User:Eliška Koutná/Sandbox 3

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= '''Prions''' =
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'''Prions'''
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<StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''>
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<StructureSection load='1qlx' size='340' side='right' caption='Human prion protein' scene='81/815943/1qlx/4'>
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== '''General intro''' ==
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Prion proteins are a common part of cell surface proteins in the mammalian nervous system, and they can, upon change of its conformation, become a highly infectious and pathogenic agent. The physiological form (PrPC) is encoded by the PRNP gene on chromosome 20 and when misfolded and aggregated, the pathological form (PrPSc) occurs, lacking any specific nucleic acid and its primary structure being determined by the PrPC form. When accumulated in the central nervous system (CNS) of mammals, PrPSc is known to be responsible for uprise of several untreatable progressive neurodegenerative diseases, generally called as transmissible spongiform encephalopathies (TSEs). These include kuru, fatal familial insomnia (FFI) and Creutzfeldt-Jacob disease (CJD) in humans, bovine spongiform encephalopathy (BSE) in cattle, scrapie in sheep and goats, transmissible mink encephalopathy (TME) in mink, feline spongiform encephalopathy (FSE) in cat or chronic wasting disease (CWD) in deer and elk <ref>DOI 10.1186/1743-422X-8-493</ref>.
== '''Protein structure''' ==
== '''Protein structure''' ==
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The PrPSc differs from PrPC solely in conformation and is its isoform. The mature PrPC consists of approx. 208 amino acids, arranged as a disordered N-terminus and a globular C-terminal domain consisting of three α-helices and a short, antiparallel β-pleated sheet <ref>PMID 10618385</ref><ref>DOI 10.1038/382180a0</ref>. There is a GPI membrane anchor at the C-terminus that tethers the protein to cell membranes and proteins that are secreted and lacking the anchor component has been proven to be unaffected by the infectious isoform <ref>DOI 10.1126/science.1110837</ref>. In contrast to the natural form of prion protein with only about 3 % of β-sheet secondary structure, the PrPSc form has about 47 % of the secondary structure in β-sheets <ref name="pan">PMID 7902575</ref> that create a core of four-rung β-solenoid fold <ref>DOI 10.3390/pathogens7010020</ref>.
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The PrPSc differs from PrPC solely in conformation and is its isoform. The mature PrPC consists of approx. 208 amino acids, arranged as a disordered N-terminus and a globular C-terminal domain consisting of <scene name='81/815943/1qlx/9'>three α-helices</scene> and a short, <scene name='81/815943/1qlx/16'>antiparallel β-pleated sheet</scene> <ref>PMID 10618385</ref><ref>DOI 10.1038/382180a0</ref>. There is a GPI membrane anchor at the C-terminus that tethers the protein to cell membranes and proteins that are secreted and lacking the anchor component has been proven to be unaffected by the infectious isoform <ref>DOI 10.1126/science.1110837</ref>. In contrast to the natural form of prion protein with only about 3 % of β-sheet secondary structure, experiments using Fourier-transform infrared (FTIR) spectroscopy, and circular dichroism spectroscopy (CD) have predicted that the PrPSc form has about<scene name='81/815943/2rnm/1'> 47 % of the secondary structure in β-sheets</scene> <ref name="pan">PMID 7902575</ref> that create a core of four-rung β-solenoid fold <ref name="wille">DOI 10.3390/pathogens7010020</ref>. Accordingly, they also differ in their properties. PrPC is soluble, has a life-span between 2 and 4 hours, and is sensitive to proteolytic cleavage – when exposed to proteases, the protein is degraded completely <ref name="pan" />. The two most important cleavage events are the α cleavage which removes the unstructured N-terminal tail and leaves the globular domain attached to the cell membrane, and the cleavage on the C-terminal end (termed PrPC shedding) which releases PrPC into the extracellular space <ref name="sigurdson">DOI 10.1146/annurev-pathmechdis- 012418-013109</ref>. Under the same conditions, PrPSc is hydrolysed by proteases only partially by forming resistant core fragment PrP 27-30 (N-terminally truncated variant) <ref name="pan" />. In addition, it is insoluble in detergents and has a very long half-life, therefore accumulates in tissues easily. It has a tendency to form aggregates and fibrillar structures and is generally susceptible to oligomerization, whereas the PrPC form mainly exist as a monomer <ref name="cohen&prusiner">DOI 10.1146/annurev.biochem.67.1.793</ref>. Monomeric PrPSc has never been isolated.
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There is a diversity in prion and prion-like assemblies that suggests no single PrPSc structure. The already mentioned core of four-rung β-solenoid fold is a model based on cryo-EM and X-ray diffraction studies of brain-derived PrPSc <ref name="table">DOI 10.1080/19336896.2019.1569450</ref>. This arrangement would result in 4 x 4.8 Å (~19 Å, 144 AAs) repeats along the axis of a protofilament which, interwined with another one, makes up the prion fibril. Which residues participate in the ß-strands that form each solenoid rung, and which ones are located in turns and connecting loops, is still not well known <ref>DOI 10.1371/journal.ppat.1005835</ref>. However, it has been shown that the protofilament is stabilized by a 3D network of hydrogen bonds that link polar zippers within a sheet, producing a motif named as a <scene name='81/815943/1qlx/17'> ‘polar clasp’</scene> <ref>DOI 10.1038/s41594-017-0018-0</ref>.
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Other considered model is the parallel in-register intermolecular β-sheet (PIRIBS) model, based on multiple solid-state NMR studies. A number of fungal prions adapt this conformation. In this model, each molecule of PrP stacks on top of the preceding molecule perfectly in register. Hence, a single molecule of PrP contributes just 4.8 Å in height to the rise of a PrP amyloid fibril <ref name="wille" />. According to in silico and in vitro experiments, this model has a reasonable ability of fibril propagation, nevertheless is not consitent with the recent cryo-EM data speaking for the four-rung β-solenoid fold in some other prion strains. On the other hand, it was also shown that PIRIBS structures might be able to template four-rung β-solenoids and four-rung β-solenoids might template PIRIBS amyloids, a mechanims that might explain mutual templating of self-propagating structures with alternative folding patterns <ref name="table" />.
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== '''Misfolding''' ==
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The fundamental event in propagation of the infectious form lies in the PrPSc template-directed misfolding of the natural form into the pathogenic, β-sheet-rich version of itself <ref name="pan" />. This process is now widely accepted as a current prion theory, and the most striking fact is that this action lacks any nucleic acid template <ref name="sigurdson" />. However, the replication cycle of PrPSc does need the PRNP gene to direct PrPC synthesis. Also, the interaction between the pathogenic and physiological form must be quite specific to propagate the conversion. The replication process itself can be explained by stochastic fluctuations in the PrPC structure, that would create the intermediate form, PrP*. This partially unfolded monomer can then switch back to the natural conformation, adopt a PrPSc one, or be degraded. Normally, there is an equilibrium between the PrPC and PrP* states which favors the physiological one. Depending on the specific cause of the disease, the PrP* state can adopt a PrPSc conformation either upon contant with a dimer of this infectious form by forming a heteromultimer which is further converted into a homomultimer of PrPSc, or through encounter with another PrP* molecule. <scene name='81/815943/1i4m/1'>This PrP*/PrP* dimer</scene> can then form an infectious dimer and initiate the replication cycle <ref name="cohen&prusiner" /><ref name="cohen">PMID 7909169</ref>. It has been found that certain host-specific RNAs can assist with the conversion into the pathogenic form <ref>DOI 10.1038/nature01979</ref>.
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A few particular residue changes have been shown to make the native structure more susceptible to the pathogenic conversion: The mutation of Val129 to Met129 has no influence on the electrostatics, however the Met group is much bulkier. Proteins with this mutation crystalized into non-swapped dimers (in contrast to the WT PrPs) and aligned to form intermolecular β-sheets. This mutation has been found in all cases of diagnosed CJDs <ref> DOI 10.1038/emboj.2009.333 </ref>
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=== Structural implications for the PrPSc propagation ===
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A β-solenoid can act as a templating agent due to its upper- and lowermost rungs containing unpaired β-strand able to propagate their hydrogen-bonding pattern into any amyloidogenic peptide they encounter. In the native, soluble proteins that contain β-solenoid structures, these are usually capped by loops or α-helices that block this propagation. When decapped, they become unstable and undergo oligomerization. Therefore, the outer rungs of PrPSc can template an incoming PrPC, modify it and this misfolded PrPC then offers a fresh surface for another native PrPC to stick to. This process can continue indefinitely.
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The fact that different strains present a transmission barrier may lie in slightly different amino acid sequence and, therefore, a variability in the main β-solenoid theme. This can have an impact on the templating properties and impose restrictions for some other strains <ref name="wille" />.
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== '''Pathogenesis''' ==
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In the case of infectious/iatrogenic diseases, pathogenic prion proteins enter the body alimentary via ingestion of affected neural tissues, or via infected materials and tissues such as during blood transfusions, corneal transplants or dura mater grafts. In this case, the exogenous PrPSc form would serve as a template to promote the conversion of PrP* and, due to its insolubility, make this exponential conversion process irreversible <ref name="cohen" />.
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Genetic, or inherited cause comprise the familial TSEs and comes from DNA mutations in the PRNP gene, which then produces mutant, unstable forms of PrPC with higher tendency of folding into the PrP* form. This further increases the chance of PrPSc forming <ref name="cohen&prusiner" />. The mutations in PRNP are autosomal dominant, highly penetrant, and consist of missense mutations, insertions and deletions <ref name="sigurdson" />. With higher probability of protein misfolding in the old age, they usually incite disease onset in the late decades of life and ultimately lead to accumulation of prion proteins and rapid development of neurodegenerative disease <ref name="khanam">DOI 10.1016/j.ejmech.2016.08.006</ref>.
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Concerning sporadic form of prion disease, the concentration of PrPSc may eventually reach a threshold level upon which a positive feedback loop would stimulate the formation of PrPSc. It requires solely a rare molecular event of formation of the PrP*/PrP* complex, or a somatic cell mutation followed by the mechanism of the initiation of inherited disease. Once formed, the replication cycle is primed for subsequent conversion <ref name="cohen&prusiner" /><ref name="cohen" />.
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Ultimately, in all cases this leads to PrPSc polymerization, forming a rod-like structures and amyloid plaques.
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== '''Prion diseases''' ==
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Up to this date, many different types of TSEs are known (see General intro), affecting many animal species as well as humans and showing various symptoms. As was mentioned in previous chapters, all prion diseases promote their negative effects through accumulation of PrPSc in the CNS. However, since most of the TSEs are transmitted by peripheral routes, either orally or transcutaneously, events critical for their pathogenesis take place at peripheral parts of the organism, especially in peripheral lymph organs. In the following text, probably the two most important prion diseases and facts known about their mechanism of infection are described.
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=== Bovine spongiform encephalopathy ===
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Commonly known as the mad cow disease, bovine spongiform encephalopathy (BSE) is a type of prion disease that affects cattle. Among major symptoms observed in affected animals are abnormal behavior, anxiety, ataxia, hypersensitivity to touch and noise and poor body condition – from movement and posture problems all the way down up to paralysis. Onset symptoms usually emerge after 4-4.5 years from the infection <ref>DOI 10.1016/B978-0-444-63945-5.00007-6</ref>. From that point, the disease is very progressive in degeneration of animal’s nervous system and leads to its death, generally within the time horizon of weeks to months <ref>PMID 15581140</ref>.
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Several types of the disease are distinguished: classic BSE (C-type BSE), L-type BSE and H-type BSE. Latter two types are considered to be sporadic, uncommon and classified as atypical since they arise spontaneously. H and L denotation has its origin in structural features of these two forms. The classic form, on the other hand, is classified as typical and arise most likely from ruminant-derived protein feed supplements (i.e. meat-and-bone meal) as epidemiological analyses of BSE-affected herds implied <ref>PMID 8030941</ref>. After oral uptake of infected feed, it was found that PrPSc gather in some intestinal lymphatic tissues (mainly in Peyer’s patches of the distal ileum and also tonsils). Infectivity of BSE subsequently slowly spreads centripetally into the CNS, probably through the peripheral nervous system. However, it still is not clear, how the disease passes from intestinal mucosa to the lymphoid system of the cattle <ref>DOI 10.1099/vir.0.82647-0</ref>.
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=== Creutzfeldt-Jacob disease ===
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Creutzfeldt-Jacob disease (CJD) is the most common human prion disease. It occurs in three distinct forms, based on the source of the disease: sporadic, acquired and inherited <ref name="knight">DOI 10.1016/bs.pmbts.2017.06.010</ref>. Sporadic form of CJD is denoted as sCJD and it predominantly affects middle aged and elderly. Its classical clinical symptoms are rapid cognitive decline, dementia, cerebellar ataxia and myoclonus terminating in an akinetic mute state <ref>DOI 10.12688/f1000research.12681.1</ref>. Due to a very rapid progress of the disease, mean survival of patients is merely six months and more than 90 % die within a year from onset of the first symptoms <ref>DOI 10.1212/01.WNL.0000160117.56690.B2</ref>. There are certain speculations about the cause of sCJD, e.g. stochastic protein folding or a somatic mutation in PRNP gene, but the true reasons remain unrevealed <ref name="knight" />.
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Acquired forms of CJD are caused by infection from exogenous source and consist of variant CJD (vCJD) and iatrogenic CJD (iCJD). Latter is caused by accidental transmission of the disease through medical and surgical procedures, mainly by cadaveric-derived human dura mater grafts (e.g. in cases of corneal transplantation <ref>PMID 4591849</ref><ref>DOI 10.1097/ICO.0b013e31816a628d</ref> or by treatment with human growth hormone (hGH) originating from sCJD affected pituitary glands <ref>DOI 10.1099/vir.0.81913-0</ref>. Additionally, few cases caused by treatment with infected human gonadotropin were also described <ref>PMID 1469410</ref>. Symptoms of iCJD are generally identical with those of sCJD. However, cases caused by infected hGH are more specific, i.e. progressive cerebellar ataxia and lower limb dysaesthesia with other features, including cognitive impairment <ref>DOI 10.1093/brain/awv235</ref>.
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The vCJD form was described for the first time during the BSE epidemic in the United Kingdom in 1996 and was termed as the “new variant CJD” <ref>PMID 8598754</ref>. It is primarily caused by ingestion of food with infectious contamination originating from BSE affected cattle <ref>DOI 10.1002/ana.20708</ref>. Nonetheless, infection can also arise from transfusion by an infected blood <ref>DOI 10.1111/vox.12371</ref> or a blood product, i.e. factor VIII important in the pathway of the blood coagulation <ref>DOI 10.1111/j.1365-2516.2009.02181.x</ref>. The BSE epidemic is the main reason for which the vCJD still occurs with highest incidence in the UK and France. Since 1996 till 25.04.2017, total count of 231 definite or probable cases of vCJD was reported <ref name="knight" />. Symptoms of vCJD are again mostly identical or very similar to those of other CJD forms, including painful sensory symptoms and involuntary movements <ref>DOI 10.1002/ana.21987</ref>. In compare with sCJD, mean survival of patients from the onset symptoms is significantly longer, approximately 14 months from the onset symptoms <ref>DOI 10.1136/jnnp.2010.232264</ref>.
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The susceptibility to infection and disease, incubation period and duration of survival in all CJD forms are dependent on several different factors including age of onset and genetic predispositions. So called PRNP-129 polymorphism is related to all CJD forms, but especially to iCJD. Its principle lies in genotype combinations of Met129 and Val129 alleles (MM, MV or VV) and in iCJD, it has substantial impact on susceptibility and incubation period of the disease caused by infection from previously mentioned treatment with hGH <ref name="brandel">DOI 10.1016/S0140-6736(03)13867-6</ref>. It appears that VV and mainly MM homozygotes are more susceptible to infection by CJD and have shorter incubation period than MV heterozygotes <ref name="brandel" /><ref name="parchi">PMID 10443888</ref>. Furthermore, supporting this hypothesis almost all definite and probable vCJD and sCJD reported cases are of MM genotype <ref name="parchi" /><ref>PMID 20109837</ref>.
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== '''Diagnosis and treatment''' ==
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To this date, there are no known treatment approaches for prion diseases, therefore these remain 100% fatal. One approach might be increasing the stability of the natural PrPC protein, but the existing compounds (like quinacrine) have been proven far too toxic <ref name="khanam" />.
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== References ==
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== '''References''' ==
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Prions

Human prion protein

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