User:Eliška Koutná/Sandbox 3

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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.
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</scene> 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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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>.
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" />.
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''' ==
== '''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. This PrP*/PrP* dimer 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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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 ===
=== Structural implications for the PrPSc propagation ===

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Prions

Human prion protein

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Eliška Koutná

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