Influence of divalent copper, manganese and zinc ions on fibril nucleation and elongation of the amyloid-like yeast prion determinant Sup35p-NM

There is a large body of evidence that divalent metal ions, particularly copper, might play a role in several protein folding pathologies like Alzheimer’s disease, Parkinson’s disease or the prion diseases. However, contribution of metal ions on pathogenesis and their molecular influence on the formation of amyloid structures is not clear. Therefore, the general influence of metals on the formation of amyloids is still controversially discussed. We have utilized the well established system of yeast Sup35p-NM to investigate the role of three different metal ions, Cu²⁺, Mn²⁺ and Zn²⁺, on amyloidogenesis. Recently, it has been shown that the prion determining region NM of the Saccharomyces cerevisiae prion protein Sup35p, which is responsible for the yeast prion phenotype [PSI⁺], specifically binds Cu²⁺ ions. We further characterized the affinity of NM for Cu²⁺, which were found to be comparable to that of other amyloidogenic proteins like the mammalian prion protein PrP. The specific binding sites could be located in the aminoterminal N-region which is known to initiate formation of amyloidogenic nuclei. In the presence of Cu²⁺, fibril nucleation was significantly delayed, probably due to influences of copper on the oligomeric ensemble of soluble Sup35p-NM, since Cu²⁺ altered the tertiary structure of soluble Sup35p-NM, while no influences on fibril elongation could be detected. The secondary structure of soluble or fibrous protein and the morphology of the fibrils were apparently not altered when assembled in presence of Cu²⁺. In contrast, Mn²⁺ and Zn²⁺ did not bind to Sup35p-NM and did not exhibit significant effects on the formation of NM amyloid fibrils.     

Effect of sodium tetrathionate on amyloid fibril: Insight into the role of disulfide bond in amyloid progression

Tissue deposition of fibrillar protein aggregates called amyloid is the root cause of several degenerative diseases. Thus identification of compounds which can prevent or reduce protein aggregation can serve as a potential therapeutic target. In the present study we have shown inhibitory effect of sodium tetrathionate toward Hen egg white lysozyme (HEWL) amyloidogenesis at pH 2.0. Our study reveals that without sulfonation, sodium tetrathionate prevents amyloid fibril progression. Moreover, it shows that formation of disulfide bonds rather than exposure of hydrophobic surface in protein plays a critical role in initiating fibrillation process. Inhibitory effect of reducing agent β-mercaptoethanol toward fibrillation process also confirms the involvement of disulfide bond in initiating HEWL amyloidogenesis. These results provide important information toward understanding key interactions that guide amyloidogenesis, which may facilitate development of potential therapeutics.     

Identification of key residues involved in fibril formation by the conserved N-terminal region of Plasmodium falciparum merozoite surface protein 2 (MSP2)

Merozoite surface protein 2 (MSP2) from the human malaria parasite Plasmodium falciparum is expressed as a GPI-anchored protein on the merozoite surface. MSP2 is assumed to have a role in erythrocyte invasion and is a leading vaccine candidate. Recombinant MSP2 forms amyloid-like fibrils upon storage, as do peptides corresponding to sequences in the conserved N-terminal region, which constitutes the structural core of fibrils formed by full-length MSP2. We have investigated the roles of individual residues in fibril formation and local ordered structure in two peptides, a recombinant 25-residue peptide corresponding to the entire N-terminal domain of mature MSP2 and an 8-residue peptide from the central region of this domain (residues 8–15). Both peptides formed fibrils that were similar to amyloid-like fibrils formed by full-length MSP2. Phe11 and Ile12 have important roles both in stabilising local structure in these peptides and promoting fibril formation; the F11A and I12A mutants of MSP2_8–15 were essentially unstructured in solution and fibril formation at pH 7.4 and 4.7 was markedly retarded. The T10A mutant showed intermediate behaviour, having a less well defined structure than wild-type and slower fibril formation at pH 7.4. The mutation of Phe11 and Ile12 in MSP2_1–25 significantly retarded but did not abolish fibril formation, indicating that these residues also play a key role in fibril formation by the entire N-terminal conserved region. These mutations had little effect on the aggregation of full-length MSP2, however, suggesting that regions outside the conserved N-terminus have unanticipated importance for fibril formation in the full-length protein.     

Conversion of non-fibrillar beta-sheet oligomers into amyloid fibrils in Alzheimer's disease amyloid peptide aggregation

Abeta(1-40) is one of the main components of the fibrils found in amyloid plaques, a hallmark of brains affected by Alzheimer's disease. It is known that prior to the formation of amyloid fibrils in which the peptide adopts a well-ordered intermolecular beta-sheet structure, peptide monomers associate forming low and high molecular weight oligomers. These oligomers have been previously described in electron microscopy, AFM, and exclusion chromatography studies. Their specific secondary structures however, have not yet been well established. A major problem when comparing aggregation and secondary structure determinations in concentration-dependent processes such as amyloid aggregation is the different concentration range required in each type of experiment. In the present study we used the dye Thioflavin T (ThT), Fourier-transform infrared spectroscopy, and electron microscopy in order to structurally characterize the different aggregated species which form during the Abeta(1-40) fibril formation process. A unique sample containing 90microM peptide was used. The results show that oligomeric species which form during the lag phase of the aggregation kinetics are a mixture of unordered, helical, and intermolecular non-fibrillar beta-structures. The number of oligomers and the amount of non-fibrillar beta-structures grows throughout the lag phase and during the elongation phase these non-fibrillar beta-structures are transformed into fibrillar (amyloid) beta-structures, formed by association of high molecular weight intermediates.     

Spontaneous aggregation and cytotoxicity of the beta-amyloid Abeta1-40: a kinetic model

The time dependency of the spontaneous aggregation of the fibrillogenic -Amyloid peptide, A^1–40, was measured by turbidity, circular dichroism, HPLC, and fluorescence polarization. The results by all methods were comparable and they were most consistent with a kinetic model where the peptide first slowly forms an activated monomeric derivative (AM), which is the only species able to initiate, by tetramerization, the formation of linear aggregates. The anti-A antibody 6E10, raised against residues 1–17, at concentrations of 200–300 nM delayed significantly the aggregation of 50 M amyloid peptide. The anti–A antibody 4G8, raised against residues 17–24, was much less active in that respect, while the antibody A162, raised against the C-terminal residues 39–43 of the full-length A was totally inactive at those concentrations. Concomitant with the aggregation experiments, we also measured the time dependency of the A^1–40–induced toxicity toward SH-EP1 cells and hippocampal neurons, evaluated by SYTOX Green fluorescence, lactate dehydrogenase release, and activation of caspases. The extent of cell damage measured by all methods reached a maximum at the same time and this maximum coincided with that of the concentration of AM. According to the kinetic scheme, the latter is the only transient peptide species whose concentration passes through a maximum. Thus, it appears that the toxic species of A^1–40 is most likely the same transient activated monomer that is responsible for the nucleation of fibril formation. These conclusions should provide a structural basis for understanding the toxicity of A^1–40 in vitro and possibly in vivo.     

A simple in vitro assay for assessing the efficacy,mechanisms and kinetics of anti-prion fibril compounds

ABSTRACT

Prion diseases are caused by the conversion of normal cellular prion proteins (PrP) into lethal prion aggregates. These prion aggregates are composed of proteinase K (PK) resistant fibrils and comparatively PK-sensitive oligomers. Currently there are no anti-prion pharmaceuticals available to treat or prevent prion disease. Methods of discovering anti-prion molecules rely primarily on relatively complex cell-based, tissue slice or animal-model assays that measure the effects of small molecules on the formation of PK-resistant prion fibrils. These assays are difficult to perform and do not detect the compounds that directly inhibit oligomer formation or alter prion conversion kinetics. We have developed a simple cell-free method to characterize the impact of anti-prion fibril compounds on both the oligomer and fibril formation. In particular, this assay uses shaking-induced conversion (ShIC) of recombinant PrP in a 96-well format and resolution enhanced native acidic gel electrophoresis (RENAGE) to generate, assess and detect PrP fibrils in a high throughput fashion. The end-point PrP fibrils from this assay can be further characterized by PK analysis and negative stain transmission electron microscopy (TEM). This cell-free, gel-based assay generates metrics to assess anti-prion fibril efficacy and kinetics. To demonstrate its utility, we characterized the action of seven well-known anti-prion molecules: Congo red, curcumin, GN8, quinacrine, chloropromazine, tetracycline, and TUDCA (taurourspdeoxycholic acid), as well as four suspected anti-prion compounds: trans-resveratrol, rosmarinic acid, myricetin and ferulic acid. These findings suggest that this in vitro assay could be useful in identifying and comprehensively assessing novel anti-prion fibril compounds.

Abbreviations: PrP, prion protein; PK, proteinase K; ShIC, shaking-induced conversion; RENAGE, resolution enhanced native acidic gel electrophoresis; TEM, transmission electron microscopy; TUDCA, taurourspdeoxycholic acid; BSE, bovine spongiform encephalopathy; CWD, chronic wasting disease; CJD, Creutzfeldt Jakob disease; GSS, Gerstmann–Sträussler–Scheinker syndrome; FFI, fatal familial insomnia; PrP^c, cellular prion protein; recPrP^C, recombinant monomeric prion protein; PrP^Sc, infectious particle of misfolded prion protein; RT-QuIC, real-time quaking-induced conversion; PMCA, Protein Misfolding Cyclic Amplification; LPS, lipopolysaccharide; EGCG, epigallocatechin gallate; GN8, 2-pyrrolidin-1-yl-N-[4-[4-(2-pyrrolidin-1-yl-acetylamino)-benzyl]-phenyl]-acetamide; DMSO, dimethyl sulfoxide; ScN2A, scrapie infected neuroblastoma cells; IC50, inhibitory concentration for 50% reduction; recMoPrP ^23?231, recombinant full-length mouse prion protein residues 23-231; EDTA; PICUP, photo-induced cross-linking of unmodified protein; BSA, bovine serum albumin;; PMSF, phenylmethanesulfonyl fluoride.     

Proportion between wild-type and mutant protein in truncated compared to full-length ATTR: An analysis on transplanted transthyretin T60A amyloidosis patients

Familial ATTR amyloidosis is caused by point mutations in the transthyretin gene. The clinical manifestations are highly varied but polyneuropathy and/or cardiomyopathy are generally the main symptoms. The amyloid fibrils can either be composed of only intact ATTR molecules or intact together with fragmented ATTR species. As plasma TTR is almost exclusively synthesized in the liver, liver transplantation is performed in order to eliminate the mutant plasma TTR. The procedure has shown best results among patients with the V30M mutation, while a rapid continued cardiac deposition of wild-type (wt) TTR has been seen for many other mutations. In this paper we investigated the proportion of wtATTR in two TTRT60A patients that underwent liver transplantation; one patient died 3 weeks after surgery, the other patient survived for 12 months. As the role of fragmented TTR species in the pathogenesis is far from understood, we investigated the proportion of wt in these species separately to the full-length molecules, which has not been done before in transplanted patients. The results show a higher proportion of wtTTR in the 12-months-surviving patient than the 3-weeks-surviving patient, but interestingly this difference in wt proportion is mainly seen among the full-length, and not the fragmented, molecules.     

Model of Alzheimer's disease amyloid-beta peptide based on a RNA binding protein

Although Alzheimer's Abeta peptide has been shown to form beta-sheet structure, a high-resolution molecular structure is still unavailable to date. A search for a sequence neighbor using Abeta(10-42) as the query in the Protein Data-Bank (PDB) revealed that an RNA binding protein, AF-Sm1 from Archaeoglobus fulgidus (PDB entry: 1i4k chain Z), shared 36% identical residues. Using AF-Sm1 as a template, we built a molecular model of Abeta(10-42) by applying comparative modeling methods. The model of Abeta(10-42) contains an antiparallel beta-sheet formed by residues 16-23 and 32-41. Hydrophobic surface constituted by residues 17-20 (LVFF) separates distinctly charged regions. Residues that interact with RNA in the AF-Sm1 crystal structure were found to be conserved in Abeta. Using a native gel we demonstrate for the first time that RNA can interact with Abeta and selectively retard the formation of fibrils or higher-order oligomers. We hypothesize that in a similar fashion to AF-Sm1, RNA interacts with Abeta in the beta-hairpin (beta-turn-beta) structure and prevents fibril formation.     

Passage of amyloid beta protein antibody across the blood-brain barrier in a mouse model of Alzheimer's disease

Vaccinations against amyloid β protein (AβP) reduce amyloid deposition and reverse learning and memory deficits in mouse models of Alzheimer’s disease. This has raised the question of whether circulating antibodies, normally restricted by the blood–brain barrier (BBB), can enter the brain [Nat. Med. 7 (2001) 369–372]. Here, we show that antibody directed against AβP does cross the BBB at a very low rate. Entry is by way of the extracellular pathways with about 0.11% of an intravenous (i.v.) dose entering the brain by 1 h. Clearance of antibody from brain increasingly dominates over time, but antibody is still detectable in brain 72 h after i.v. injection. Uptake and clearance is not altered in mice overexpressing AβP. This ability to enter and exit the brain even in the presence of increased brain ligand supports the use of antibody in the treatment of Alzheimer’s and other diseases of the brain.     

A computational model to explore the role of angiogenic impairment on endochondral ossification during fracture healing

While it is well established that an adequate blood supply is critical to successful bone regeneration, it remains poorly understood how progenitor cell fate is affected by the altered conditions present in fractures with disrupted vasculature. In this study, computational models were used to explore how angiogenic impairment impacts oxygen availability within a fracture callus and hence regulates mesenchymal stem cell (MSC) differentiation and bone regeneration. Tissue differentiation was predicted using a previously developed algorithm which assumed that MSC fate is governed by oxygen tension and substrate stiffness. This model was updated based on the hypothesis that cell death, chondrocyte hypertrophy and endochondral ossification are regulated by oxygen availability. To test this, the updated model was used to simulate the time course of normal fracture healing, where it successfully predicted the observed quantity and spatial distribution of bone and cartilage at 10 and 20 days post-fracture (dpf). It also predicted the ratio of cartilage which had become hypertrophic at 10 dpf. Following this, three models of fracture healing with increasing levels of angiogenic impairment were developed. Under mild impairment, the model predicted experimentally observed reductions in hypertrophic cartilage at 10 dpf as well as the persistence of cartilage at 20 dpf. Models of more severe impairment predicted apoptosis and the development of fibrous tissue. These results provide insight into how factors specific to an ischemic callus regulate tissue regeneration and provide support for the hypothesis that chondrocyte hypertrophy and endochondral ossification during tissue regeneration are inhibited by low oxygen.     

A general kinetic analysis of transport Tests of the carrier model based on predicted relations among experimental parameters

The analysis of transport kinetics has lacked both a unified treatment in which general rate equations are written entirely in terms of experimental parameters, and a convention by which these parameters may be designated in a concise yet immediately recognizable manner. Such a treatment is presented here in an easily accessible form, and a simple system of nomenclature is proposed resembling that in use in enzyme kinetics. The treatment is independent of assumptions about rate-limiting steps in transport, and applies to both active and facilitated systems, including obligatory exchange. A single substrate is characterized by twelve different parameters, only five of which are required in theory to calculate the others. If a second substrate is present on the trans side of the membrane there are six more parameters. All eighteen parameters are linked by multiple relationships which provide a complete set of rejection criteria for the generalized form of the mobile carrier. Relationships among parameters are also defined that give information on the rate-limiting steps in transport. Equations governing any individual experiment, involving only experimental parameters, are easily written out from the general expressions, for example under conditions of zero trans and infinite trans flux, equilibrium exchange, or competitive inhibition.     

Protein misfolding detected early in pathogenesis of transgenic mouse model of Huntington disease using amyloid seeding assay

Huntington disease (HD) is one of several fatal neurodegenerative disorders associated with misfolded proteins. Here, we report a novel method for the sensitive detection of misfolded huntingtin (HTT) isolated from the brains of transgenic (Tg) mouse models of HD and humans with HD using an amyloid seeding assay (ASA), which is based on the propensity of misfolded proteins to act as a seed and shorten the nucleation-associated lag phase in the kinetics of amyloid formation in vitro. Using synthetic polyglutamine peptides as the substrate for amyloid formation, we found that partially purified misfolded HTT obtained from end-stage brain tissue of two Tg HD mouse models and brain tissue of post-mortem human HD patients was capable of specifically accelerating polyglutamine amyloid formation compared with unseeded reactions and controls. Alzheimer and prion disease brain tissues did not do so, demonstrating the specificity of the ASA. It is unclear whether early intermediates or later conformational species in the protein misfolding process act as seeds in the ASA for HD. However, we were able to detect misfolded protein in the brains of YAC128 mice early in disease pathogenesis (11 weeks of age), whereas large inclusion bodies have not been observed in the brains of these mice by histology until 78 weeks of age, much later in the pathogenic process. The sensitive detection of misfolded HTT protein early in the disease pathogenesis in the YAC128 Tg mouse model strengthens the argument for a causative role of protein misfolding in HD.     

Identification of tissue differentiation rates in a mechanobiological model of fracture healing

As a basis for model-based analysis of the processes in secondary fracture healing, a dynamical model is presented that characterises the physiological status in the fracture area by the location-dependent composition of tissues. Five types of tissue are distinguished: connective tissue, cartilage, bone, haematoma and avascular bone. A rule base is given that describes dynamical tissue differentiation processes. The rules consider not only a mechanical stimulus but also osteogenic and a vasculative factors as biological stimuli. Within this model structure, it is possible, e.g., to distinguish intramembranous from endochondral ossification processes. An objective function is introduced to assess accordance between the model-based simulation results and reference healing stages. By minimising this objective function, relevant tissue differentiation rates can be determined. For a reference process of secondary fracture healing it could be shown that the intramembranous ossification rate of 0.313%/day (from connective tissue to bone) is much smaller than the endochondral ossification rate of 1.136%/day (from cartilage to bone). In order to verify the model approach, it is transferred to simulate long bone distraction. Results show that healing patterns of bone distraction can be predicted. Using this method, it is possible to identify model parameters for individual subjects. This will allow a patient-specific analysis of tissue healing processes in future.     

A hydraulic-photosynthetic model based on extended HLH and its application to Coast redwood (Sequoia sempervirens)

Although recent investigations [Ryan, M.G., Yoder, B.J., 1997. Hydraulic limits to tree height and tree growth. Bioscience 47, 235-242; Koch, G.W., Sillett, S.C.,Jennings, G.M.,Davis, S.D., 2004. The limits to tree height. Nature 428, 851-854; Niklas, K.J., Spatz, H., 2004. Growth and hydraulic (not mechanical) constraints govern the scaling of tree height and mass. Proc. Natl Acad. Sci. 101, 15661-15663; Ryan, M.G., Phillips, N., Bond, B.J., 2006. Hydraulic limitation hypothesis revisited. Plant Cell Environ. 29, 367-381; Niklas, K.J., 2007. Maximum plant height and the biophysical factors that limit it. Tree Physiol. 27, 433-440; Burgess, S.S.O., Dawson, T.E., 2007. Predicting the limits to tree height using statistical regressions of leaf traits. New Phytol. 174, 626-636] suggested that the hydraulic limitation hypothesis (HLH) is the most plausible theory to explain the biophysical limits to maximum tree height and the decline in tree growth rate with age, the analysis is largely qualitative or based on statistical regression. Here we present an integrated biophysical model based on the principle that trees develop physiological compensations (e.g. the declined leaf water potential and the tapering of conduits with heights [West, G.B., Brown, J.H., Enquist, B.J., 1999. A general model for the structure and allometry of plant vascular systems. Nature 400, 664-667]) to resist the increasing water stress with height, the classical HLH and the biochemical limitations on photosynthesis [von Caemmerer, S., 2000. Biochemical Models of Leaf Photosynthesis. CSIRO Publishing, Australia]. The model has been applied to the tallest trees in the world (viz. Coast redwood (Sequoia sempervirens)). Xylem water potential, leaf carbon isotope composition, leaf mass to area ratio at different heights derived from the model show good agreements with the experimental measurements of Koch et al. [2004. The limits to tree height. Nature 428, 851-854]. The model also well explains the universal trend of declining growth rate with age.     

Osteoporosis influences the late period of fracture healing in a rat model prepared by ovariectomy and low calcium diet

To elucidate the influence of osteoporosis on the fracture healing, we produced a rat osteoporosis model by ovariectomy and by maintaining a low calcium diet; and monitored the healing process radiographically, histologically, and biomechanically for 12 weeks. Radiologic, histologic and biomechanical findings of the fracture areas 6 weeks after making the fractures were almost identical in both the osteoporosis group and the control group. However, 12 weeks after making the fractures, newly generated bones in the osteoporosis group showed histological osteoporotic changes and their bone mineral density on the fracture site decreased. These findings show that estrogen-deficient and low calcium conditions greatly affect the bone in the later period of the healing process, but do not affect remarkably the early healing period. This is clinically important when we consider fracture treatments for patients with osteoporosis due to menopause.     

Molecular crowding limits the role of fetal hemoglobin in therapy for sickle cell disease

The dominant assumption central to most treatments for sickle cell anemia has been that replacement of sickle hemoglobin (HbS) by fetal hemoglobin (HbF) would have major clinical benefit. Using laser photolysis, we have measured polymerization kinetics including rates of homogeneous and heterogeneous nucleation on mixtures of 20% and 30% HbF with HbS. We find that the present model for polymerization, including molecular crowding, can accurately predict the rates of such mixtures, by using the single assumption that no significant amount of HbF enters the polymer. The effects of replacing HbS by HbF on the rates of polymer formation are found to be significantly lower than previous measurements appeared to indicate because the impact of the replacement is also highly dependent on the total hemoglobin concentration. This is because the molecular crowding of non-polymerizing HbF offsets substantially the effects of decreasing the concentration of HbS concentration, an effect that increases with concentration. Most strikingly, the demonstrated benefit of hydroxyurea therapy in slowing the kinetics of intracellular polymerization cannot be primarily due to enhanced HbF, but must have some other origin, which could itself represent a promising therapeutic approach.     

Discussion of the role of the extracellular signal-regulated kinase-phospholipase A2 pathway in production of reactive oxygen species in Alzheimer's disease

In this paper we show that exposure of a rat brain synaptosome fraction to the amyloid beta peptide fragment A(25-35), but not the inverted peptide A(35-25), stimulated production of reactive oxygen species (ROS) in a concentration- and time-dependent manner. The ROS formation was attenuated by the tyrosine kinase inhibitor genistein, the mitogen-activated protein kinase inhibitor U0126, and the phospholipase A₂ (PLA₂) inhibitor 7,7-dimethyl-(5Z,8Z)-eicosadienoic acid. This strongly suggests that A(25-35) stimulated ROS production through an extracellular signal-regulated kinase-PLA₂-dependent pathway. The interaction between these enzymes and their possible involvement in free radical formation in Alzheimer's disease are discussed.     

Osteoporosis,the risk of vertebral fracture,and periodontal disease in an elderly group in Mexico City

doi: 10.1111/j.1741‐2358.2009.00342.x
Osteoporosis, the risk of vertebral fracture, and periodontal disease in an elderly group in Mexico City Objectives: The aims of this study were to identify the possible association of osteoporosis, fracture risk and periodontitis, and consider the role of pharmacological treatment of osteoporosis and the periodontal condition. Methods: Patients aged 60 and older from the Mexican National Medical Science and Nutrition Institute Salvador Zubirán participated in the study. DXA was used to assess osteoporosis and risk of vertebral fracture. A modified version of the extent and severity index (ESI) was applied to evaluate periodontitis (cut‐off point for attachment loss ≥ 4 mm) and all teeth were examined. Results: One hundred and sixty‐six patients were examined, 88.6% were females, 47.0% had osteoporosis and 38.6% showed a high risk of fracture. The modified ESI was 5.13 mm (SD 1.4), 57.8% (SD 29.7). The model for periodontitis severity showed an association with oral hygiene (OR = 1.85) and use of osteoporosis medication (OR = 0.43). The model for the extent of periodontitis identified an association with smoking (OR = 2.37), osteoporosis (OR = 1.82) and osteoporosis medication (OR = 0.36). The model for tooth loss detected an association with fracture risk (OR = 3.02) and osteoporosis medication (OR = 0.33). Conclusion: Periodontitis extent was associated with osteoporosis, and tooth loss with fracture risk.