Browse
Submit Data
Databases
API
Help

Dataset Information

22 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Differential effects of divalent cations on elk prion protein fibril formation and stability.

ABSTRACT: Misfolding of the normally folded prion protein of mammals (PrPC) into infectious fibrils causes a variety of diseases, from scrapie in sheep to chronic wasting disease (CWD) in cervids. The misfolded form of PrPC, termed PrPSc, or in this case PrPCWD, interacts with PrPC to create more PrPCWD. This process is not clearly defined but is affected by the presence and interactions of biotic and abiotic cofactors. These include nucleic acids, lipids, glycosylation, pH, and ionic character. PrPC has been shown to act as a copper-binding protein in vivo, though it also binds to other divalents as well. The significance of this action has not been conclusively elucidated. Previous reports have shown that metal binding sites occur throughout the N-terminal region of PrPC. Other cations like manganese have also been shown to affect PrPC abundance in a transcript-independent fashion. Here, we examined the ability of different divalent cations to influence the stability and in vitro conversion of two variants of PrP from elk (L/M132, 26-234). We find that copper and zinc de-stabilize PrP. We also find that PrP M132 exhibits a greater degree of divalent cation induced destabilization than L132. This supports findings that leucine at position 132 confers resistance to CWD, while M132 is susceptible. However, in vitro conversion of PrP is equally suppressed by either copper or zinc, in both L132 and M132 backgrounds. This report demonstrates the complex importance of ionic character on the PrPC folding pathway selection on the route to PrPSc formation.

SUBMITTER: Samorodnitsky D

PROVIDER: S-EPMC5871030 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Differential stability of DNA crossovers in solution mediated by divalent cations.

Project description:The assembly of DNA duplexes into higher-order structures plays a major role in many vital cellular functions such as recombination, chromatin packaging and gene regulation. However, little is currently known about the molecular structure and stability of direct DNA-DNA interactions that are required for such functions. In nature, DNA helices minimize electrostatic repulsion between double helices in several ways. Within crystals, B-DNA forms either right-handed crossovers by groove-backbone interaction or left-handed crossovers by groove-groove juxtaposition. We evaluated the stability of such crossovers at various ionic concentrations using large-scale atomistic molecular dynamics simulations. Our results show that right-handed DNA crossovers are thermodynamically stable in solution in the presence of divalent cations. Attractive forces at short-range stabilize such crossover structures with inter-axial separation of helices less than 20 A. Right-handed crossovers, however, dissociate swiftly in the presence of monovalent ions only. Surprisingly, left-handed crossovers, assembled by sequence-independent juxtaposition of the helices, appear unstable even at the highest concentration of Mg(2+)studied here. Our study provides new molecular insights into chiral association of DNA duplexes and highlights the unique role divalent cations play in differential stabilization of crossover structures. These results may serve as a rational basis to understand the role DNA crossovers play in biological processes.

| S-EPMC2896531 | biostudies-literature

Prion protein glycans reduce intracerebral fibril formation and spongiosis in prion disease.

Project description:Posttranslational modifications (PTMs) are common among proteins that aggregate in neurodegenerative disease, yet how PTMs impact the aggregate conformation and disease progression remains unclear. By engineering knockin mice expressing prion protein (PrP) lacking 2 N-linked glycans (Prnp180Q/196Q), we provide evidence that glycans reduce spongiform degeneration and hinder plaque formation in prion disease. Prnp180Q/196Q mice challenged with 2 subfibrillar, non-plaque-forming prion strains instead developed plaques highly enriched in ADAM10-cleaved PrP and heparan sulfate (HS). Intriguingly, a third strain composed of intact, glycophosphatidylinositol-anchored (GPI-anchored) PrP was relatively unchanged, forming diffuse, HS-deficient deposits in both the Prnp180Q/196Q and WT mice, underscoring the pivotal role of the GPI-anchor in driving the aggregate conformation and disease phenotype. Finally, knockin mice expressing triglycosylated PrP (Prnp187N) challenged with a plaque-forming prion strain showed a phenotype reversal, with a striking disease acceleration and switch from plaques to predominantly diffuse, subfibrillar deposits. Our findings suggest that the dominance of subfibrillar aggregates in prion disease is due to the replication of GPI-anchored prions, with fibrillar plaques forming from poorly glycosylated, GPI-anchorless prions that interact with extracellular HS. These studies provide insight into how PTMs impact PrP interactions with polyanionic cofactors, and highlight PTMs as a major force driving the prion disease phenotype.

| S-EPMC7269597 | biostudies-literature

Prion protein NMR structures of elk and of mouse/elk hybrids.

Project description:The NMR structure of the recombinant elk prion protein (ePrP), which represents the cellular isoform (ePrPC) in the healthy organism, is described here. As anticipated from the highly conserved amino acid sequence, ePrPC has the same global fold as other mammalian prion proteins (PrPs), with a flexibly disordered "tail" of residues 23-124 and a globular domain 125-226 with three alpha-helices and a short antiparallel beta-sheet. However, ePrPC shows a striking local structure variation when compared with most other mammalian PrPs, in particular human, bovine, and mouse PrPC. A loop of residues 166-175, which links the beta-sheet with the alpha2-helix and is part of a hypothetical "protein X" epitope, is outstandingly well defined, whereas this loop is disordered in the other species. Based on NMR structure determinations of two mouse PrP variants, mPrP[N174T] and mPrP[S170N,N174T], this study shows that the structured loop in ePrPC relates to these two local amino acid exchanges, so that mPrP[S170N,N174T] exactly mimics ePrPC. These results are evaluated in the context of recent reports on chronic wasting disease (CWD) in captive and free-ranging deer and elk in the U.S. and Canada, and an animal model is proposed for support of future research on CWD.

| S-EPMC545551 | biostudies-literature

Differential stability of the bovine prion protein upon urea unfolding.

Project description:Prion diseases, or transmissible spongiform encephalopathies, are a group of infectious neurological diseases associated with the structural conversion of an endogenous protein (PrP) in the central nervous system. There are two major forms of this protein: the native and noninfectious cellular form, PrP(C); and the misfolded, infectious, and proteinase K-resistant form, PrP(Sc). The C-terminal domain of PrP(C) is mainly alpha-helical in structure, whereas PrP(Sc) in known to aggregate into an assembly of beta-sheets, forming amyloid fibrils. To identify the regions of PrP(C) potentially involved in the initial steps of the conversion to the infectious conformation, we have used high-resolution NMR spectroscopy to characterize the stability and structure of bovine recombinant PrP(C) (residues 121 to 230) during unfolding with the denaturant urea. Analysis of the 800 MHz (1)H NMR spectra reveals region-specific information about the structural changes occurring upon unfolding. Our data suggest that the dissociation of the native beta-sheet of PrP(C) is a primary step in the urea-induced unfolding process, while strong hydrophobic interactions between helices alpha1 and alpha3, and between alpha2 and alpha3, stabilize these regions even at very high concentrations of urea.

| S-EPMC2786980 | biostudies-literature

Influence of specific HSP70 domains on fibril formation of the yeast prion protein Ure2.

Project description:Ure2p is the protein determinant of the Saccharomyces cerevisiae prion state [URE3]. Constitutive overexpression of the HSP70 family member SSA1 cures cells of [URE3]. Here, we show that Ssa1p increases the lag time of Ure2p fibril formation in vitro in the presence or absence of nucleotide. The presence of the HSP40 co-chaperone Ydj1p has an additive effect on the inhibition of Ure2p fibril formation, whereas the Ydj1p H34Q mutant shows reduced inhibition alone and in combination with Ssa1p. In order to investigate the structural basis of these effects, we constructed and tested an Ssa1p mutant lacking the ATPase domain, as well as a series of C-terminal truncation mutants. The results indicate that Ssa1p can bind to Ure2p and delay fibril formation even in the absence of the ATPase domain, but interaction of Ure2p with the substrate-binding domain is strongly influenced by the C-terminal lid region. Dynamic light scattering, quartz crystal microbalance assays, pull-down assays and kinetic analysis indicate that Ssa1p interacts with both native Ure2p and fibril seeds, and reduces the rate of Ure2p fibril elongation in a concentration-dependent manner. These results provide new insights into the structural and mechanistic basis for inhibition of Ure2p fibril formation by Ssa1p and Ydj1p.

| S-EPMC3638396 | biostudies-literature

Fibril formation of the rabbit/human/bovine prion proteins.

Project description:Prion diseases are infectious fatal neurodegenerative diseases including Creutzfeldt-Jakob disease in humans and bovine spongiform encephalopathy in cattle. The misfolding and conversion of cellular PrP in such mammals into pathogenic PrP is believed to be the key procedure. Rabbits are among the few mammalian species that exhibit resistance to prion diseases, but little is known about the molecular mechanism underlying such resistance. Here, we report that the crowding agents Ficoll 70 and dextran 70 have different effects on fibrillization of the recombinant full-length PrPs from different species: although these agents dramatically promote fibril formation of the proteins from human and cow, they significantly inhibit fibrillization of the rabbit protein by stabilizing its native state. We also find that fibrils formed by the rabbit protein contain less β-sheet structure and more α-helix structure than those formed by the proteins from human and cow. In addition, amyloid fibrils formed by the rabbit protein do not generate a proteinase K-resistant fragment of 15-16-kDa, but those formed by the proteins from human and cow generate such proteinase K-resistant fragments. Together, these results suggest that the strong inhibition of fibrillization of the rabbit PrP by the crowded physiological environment and the absence of such a protease-resistant fragment for the rabbit protein could be two of the reasons why rabbits are resistant to prion diseases.

| S-EPMC3177062 | biostudies-literature

Molecular basis for amyloid fibril formation and stability.

Project description:The molecular structure of the amyloid fibril has remained elusive because of the difficulty of growing well diffracting crystals. By using a sequence-designed polypeptide, we have produced crystals of an amyloid fiber. These crystals diffract to high resolution (1 A) by electron and x-ray diffraction, enabling us to determine a detailed structure for amyloid. The structure reveals that the polypeptides form fibrous crystals composed of antiparallel beta-sheets in a cross-beta arrangement, characteristic of all amyloid fibers, and allows us to determine the side-chain packing within an amyloid fiber. The antiparallel beta-sheets are zipped together by means of pi-bonding between adjacent phenylalanine rings and salt-bridges between charge pairs (glutamic acid-lysine), thus controlling and stabilizing the structure. These interactions are likely to be important in the formation and stability of other amyloid fibrils.

| S-EPMC544296 | biostudies-literature

Strength of Humic Acid Aggregates: Effects of Divalent Cations and Solution pH.

Project description:Aggregation-dispersion, charging, and aggregate strength of Leonardite humic acid (LHA) were investigated in CaCl2 and MgCl2 solutions as a function of pH and ionic strength (I). The strength or the withstanding force of aggregates of humic substances (HSs) against breakage is important because this force influences the transport and distribution of pollutants and nutrients along with HSs through the change in the size of HS aggregates as a transport unit. We observed the dominancy of aggregation of LHA at high pH than at low pH in every case of CaCl2 and MgCl2 solutions. This observation suggests the higher binding efficiency of these divalent ions at high pH, though there was no obvious relation with electrophoretic mobility and aggregation of LHA. Further, we first revealed the numerical value of the strength of HS aggregates by using a simple experimental setup of aggregate breakup under laminar converging flow through a capillary tube. The obtained values of the strength of LHA aggregates were higher in the presence of CaCl2 solution than MgCl2 solution, and the strength increased with pH. The highest strengths of LHA aggregates in 30 mM (I) CaCl2 and MgCl2 solutions were around 5.8 and 2.4 nN, respectively, at pH around 9.

| S-EPMC6648436 | biostudies-literature

Enhanced Electrochemical Stability of Molten Li Salt Hydrate Electrolytes by the Addition of Divalent Cations.

Project description:Water can be an attractive solvent for Li-ion battery electrolytes owing to numerous advantages such as high polarity, nonflammability, environmental benignity, and abundance, provided that its narrow electrochemical potential window can be enhanced to a similar level to that of typical nonaqueous electrolytes. In recent years, significant improvements in the electrochemical stability of aqueous electrolytes have been achieved with molten salt hydrate electrolytes containing extremely high concentrations of Li salt. In this study, we investigated the effect of divalent salt additives (magnesium and calcium bis(trifluoromethanesulfonyl)amides) in a molten salt hydrate electrolyte (21 mol kg-1 lithium bis(trifluoromethanesulfonyl)amide) on the electrochemical stability and aqueous lithium secondary battery performance. We found that the electrochemical stability was further enhanced by the addition of the divalent salt. In particular, the reductive stability was increased by more than 1 V on the Al electrode in the presence of either of the divalent cations. Surface characterization with X-ray photoelectron spectroscopy suggests that a passivation layer formed on the Al electrode consists of inorganic salts (most notably fluorides) of the divalent cations and the less-soluble solid electrolyte interphase mitigated the reductive decomposition of water effectively. The enhanced electrochemical stability in the presence of the divalent salts resulted in a more-stable charge-discharge cycling of LiCoO2 and Li4Ti5O12 electrodes.

| S-EPMC6130271 | biostudies-literature

Divalent cations promote TALE DNA-binding specificity.

Project description:Recent advances in gene editing have been enabled by programmable nucleases such as transcription activator-like effector nucleases (TALENs) and CRISPR-Cas9. However, several open questions remain regarding the molecular machinery in these systems, including fundamental search and binding behavior as well as role of off-target binding and specificity. In order to achieve efficient and specific cleavage at target sites, a high degree of target site discrimination must be demonstrated for gene editing applications. In this work, we studied the binding affinity and specificity for a series of TALE proteins under a variety of solution conditions using in vitro fluorescence methods and molecular dynamics (MD) simulations. Remarkably, we identified that TALEs demonstrate high sequence specificity only upon addition of small amounts of certain divalent cations (Mg2+, Ca2+). However, under purely monovalent salt conditions (K+, Na+), TALEs bind to specific and non-specific DNA with nearly equal affinity. Divalent cations preferentially bind to DNA over monovalent cations, which attenuates non-specific interactions between TALEs and DNA and further stabilizes specific interactions. Overall, these results uncover new mechanistic insights into the binding action of TALEs and further provide potential avenues for engineering and application of TALE- or TALEN-based systems for genome editing and regulation.

| S-EPMC7026652 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data