Rich Isoform Research Articles

A valine-to-lysine substitution at position 210 induces structural conversion of prion protein into a β-sheet rich oligomer

Prion diseases are fatal neurodegenerative diseases associated with structural conversion of α-helical prion protein (PrP) into its β-sheet rich isoform (PrPSc). Previous genetic analyses have indicated that several amino acid residues involved in the hydrophobic core of PrP (such as V180, F198, and V210) play a critical role in the development of prion diseases. To understand how these hydrophobic residues would contribute to the α-to-β conversion process of PrP, we substituted the V210 residue with bulkier (V210F, V210I, and V210L), smaller (V210A), and charged amino acids (V210K) and characterized its effects. Interestingly, although most of the mutations had little or no effect on the biochemical properties of PrP, the V210K mutation induced structural conversion of PrP into a β-structure. The β-inducing effect was prominent and observed even under a physiological condition (i.e., in the absence of denaturant, acidic pH, reducing agent, and high temperature) in contrast to the disease-associated mutations in the PrP gene. We also examined structural features of V210K PrP using guanidine-hydrochloride unfolding, dynamic light scattering, 8-anilino-1-naphthalene sulfonate fluorescence, and electron microscopy, and revealed that V210K PrP assembles into a non-fibrillar β-rich oligomer. Thus, the α-to-β conversion can be induced by introduction of a charged residue into the hydrophobic core, which provide novel insight into the structural dynamics of PrP.

Aggregation Propensity of Prion is Kinetically Controlled by Intramolecular Diffusion of Protein Chain

Prion disease are rapidly progressive neurodegenerative disorders like Alzheimer's disease and Parkinson disease that are attributed to misfolding followed by ordered aggregation and accumulation of protein deposits in neuronal cells. According to the “protein only” hypothesis, the central event in prion pathogenesis is the conformational conversion of the cellular α-helical rich isoform, PrPC, into misfolded β-sheet rich isoform, PrPSc. Here we present a novel way to understand the molecular basis of Prion misfolding and aggregation, by investigating the early stage intramolecular backbone reconfiguration of monomer. Our hypothesis is that when reconfiguration is much faster or much slower than bimolecular diffusion, biomolecular association is not stable, but as the reconfiguration rate becomes similar to the rate of biomolecular diffusion, the association is more stable and subsequent aggregation is faster. We are investigating the effects of reducing agent, pH and denaturant on reconfiguration dynamics of the Hamster and Rabbit Prion protein. This work not only provides a better understanding of early stage conformational dynamics, but also provides a way forward for a novel therapeutic strategy of drug development which can bind monomers and prevent aggregation at the earliest step.

Improved synthesis of a quaterthiophene-triazine-diamine derivative, a promising molecule to study pathogenic prion proteins

The 6,6′-([2,2′:5′,2″:5″,2‴-quaterthiophene]-5,5‴-diyl)bis(1,3,5-triazine-2,4-diamine) (MR100), has been previously investigated in our research group through its biological activities toward pathogenic prion proteins (PrPSc). This compound presents a high affinity to protein strains and interacts selectively with at least one β-sheet rich isoform of prion protein. Herein we present the improved total synthesis of MR100, through a palladium-catalyzed direct double arylation using the concerted metalation deprotonation mechanism (CMD).

Nucleic acid induced unfolding of recombinant prion protein globular fragment is pH dependent.

Nucleic acid can catalyze the conversion of α-helical cellular prion protein to β-sheet rich Proteinase K resistant prion protein oligomers and amyloid polymers in vitro and in solution. Because unfolding of a protein molecule from its ordered α-helical structure is considered to be a necessary step for the structural conversion to its β-sheet rich isoform, we have studied the unfolding of the α-helical globular 121-231 fragment of mouse recombinant prion protein in the presence of different nucleic acids at neutral and acid pH. Nucleic acids, either single or double stranded, do not have any significant effect on the secondary structure of the protein fragment at neutral pH; however the protein secondary structure is modified by the nucleic acids at pH 5. Nucleic acids do not show any significant effect on the temperature induced unfolding of the globular prion protein domain at neutral pH which, however, undergoes a gross conformational change at pH 5 as evidenced from the lowering of the midpoint of thermal denaturation temperatures, Tm, of the protein. The extent of Tm decrease shows a dependence on the nature of nucleic acid. The interaction of nucleic acid with the nonpolar groups exposed from the protein interior at pH 5 probably contributes substantially to the unfolding process of the protein.

Human Prion Protein Conformational Changes Susceptibility: A Molecular Dynamics Simulation Study

Prion proteins are related to the development of incurable and invariably fatal neurodegenerative diseases in humans and animals. The pathogenicity involves the conversion of the host-encoded-alpha rich isoform of prion protein, PrPC, into a misfolded beta-strand rich conformer, PrPSc. Although it has already been described that many punctual mutations alter the stability of PrPC, making it more prone to adopt an abnormal misfolded structure, the majority of cases reported among general population are sporadic in wild-type organisms. Thus, in this work we studied the dynamics and stability profiles of wild-type human prion protein by Molecular Dynamics (MD) simulation at different solvent temperatures. This analysis brought out certain residues and segments of the prion protein as critical to conformational changes; these results are consistent with experimental reports showing that protein mutants in those positions are related to the development of disease.

Atypical and Classical Forms of the Disease-Associated State of the Prion Protein Exhibit Distinct Neuronal Tropism, Deposition Patterns, and Lesion Profiles

A number of disease-associated PrP forms characterized by abnormally short proteinase K-resistant fragments (atypical PrPres) were recently described in prion diseases. The relationship between atypical PrPres and PrP(Sc), and their role in etiology of prion diseases, remains unknown. We examined the relationship between PrP(Sc) and atypical PrPres, a form characterized by short C-terminal proteinase K-resistant fragments, in a prion strain of synthetic origin. We found that the two forms exhibit distinct neuronal tropism, deposition patterns, and degree of pathological lesions. Immunostaining of brain regions demonstrated a partial overlap in anatomic involvement of the two forms and revealed the sites of their selective deposition. The experiments on amplification in vitro suggested that distinct neuronal tropism is attributed to differences in replication requirements, such as preferences for different cellular cofactors and PrP(C) glycoforms. Remarkably, deposition of atypical PrPres alone was not associated with notable pathological lesions, suggesting that it was not neurotoxic, but yet transmissible. Unlike PrP(Sc), atypical PrPres did not show significant perineuronal, vascular, or perivascular immunoreactivity. However, both forms showed substantial synaptic immunoreactivity. Considering that atypical PrPres is not associated with substantial lesions, this result suggests that not all synaptic disease-related PrP states are neurotoxic. The current work provides important new insight into our understanding of the structure-pathogenicity relationships of transmissible PrP states.

Burial of the Polymorphic Residue 129 in Amyloid Fibrils of Prion Stop Mutants

Misfolding of the natively α-helical prion protein into a β-sheet rich isoform is related to various human diseases such as Creutzfeldt-Jakob disease and Gerstmann-Sträussler-Scheinker syndrome. In humans, the disease phenotype is modified by a methionine/valine polymorphism at codon 129 of the prion protein gene. Using a combination of hydrogen/deuterium exchange coupled to NMR spectroscopy, hydroxyl radical probing detected by mass spectrometry, and site-directed mutagenesis, we demonstrate that stop mutants of the human prion protein have a conserved amyloid core. The 129 residue is deeply buried in the amyloid core structure, and its mutation strongly impacts aggregation. Taken together the data support a critical role of the polymorphic residue 129 of the human prion protein in aggregation and disease.

Biochemical properties of highly neuroinvasive prion strains

Prion diseases are fatal neurodegenerative diseases caused by the conformational conversion of the cellular prion protein, PrPC, into an aggregated, β‐sheet rich isoform, PrPSc. Prion pathogenesis can vary dramatically depending on the strain, thought to be conformational variants of PrPSc, yet the structural basis for the differences in pathogenesis in unclear. Using an array of mouseadapted prion strains, here we define the neuropathology and biochemical features of prion strains that efficiently or poorly invade the CNS from their peripheral entry site. In brain sections, we find that the highly neuroinvasive prion strains primarily form diffuse aggregates that do not bind to the amyloid binding dye, Congo red. Biochemically these aggregates are conformationally unstable in denaturing conditions. These neuroinvasive strains also efficiently generate PrPSc over short incubation periods. In contrast, the poorly neuroinvasive strains formed dense, Congo red binding aggregates that were conformationally stable. Our findings indicate that the most neuroinvasive, efficiently spreading strains are also the least conformationally stable, and support the concept that the unstable nature of the most rapidly converting prions may be a feature linked to their efficient spread into the CNS.

Iron content of ferritin modulates its uptake by intestinal epithelium: implications for co-transport of prions

The spread of Chronic Wasting Disease (CWD) in the deer and elk population has caused serious public health concerns due to its potential to infect farm animals and humans. Like other prion disorders such a sporadic Creutzfeldt-Jakob-disease of humans and Mad Cow Disease of cattle, CWD is caused by PrP-scrapie (PrPSc), a β-sheet rich isoform of a normal cell surface glycoprotein, the prion protein (PrPC). Since PrPSc is sufficient to cause infection and neurotoxicity if ingested by a susceptible host, it is important to understand the mechanism by which it crosses the stringent epithelial cell barrier of the small intestine. Possible mechanisms include co-transport with ferritin in ingested food and uptake by dendritic cells. Since ferritin is ubiquitously expressed and shares considerable homology among species, co-transport of PrPSc with ferritin can result in cross-species spread with deleterious consequences. We have used a combination of in vitro and in vivo models of intestinal epithelial cell barrier to understand the role of ferritin in mediating PrPSc uptake and transport. In this report, we demonstrate that PrPSc and ferritin from CWD affected deer and elk brains and scrapie from sheep resist degradation by digestive enzymes, and are transcytosed across a tight monolayer of human epithelial cells with significant efficiency. Likewise, ferritin from hamster brains is taken up by mouse intestinal epithelial cells in vivo, indicating that uptake of ferritin is not limited by species differences as described for prions. More importantly, the iron content of ferritin determines its efficiency of uptake and transport by Caco-2 cells and mouse models, providing insight into the mechanism(s) of ferritin and PrPSc uptake by intestinal epithelial cells.

Beta-Barrel Hypothesis: Structural Insights to Oligomeric Prion Conformation

The denaturation of prion protein (PrP) and the concurrent formation of beta-sheet rich isoform has been accredited to the etiology of the prion diseases. Accumulating biochemical evidences underline the critical role of oligomeric PrP conformations emerging from the early stage of the denaturation process. However detailed structural information on the oligomeric isoforms remains elusive, which hampers precise description of the pathological process. Recently we proposed a new structural hypothesis for the oligomeric PrP species comprised of a short PrP construct (Human PrP 175-217) based on experimental findings. We postulated that 1) monomers adopt beta-hairpin conformation and 2) assemble as beta-barrel quaternary structure. These assumptions provided a comprehensive explanation for the experimental findings suggesting beta-sheet rich structure including circular dichroism (CD) spectrum and Fourier transformed infra-red spectroscopy (FTIR) as well as the presence of disulfide bridge between CYS-179 and CYS-214. To be more specific, we constructed various beta-barrel models differing in number of monomers, inter-molecular hydrogen bond pattern and side-chains facing exterior of the barrel. Those models were refined extensively using a protein structure prediction tool (Rosetta). Structural energy profile of the predicted oligomer models was consistently lower than that of native like monomer or oligomers comprised of partially denatured monomers. Also the smallest stable oligomer was predicted to be an octamer, which is in good agreement with available mass spectrometric data. Finally, we discussed a possible generality between protein denaturation and amyloidogenesis problems in general, by comparing our model with a oligomeric assembly model for the pathological amyloid beta protein (Abeta).

Abnormal brain iron homeostasis in human and animal prion disorders.

Neurotoxicity in all prion disorders is believed to result from the accumulation of PrP-scrapie (PrPSc), a β-sheet rich isoform of a normal cell-surface glycoprotein, the prion protein (PrPC). Limited reports suggest imbalance of brain iron homeostasis as a significant associated cause of neurotoxicity in prion-infected cell and mouse models. However, systematic studies on the generality of this phenomenon and the underlying mechanism(s) leading to iron dyshomeostasis in diseased brains are lacking. In this report, we demonstrate that prion disease–affected human, hamster, and mouse brains show increased total and redox-active Fe (II) iron, and a paradoxical increase in major iron uptake proteins transferrin (Tf) and transferrin receptor (TfR) at the end stage of disease. Furthermore, examination of scrapie-inoculated hamster brains at different timepoints following infection shows increased levels of Tf with time, suggesting increasing iron deficiency with disease progression. Sporadic Creutzfeldt-Jakob disease (sCJD)–affected human brains show a similar increase in total iron and a direct correlation between PrP and Tf levels, implicating PrPSc as the underlying cause of iron deficiency. Increased binding of Tf to the cerebellar Purkinje cell neurons of sCJD brains further indicates upregulation of TfR and a phenotype of neuronal iron deficiency in diseased brains despite increased iron levels. The likely cause of this phenotype is sequestration of iron in brain ferritin that becomes detergent-insoluble in PrPSc-infected cell lines and sCJD brain homogenates. These results suggest that sequestration of iron in PrPSc–ferritin complexes induces a state of iron bio-insufficiency in prion disease–affected brains, resulting in increased uptake and a state of iron dyshomeostasis. An additional unexpected observation is the resistance of Tf to digestion by proteinase-K, providing a reliable marker for iron levels in postmortem human brains. These data implicate redox-iron in prion disease–associated neurotoxicity, a novel observation with significant implications for prion disease pathogenesis.

Modulation of proteinase K-resistant prion protein in cells and infectious brain homogenate by redox iron: implications for prion replication and disease pathogenesis.

The principal infectious and pathogenic agent in all prion disorders is a beta-sheet-rich isoform of the cellular prion protein (PrP(C)) termed PrP-scrapie (PrP(Sc)). Once initiated, PrP(Sc) is self-replicating and toxic to neuronal cells, but the underlying mechanisms remain unclear. In this report, we demonstrate that PrP(C) binds iron and transforms to a PrP(Sc)-like form (*PrP(Sc)) when human neuroblastoma cells are exposed to an inorganic source of redox iron. The *PrP(Sc) thus generated is itself redox active, and it induces the transformation of additional PrP(C), simulating *PrP(Sc) propagation in the absence of brain-derived PrP(Sc). Moreover, limited depletion of iron from prion disease-affected human and mouse brain homogenates and scrapie-infected mouse neuroblastoma cells results in 4- to 10-fold reduction in proteinase K (PK)-resistant PrP(Sc), implicating redox iron in the generation, propagation, and stability of PK-resistant PrP(Sc). Furthermore, we demonstrate increased redox-active ferrous iron levels in prion disease-affected brains, suggesting that accumulation of PrP(Sc) is modulated by the combined effect of imbalance in brain iron homeostasis and the redox-active nature of PrP(Sc). These data provide information on the mechanism of replication and toxicity by PrP(Sc), and they evoke predictable and therapeutically amenable ways of modulating PrP(Sc) load.

Cerebral Amyloidoses: Molecular Pathways and Therapeutic Challenges

Alzheimer disease (AD) and Creutzfeldt-Jakob disease (CJD) are sporadic and genetic neurodegenerative conditions characterized by brain accumulation and deposition of protein aggregates. In AD, the key pathogenic event is linked to the formation of a 4-kDa amyloid beta (Abeta) peptide, generated by sequential cleavages of the amyloid precursor protein (APP). In CJD and other prion diseases, the process is initiated by conformational changes of the cellular prion protein, or PrP(C), into a beta-sheet rich isoform, named PrP(Sc), which acquires protease-resistance and detergent insolubility. Once generated, Abeta and PrP(Sc) are highly prone to misassembly under thermodynamically favourable oligomeric forms and protofibril/fibril structures. The variety of physicochemical states exhibited by Abeta and PrP(Sc) is accounted for by distinct molecular forms with different amino and/or carboxyl termini and alternative conformations. Unlike Abeta, PrP(Sc) is also infectious, and this feature poses public health concerns, as in the case of iatrogenic and variant CJD (vCJD). Several lines of evidence suggest that Abeta and PrP(Sc) are the main factors responsible for death of selected neuronal populations in brains of AD and prion disease's victims. Therefore, in addition to symptomatic treatment of dementia, therapeutic efforts are currently aimed at testing the efficacy of disease-modifying, anti-amyloid therapies. Experimental and clinical therapeutic interventions include passive and active immunization against amyloidogenic peptides, non immunological strategies, as well as drugs enhancing the nonamyloidogenic protein processing. In this review, we focus on molecular mechanisms of AD and prion diseases, and on novel treatment approaches.