Browse
Submit Data
Databases
API
Help

Dataset Information

15 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Formation and growth of oligomers: a Monte Carlo study of an amyloid tau fragment.

ABSTRACT: Small oligomers formed early in the process of amyloid fibril formation may be the major toxic species in Alzheimer's disease. We investigate the early stages of amyloid aggregation for the tau fragment AcPHF6 (Ac-VQIVYK-NH2) using an implicit solvent all-atom model and extensive Monte Carlo simulations of 12, 24, and 36 chains. A variety of small metastable aggregates form and dissolve until an aggregate of a critical size and conformation arises. However, the stable oligomers, which are beta-sheet-rich and feature many hydrophobic contacts, are not always growth-ready. The simulations indicate instead that these supercritical oligomers spend a lengthy period in equilibrium in which considerable reorganization takes place accompanied by exchange of chains with the solution. Growth competence of the stable oligomers correlates with the alignment of the strands in the beta-sheets. The larger aggregates seen in our simulations are all composed of two twisted beta-sheets, packed against each other with hydrophobic side chains at the sheet-sheet interface. These beta-sandwiches show similarities with the proposed steric zipper structure for PHF6 fibrils but have a mixed parallel/antiparallel beta-strand organization as opposed to the parallel organization found in experiments on fibrils. Interestingly, we find that the fraction of parallel beta-sheet structure increases with aggregate size. We speculate that the reorganization of the beta-sheets into parallel ones is an important rate-limiting step in the formation of PHF6 fibrils.

SUBMITTER: Li DW

PROVIDER: S-EPMC2583953 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

A Monte Carlo Study of the Early Steps of Functional Amyloid Formation.

Project description:In addition to their well-known roles in neurodegenerative diseases and amyloidoses, amyloid structures also assume important functional roles in the cell. Although functional amyloid shares many physiochemical properties with its pathogenic counterpart, it is evolutionarily optimized to avoid cytotoxicity. This makes it an interesting study case for aggregation phenomenon in general. One of the most well-known examples of a functional amyloid, E. coli curli, is an essential component in the formation of bacterial biofilm, and is primarily formed by aggregates of the protein CsgA. Previous studies have shown that the minor sequence variations observed in the five different subrepeats (R1-R5), which comprise the CsgA primary sequence, have a substantial influence on their individual aggregation propensities. Using a recently described diffusion-optimized enhanced sampling approach for Monte Carlo simulations, we here investigate the equilibrium properties of the monomeric and dimeric states of these subrepeats, to probe whether structural properties observed in these early stage oligomers are decisive for the characteristics of the resulting aggregate. We show that the dimerization propensities of these peptides have strong correlations with their propensity for amyloid formation, and provide structural insights into the inter- and intramolecular contacts that appear to be essential in this process.

| S-EPMC4706413 | biostudies-literature

Fragment Pose Prediction Using Non-equilibrium Candidate Monte Carlo and Molecular Dynamics Simulations.

Project description:Part of early stage drug discovery involves determining how molecules may bind to the target protein. Through understanding where and how molecules bind, chemists can begin to build ideas on how to design improvements to increase binding affinities. In this retrospective study, we compare how computational approaches like docking, molecular dynamics (MD) simulations, and a non-equilibrium candidate Monte Carlo (NCMC)-based method (NCMC + MD) perform in predicting binding modes for a set of 12 fragment-like molecules, which bind to soluble epoxide hydrolase. We evaluate each method's effectiveness in identifying the dominant binding mode and finding additional binding modes (if any). Then, we compare our predicted binding modes to experimentally obtained X-ray crystal structures. We dock each of the 12 small molecules into the apo-protein crystal structure and then run simulations up to 1 μs each. Small and fragment-like molecules likely have smaller energy barriers separating different binding modes by virtue of relatively fewer and weaker interactions relative to drug-like molecules and thus likely undergo more rapid binding mode transitions. We expect, thus, to see more rapid transitions between binding modes in our study. Following this, we build Markov State Models to define our stable ligand binding modes. We investigate if adequate sampling of ligand binding modes and transitions between them can occur at the microsecond timescale using traditional MD or a hybrid NCMC+MD simulation approach. Our findings suggest that even with small fragment-like molecules, we fail to sample all the crystallographic binding modes using microsecond MD simulations, but using NCMC+MD, we have better success in sampling the crystal structure while obtaining the correct populations.

| S-EPMC7325745 | biostudies-literature

Intraneuronal Tau Misfolding Induced by Extracellular Amyloid-β Oligomers.

Project description:Abnormal folding and aggregation of the microtubule-associated protein, tau, is a hallmark of several neurodegenerative disorders, including Alzheimer's disease (AD). Although normal tau is an intrinsically disordered protein, it does exhibit tertiary structure whereby the N- and C-termini are often in close proximity to each other and to the contiguous microtubule-binding repeat domains that extend C-terminally from the middle of the protein. Unfolding of this paperclip-like conformation might precede formation of toxic tau oligomers and filaments, like those found in AD brain. While there are many ways to monitor tau aggregation, methods to monitor changes in tau folding are not well established. Using full length human 2N4R tau doubly labeled with the Förster resonance energy transfer (FRET) compatible fluorescent proteins, Venus and Teal, on the N- and C-termini, respectively (Venus-Tau-Teal), intensity and lifetime FRET measurements were able to distinguish folded from unfolded tau in living cells independently of tau-tau intermolecular interactions. When expression was restricted to low levels in which tau-tau aggregation was minimized, Venus-Tau-Teal was sensitive to microtubule binding, phosphorylation, and pathogenic oligomers. Of particular interest is our finding that amyloid-β oligomers (AβOs) trigger Venus-Tau-Teal unfolding in cultured mouse neurons. We thus provide direct experimental evidence that AβOs convert normally folded tau into a conformation thought to predominate in toxic tau aggregates. This finding provides further evidence for a mechanistic connection between Aβ and tau at seminal stages of AD pathogenesis.

| S-EPMC7464573 | biostudies-literature

Polypeptide-Nanoparticle Interactions and Corona Formation Investigated by Monte Carlo Simulations.

Project description:Biomacromolecule activity is usually related to its ability to keep a specific structure. However, in solution, many parameters (pH, ionic strength) and external compounds (polyelectrolytes, nanoparticles) can modify biomacromolecule structure as well as acid/base properties, thus resulting in a loss of activity and denaturation. In this paper, the impact of neutral and charged nanoparticles (NPs) is investigated by Monte Carlo simulations on polypeptide (PP) chains with primary structure based on bovine serum albumin. The influence of pH, salt valency, and NP surface charge density is systematically studied. It is found that the PP is extended at extreme pH, when no complex formation is observed, and folded at physiological pH. PP adsorption around oppositely-charged NPs strongly limits chain structural changes and modifies its acid/base properties. At physiological pH, the complex formation occurs only with positively-charged NPs. The presence of salts, in particular those with trivalent cations, introduces additional electrostatic interactions, resulting in a mitigation of the impact of negative NPs. Thus, the corona structure is less dense with locally-desorbed segments. On the contrary, very limited impact of salt cation valency is observed when NPs are positive, due to the absence of competitive effects between multivalent cations and NP.

| S-EPMC6432162 | biostudies-literature

MERIT: Controlling Monte-Carlo error rate in large-scale Monte-Carlo hypothesis testing.

Project description:The use of Monte-Carlo (MC) p$$ p $$ -values when testing the significance of a large number of hypotheses is now commonplace. In large-scale hypothesis testing, we will typically encounter at least some p$$ p $$ -values near the threshold of significance, which require a larger number of MC replicates than p$$ p $$ -values that are far from the threshold. As a result, some incorrect conclusions can be reached due to MC error alone; for hypotheses near the threshold, even a very large number (eg, 106$$ 1{0}^6 $$ ) of MC replicates may not be enough to guarantee conclusions reached using MC p$$ p $$ -values. Gandy and Hahn (GH)6-8 have developed the only method that directly addresses this problem. They defined a Monte-Carlo error rate (MCER) to be the probability that any decisions on accepting or rejecting a hypothesis based on MC p$$ p $$ -values are different from decisions based on ideal p$$ p $$ -values; their method then makes decisions by controlling the MCER. Unfortunately, the GH method is frequently very conservative, often making no rejections at all and leaving a large number of hypotheses "undecided". In this article, we propose MERIT, a method for large-scale MC hypothesis testing that also controls the MCER but is more statistically efficient than the GH method. Through extensive simulation studies, we demonstrate that MERIT controls the MCER while making more decisions that agree with the ideal p$$ p $$ -values than GH does. We also illustrate our method by an analysis of gene expression data from a prostate cancer study.

| S-EPMC10909586 | biostudies-literature

Streaming Variational Monte Carlo.

Project description:Nonlinear state-space models are powerful tools to describe dynamical structures in complex time series. In a streaming setting where data are processed one sample at a time, simultaneous inference of the state and its nonlinear dynamics has posed significant challenges in practice. We develop a novel online learning framework, leveraging variational inference and sequential Monte Carlo, which enables flexible and accurate Bayesian joint filtering. Our method provides an approximation of the filtering posterior which can be made arbitrarily close to the true filtering distribution for a wide class of dynamics models and observation models. Specifically, the proposed framework can efficiently approximate a posterior over the dynamics using sparse Gaussian processes, allowing for an interpretable model of the latent dynamics. Constant time complexity per sample makes our approach amenable to online learning scenarios and suitable for real-time applications.

| S-EPMC10082974 | biostudies-literature

Amyloid β-protein oligomers promote the uptake of tau fibril seeds potentiating intracellular tau aggregation.

Project description:BackgroundRepeated failure of drug candidates targeting Alzheimer's disease (AD) in clinical trials likely stems from a lack of understanding of the molecular mechanisms underlying AD pathogenesis. Recent research has highlighted synergistic interactions between aggregated amyloid-β (Aβ) and tau proteins in AD, but the molecular details of how these interactions drive AD pathology remain elusive and speculative.MethodsHere, we test the hypothesis that Aβ potentiates intracellular tau aggregation, and show that oligomeric Aβ specifically exacerbates proteopathic seeding by tau. Using tau-biosensor cells, we show that treatment with sub-toxic concentrations of Aβ oligomers, but not monomers or fibrils, "primes" cells, making them more susceptible to tau seeding. The treatment with Aβ oligomers enhances intracellular tau aggregation in a dose-dependent manner when the cells are seeded with either recombinant or brain-derived tau fibrils, whereas little or no aggregation is observed in the absence of Aβ-oligomer priming.ResultsPriming by Aβ oligomers appears to be specific to tau, as α-synuclein seeding is unaffected by this treatment. Aβ oligomer-enhanced tau seeding also occurs in primary mouse neurons and human neuroblastoma cells. Using fluorescently labeled tau seeds, we find that treatment with Aβ oligomers significantly enhances the cellular uptake of tau seeds, whereas a known tau-uptake inhibitor blocks the effect of Aβ on tau uptake.ConclusionThe ability of Aβ to promote tau seeding suggests a specific and plausible mechanism by which extracellular Aβ initiates a deleterious cascade that is unique to AD. These data suggest that the Aβ-mediated potentiation of tau uptake into cells should also be taken into account when designing Aβ-targeted therapeutics.

| S-EPMC6800506 | biostudies-literature

Amyloid oligomers exacerbate tau pathology in a mouse model of tauopathy.

Project description:We aimed to investigate the influence of oligomeric forms of ?-amyloid (A?) and the influence of the duration of exposure on the development of tau phosphorylation.A? oligomers were injected intracranially either acutely into 5-month-old rTg4510 mice and tissue was collected 3 days later, or chronically into 3-month-old mice and tissue was collected 2 months later. Several forms of phosphorylated tau (p-tau), GSK3 (glycogen synthase kinase-3) and microglial and astrocyte activation were measured.Acute injections of A? oligomers had no effect on p-tau epitopes but did result in elevation of phosphorylated/activated GSK3 (pGSK3). Chronic infusion of A? oligomers into the right hippocampus resulted in 3- to 4-fold elevations in several p-tau isoforms with no changes in total tau levels. A significant elevation in pGSK3 accompanied these changes. Microglial staining with CD68 paralleled the increase in tau phosphorylation, however, CD45 staining was unaffected by A?. Control experiments revealed that the infusion of A? from the minipumps was largely complete by 10 days after implantation. Thus, the elevation in p-tau 2 months after implantation implies that the changes are quite persistent.Soluble A?(1-42) oligomers have long-lasting effects on tau phosphorylation in the rTg4510 model, possibly due to elevations in GSK3. These data suggest that even brief elevations in A? production, may have enduring impact on the risk for tauopathy.

| S-EPMC3739054 | biostudies-literature

Passive Immunotherapies Targeting Amyloid Beta and Tau Oligomers in Alzheimer's Disease.

Project description:Alzheimer's disease (AD) is historically difficult to treat, in part because of the inaccessible nature of brain pathology. Amyloid beta and tau proteins drive pathology by forming toxic oligomers that eventually deposit as insoluble amyloid plaques and neurofibrillary tangles. Recent clinical studies suggest that effective drugs must specifically target oligomers, not native monomers or insoluble fibrils. Passive immunotherapy is a promising pharmaceutical strategy used to specifically target these oligomers in situ. Using the specificity of antibodies coupled with the natural power of the body's immune response, this treatment provides an opportunity for safe clearance of pathogenic protein species from the brain. Passive immunotherapies against amyloid beta and tau oligomers have progressed to clinical trials, with many currently in progress. Biochemical studies of antibody-oligomer complexes have helped identify previously unknown toxic epitopes, thus providing knowledge to the AD field as a whole. This mini-review focuses on the efforts to develop passive immunotherapy treatments for AD and discusses the knowledge gained from recent failures and clinical trials in progress.

| S-EPMC6937375 | biostudies-literature

Addressing nonlinearities in Monte Carlo.

Project description:Monte Carlo is famous for accepting model extensions and model refinements up to infinite dimension. However, this powerful incremental design is based on a premise which has severely limited its application so far: a state-variable can only be recursively defined as a function of underlying state-variables if this function is linear. Here we show that this premise can be alleviated by projecting nonlinearities onto a polynomial basis and increasing the configuration space dimension. Considering phytoplankton growth in light-limited environments, radiative transfer in planetary atmospheres, electromagnetic scattering by particles, and concentrated solar power plant production, we prove the real-world usability of this advance in four test cases which were previously regarded as impracticable using Monte Carlo approaches. We also illustrate an outstanding feature of our method when applied to acute problems with interacting particles: handling rare events is now straightforward. Overall, our extension preserves the features that made the method popular: addressing nonlinearities does not compromise on model refinement or system complexity, and convergence rates remain independent of dimension.

| S-EPMC6125312 | 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