Nucleated Polymerization Research Articles

Multiple aspects of amyloid dynamics in vivo integrate to establish prion variant dominance in yeast.

Prion variants are self-perpetuating conformers of a single protein that assemble into amyloid fibers and confer unique phenotypic states. Multiple prion variants can arise, particularly in response to changing environments, and interact within an organism. These interactions are often competitive, with one variant establishing phenotypic dominance over the others. This dominance has been linked to the competition for non-prion state protein, which must be converted to the prion state via a nucleated polymerization mechanism. However, the intrinsic rates of conversion, determined by the conformation of the variant, cannot explain prion variant dominance, suggesting a more complex interaction. Using the yeast prion system [PSI+ ], we have determined the mechanism of dominance of the [PSI+ ]Strong variant over the [PSI+ ]Weak variant in vivo. When mixed by mating, phenotypic dominance is established in zygotes, but the two variants persist and co-exist in the lineage descended from this cell. [PSI+ ]Strong propagons, the heritable unit, are amplified at the expense of [PSI+ ]Weak propagons, through the efficient conversion of soluble Sup35 protein, as revealed by fluorescence photobleaching experiments employing variant-specific mutants of Sup35. This competition, however, is highly sensitive to the fragmentation of [PSI+ ]Strong amyloid fibers, with even transient inhibition of the fragmentation catalyst Hsp104 promoting amplification of [PSI+ ]Weak propagons. Reducing the number of [PSI+ ]Strong propagons prior to mating, similarly promotes [PSI+ ]Weak amplification and conversion of soluble Sup35, indicating that template number and conversion efficiency combine to determine dominance. Thus, prion variant dominance is not an absolute hierarchy but rather an outcome arising from the dynamic interplay between unique protein conformations and their interactions with distinct cellular proteostatic niches.

Tau fibrils induce nanoscale membrane damage and nucleate cytosolic tau at lysosomes

The prion-like spread of protein aggregates is a leading hypothesis for the propagation of neurofibrillary lesions in the brain, including the spread of tau inclusions associated with Alzheimer's disease. The mechanisms of cellular uptake of tau seeds and subsequent nucleated polymerization of cytosolic tau are major questions in the field, and the potential for coupling between the entry and nucleation mechanisms has been little explored. We found that in primary astrocytes and neurons, endocytosis of tau seeds leads to their accumulation in lysosomes. This in turn leads to lysosomal swelling, deacidification, and recruitment of ESCRT proteins, but not Galectin-3, to the lysosomal membrane. These observations are consistent with nanoscale damage of the lysosomal membrane. Live cell imaging and STORM superresolution microscopy further show that the nucleation of cytosolic tau occurs primarily at the lysosome membrane under these conditions. These data suggest that tau seeds escape from lysosomes via nanoscale damage rather than wholesale rupture and that nucleation of cytosolic tau commences as soon as tau fibril ends emerge from the lysosomal membrane.

The melt memory effects in polymer crystallization

AbstractThis paper presents a systematic review of the literature on the melt memory effects observed in polymers, an area that has engendered considerable debate for over 50 years. Recent advances in experimental techniques have provided fresh insights into how a polymer's thermal history influences its recrystallization behavior. It has been observed that given other conditions unchanged, the crystallization temperature during recrystallization decreases with an increase in the melt temperature Ts above the melting point Tm until a critical melt temperature is attained. This phenomenon also extends to the half‐time of crystallization and the secondary structures, such as lamellar thickness, of semi‐crystalline polymers. Despite these findings, a comprehensive constitutive model that encapsulates polymer melt memory effects remains elusive. Cutting‐edge instrumentation, including in situ small and wide‐angle X‐ray scattering, temperature‐controlled Fourier transform infrared spectroscopy, and flash differential scanning calorimetry, have posed significant challenges to the traditional nucleation and growth models established in the 1970s. These models are foundational to our understanding of polymer crystallization, which is an integral part of polymer processing and production. In this review, the historical contours of this discourse are traced, with an examination of both the recent experimental breakthroughs and theoretical advancements pertinent to polymer melt memory effects. This paper delves into the prevailing theories of polymer nucleation and crystallization and engages with theoretical discussions and numerical simulations that attempt to elucidate and rationalize these melt memory phenomena.

Fully time-dependent cloud formation from a non-equilibrium gas-phase in exoplanetary atmospheres

Context. Recent observations suggest the presence of clouds in exoplanet atmospheres, but they have also shown that certain chemical species in the upper atmosphere might not be in chemical equilibrium. Present and future interpretation of data from, for example, CHEOPS, JWST, PLATO, and Ariel require a combined understanding of the gas-phase and the cloud chemistry. Aims. The goal of this work is to calculate the two main cloud formation processes, nucleation, and bulk growth consistently from a non-equilibrium gas phase. The aim is also to explore the interaction between a kinetic gas-phase and cloud microphysics. Methods. The cloud formation is modelled using the moment method and kinetic nucleation, which are coupled to a gas-phase kinetic rate network. Specifically, the formation of cloud condensation nuclei is derived from cluster rates that include the thermochemical data of (TiO2)N from N = 1 to 15. The surface growth of nine bulk Al, Fe, Mg, O, Si, S, and Ti binding materials considers the respective gas-phase species through condensation and surface reactions as derived from kinetic disequilibrium. The effect of the completeness of rate networks and the time evolution of the cloud particle formation is studied for an example exoplanet, HD 209458 b. Results. A consistent, fully time-dependent cloud formation model in chemical disequilibrium with respect to nucleation, bulk growth, and the gas-phase is presented and first test cases are studied. This model shows that cloud formation in exoplanet atmospheres is a fast process. This confirms previous findings that the formation of cloud particles is a local process. Tests on selected locations within the atmosphere of the gas-giant HD 209458 b show that the cloud particle number density and volume reach constant values within 1 s. The complex kinetic polymer nucleation of TiO2 confirms results from classical nucleation models. The surface reactions of SiO[s] and SiO2[s] can create a catalytic cycle that dissociates H2 to 2 H, resulting in a reduction of the CH4 number densities.

Gelsolin from mussel's catch muscle

Proteins of the gelsolin family are Ca2+-dependent, multifunctional, actin-binding proteins containing three (S1–S3, about 40 kDa) or six (S1–S6, about 80 kDa) highly conserved repeats in the amino acid sequence. The pattern of interaction of these proteins with actin is complex: they can sever actin filaments; promote polymer nucleation after binding to two actin monomers; and cap the growing barbed end of actin filaments. In the present study, an actin polymerizing factor (46 kDa) from the adductor muscle of a bivalve mollusc has been discovered and identified for the first time. This protein has turned out to belong to the gelsolin family of actin regulatory proteins. The expression of gelsolin-like proteins in the tissues of bivalves was predicted after analyzing their proteome, but this is the first study where an actually expressed protein has been found. A primary determination of its physicochemical properties such as molecular weight, charge, resistance to urea, influence on actin polymerization by viscosity, and light scattering is carried out and the molecular structure analyzed.

Stabilized Ti3C2Tx-doped 3D vesicle polypyrrole coating for efficient protection toward copper in artificial seawater

A closed 3D vesicle polypyrrole-based composite coating (PPy-STi) was electropolymerized on copper with the support of sodium dodecyl sulfate (SDS)-stabilized Ti3C2Tx-MXene via an inverted-electrode cyclic voltammetry route. Due to the promoted polymer nucleation effect of SDS and active catalysis of hydrogen evolution by well-dispersed Ti3C2Tx, a unique vesicle-like architecture of PPy-STi were formed with twisted diffusion pathways, which endowed a strong barrier against aggressive species. Meanwhile the stabilized Ti3C2Tx with high metallic conductivity facilitated the overall electroactivity of PPy-STi coating, yielding much improved anodic protection for copper in artificial seawater (ASW). Relying on the tolerant physical barrier and robust anodic protection capacity of PPy-STi, the coated copper could sustain its passivated state during 10 days of immersion in ASW. The integration of MXenes in conductive polymer coating with enhanced protection characteristics may provide a new strategy to improve the corrosion resistance of electronic devices in the harsh environment.

Eco-evolutionary trade-offs in the dynamics of prion strain competition.

Prion and prion-like molecules are a type of self-replicating aggregate protein that have been implicated in a variety of neurodegenerative diseases. Over recent decades, the molecular dynamics of prions have been characterized both empirically and through mathematical models, providing insights into the epidemiology of prion diseases and the impact of prions on the evolution of cellular processes. At the same time, a variety of evidence indicates that prions are themselves capable of a form of evolution, in which changes to their structure that impact their rate of growth or fragmentation are replicated, making such changes subject to natural selection. Here we study the role of such selection in shaping the characteristics of prions under the nucleated polymerization model (NPM). We show that fragmentation rates evolve to an evolutionary stable value which balances rapid reproduction of PrPSc aggregates with the need to produce stable polymers. We further show that this evolved fragmentation rate differs in general from the rate that optimizes transmission between cells. We find that under the NPM, prions that are both evolutionary stable and optimized for transmission have a characteristic length of three times the critical length below which they become unstable. Finally, we study the dynamics of inter-cellular competition between strains, and show that the eco-evolutionary trade-off between intra- and inter-cellular competition favours coexistence.

Filler-induced heterogeneous nucleation of polymer crystals investigated by molecular dynamics simulations

Filler particles are known to act as nucleants for polymer crystallisation yet the connection between the filler surface properties and polymer crystallisation are not well understood. In this work, molecular dynamics simulations were used to investigate homogeneous and heterogeneous polymer nucleation and crystallisation using a generic linear bead–spring polymer model with a bond bending potential. The polymer systems were equilibrated at high temperature and then cooled at a constant rate. Without a surface present, polymers with stiff chains were found to crystallise more readily than more flexible polymers. The degree of crystallinity was estimated based on the mass fraction of straight chain segments which we equate to stem mass fraction. At a temperature Tc a sharp increase in density, radius of gyration and stem mass fraction occurred. After cooling, the systems were reheated and some systems showed hysteresis with a sharp decrease in these properties occurring upon melting at Tm>Tc. For slower heating rates, crystal growth occurred during heating from between the glass transition temperature, Tg, and Tc until just before melting at Tm. The presence of an isotropic surface was found to promote crystallisation in flexible systems that did not crystallise in the bulk, where the stem mass fraction and Tc increased with the interaction strength between the surface and the polymer beads. Changes in Tc and degree of crystallinity with cooling rate are consistent with experimental observations. This model captures polymer crystallisation phenomena and provides insight into heterogeneous nucleation, demonstrating that strong interfacial interactions promote crystallisation, thus aiding the choice or design of nucleants for control of polymer crystallisation and microstructure.

The effect of surface nucleation modulation on the mechanical and biocompatibility of metal-polymer biomaterials.

The deployment of hernia repair patches in laparoscopic procedures is gradually increasing. In this technology, however, understanding the new phases of titanium from the parent phase on polymer substrates is essential to control the microstructural transition and material properties. It remains a challenging area of condensed matter physics to predict the kinetic and thermodynamic properties of metals on polymer substrates from the molecular scale due to the lack of understanding of the properties of the metal-polymer interface. However, this paper revealed the mechanism of nucleation on polymer substrates and proposed for the first record a time-dependent regulatory mechanism for the polymer-titanium interface. The interconnection between polymer surface chain entanglement, nucleation and growth patterns, crystal structure and surface roughness were effectively unified. The secondary regulation of mechanical properties was accomplished simultaneously to satisfy the requirement of biocompatibility. Titaniumized polypropylene patches prepared by time-dependent magnetron sputtering technology demonstrated excellent interfacial mechanical properties and biocompatibility. In addition, modulation by low-temperature plasma metal deposition opened a new pathway for biomaterials. This paper provides a solid theoretical basis for the research of titanium nanofilms on medical polypropylene substrates and the medical industry of implantable biomaterials, which will be of great value in the future.

Effect of Different Initial CaO/SiO2 Molar Ratios and Curing Times on the Preparation and Formation Mechanism of Calcium Silicate Hydrate.

To better understand the pozzolanic activity in fly ash used as a supplementary cementitious material in cement or concrete, calcium silicate hydrate (C-S-H) has been synthesized by adding silica fume to a supersaturated calcium hydroxide solution prepared by mixing calcium oxide and ultrapure water. Thermogravimetric analysis results have revealed the variation in the weight loss due to C-S-H in the samples and the conversion ratio of calcium oxide (the μCaO value), which represents the proportion of calcium oxide in the initial reaction mixture used to produce C-S-H, with curing time. The weight loss due to C-S-H and the μCaO value were both maximized (13.5% and 90.4%, respectively) when the initial C/S molar ratio was 1.0 and the curing time was 90 d. X-ray diffraction (XRD) analysis has indicated that C-S-H in the samples after curing for 7 d had the composition Ca1.5SiO3.5·xH2O. 29Si magic angle spinning (MAS) nuclear magnetic resonance (NMR) analysis has revealed that the degree of polymerization of C-S-H increased with an increase in curing time for samples with an initial C/S molar ratio of 1.0. The ratio of internal to terminal tetrahedra (Q2/Q1) increased from 2.29 to 4.28 with the increase in curing time from 7 d to 90 d. At curing times ≥ 28 d, a leaf-like C-S-H structure was observed by scanning electron microscopy (SEM). An ectopic nucleation-polymerization reaction process is proposed for the formation mechanism of C-S-H.

Synergy of Fiber Surface Chemistry and Flow: Multi-Phase Transcrystallization in Fiber-Reinforced Thermoplastics.

Fiber-reinforced polymer composites are largely employed for their improved strength with respect to unfilled matrices. Considering semi-crystalline materials under relevant processing conditions, the applied pressure and flow induce shear stresses at the fiber-polymer interface. These stresses may strongly enhance the nucleation ability of the fiber surface with respect to the quiescent case. It is thus possible to assume that the fiber features are no longer of importance and that crystallization is dominated by the effect of flow. However, by making use of an advanced experimental technique, i.e., polarization-modulated synchrotron infrared microspectroscopy (PM-SIRMS), we are able to show that the opposite is true for the industrially relevant case of isotactic polypropylene (iPP). With PM-SIRMS, the local chain orientation is measured with micron-size spatial resolution. This orientation can be related to the polymer nucleation density along the fiber surface. For various combinations of an iPP matrix and fiber, the degree of orientation in the cylindrical layer that develops during flow correlates well with the differences in nucleation density found in quiescent conditions. This result shows that the morphological development during processing of polymer composites is not solely determined by the flow field, nor by the nucleating ability of the fiber surface alone, but rather by a synergistic combination of the two. In addition, using finite element modeling, it is demonstrated that, under the experimentally applied flow conditions, the interphase structure formation is mostly dominated by the rheological characteristics of the material rather than perturbations in experimental conditions, such as shear rate, layer thickness, and temperature. This once again highlights the importance of matrix-filler interplay during flow and, thus, of material selection in the design of hybrid and lightweight composite technologies.

POP1 inhibits MSU-induced inflammasome activation and ameliorates gout.

Canonical inflammasomes are innate immune protein scaffolds that enable the activation of inflammatory caspase-1, and subsequently the processing and release of interleukin (IL)-1β, IL-18, and danger signals, as well as the induction of pyroptotic cell death. Inflammasome assembly and activation occurs in response to sensing of infectious, sterile and self-derived molecular patterns by cytosolic pattern recognition receptors, including the Nod-like receptor NLRP3. While these responses are essential for host defense, excessive and uncontrolled NLRP3 inflammasome responses cause and contribute to a wide spectrum of inflammatory diseases, including gout. A key step in NLRP3 inflammasome assembly is the sequentially nucleated polymerization of Pyrin domain (PYD)- and caspase recruitment domain (CARD)-containing inflammasome components. NLRP3 triggers polymerization of the adaptor protein ASC through PYD-PYD interactions, but ASC polymerization then proceeds in a self-perpetuating manner and represents a point of no return, which culminates in the activation of caspase-1 by induced proximity. In humans, small PYD-only proteins (POPs) lacking an effector domain regulate this key process through competitive binding, but limited information exists on their physiological role during health and disease. Here we demonstrate that POP1 expression in macrophages is sufficient to dampen MSU crystal-mediated inflammatory responses in animal models of gout. Whether MSU crystals are administered into a subcutaneous airpouch or into the ankle joint, the presence of POP1 significantly reduces neutrophil infiltration. Also, airpouch exudates have much reduced IL-1β and ASC, which are typical pro-inflammatory indicators that can also be detected in synovial fluids of gout patients. Exogenous expression of POP1 in mouse and human macrophages also blocks MSU crystal-induced NLRP3 inflammasome assembly, resulting in reduced IL-1β and IL-18 secretion. Conversely, reduced POP1 expression in human macrophages enhances IL-1β secretion. We further determined that the mechanism for the POP1-mediated inhibition of NLRP3 inflammasome activation is through its interference with the crucial NLRP3 and ASC interaction within the inflammasome complex. Strikingly, administration of an engineered cell permeable version of POP1 was able to ameliorate MSU crystal-mediated inflammation in vivo, as measured by neutrophil infiltration. Overall, we demonstrate that POP1 may play a crucial role in regulating inflammatory responses in gout.

Dual control of formin-nucleated actin assembly by the chromatin and ER in mouse oocytes

The first asymmetric meiotic cell divisions in mouse oocytes are driven by formin 2 (FMN2)-nucleated actin polymerization around the spindle. In this study, we investigated how FMN2 is recruited to the spindle peripheral ER and how its activity is regulated in mouse meiosis I (MI) oocytes. We show that this process is regulated by the Ran GTPase, a conserved mediator of chromatin signal, and the ER-associated protein VAPA. FMN2 contains a nuclear localization sequence (NLS) within a domain (SLD) previously shown to be required for FMN2 localization to the spindle periphery. FMN2 NLS is bound to the importin α1/β complex, and the disruption of this interaction by RanGTP is required for FMN2 accumulation in the area proximal to the chromatin and the MI spindle. The importin-free FMN2 is then recruited to the surface of ER around the spindle through the binding of the SLD with the ER-membrane protein VAPA. We further show that FMN2 is autoinhibited through an intramolecular interaction between the SLD with the C-terminal formin homology 2 (FH2) domain that nucleates actin filaments. VAPA binding to SLD relieves the autoinhibition of FMN2, leading to localized actin polymerization. This dual control of formin-mediated actin assembly allows actin polymerization to initiate the movement of the meiotic spindle toward the cortex, an essential step in the maturation of the mammalian female gamete.

Fluorescence Lifetime Measurement of Prefibrillar Sickle Hemoglobin Oligomers as a Platform for Drug Discovery in Sickle Cell Disease.

The molecular origin of sickle cell disease (SCD) has been known since 1949, but treatments remain limited. We present the first high-throughput screening (HTS) platform for discovering small molecules that directly inhibit sickle hemoglobin (HbS) oligomerization and improve blood flow, potentially overcoming a long-standing bottleneck in SCD drug discovery. We show that at concentrations far below the threshold for nucleation and rapid polymerization, deoxygenated HbS forms small assemblies of multiple α2β2 tetramers. Our HTS platform leverages high-sensitivity fluorescence lifetime measurements that monitor these temporally stable prefibrillar HbS oligomers. We show that this approach is sensitive to compounds that inhibit HbS polymerization with or without modulating hemoglobin oxygen binding affinity. We also report the results of a pilot small-molecule screen in which we discovered and validated several novel inhibitors of HbS oligomerization.

Entanglement on Nucleation Barrier of Polymer Crystal

We propose a theoretical approach to quantitatively account for the role of entanglement in the nucleation of polymer melts, which is the unique feature of polymer differentiated from small molecules. By performing molecular dynamics simulations, we obtain the nucleation barriers of polymer systems with different entanglement densities, which exhibits an opposite trend compared to the prediction of the classic nucleation theory (CNT). To amend the deficiency of the CNT in polymer crystallization, we introduce the entanglement free energy to reflect the role of entanglement in polymer nucleation. Specifically, the polymer nucleation not only involves free energies of monomers inside and on the surface of a nucleus as considered in the CNT, but also affects the entanglement network around the nucleus. Our theoretical approach provides a reasonable interpretation for the unsolved nucleation phenomena of polymers in simulations and experiments.

Nucleation and crystallization of poly(L-lactide) assisted by terminal hydrogen-bonding segments

The role of hydrogen bonding (H-bonding) in polymer nucleation and crystallization is not yet so clear. To understand this physical issue, a series of poly (L-lactide) (PLLA) with different amount of terminal oxamide segments (OXA, -NHCOCONH-) were tailor-made as model H-bonding polymers (PLLAnOXA, n is the number of –NHCO–), and then the influence of H-bonding on the polymer nucleation and crystallization were investigated by a combination of experiments and molecular dynamics (MD) simulations. Compared with PLLA, much more types of H-bonds are created between the OXA segments and either the PLLA chains or the other OXA segments in the PLLAnOXA systems. A segment can be immobilized in the melt by H-bonding induced topological constraint and/or steric hindrance leading to a certain extent of reduction in entropy. Thus, the pair of H-bonded segments acting as a precursor of the “first stems” is expected to inducing local ordered structures (LOS) at elevated temperatures, which further facilitates the formation of both primary and secondary nuclei. As a consequence, the nOXA segments induced H-bonds not only significantly enhanced the crystallization temperature (Tc, from 100 °C to 112 °C) and the crystallinity (Xc, from 10% to 52%) of PLLA, but also increases the crystal growth rate (G) by nearly 10 times (from 0.25 to 2.66 μm min−1 at 150 °C). Moreover, a HI-MS (H-bond induced multi-stage) nucleation phenomenon in the melt of the PLLAnOXA was revealed by in-situ small-angle X-ray scattering (SAXS) under both non-isothermal (1 °C/min) and isothermal (135 °C) conditions. The HI-MS nucleation mechanism is well correlated to the nOXA induced multi-types of H-bonds which possess different thermodynamical stability at a certain high temperature. Therefore, this work not only provides a new route to make rapid crystallizing PLLA via hybridizing H-bonding segments, but also provides a molecular-level insight in the H-bonding assisted nucleation of semi-crystalline polymers in general.

Polyhydroxybutyrate: a review of experimental and simulation studies of the effect of fillers on crystallinity and mechanical properties

AbstractPolyhydroxybutyrate (PHB) is a sustainable polymer that is a promising candidate for replacing petroleum‐based plastics in food packaging. Fillers are used to improve the mechanical properties of PHB composites, simultaneously changing the crystallinity of the polymer matrix. However, it is not well understood how fillers affect crystallisation and microstructure, and thus the resulting mechanical properties of the composite. This review summarises simulation work on polymer nucleation and crystallisation and how nucleation is influenced by different types of polymer–filler interfaces. Experimental studies of PHB composites with a wide variety of fillers are reviewed to find trends between the filler type, crystallinity and mechanical properties. It is clear that fillers act as nucleants that increase the number of spherulites while reducing spherulite size. This behaviour is apparent for almost all fillers regardless of filler chemistry or topology. However, the data obtained from the literature do not seem to produce strong conclusions about the effect of the degree of crystallinity on the tensile properties of PHB–filler composites, although there are some weak trends that indicate the importance of microstructure. In order to enable prediction and control of PHB composite properties, further systematic studies are required to elucidate the effect of specific filler types and the connection between crystallinity, microstructure and mechanical properties. © 2022 The Authors. Polymer International published by John Wiley & Sons Ltd on behalf of Society of Industrial Chemistry.

Kinetics-controlled regulation for homogeneous nucleation and growth of colloidal polymer and carbon nanospheres.

Size regulation of uniform polymer nanospheres (PNSs) and carbon nanospheres (CNSs) below 100 nm has been difficult and is limited by multiple factors, such as ongoing nucleation, Ostwald ripening, minimization of surface energy, and high viscosity during the nucleation and growth process. In this study, a kinetics-controlled regulation is reported for the synthesis of monodispersed PNSs and corresponding CNSs with adjustable size below 100 nm. During the synthesis of PNSs, three distinct stages including surface energy control, surface tension control and viscosity control have been observed, where the concentration of block copolymer F127 (CF127) plays a vital role in affecting the nucleation rate of PNSs and tunes the diffusion rate of monomers and migration of particles during the nucleation and growth process. As a consequence, the size of monodisperse CNSs can be customized from 100 nm down to 41 nm with PDI below 5%.

Modeling and Designing Particle-Regulated Amyloid-like Assembly of Synthetic Polypeptides in Aqueous Solution.

In cells, actin and tubulin polymerization is regulated by nucleation factors, which promote the nucleation and subsequent growth of protein filaments in a controlled manner. Mimicking this natural mechanism to control the supramolecular polymerization of macromolecular monomers by artificially created nucleation factors remains a largely unmet challenge. Biological nucleation factors act as molecular scaffolds to boost the local concentrations of protein monomers and facilitate the required conformational changes to accelerate the nucleation and subsequent polymerization. An accelerated assembly of synthetic poly(l-glutamic acid) into amyloid fibrils catalyzed by cationic silica nanoparticle clusters (NPCs) as artificial nucleation factors is demonstrated here and modeled as supramolecular polymerization with a surface-induced heterogeneous nucleation pathway. Kinetic studies of fibril growth coupled with mechanistic analysis demonstrate that the artificial nucleators predictably accelerate the supramolecular polymerization process by orders of magnitude (e.g., shortening the assembly time by more than 10 times) when compared to the uncatalyzed reaction, under otherwise identical conditions. Amyloid-like fibrillation was supported by a variety of standard characterization methods. Nucleation followed a Michaelis-Menten-like scheme for the cationic silica NPCs, while the corresponding anionic or neutral nanoparticles had no effect on fibrillation. This approach shows the effectiveness of charge-charge interactions and surface functionalities in facilitating the conformational change of macromolecular monomers and controlling the rates of nucleation for fibril growth. Molecular design approaches like these inspire the development of novel materials via biomimetic supramolecular polymerizations.

Non-monotonic fibril surface occlusion by GFP tags from coarse-grained molecular simulations

The pathological growth of amyloid fibrils in neurons underlies the progression of neurodegenerative diseases including Alzheimer’s and Parkinson’s disease. Fibrils form when soluble monomers oligomerise in the cytoplasm. Their subsequent growth occurs via nucleated polymerization mechanisms involving the free ends of the fibrils augmented by secondary nucleation of new oligomers at their surface. Amyloid fibrils possess a complex interactome with diffusing cytoplasmic proteins that regulates many aspects of their growth, seeding capacity, biochemical activity and transition to pathological inclusions in diseased brains. Changes to their surface are also expected to modify their interactome, pathogenicity and spreading in the brain. Many assays visualise fibril formation, growth and inclusion formation by decorating monomeric proteins with fluorescent tags such as GFP. Recent studies from our group suggest that tags with sizes comparable to the fibril radius may modify the fibril surface accessibility and thus their PTM pattern, interactome and ability to form inclusions. Using coarse-grained molecular simulations of a single alpha synuclein fibril tagged with GFP we find that thermal fluctuations of the tags create a non-monotonic, size-dependent sieve around the fibril that perturbs its interactome with diffusing species. Our results indicate that experiments using tagged and untagged monomers to study the growth and interactome of fibrils should be compared with caution, and the confounding effects of the tags are more complex than a reduction in surface accessibility. The prevalence of fluorescent tags in amyloid fibril growth experiments suggests this has implications beyond the specific alpha synuclein fibrils we model here.