User:Eliška Koutná/Sandbox 3

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== '''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 <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 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 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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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<scene name='81/815943/2rnm/1'> 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</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>.
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" />.

Revision as of 09:04, 24 May 2019

Prions

Human prion protein

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Eliška Koutná

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