SciCombinator

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Concept: Aggregate data

166

Aggregation of TAR DNA-binding protein 43 (TDP-43) is a pathological signature of amyotrophic lateral sclerosis (ALS). Although accumulating evidence suggests the involvement of RNA recognition motifs (RRMs) in TDP-43 proteinopathy, it remains unclear how native TDP-43 is converted to pathogenic forms. To elucidate the role of homeostasis of RRM1 structure in ALS pathogenesis, conformations of RRM1 under high pressure were monitored by NMR. We first found that RRM1 was prone to aggregation and had three regions showing stable chemical shifts during misfolding. Moreover, mass-spectrometric analysis of aggregated RRM1 revealed that one of the regions was located on protease-resistant β-strands containing two cysteines (C173 and C175), indicating that this region served as a core assembly interface in RRM1 aggregation. Although a fraction of RRM1 aggregates comprised disulfide-bonded oligomers, the substitution of cysteine(s) to serine(s) (C/S) resulted in unexpected acceleration of amyloid fibrils of RRM1 and disulfide-independent aggregate formation of full-length TDP-43. Notably, TDP-43 aggregates with RRM1-C/S required C-terminus, and replicated cytopathologies of ALS, including mislocalization, impaired RNA splicing, ubiquitination, phosphorylation, and motor neuron toxicity. Furthermore, RRM1-C/S accentuated inclusions of familial ALS-linked TDP-43 mutants in C-terminus. The relevance of RRM1-C/S-induced TDP-43 aggregates in ALS pathogenesis was verified by immunolabeling of inclusions of ALS patients and cultured cells overexpressing the RRM1-C/S TDP-43 with antibody targeting a misfolding-relevant regions. Our results indicate that cysteines in RRM1 crucially govern the conformation of TDP-43, and aberrant self-assembly of RRM1 at amyloidogenic regions contributes to pathogenic conversion of TDP-43 in ALS.

Concepts: DNA, Protein, Amyloid, Amyotrophic lateral sclerosis, Aggregate, Aggregate data, RNA splicing, Proteopathy

39

Tactoids are nuclei of an orientationally ordered nematic phase that emerge upon cooling the isotropic phase. In addition to providing a natural setting for exploring chromonics under confinement, we show that tactoids can also serve as optical probes to delineate the role of temperature and concentration in the aggregation behavior of chromonics. For high concentrations, we observe the commonly reported elongated bipolar tactoids. As the concentration is lowered, breaking of achiral symmetry in the director configuration is observed with a predominance of twisted bipolar tactoids. On further reduction of concentration, a remarkable transformation of the director configuration occurs, wherein it conforms to a unique splay-minimizing configuration. Based on a simple model, we arrive at an interesting result that lower concentrations have longer aggregates at the same reduced temperature. Hence, the splay deformation that scales linearly with the aggregate length becomes prohibitive for lower concentrations and is relieved via twist and bend deformations in this unique configuration. Raman scattering measurements of the order parameters independently verify the trend in aggregate lengths and provide a physical picture of the nematic-biphasic transition.

Concepts: Fundamental physics concepts, Electrochemistry, Scattering, Aggregate, Aggregate data, Raman scattering, Liquid crystal, Phase diagram

37

The aggregation of amyloid-Aβ (Aβ) on lipid bilayers has been implicated as a mechanism by which Aβ exerts its toxicity in Alzheimer’s disease (AD). Lipid bilayer thinning has been observed during both oxidative stress and protein aggregation in AD, but whether these pathological modifications of the bilayer correlate with Aβ misfolding is unclear. Here, we studied peptide-lipid interactions in synthetic bilayers of the short-chain lipid dilauroyl phosphatidylcholine (DLPC) as a simplified model for diseased bilayers to determine their impact on Aβ aggregate, protofibril, and fibril formation. Aβ aggregation and fibril formation in membranes composed of dioleoyl phosphatidylcholine (DOPC) or 1- palmitoyl-2-oleoyl phosphatidylcholine (POPC) mimicking normal bilayers served as controls. Differences in aggregate formation and stability were monitored by a combination of thioflavin-T fluorescence, circular dichroism, AFM, TEM, and NMR. Despite the ability of all three lipid bilayers to catalyze aggregation, DLPC accelerates aggregation at much lower concentrations uniquely ablates the fibrillation of Aβ at low μM concentrations. DLPC stabilized globular, membrane-associated oligomers which could disrupt the bilayer integrity. DLPC bilayers also remodeled preformed amyloid fibrils into a pseudo-unfolded, molten globule state which resembled on-pathway, protofibrillar aggregates. While the stabilized, membrane-associated oligomers were found to be nontoxic, the remodeled species displayed toxicity similar to that of conventionally prepared aggregates. These results provide mechanistic insights into the roles that pathologically thin bilayers may play in Aβ aggregation on neuronal bilayers and pathological lipid oxidation may contribute to Aβ misfolding.

Concepts: Protein, Redox, Electrochemistry, Aggregate, Aggregate data, Lipid, Toxicity, Lipid bilayer

28

The time-evolutions of nanoparticle hydrodynamic radius and aggregate fractal dimension during the aggregation of fullerene (C(60)) nanoparticles (FNPs) were measured via simultaneous multiangle static and dynamic light scattering. The FNP aggregation behavior was determined as a function of monovalent (NaCl) and divalent (CaCl(2)) electrolyte concentration, and the impact of addition of dissolved natural organic matter (humic acid) to the solution was also investigated. In the absence of humic acid, the fractal dimension decreased over time with monovalent and divalent salts, suggesting that aggregates become slightly more open and less compact as they grow. Although the aggregates become slightly more open, the magnitude of the fractal dimension suggests intermediate aggregation between the diffusion- and reaction-limited regimes. We observed different aggregation behavior with monovalent and divalent salts upon the addition of humic acid to the solution. For NaCl-induced aggregation, the introduction of humic acid significantly suppressed the aggregation rate of FNPs at NaCl concentrations lower than 150mM. In this case, the aggregation was intermediate or reaction-limited even at NaCl concentrations as high as 500mM, giving rise to aggregates with a fractal dimension of 2.0. For CaCl(2)-induced aggregation, the introduction of humic acid enhanced the aggregation of FNPs at CaCl(2) concentrations greater than about 5mM due to calcium complexation and bridging effects. Humic acid also had an impact on the FNP aggregate structure in the presence of CaCl(2), resulting in a fractal dimension of 1.6 for the diffusion-limited aggregation regime. Our results with CaCl(2) indicate that in the presence of humic acid, FNP aggregates have a more open and loose structure than in the absence of humic acid. The aggregation results presented in this paper have important implications for the transport, chemical reactivity, and toxicity of engineered nanoparticles in aquatic environments.

Concepts: Chemistry, Soil, Aggregate, Aggregate data, Light scattering, Humus, Natural organic matter, Fractal

26

The 5-phosphoinositide phosphatase Sac3, whose loss-of-function mutations are linked to neurodegenerative disorders, forms a stable cytosolic complex with the scaffolding protein ArPIKfyve. The ArPIKfyve-Sac3 heterodimer interacts with the phosphoinositide 5-kinase PIKfyve in a ubiquitous ternary complex that couples PtdIns(3,5)P(2) synthesis with turnover at endosomal membranes, thereby regulating the housekeeping endocytic transport in eukaryotes. Neuron-specific associations of the ArPIKfyve-Sac3 heterodimer, which may shed light on neuropathological mechanisms triggered by Sac3 dysfunction, are unknown. Here we conducted mass spectrometry analysis for brain-derived interactors of ArPIKfyve-Sac3 and unraveled the α-synuclein-interacting protein Synphilin-1 (Sph1) as a new component of the ArPIKfyve-Sac3 complex. Sph1, a predominantly neuronal protein that facilitates aggregation of α-synuclein, is a major component of Lewy body inclusions in neurodegenerative α-synucleinopathies. Modulations in ArPIKfyve/Sac3 protein levels by RNA silencing or overexpression in several mammalian cell lines, including human neuronal SH-SY5Y or primary mouse cortical neurons, revealed that the ArPIKfyve-Sac3 complex specifically altered aggregation properties of Sph1-GFP. This effect required an active Sac3 phosphatase and proceeded through mechanisms that involved increased Sph1-GFP partitioning into the cytosol and removal of Sph1-GFP aggregates by basal autophagy but not by the proteasomal system. If uncoupled from ArPIKfyve elevation, overexpressed Sac3 readily aggregated, markedly enhancing the aggregation potential of Sph1-GFP. These data identify a novel role of the ArPIKfyve-Sac3 complex in the mechanisms controlling aggregate formation of Sph1 and suggest that Sac3 protein deficiency or overproduction may facilitate aggregation of aggregation-prone proteins, thereby precipitating the onset of multiple neuronal disorders.

Concepts: Cell nucleus, Cell, Mutation, Cell membrane, Ribosome, Cerebral cortex, Aggregate, Aggregate data

9

The aggregation of amyloid-β peptides into protein fibres is one of the main neuropathological features of Alzheimer’s disease (AD). While imaging of amyloid-β aggregate morphology in vitro is extremely important for understanding AD pathology and in the development of aggregation inhibitors, unfortunately, potentially highly toxic, early aggregates are difficult to observe by current electron microscopy and atomic force microscopy (AFM) methods, due to low contrast and variability of peptide attachment to the substrate. Here, we use a poly-L-Lysine (PLL) surface that captures all protein components from monomers to fully formed fibres, followed by nanomechanical mapping via ultrasonic force microscopy (UFM), which marries high spatial resolution and nanomechanical contrast with the non-destructive nature of tapping mode AFM. For the main putative AD pathogenic component, Aβ1-42, the PLL-UFM approach reveals the morphology of oligomers, protofibrils and mature fibres, and finds that a fraction of small oligomers is still present at later stages of fibril assembly.

Concepts: Alzheimer's disease, Protein, Peptide bond, Peptide, Aggregate, Aggregate data, Scanning tunneling microscope, Oligomer

5

South Africa has a large burden of rifampicin-resistant tuberculosis (RR-TB), with 18,734 patients diagnosed in 2014. The number of diagnosed patients has increased substantially with the introduction of the Xpert MTB/RIF test, used for tuberculosis (TB) diagnosis for all patients with presumptive TB. Routine aggregate data suggest a large treatment gap (pre-treatment loss to follow-up) between the numbers of patients with laboratory-confirmed RR-TB and those reported to have started second-line treatment. We aimed to assess the impact of Xpert MTB/RIF implementation on the delay to treatment initiation and loss to follow-up before second-line treatment for RR-TB across South Africa.

Concepts: HIV, AIDS, Cohort study, Evaluation methods, Tuberculosis, Aggregate data, Statistical terminology, Delays

5

Tau aggregation occurs in neurodegenerative diseases including Alzheimer’s disease and many other disorders collectively termed tauopathies. trans-cellular propagation of tau pathology, mediated by extracellular tau aggregates, may underlie pathogenesis of these conditions. P301S tau transgenic mice express mutant human tau protein and develop progressive tau pathology. Using a cell-based biosensor assay, we screened anti-tau monoclonal antibodies for their ability to block seeding activity present in P301S brain lysates. We infused three effective antibodies or controls into the lateral ventricle of P301S mice for 3 months. The antibodies markedly reduced hyperphosphorylated, aggregated, and insoluble tau. They also blocked development of tau seeding activity detected in brain lysates using the biosensor assay, reduced microglial activation, and improved cognitive deficits. These data imply a central role for extracellular tau aggregates in the development of pathology. They also suggest that immunotherapy specifically designed to block trans-cellular aggregate propagation will be a productive treatment strategy.

Concepts: Alzheimer's disease, Brain, Neurology, Aggregate, Aggregate data, Tau protein, Tauopathy, Proteopathy

4

Aging has been associated with a progressive decline of proteostasis, but how this process affects proteome composition remains largely unexplored. Here, we profiled more than 5,000 proteins along the lifespan of the nematode C. elegans. We find that one-third of proteins change in abundance at least 2-fold during aging, resulting in a severe proteome imbalance. These changes are reduced in the long-lived daf-2 mutant but are enhanced in the short-lived daf-16 mutant. While ribosomal proteins decline and lose normal stoichiometry, proteasome complexes increase. Proteome imbalance is accompanied by widespread protein aggregation, with abundant proteins that exceed solubility contributing most to aggregate load. Notably, the properties by which proteins are selected for aggregation differ in the daf-2 mutant, and an increased formation of aggregates associated with small heat-shock proteins is observed. We suggest that sequestering proteins into chaperone-enriched aggregates is a protective strategy to slow proteostasis decline during nematode aging.

Concepts: Protein, Gene, Amino acid, Ribosome, Cytoplasm, Messenger RNA, Aggregate, Aggregate data

3

Aggregates of proteins containing polyglutamine (polyQ) repeats are strongly associated with several neurodegenerative diseases. The length of the repeats correlates with the severity of the disease. Previous studies have shown that pure polyQ peptides aggregate by nucleated growth polymerization and that the size of the critical nucleus (n*) decreases from tetrameric to dimeric and monomeric as length increases from Q18 to Q26. Why the critical nucleus size changes with repeat-length has been unclear. Using AWSEM (the Associative memory, Water mediated, Structure and Energy Model), we construct the aggregation free energy landscapes for polyQ peptides of different repeat-lengths. These studies show that the monomer of the shorter repeat-length (Q20) prefers an extended conformation and that its aggregation indeed has a trimeric nucleus (n*∼ 3), while a longer repeat-length monomer (Q30) prefers a β-hairpin conformation which then aggregates in a downhill fashion at 0.1mM. For an intermediate length peptide (Q26), there is an equal preference for hairpin and extended forms in the monomer which leads to a mixed inhomogeneous nucleation mechanism for fibrils. The predicted changes of monomeric structure and nucleation mechanism are confirmed by studying the aggregation free energy profile for a polyglutamine repeat with site specific PG mutations that favor the hairpin form giving results in harmony with experiments on this system.

Concepts: DNA, Protein, Polymer chemistry, Aggregate, Aggregate data, Dimer, Monomer, Polymerization