Growth Of Oligomers Research Articles

Assembly mechanism of the inflammasome sensor AIM2 revealed by single molecule analysis

Pathogenic dsDNA prompts AIM2 assembly leading to the formation of the inflammasome, a multimeric complex that triggers the inflammatory response. The recognition of foreign dsDNA involves AIM2 self-assembly concomitant with dsDNA binding. However, we lack mechanistic and kinetic information on the formation and propagation of the assembly, which can shed light on innate immunity’s time response and specificity. Combining optical traps and confocal fluorescence microscopy, we determine here the association and dissociation rates of the AIM2-DNA complex at the single molecule level. We identify distinct mechanisms for oligomer growth via the binding of incoming AIM2 molecules to adjacent dsDNA or direct interaction with bound AIM2 assemblies, resembling primary and secondary nucleation. Through these mechanisms, the size of AIM2 oligomers can increase fourfold in seconds. Finally, our data indicate that single AIM2 molecules do not diffuse/scan along the DNA, suggesting that oligomerization depends on stochastic encounters with DNA and/or DNA-bound AIM2.

Synthesis of Prepolymers of Poly(glycerol-co-diacids) Based on Sebacic and Succinic Acid Mixtures.

In this study, poly(glycerol-co-diacids) prepolymers were produced using different ratios of glycerol (G), sebacic acid (S), and succinic acid (Su) (molar ratios: GS 1:1, GSSu 1:0.9:0.1, GSSu 1:0.8:0.2, GSSu 1:0.5:0.5, GSSu 1:0.2:0.8, GSSu 1:0.1:0.9, GSu 1:1). All polycondensation reactions were performed at 150 °C until reaching a degree of polymerization of ≈55%, inferred by the water volume collected from a reactor. We concluded that the reaction time is correlated with the ratio of diacids used, that is, the increase in succinic acid is proportional to a decrease in the duration of the reaction. In fact, the reaction of poly(glycerol sebacate) (PGS 1:1) is twice as slow as the reaction of poly(glycerol succinate) (PGSu 1:1). The obtained prepolymers were analyzed by electrospray ionization mass spectrometry (ESI-MS) and 1H and 13C nuclear magnetic resonance (NMR). Besides its catalytic influence in poly(glycerol)/ether bond formation, the presence of succinic acid also contributes to a mass growth of ester oligomers, the formation of cyclic structures, a greater number of oligomers detected, and a difference in mass distribution. When compared with PGS (1:1), and even at lower ratios, the prepolymers produced with succinic acid presented mass peak characteristics of oligomer species with a glycerol unit as its end group in higher abundance. Generally, the most abundant oligomers have molecular weights between 400 and 800 g/mol.

Aluminium catalysed oligomerisation in cement-forming silicate systems.

Alumino-silicates form the backbone of structural materials including cements and the concrete they form. However, the nanoscale aspects of the oligomerisation mechanisms elongating the (alumino-)silicate chains is not fully clarified; the role of aluminium in particular. Herein, we explore and contrast the growth of silicate and alumino-silicate oligomers by both neutral and anionic mechanisms, with focus on the influence of Al on oligomer structure and stability. Further, the spontaneity of chain lengthening in the absence and presence of Al of differing coordination (Al-IV, V, VI) was characterised. Result trends showed Al-IV facilitating oligomerisation in neutral conditions, with respect to Si only systems, effectively promoting longer chain formation and stabilisation. The anionic pathway similarly showed Al reducing the overall energetic barriers to oligomerisation. In both conditions, Al's coordinative and structural flexibility, at O-Al-O hinge points in particular, was responsible for the lowering of the energetic expense for oligomerisation. The results and implications resolved herein are informative for chain formation and stability for bulk material properties of alumino-silicate materials such as cements, where the aluminosilicate systems are dominated by short chains of 2-5 units in length.

Exploring the Interplay between Disordered and Ordered Oligomer Channels on the Aggregation Energy Landscapes of α-Synuclein.

The abnormal aggregation of α-synulcein is associated with multiple neurodegenerative diseases such as Parkinson's disease. The hydrophobic non-amyloid component (NAC) region of α-synuclein comprises the core of the fibril in vitro and in vivo. In this work, we study the aggregation landscape of the hydrophobic NAC region of α-synuclein using a transferrable coarse-grained force field, the associative memory water-mediated structure, and energy model (AWSEM). Using structural similarity, we can group metastable states on the free energy landscape of aggregation into three types of oligomers: disordered oligomers, prefibrillar oligomers with disordered tips, and ordered prefibrillar oligomers. The prefibrillar oligomers with disordered tips have more in-register parallel β strands than do the fully disordered oligomers but have fewer in-register parallel β strands than the ordered prefibrillar oligomers. Along with the ordered prefibrillar species, the disordered oligomeric states dominate at small oligomer sizes while the prefibrillar species with disordered tips thermodynamically dominate with the growth of oligomers. The topology of the aggregation landscape and observations in simulations suggest there is backtracking between ordered prefibrillar oligomers and other kinds of oligomers as the aggregation proceeds. The significant structural differences between the ordered prefibrillar oligomers and the disordered oligomers support the idea that the growth of these two kinds of oligomers involves kinetically independent parallel pathways. In contrast, the overall structural similarity between the fully ordered prefibrillar oligomers and the prefibrillar oligomers with disordered tips implies that two channels can interconvert on slower time scales. We also evaluate the effects of phosphorylation on the aggregation free energy landscape using statistical mechanical perturbation theory.

Anti-IAPP Monoclonal Antibody Improves Clinical Symptoms in a Mouse Model of Type 2 Diabetes.

Type 2 Diabetes Mellitus (T2DM) is a chronic progressive disease, defined by insulin resistance and insufficient insulin secretion to maintain normoglycemia. Amyloidogenic aggregates are a hallmark of T2DM patients; they are cytotoxic for the insulin producing β-cells, and cause inflammasome-dependent secretion of IL-1β. To avoid the associated β-cell loss and inflammation in advanced stage T2DM, we developed a novel monoclonal therapy targeting the major component of aggregates, islet amyloid polypeptide (IAPP). The here described monoclonal antibody (mAb) m81, specific for oligomeric and fibrils, but not for soluble free IAPP, is able to prevent oligomer growth and aggregate formation in vitro, and blocks islet inflammation and disease progression in vivo. Collectively, our data show that blocking fibril formation and prevention of new amyloidogenic aggregates by monoclonal antibody therapy may be a potential therapy for T2DM.

The first step of arsenoplatin-1 aggregation in solution unveiled by solving the crystal structure of its protein adduct.

Arsenoplatin-1 (AP-1) is an innovative dual-action anticancer agent that contains a platinum(ii) center coordinated to an arsenous acid moiety. We found that AP-1 spontaneously aggregates in aqueous solutions generating oligomeric species of increasing length. Afterward, we succeeded in solving the crystal structure of the adduct formed between the model protein lysozyme and an early AP-1 oligomer that turned out to be a trimer. Remarkably, this crystal structure traps an early stage of AP-1 aggregation offering detailed insight into the molecular process of the oligomer's growth.

Soy Protein Isolate Non-Isocyanates Polyurethanes (NIPU) Wood Adhesives

Soy-protein isolate (SPI) was used to prepare non-isocyanate polyurethane (NIPU) thermosetting adhesives for wood panels by reacting it with dimethyl carbonate (DMC) and hexamethylene diamine. Both linear as well as branched oligomers were obtained and identified, indicating how such oligomer structures could further cross-link to form a hardened network. Unusual structures were observed, namely carbamic acid-derived urethane linkages coupled with lactam structures. The curing of the adhesive was followed by thermomechanical analysis (TMA). It appeared to follow a two stages process: First, at a lower temperature (maximum 130°C), the growth of linear oligomers occurred, finally forming a physically entangled network. This appeared to collapse and disentangle, causing a decrease of MOE, as the temperature increases. This appears to be due to the ever more marked Brownian movements of the linear oligomer chains with the increase of the temperature. Second, chemical cross-linking of the chains appeared to ensue, forming a hardened network. This was shown by the thermomechanical analysis (TMA) showing two distinct MOE maxima peaks, one around 130°C and the other around 220°C, with a very marked MOE decrease between the two. Plywood panels were prepared and bonded with the SPI-NIPU wood adhesive and the results obtained are presented. The adhesive appeared to pass comfortably the requirements for dry strength of relevant standards, showing to be suitable for interior grade plywood panels. It did not pass the requirements for wet tests. However, addition of 15% of glycerol diglycidyl ether improved the wet tests results but still not enough to satisfy the standards requirements.

Solar transparent radiators based on in-plane worm-like assemblies of metal nanoparticles

Windows with solar heating capacity can facilitate the indoors–outdoors thermal balance and improve the thermal energy efficiency of buildings, thus reducing the energy consumption in winter; however, their development has been hindered by the narrow light absorption and limited transparency of photothermal materials. In this study, transparent solar thermal surfaces on window glazing are constructed by the in-plane linear assembly of thermoplasmonics under a hierarchical electrostatic field. First results with gold nanoparticles (Au NPs) demonstrated that the hierarchical electrostatic field induced the random generation and chain growth of NP oligomers to yield controlled in-plane nanoassemblies. The linear morphology of these nanoassemblies enhanced the local electric field along the NP chains and caused additional plasmon absorption in the near-infrared spectral region, thereby improving the photothermal conversion effect without sacrificing the transparency. The solar thermal surface with Au NP assemblies increased the window glazing temperature by up to 9.8 °C under natural solar irradiation, while maintaining a high visible transmittance (>65%). The temperature increment was within the ballpark of the highest reported values and satisfied the standard requirements for thermal insulation of buildings in cold climates. This work extends new applications of linear nanoassemblies in solar energy harvesting and related energy conversion technologies.

Enzymatic Polycondensation of 1,6-Hexanediol and Diethyl Adipate: A Statistical Approach Predicting the Key-Parameters in Solution and in Bulk.

Among the various catalysts that can be used for polycondensation reactions, enzymes have been gaining interest for three decades, offering a green and eco-friendly platform towards the sustainable design of renewable polyesters. However, limitations imposed by their delicate nature, render them less addressed. As a case study, we compare herein bulk and solution polycondensation of 1,6-hexanediol and diethyl adipate catalyzed by an immobilized lipase from Candida antarctica. The influence of various parameters including time, temperature, enzyme loading, and vacuum was assessed in the frame of a two-step polymerization with the help of response surface methodology, a statistical technique that investigates relations between input and output variables. Results in solution (diphenyl ether) and bulk conditions showed that a two-hour reaction time was enough to allow adequate oligomer growth for the first step conducted under atmospheric pressure at 100 °C. The number-average molecular weight (Mn) achieved varied between 5000 and 12,000 g·mol−1 after a 24 h reaction and up to 18,500 g∙mol−1 after 48 h. The statistical analysis showed that vacuum was the most influential factor affecting the Mn in diphenyl ether. In sharp contrast, enzyme loading was found to be the most influential parameter in bulk conditions. Recyclability in bulk conditions showed a constant Mn of the polyester over three cycles, while a 17% decrease was noticed in solution. The following work finally introduced a statistical approach that can adequately predict the Mn of poly(hexylene adipate) based on the choice of parameter levels, providing a handy tool in the synthesis of polyesters where the control of molecular weight is of importance.

Silica scaling of reverse osmosis membranes preconditioned by natural organic matter

Reverse osmosis (RO) membranes were preconditioned in this study with humic acid, sodium alginate, or bovine serum albumin, and subsequently examined for silica scaling using the water matrix representative of concentrated brackish groundwater. The results suggested that water matrix combined with organic foulants affected silica scaling. High ambient pH favored the moderate silica ionization and thus the silica homogeneous polymerization to potentially form low molecular weight silica oligomers. The resulting scaling layer was dense and highly impermeable. Under the high Ca proportion at a given hardness, membrane scaling was enhanced through the Ca-induced silica scaling and the formation of intermolecular bridges between adjacent silica species. In contrast, high Mg hardness may facilitate the sustainable growth of silica oligomers to form the ringed high molecular weight oligomers by reducing the required energy for chain deformation. The deposition of these oligomers caused a loose scaling layer with reduced hydraulic resistance to water permeation. During the scaling tests under similar water matrix, the membranes slightly fouled by organics suffered severe flux decline due to an available space provided by the pre-existing organic fouling layer for subsequent silica scaling.

Growth of New Linear Phenylene-Oxazole Oligomers with a Central Benzothiadiazole Fragment from Solutions of Crystals

For the first time, the results on the solubility and growth of new oligomers with a single conjugated core from solutions of organic crystals are reported. The new oligomers consist of benzothiadiazole, phenylene, and oxazole units and have various terminal substituents. Using DSC and TGA methods, melting parameters are found and thermal stability upon heating is studied.

The Mitochondrial Peptide Humanin Targets but Does Not Denature Amyloid Oligomers in Type II Diabetes.

Mitochondrially derived peptides (MDPs) such as humanin (HN) have shown a remarkable ability to modulate neurological amyloids and apoptosis-associated proteins in cells and animal models. Recently, we found that humanin-like peptides also inhibit amyloid formation outside of neural environments in islet amyloid polypeptide (IAPP) fibrils and plaques, which are hallmarks of Type II diabetes. However, the biochemical basis for regulating amyloids through endogenous MDPs remains elusive. One hypothesis is that MDPs stabilize intermediate amyloid oligomers and discourage the formation of insoluble fibrils. To test this hypothesis, we carried out simulations and experiments to extract the dominant interactions between the S14G-HN mutant (HNG) and a diverse set of IAPP structures. Replica-exchange molecular dynamics suggests that MDPs cap the growth of amyloid oligomers. Simulations also indicate that HNG-IAPP heterodimers are 10 times more stable than IAPP homodimers, which explains the substoichiometric ability of HNG to inhibit amyloid growth. Despite this strong attraction, HNG does not denature IAPP. Instead, HNG binds IAPP near the disordered NFGAIL motif, wedging itself between amyloidogenic fragments. Shielding of NFGAIL-flanking fragments reduces the formation of parallel IAPP β-sheets and subsequent nucleation of mature amyloid fibrils. From ThT spectroscopy and electron microscopy, we found that HNG does not deconstruct mature IAPP fibrils and oligomers, consistent with the simulations and our proposed hypothesis. Taken together, this work provides new mechanistic insight into how endogenous MDPs regulate pathological amyloid growth at the molecular level and in highly substoichiometric quantities, which can be exploited through peptidomimetics in diabetes or Alzheimer's disease.

Understanding the Origin of 2D Self-Assembly of Tricarbazole Macrocycles: An Integrated Quantum Mechanical/Molecular Dynamics Study

The intermolecular interactions underlying self-assembly are important for designing supramolecular architectures with defined function and composition over various length scales. Here, an integrated quantum mechanical/molecular dynamics (QM/MD) approach is introduced to explore the intermolecular interactions governing the two-dimensional self-assembly of a shape-persistent macrocycle, that is, tricarbazolo triazolophane (tricarb), on highly ordered pyrolytic graphite (HOPG). Three structural motifs (row, zig-zag, and rosette) for the self-association and growth of tricarb oligomers are analyzed using dispersion-corrected density functional theory to reveal their relative stability. QM analysis shows that the major factor in the self-assembly, via H-bonding contributions to the interaction energies, originates from favorable local dipole orientations between triazole units in the zig-zag and rosette motifs. Closing of the macrocyclic loop leads to the formation of a tertiary structure, which induces stab...

Mechanisms of Protein Fibril Formation in Amyloid Beta and Lysozyme Proteins

Rigid fibril (RFs) formation of amyloid proteins is a precursor to many degenerative disorders, thus understanding the kinetics behind their generation could yield important information with respect to disease pathology. These amyloid proteins exhibit what is known as the “critical oligomer concentration” (COC), exhibiting similar behavior as that of micelle formation by surfactants. At low concentrations these proteins generate only smaller oligomeric species and RFs, upon crossing the COC the growth of globular oligomers (gOs) and curvilinear fibrils (CFs) begin, aggregate species that have been shown to be strongly correlated with disease pathology. Below the COC, RFs result in a sigmoidal rise with an initial lag period generated by delayed polymer nucleation. Above the COC, the rapid generation of gOs/CFs result in the elimination of the initial lag period, followed by a secondary rise due to RF growth, producing a biphasic onset. Here, we simulate the growth kinetics of amyloid beta and lysozyme proteins utilizing the theory of nucleated polymerization with off-pathway aggregation, with the assumption that on-pathway nucleation and off-pathway aggregation occur so rapidly that they can be represented as a single step. We show that in order to simulate experimental fibril formation, the primary nucleation rate must be significantly decreased at initial monomer concentration where there is a significant amount of off-pathway aggregates, resulting in a corresponding increase in initial lag periods. In addition, attempting similar fitting with models of the same type produce comparable trends, further supporting our initial findings, and hinting at a possibly inhibitory effect on RF growth by gOs/CFs.

Water-Chloroform Interface Assisted Microstructure Tuning of Polypyrrole-Silver Sheets.

The liquid-liquid interface of two immiscible solvents remarkably controls the morphology of polymeric nanostructures as compared to the polymerization in single solvent systems. The polymerization of pyrrole in the water-chloroform medium using silver nitrate (AgNO3) as oxidant yields polypyrrole/silver (PPy/Ag) sheets. The water-chloroform interface acts as a template for the growth of PPy/Ag hybrids into sheets by preventing the secondary growth of silver associated pyrrole oligomers in a three-dimensional (3-D) manner. On the contrary, the 3-D growth of pyrrole oligomers into spherical shapes at the water-chloroform interface is observed when ammonium persulfate (APS) is used as the oxidant. Transmission electron microscopic and scanning electron microscopic images reveal the sheetlike morphology of PPy/Ag with a relatively uniform distribution of Ag NPs (∼100 nm) on PPy sheets. The ratio of aqueous-organic bisolvent and the concentration/type of oxidant have a distinct effect on morphology, crystallinity, and electrical properties of PPy/Ag sheets. The dispersed PPy/Ag sheets are stable in moderately polar solvents up to 2 weeks. The electrochemical behavior of PPy/Ag sheets is confirmed by H2O2 sensing capability through cyclic voltammetry experiments. The antibacterial activity toward E. coli and S. aureus is quantitatively assessed using the minimum bactericidal concentration (MBC) determination.

Influence of Postsynthesis Heat Treatment on Vapor-Phase-Polymerized Conductive Polymers.

The effect of thermal treatment on the structure and electrical/optical properties of vapor phase-polymerized poly(3,4-ethylenedioxythiophene):tosylate (PEDOT:Tos) and polypyrrole:tosylate (PPy:Tos) polymer films was investigated. Thermal treatment was applied postpolymerization but prior to washing the embedded oxidant layer out of the polymer film. Structural and chemical changes arising from the treatment were studied in the context of their conductive and electrochromic behavior. Spectroscopic analysis indicated a rise in the doping levels of both conductive polymers when exposed to thermal treatment. Additionally, an increase in the film thickness was recorded after the oxidant and other unbound species were removed from the polymer layer using an ethanol rinse. As such, a strong indication that polymerization continued even in the absence of (external) monomer vapor was present. This film thickness increase was most pronounced for PPy:Tos but also present in the PEDOT:Tos film. Heat-treated films exhibited enhanced cohesion, making them more robust and therefore increasing the viability for the material to be used in the optoelectronics area. This robustness, due to additional (cross-linking) oligomer growth, came at the expense of lower conductivity relative to their untreated counterparts.

Theoretical Insights into the Interaction of Oxygenated Organic Molecules and Cobalt(II) Precursor with γ-Al2O3Surfaces

The interaction of two common oxygenates, ethylene glycol (EG) and acetic acid (AA), with the main exposed (100) and (110) surfaces of γ-Al2O3 are investigated by quantifying the thermochemistry of the drying process. Using density functional theory (DFT) calculations, we determine adsorption free energies and identify the adsorption modes and sites for both molecules interacting with the (100) and (110) surfaces of γ-Al2O3 at various coverages. While the affinity of both molecules is stronger for the (100) surface after drying, EG is more strongly adsorbed on alumina surfaces than AA. EG preferentially interacts through hydrogen bonds on the hydroxyl nests of the (100) and (110) surfaces, while it may also interact through Al–O bonds on the (110) surface at low coverage. AA is predominantly deprotonated and interacts as acetate anions through hydrogen bonds on the (110) and (100) surfaces and through Al–O bonds on the (100) surface at low coverage. We then propose a quantitative comparison of the interaction of Co2+ hexaaquo precursor with the same γ-Al2O3 surfaces. The adsorption configurations of the two organic molecules which may hinder the epitaxial growth of cobalt oligomers on alumina surfaces are identified. However, the thermodynamic analysis shows that EG and AA are less stable than the Co precursors after drying. The strong stabilization of Co precursors is attributed to its epitaxial relationship with the dried alumina surfaces as found in [Angew. Chem. Int. Ed. 2015, 54, 6824–6827] and also to a favorable entropy change during the drying process (vapor release and nitrate counterion decomposition in the gas phase). We finally discuss how these effects can be circumvented by changing the conditions of preparation and drying.

Oleuropein aglycone stabilizes the monomeric \u03b1-synuclein and favours the growth of non-toxic aggregates

α-synuclein plays a key role in the pathogenesis of Parkinson’s disease (PD); its deposits are found as amyloid fibrils in Lewy bodies and Lewy neurites, the histopathological hallmarks of PD. Amyloid fibrillation is a progressive polymerization path starting from peptide/protein misfolding and proceeding through the transient growth of oligomeric intermediates widely considered as the most toxic species. Consequently, a promising approach of intervention against PD might be preventing α-synuclein build-up, misfolding and aggregation. A possible strategy involves the use of small molecules able to slow down the aggregation process or to alter oligomer conformation favouring the growth of non-pathogenic species. Here, we show that oleuropein aglycone (OleA), the main olive oil polyphenol, exhibits anti-amyloidogenic power in vitro by interacting with, and stabilizing, α-synuclein monomers thus hampering the growth of on-pathway oligomers and favouring the growth of stable and harmless aggregates with no tendency to evolve into other cytotoxic amyloids. We investigated the molecular basis of such interference by both biophysical techniques and limited proteolysis; aggregate morphology was monitored by electron microscopy. We also found that OleA reduces the cytotoxicity of α-synuclein aggregates by hindering their binding to cell membrane components and preventing the resulting oxidative damage to cells.

Length-Dependent Manifestation of Vibration Modes Regulates a Specific Intermediate Morphology of Aβ17-42 in Different Environments.

Various cytotoxic mechanisms for neurodegenerative disease are induced by specific conformations of Aβ intermediates. The efforts to understand the diverse intermediate forms of amyloid oligomers have been focused on understanding the aggregation mechanism of specific morphologies for Aβ intermediates. However, these are still not easy tasks to be accomplished because the diverse conformations of Aβ intermediates can be altered during the aggregation process, even though the same Aβ monomers are present. Thus, efforts to reveal the conformational change mechanism could be a fundamental process to understand the formation of diverse Aβ intermediate conformations. Here, we evaluate the conformational characteristics of Aβ17-42 fibrillar oligomers in different environments according to the length. We observed that Aβ fibrillar oligomers optimize their inherent hydrogen bonds and configurational entropy to stabilize their structure according to the simulation time and their length increase. In addition, we revealed the role of the expressed vibration mode shape in the fibrillar oligomers' elongation and deformation processes. Our results suggest that limitations in amyloid oligomer growth and transformations of their morphologies can be regulated and controlled by modifying the vibration features.

Controlled Functionalization of Reduced Graphene Oxide Enabled by Microfluidic Reactors

We report the use of microfluidics to functionalize suspended reduced graphene oxide flakes through the addition of aryl radical, generated in situ by reaction between aryl amines and isopentyl nitrite. Microfluidic enabled a tight control of temperature, reaction times and stoichiometric ratios, making it possible to tune the growth of oligomers on the surface of the flakes, which in turn affects the interactions of the functional material with the surrounding environment. The results suggest that shear stress phenomena within the reactor may play a role in the chemistry of graphene materials, by providing a constant driving force towards exfoliation of the layered structures. Scale up of the functionalization process is also reported, along with the grafting of dyes based on squaric acid cores. Photophysical characterization of the dye-modified flakes proves that the microfluidic approach is a viable method towards the development of new materials with tailored properties.