Filamentous Aggregates Are Fragmented by the Proteasome Holoenzyme.

Filamentous aggregates (fibrils) are regarded as the final stage in the assembly of amyloidogenic proteins and are formed in many neurodegenerative diseases. Accumulation of aggregates occurs as a result of an imbalance between their formation and removal. Here we use single-aggregate imaging to show that large fibrils assembled from full-length tau are substrates of the 26S proteasome holoenzyme, which fragments them into small aggregates. Interestingly, although degradation of monomeric tau is not inhibited by adenosine 5'-(3-thiotriphosphate) (ATPγS), fibril fragmentation is predominantly dependent on the ATPase activity of the proteasome. The proteasome holoenzyme also targets fibrils assembled from α-synuclein, suggesting that its fibril-fragmenting function may be a general mechanism. The fragmented species produced by the proteasome shows significant toxicity to human cell lines compared with intact fibrils. Together, our results indicate that the proteasome holoenzyme possesses a fragmentation function that disassembles large fibrils into smaller and more cytotoxic species.Wellcome Trust, Sir Henry Wellcome Fellowship (101585/Z/13/Z) to Yu Y

Realistic atomistic structure of amorphous silicon from machine-learning-driven molecular dynamics

Amorphous silicon (a-Si) is a widely studied noncrystalline material, and yet the subtle details of its atomistic structure are still unclear. Here, we show that accurate structural models of a-Si can be obtained using a machine-learning-based interatomic potential. Our best a-Si network is obtained by simulated cooling from the melt at a rate of 1011 K/s (that is, on the 10 ns time scale), contains less than 2% defects, and agrees with experiments regarding excess energies, diffraction data, and 29Si NMR chemical shifts. We show that this level of quality is impossible to achieve with faster quench simulations. We then generate a 4096-atom system that correctly reproduces the magnitude of the first sharp diffraction peak (FSDP) in the structure factor, achieving the closest agreement with experiments to date. Our study demonstrates the broader impact of machine-learning potentials for elucidating structures and properties of technologically important amorphous materials

ThX - a next-generation probe for the early detection of amyloid aggregates.

Neurodegenerative diseases such as Alzheimer's and Parkinson's are associated with protein misfolding and aggregation. Recent studies suggest that the small, rare and heterogeneous oligomeric species, formed early on in the aggregation process, may be a source of cytotoxicity. Thioflavin T (ThT) is currently the gold-standard fluorescent probe for the study of amyloid proteins and aggregation processes. However, the poor photophysical and binding properties of ThT impairs the study of oligomers. To overcome this challenge, we have designed Thioflavin X, (ThX), a next-generation fluorescent probe which displays superior properties; including a 5-fold increase in brightness and 7-fold increase in binding affinity to amyloidogenic proteins. As an extrinsic dye, this can be used to study unique structural amyloid features both in bulk and on a single-aggregate level. Furthermore, ThX can be used as a super-resolution imaging probe in single-molecule localisation microscopy. Finally, the improved optical properties (extinction coefficient, quantum yield and brightness) of ThX can be used to monitor structural differences in oligomeric species, not observed via traditional ThT imaging

Structural Simplicity as a Restraint on the Structure of Amorphous Silicon

Understanding the structural origins of the properties of amorphous materials remains one of the most important challenges in structural science. In this study we demonstrate that local ‘structural simplicity’, embodied by the degree to which atomic environments within a material are similar to each other, is powerful concept for rationalising the structure of canonical amorphous material amorphous silicon (a-Si). We show, by restraining a reverse Monte Carlo refinement against pair distribution function (PDF) data to be simpler, that the simplest model consistent with the PDF is a continuous random network (CRN). A further effect of producing a simple model of a-Si is the generation of a (pseudo)gap in the electronic density of states, suggesting that structural ho- mogeneity drives electronic homogeneity. That this method produces models of a-Si that approach the state-of-the-art without the need for chemically specific restraints (beyond the assumption of homogeneity) suggests that simplicity-based refinement approaches may allow experiment-driven structural modelling techniques to be developed for the wide variety of amorphous semiconductors with strong local order.Sidney Sussex College, Cambridge to M.J.C.; EPSRC to C.P.G. and R.P.K. under Grant No. EP/K030132/1 EPSRC (EP/G004528/2) and ERC (Grant Ref: 279705) to M.J.C and A.L.G.. A.P.B. was supported by a Leverhulme Early Career Fellowship with joint funding from the Isaac Newton Trust. Via our membership of the UK’s HEC Materials Chemistry Consortium, which is funded by the EPSRC (EP/L000202), this work used the ARCHER UK National Supercomputing Service (http://archer.ac.uk)

Formation of pre-pore complexes of pneumolysin is accompanied by a decrease in short-range order of lipid molecules throughout vesicle bilayers.

Oligomers of pneumolysin form transmembrane channels in cholesterol-containing lipid bilayers. The mechanism of pore formation involves a multistage process in which the protein, at first, assembles into a ring-shaped complex on the outer-bilayer leaflet. In a subsequent step, the complex inserts into the membrane. Contrary to most investigations of pore formation that have focussed on protein changes, we have deduced how the lipid-packing order is altered in different stages of the pore-forming mechanism. An optical tweezing apparatus was used, in combination with microfluidics, to isolate large-unilamellar vesicles and control exposure of the bilayer to pneumolysin. By monitoring Raman-scattered light from a single-trapped liposome, the effect of the protein on short-range order and rotational diffusion of lipids could be inferred from changes in the envelope of the C-H stretch. A significant change in the lipid-packing order takes place during assembly of pre-pore oligomers. We were not able to detect a change in the lipid-packing order during the initial stage of protein binding, or any further change during the insertion of oligomers. Pre-pore complexes induce a transformation in which a bilayer, resembling a liquid-ordered phase is changed into a bilayer resembling a fluid-liquid-disordered phase surrounding ordered microdomains enriched in cholesterol and protein complexes

ThX-a next-generation probe for the early detection of amyloid aggregates

Neurodegenerative diseases such as Alzheimer's and Parkinson's are associated with protein misfolding and aggregation. Recent studies suggest that the small, rare and heterogeneous oligomeric species, formed early on in the aggregation process, may be a source of cytotoxicity. Thioflavin T (ThT) is currently the gold-standard fluorescent probe for the study of amyloid proteins and aggregation processes. However, the poor photophysical and binding properties of ThT impairs the study of oligomers. To overcome this challenge, we have designed Thioflavin X, (ThX), a next-generation fluorescent probe which displays superior properties; including a 5-fold increase in brightness and 7-fold increase in binding affinity to amyloidogenic proteins. As an extrinsic dye, this can be used to study unique structural amyloid features both in bulk and on a single-aggregate level. Furthermore, ThX can be used as a super-resolution imaging probe in single-molecule localisation microscopy. Finally, the improved optical properties (extinction coefficient, quantum yield and brightness) of ThX can be used to monitor structural differences in oligomeric species, not observed via traditional ThT imaging.</p