Seeded propagation of amyloid-beta (Aβ) pathology is suggested to contribute to the progression of Alzheimer's disease. Local overproduction of aggregation-prone Aβ variants could explain the focal ...initiation of a seeding cascade that subsequently triggers widespread pathology. Several animal models support this seeding concept by demonstrating accelerated Aβ deposition following inoculation with Aβ-containing homogenates, however its role in progressive neurodegeneration remains unclear. Here, we present a non-invasive approach to study Aβ seeding processes in vivo using Drosophila models. We show that small amounts of aggregation-competent Aβ
seeds, generated in selected neuronal clusters, can induce the deposition of the pan-neuronally expressed and otherwise soluble Aβ
. Moreover, our models visualize the accelerated formation and propagation of amyloid pathology throughout the brain, which correlates with severe neurotoxicity. Taken together, these in vivo models provide mechanistic insights into disease-related processes and represent versatile genetic tools to determine novel modifiers of the Aβ seeding cascade.Seeding of amyloid beta from one brain region to another is thought to contribute to the progression of Alzheimer's disease, although to date most studies have depended on inoculation of animals with exogenous amyloid. Here the authors describe a genetic seed and target system in Drosophila which may be useful for the mechanistic study of seeding of amyloid in vivo.
Protein aggregation has now become recognised as an important and generic aspect of protein energy landscapes. Since the discovery that numerous human diseases are caused by protein aggregation, the ...biophysical characterisation of misfolded states and their aggregation mechanisms has received increased attention. Utilising experimental techniques and computational approaches established for the analysis of protein folding reactions has ensured rapid advances in the study of pathways leading to amyloid fibrils and amyloid-related aggregates. Here we describe recent experimental and theoretical advances in the elucidation of the conformational properties of dynamic, heterogeneous and/or insoluble protein ensembles populated on complex, multidimensional protein energy landscapes. We discuss current understanding of aggregation mechanisms in this context and describe how the synergy between biochemical, biophysical and cell-biological experiments are beginning to provide detailed insights into the partitioning of non-native species between protein folding and aggregation pathways.
Abstract The identification of protein binding residues helps to understand their biological processes as protein function is often defined through ligand binding, such as to other proteins, small ...molecules, ions, or nucleotides. Methods predicting binding residues often err for intrinsically disordered proteins or regions (IDPs/IDPRs), often also referred to as molecular recognition features (MoRFs). Here, we presented a novel machine learning (ML) model trained to specifically predict binding regions in IDPRs. The proposed model, IDBindT5, leveraged embeddings from the protein language model (pLM) ProtT5 to reach a balanced accuracy of 57.2 ± 3.6% (95% confidence interval). Assessed on the same data set, this did not differ at the 95% CI from the state-of-the-art (SOTA) methods ANCHOR2 and DeepDISOBind that rely on expert-crafted features and evolutionary information from multiple sequence alignments (MSAs). Assessed on other data, methods such as SPOT-MoRF reached higher MCCs. IDBindT5’s SOTA predictions are much faster than other methods, easily enabling full-proteome analyses. Our findings emphasize the potential of pLMs as a promising approach for exploring and predicting features of disordered proteins. The model and a comprehensive manual are publicly available at https://github.com/jahnl/binding_in_disorder .
BACKGROUND AND AIMS: Rice plants (Oryza sativa L.) contain large quantities of silicon (Si) in form of phytoliths, which increase their resistance to abiotic and biotic stresses. The Si cycle through ...rice fields is hardly studied. We tested how increasing Si availability affects rice growth and the decomposability of the straw. Secondly we tested the role of straw recycling for Si availability. METHODS: In a field experiment, we applied three levels of silica gel during one rice cropping season. In a follow-up laboratory experiment, we used straw produced in the field experiment, having different Si concentrations, and studied straw decomposition, straw Si release, and Si uptake by plants. RESULTS: Silicon fertilization increased Si contents, biomass production, and grain yield of rice plants. Increased Si uptake by rice decreased concentrations of C and some essential nutrients (N, P, K, Ca, and Mg) in the straw, and increased straw decomposability and Si release. CONCLUSIONS: Fertilization with silica gel is an option to improve Si supply to rice plants growing on weathered soils with low levels of plant-available Si. Phytoliths from fresh rice straw dissolve fast in soil, thus, recycling of rice straw is an important source of plant-available Si.
The Yin and Yang of protein folding Jahn, Thomas R.; Radford, Sheena E.
The FEBS journal,
December 2005, Letnik:
272, Številka:
23
Journal Article
Recenzirano
Odprti dostop
The study of protein aggregation saw a renaissance in the last decade, when it was discovered that aggregation is the cause of several human diseases, making this field of research one of the most ...exciting frontiers in science today. Building on knowledge about protein folding energy landscapes, determined using an array of biophysical methods, theory and simulation, new light is now being shed on some of the key questions in protein‐misfolding diseases. This review will focus on the mechanisms of protein folding and amyloid fibril formation, concentrating on the role of partially folded states in these processes, the complexity of the free energy landscape, and the potentials for the development of future therapeutic strategies based on a full biophysical description of the combined folding and aggregation free‐energy surface.
Abstract
The deposition of tau aggregates throughout the brain is a pathological characteristic within a group of neurodegenerative diseases collectively termed tauopathies, which includes ...Alzheimer’s disease. While recent findings suggest the involvement of unconventional secretory pathways driving tau into the extracellular space and mediating the propagation of the disease-associated pathology, many of the mechanistic details governing this process remain elusive. In the current study, we provide an in-depth characterization of the unconventional secretory pathway of tau and identify novel molecular determinants that are required for this process. Here, using
Drosophila
models of tauopathy, we correlate the hyperphosphorylation and aggregation state of tau with the disease-related neurotoxicity. These newly established systems recapitulate all the previously identified hallmarks of tau secretion, including the contribution of tau hyperphosphorylation as well as the requirement for PI(4,5)P
2
triggering the direct translocation of tau. Using a series of cellular assays, we demonstrate that both the sulfated proteoglycans on the cell surface and the correct orientation of the protein at the inner plasma membrane leaflet are critical determinants of this process. Finally, we identify two cysteine residues within the microtubule binding repeat domain as novel
cis
-elements that are important for both unconventional secretion and trans-cellular propagation of tau.
We compare the performance of three most accepted reagents for organic matter removal: hydrogen peroxide (H2O2), sodium hypochlorite (NaOCl) and disodium peroxodisulfate (Na2S2O8). Removal of organic ...matter from soil is mostly incomplete with the efficiency of removal depending on reaction conditions and sample properties. Generally, NaOCl and Na2S2O8 are more effective in organic C removal than H2O2. Alkaline conditions and additives favoring dispersion and/or desorption of organic matter, such as sodium pyrophosphate, seem to be crucial for C removal. Pyrophosphate and additives for pH control (bicarbonate) may irreversibly adsorb to mineral surfaces. In soils with a large proportion of organic matter bound to the mineral matrix, for example subsoils, or rich in clay-sized minerals (Fe oxides, poorly crystalline Fe and Al phases, expandable phyllosilicates), C removal can be little irrespective of the reagents used. Residual organic C seems to seems to represent largely refractory organic matter, and comprises mainly pyrogenic materials and aliphatic compounds. If protected by close association with minerals, other organic constituents such as low-molecular weight carboxylic acids, lignin-derived and N-containing compounds may escape chemical destruction. For determination of mineral phase properties, treatment with H2O2 should be avoided since it may promote organic-assisted dissolution of poorly crystalline minerals at low pH, disintegration of expandable clay minerals, and transformation of vermiculite into mica-like products due to NH4(+) fixation. Sodium hypochlorite and Na2S2O8 are less harmful for minerals than H2O2. While the NaOCl procedure (pH 9.5) may dissolve Al hydroxides, alkaline conditions favor the precipitation of metals released upon destruction of organic matter. Prolonged heating to >40 degrees C during any treatment may transform poorly crystalline minerals into more crystalline ones. Sodium hypochlorite can be used at 25 degrees C, thus preventing heat-induced mineral alteration.
Transmission electron microscopic image of iron isomaltoside 1000.
The treatment of iron deficiency anemia with polynuclear iron formulations is an established therapy in patients with chronic kidney ...disease but also in other disease areas like gastroenterology, cardiology, oncology, pre/post operatively and obstetrics’ and gynecology. Parenteral iron formulations represent colloidal systems in the lower nanometer size range which have traditionally been shown to consist of an iron core surrounded by a carbohydrate shell. In this publication, we for the first time describe the novel matrix structure of iron isomaltoside 1000 which differs from the traditional picture of an iron core surrounded by a carbohydrate. Despite some structural similarities between the different iron formulations, the products differ significantly in their physicochemical properties such as particle size, zeta potential, free and labile iron content, and release of iron in serum. This study compares the physiochemical properties of iron isomaltoside 1000 (Monofer®) with the currently available intravenous iron preparations and relates them to their biopharmaceutical properties and their approved clinical applications. The investigated products encompass low molecular weight iron dextran (CosmoFer®), sodium ferric gluconate (Ferrlecit®), iron sucrose (Venofer®), iron carboxymaltose (Ferinject®/Injectafer®), and ferumoxytol (Feraheme®) which are compared to iron isomaltoside 1000 (Monofer®). It is shown that significant and clinically relevant differences exist between sodium ferric gluconate and iron sucrose as labile iron formulations and iron dextran, iron carboxymaltose, ferumoxytol, and iron isomaltoside 1000 as stable polynuclear formulations. The differences exist in terms of their immunogenic potential, safety, and convenience of use, the latter being expressed by the opportunity for high single-dose administration and short infusion times. Monofer is a new parenteral iron product with a very low immunogenic potential and a very low content of labile and free iron. This enables Monofer, as the only IV iron formulation, to be administered as a rapid high dose infusion in doses exceeding 1000
mg without the application of a test dose. This offers considerable dose flexibility, including the possibility of providing full iron repletion in a single infusion (one-dose iron repletion).
Summary
Soil minerals are known to influence the biological stability of soil organic matter (SOM). Our study aimed to relate properties of the mineral matrix to its ability to protect organic C ...against decomposition in acid soils. We used the amount of hydroxyl ions released after exposure to NaF solution to establish a reactivity gradient spanning 12 subsoil horizons collected from 10 different locations. The subsoil horizons represent six soil orders and diverse geological parent materials. Phyllosilicates were characterized by X‐ray diffraction and pedogenic oxides by selective dissolution procedures. The organic carbon (C) remaining after chemical removal of an oxidizable fraction of SOM with NaOCl solution was taken to represent a stable organic carbon pool. Stable organic carbon was confirmed as older than bulk organic carbon by a smaller radiocarbon (14C) content after oxidation in all 12 soils. The amount of stable organic C did not depend on clay content or the content of dithionite–citrate‐extractable Fe. The combination of oxalate‐extractable Fe and Al explained the greatest amount of variation in stable organic C (R2 = 0.78). Our results suggest that in acid soils, organic matter is preferentially protected by interaction with poorly crystalline minerals represented by the oxalate‐soluble Fe and Al fraction. This evidence suggests that ligand exchange between mineral surface hydroxyl groups and negatively charged organic functional groups is a quantitatively important mechanism in the stabilization of SOM in acid soils. The results imply a finite stabilization capacity of soil minerals for organic matter, limited by the area density of reactive surface sites.
Although most proteins can assemble into amyloid-like fibrils in vitro under extreme conditions, how proteins form amyloid fibrils in vivo remains unresolved. Identifying rare aggregation-prone ...species under physiologically relevant conditions and defining their structural properties is therefore an important challenge. By solving the folding mechanism of the naturally amyloidogenic protein beta-2-microglobulin at pH 7.0 and 37 degrees C and correlating the concentrations of different species with the rate of fibril elongation, we identify a specific folding intermediate, containing a non-native trans-proline isomer, as the direct precursor of fibril elongation. Structural analysis using NMR shows that this species is highly native-like but contains perturbation of the edge strands that normally protect beta-sandwich proteins from self-association. The results demonstrate that aggregation pathways can involve self-assembly of highly native-like folding intermediates, and have implications for the prevention of this, and other, amyloid disorders.
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