Spatial control of irreversible protein aggregation

Liquid cellular compartments spatially segregate from the cytoplasm and can regulate aberrant protein aggregation, a process linked to several medical conditions, including Alzheimer's and Parkinson's diseases. Yet the mechanisms by which these droplet-like compartments affect protein aggregation remain unknown. Here, we combine kinetic theory of protein aggregation and liquid-liquid phase separation to study the spatial control of irreversible protein aggregation in the presence of liquid compartments. We find that, even for weak interactions between the compartment constituents and the aggregating monomers, aggregates are strongly enriched inside the liquid compartment relative to the surrounding cytoplasm. We show that this enrichment is caused by a positive feedback mechanism of aggregate nucleation and growth which is mediated by a flux maintaining the phase equilibrium between the compartment and the cytoplasm. Our model predicts that the compartment volume that maximizes aggregate enrichment in the compartment is determined by the reaction orders of aggregate nucleation. The underlying mechanism of aggregate enrichment could be used to confine cytotoxic protein aggregates inside droplet-like compartments suggesting potential new avenues against aberrant protein aggregation. Our findings could also represent a common mechanism for the spatial control of irreversible chemical reactions in general

Estimation and Application of 2-D Scattering Matrices for Sparse Array Imaging of Impact Damage in Composite Panels

Reliable detection of hidden damage in composites is important for failure prevention in the aerospace industry since these materials are being more frequently used in high stress applications. Structural health monitoring (SHM) via guided wave sensors mounted on or embedded within a composite structure can help detect and localize damage in real-time while also reducing overall maintenance costs. One approach to guided wave SHM is sparse array imaging via the minimum variance algorithm, and it has been shown in prior work that incorporating estimated scattering from expected defects can improve the quality of damage localization and characterization [1]. For this study, impacts were applied to induce delaminations within a composite panel. Wavefield data were recorded on a circle centered at the damage location from multiple incident directions before and after the impacts. Baseline subtraction [2] is used to estimate scattering patterns for each incident direction, and these patterns are combined and interpolated to form a full 2-D scattering matrix. This matrix is then incorporated into the minimum variance imaging algorithm, and imaging efficacy is evaluated for both these impacts and impact damage in other similar composite plates. Results are compared to images generated using simpler scattering assumptions

Angle-Beam Shear Wave Scattering from Buried Crack-like Defects in Bonded Specimens

Ultrasonic wavefield imaging, which refers to the measurement of wave motion on a 2-D rectilinear grid resulting from a fixed source, has been previously applied to angle-beam shear wave propagation in simple plates with through-holes and far-surface notches [1]. In this prior work scattered waves were analyzed using baseline subtraction of wavefields acquired before and after a notch was introduced [2]. In practice, however, defects of interest often occur between bonded layers and it is generally not possible to record data from the same specimen in both the undamaged and damaged states, making direct baseline subtraction infeasible. This present work considers measurement of angle-beam waves in several bonded specimens with and without buried defects originating from fastener holes. The experimental methodology is explained, which includes specimen fabrication details and wavefield measurement methods. Data from fastener holes with and without simulated damage in the form of notches are compared, and techniques used to analyze differences are discussed. Despite unavoidable deviations from specimen-to-specimen caused by factors such as variations in bonding, transducer mounting, and fastener hole machining, it is shown that scattering from buried notches can be clearly visualized in the recorded wavefield data

Aggregation controlled by condensate rheology

Biomolecular condensates in living cells can exhibit a complex rheology, including viscoelastic and glassy behavior. This rheological behavior of condensates was suggested to regulate polymerization of cytoskeletal filaments and aggregation of amyloid fibrils. Here, we theoretically investigate how the rheological properties of condensates can control the formation of linear aggregates. To this end, we propose a kinetic theory for linear aggregation in coexisting phases, which accounts for the aggregate size distribution and the exchange of aggregates between inside and outside of condensates. The rheology of condensates is accounted in our model via aggregate mobilities that depend on aggregate size. We show that condensate rheology determines whether aggregates of all sizes or dominantly small aggregates are exchanged between condensate inside and outside on the timescale of aggregation. As a result, the ratio of aggregate numbers inside to outside of condensates differs significantly. Strikingly, we also find that weak variations in the rheological properties of condensates can lead to a switch-like change of the number of aggregates. These results suggest a possible physical mechanism for how living cells could control linear aggregation in a switch-like fashion through variations in condensate rheology

Mechanics and kinetics of dynamic instability.

During dynamic instability, self-assembling microtubules (MTs) stochastically alternate between phases of growth and shrinkage. This process is driven by the presence of two distinct states of MT subunits, GTP- and GDP-bound tubulin dimers, that have different structural properties. Here, we use a combination of analysis and computer simulations to study the mechanical and kinetic regulation of dynamic instability in three-dimensional (3D) self-assembling MTs. Our model quantifies how the 3D structure and kinetics of the distinct states of tubulin dimers determine the mechanical stability of MTs. We further show that dynamic instability is influenced by the presence of quenched disorder in the state of the tubulin subunit as reflected in the fraction of non-hydrolysed tubulin. Our results connect the 3D geometry, kinetics and statistical mechanics of these tubular assemblies within a single framework, and may be applicable to other self-assembled systems where these same processes are at play

Universality of filamentous aggregation phenomena.

We use perturbative renormalization group theory to study the kinetics of protein aggregation phenomena in a unified manner across multiple timescales. Using this approach, we find that, irrespective of the specific molecular details or experimental conditions, filamentous assembly systems display universal behavior in time. Moreover, we show that the universality classes for protein aggregation correspond to simple autocatalytic processes and that the diversity of behavior in these systems is determined solely by the reaction order for secondary nucleation with respect to the protein concentration, which labels all possible universality classes. We validate these predictions on experimental data for the aggregation of several different proteins at several different initial concentrations, which by appropriate coordinate transformations we are able to collapse onto universal kinetic growth curves. These results establish the power of the perturbative renormalization group in distilling the ultimately simple temporal behavior of complex protein aggregation systems, creating the possibility to study the kinetics of general self-assembly phenomena in a unified fashion

Enhanced potency of aggregation inhibitors mediated by liquid condensates

Liquid condensates are membraneless organelles that form via phase separation in living cells. These condensates provide unique heterogeneous environments that have much potential in regulating a range of biochemical processes from gene expression to filamentous protein aggregation—a process linked to Alzheimer's and Parkinson's diseases. Here we theoretically study the physical interplay between protein aggregation, its inhibition, and liquid-liquid phase separation. Our key finding is that the action of protein aggregation inhibitors can be strongly enhanced by liquid condensates. The physical mechanism of this enhancement relies on the partitioning and colocalization of inhibitors with their targets inside the liquid condensate. Our theory uncovers how the physicochemical properties of condensates can be used to modulate inhibitor potency, and we provide experimentally testable conditions under which drug potency is maximal. Our findings suggest design principles for protein aggregation inhibitors with respect to their phase-separation properties