-ordered specimens, information on the atomic structure of the fibril.
|1. Due to a lack of contrast, images often have a very low signal-to-noise ratio, requiring highly advanced detection hardware and image processing;
2. Sample preparation can be difficult, not only to optimize thickness, but also to optimize particle distribution;
3. The most advanced cryo-EM equipment is very expensive.
|Nature of Monomeric Species||Description||References|
|Normally folded proteins may retain a substantial tendency to aggregate through direct assembly of monomers in their native state when the native state exposes complementary surfaces.|||
|Conformationally altered monomer||The native monomer has very low propensity to associate. Partial unfolding or conformational changes of the native monomer are required, resulting in a non-native species prone to aggregate.|||
|Chemically modified monomer||Chemical modifications (deamidation, isomerization, hydrolysis, oxidation, photolysis, etc.) may cause conformational changes in native monomers, leading to species with high propensity to aggregate.|||
|Nature of Aggregation Interfaces||Description||References|
|Hydrophobic–hydrophilic interfaces may induce aggregation reactions.|||
|Mechanical stress (agitation, stirring, pumping, or shaking) has been associated with cavitation which generates air bubbles and, consequently, the formation of an air-water interface which facilitates protein denaturation and aggregation.|||
|The use of beads during agitation accelerates the aggregation process by enhancing cavitation.|||
|Solid-liquid interfaces may facilitate monomer encounters and initial monomer to monomer association and later further aggregation.|
|In vitro, interaction with glass, silicone, graphite, polypropylene, Teflon, mica, gold, etc. might lead to protein partial unfolding and aggregation.|||
|In vitro and in vivo, flow through tubes and vessels produce shear forces that may lead to protein partial unfolding and aggregation.|||
|Freeze-thaw cycles create new ice-water interfaces which may induce protein partial unfolding and aggregation.|||
|Presence of metal ions, in particular, Cu2+ and Zn2+, may promote aggregation of protein monomers bearing metal-ion binding sites or binding residues (e.g., histidines).|||
|Monomer association at the surface of biomembranes or biomolecules may also enhance aggregation.|||