Amyloid formation and depolymerization of tumor suppressor p16INK4a are regulated by a thiol-dependent redox mechanism.

The conversion of a soluble protein into polymeric amyloid structures is a process that is poorly understood. Here, we describe a fully redox-regulated amyloid system in which cysteine oxidation of the tumor suppressor protein p16INK4a leads to rapid amyloid formation. We identify a partially-structured disulfide-bonded dimeric intermediate species that subsequently assembles into fibrils. The stable amyloid structures disassemble when the disulfide bond is reduced. p16INK4a is frequently mutated in cancers and is considered highly vulnerable to single-point mutations. We find that multiple cancer-related mutations show increased amyloid formation propensity whereas mutations stabilizing the fold prevent transition into amyloid. The complex transition into amyloids and their structural stability is therefore strictly governed by redox reactions and a single regulatory disulfide bond.

A model of microtubule depolymerization by kinesin-8 motor proteins.

The dimeric kinesin-8 motors have the biological function of depolymerizing microtubules (MTs) from the plus end. However, the molecular mechanism of the depolymerization promoted by the kinesin-8 motors is still undetermined. Here, a model is proposed for the MT depolymerization by the kinesin-8 motors. Based on the model, the dynamics of depolymerization in the presence of the single motor at the MT plus end under no load and under load on the motor is studied theoretically. The dynamics of depolymerization in the presence of multiple motors at the MT plus end is also analyzed. The theoretical results explain well the available experimental data. The studies can also be applicable to other families of kinesin motors such as kinesin-13 mitotic centromere-associated kinesin motors that have the ability to depolymerize MTs.

Performance of a polymerization-based electrochemically assisted persulfate process on a real coking wastewater treatment.

Industrial wastewater should be treated with caution due to its potential environmental risks. In this study, a polymerization-based cathode/Fe3+/peroxydisulfate (PDS) process was employed for the first time to treat a raw coking wastewater, which can achieve simultaneous organics abatement and recovery by converting organic contaminants into separable solid organic-polymers. The results confirm that several dominant organic contaminants in coking wastewater such as phenol, cresols, quinoline and indole can be induced to polymerize by self-coupling or cross-coupling. The total chemical oxygen demand (COD) abatement from coking wastewater is 46.8% and the separable organic-polymer formed from organic contaminants accounts for 62.8% of the abated COD. Dissolved organic carbon (DOC) abatement of 41.9% is achieved with about 89% less PDS consumption than conventional degradation-based process. Operating conditions such as PDS concentration, Fe3+ concentration and current density can affect the COD/DOC abatement and organic-polymer yield by regulating the generation of reactive radicals. ESI-MS result shows that some organic-polymers are substituted by inorganic ions such as Cl-, Br-, I-, NH4+, SCN- and CN-, suggesting that these inorganic ions may be involved in the polymerization. The specific consumption of this coking wastewater treatment is 27 kWh/kg COD and 95 kWh/kg DOC. The values are much lower than those of the degradation-based processes in treating the same coking wastewater, and also are lower than those of most processes previously reported for coking wastewater treatment.

Engineering Interfacial Integrity with Hydrolytic-Resistant, Self-Reinforcing Dentin Adhesive.

The leading cause of composite restoration failure is secondary caries, and although caries is a multifactorial problem, weak, damage-prone adhesives play a pivotal role in the high susceptibility of composite restorations to secondary caries. Our group has developed synthetic resins that capitalize on free-radical polymerization and sol-gel reactions to provide dental adhesives with enhanced properties. The resins contain γ-methacryloxypropyltrimethoxysilane (MPS) as the Si-based compound. This study investigated the properties of methacrylate-based resins containing methacryloxymethyltrimethoxysilane (MMeS) as a short-chain alternative. The degree of conversion (DC), polymerization kinetics, water sorption, mechanical properties, and leachates of MMeS- and MPS-resins with 55 and 30 wt% BisGMA-crosslinker were determined. The formulations were used as model adhesives, and the adhesive/dentin (a/d) interfaces were analyzed using chemometrics-assisted micro-Raman spectroscopy. The properties of the 55 wt% formulations were comparable. In the 30 wt% BisGMA formulations, the MMeS-resin exhibited faster polymerization, lower DC, reduced leachates, and increased storage and loss moduli, glass transition (Tg), crosslink density, and heterogeneity. The spectroscopic results indicated a comparable spatial distribution of resin, mineralized, and demineralized dentin across the a/d interfaces. The hydrolytically stable experimental short-chain-silane-monomer dental adhesive provides enhanced mechanical properties through autonomous strengthening and offers a promising strategy for the development of restorative dental materials with extended service life.

Molecular dynamics simulations in pre-polymerization mixtures for peptide recognition.

CONTEXT: Molecularly imprinted polymers (MIPs) have promising applications as synthetic antibodies for protein and peptide recognition. A critical aspect of MIP design is the selection of functional monomers and their adequate proportions to achieve materials with high recognition capacity toward their targets. To contribute to this goal, we calibrated a molecular dynamics protocol to reproduce the experimental trends in peptide recognition of 13 pre-polymerization mixtures reported in the literature for the peptide toxin melittin. METHODS: Three simulation conditions were tested for each mixture by changing the box size and the number of monomers and cross-linkers surrounding the template in a solvent-explicit environment. Fully atomistic MD simulations of 350 ns were conducted with the AMBER20 software, with ff19SB parameters for the peptide, gaff2 parameters for the monomers and cross-linkers, and the OPC water model. Template-monomer interaction energies under the LIE approach showed significant differences between high-affinity and low-affinity mixtures. Simulation systems containing 100 monomers plus cross-linkers in a cubic box of 90 Å3 successfully ranked the mixtures according to their experimental performance. Systems with higher monomer densities resulted in non-specific intermolecular contacts that could not account for the experimental trends in melittin recognition. The mixture with the best recognition capacity showed preferential binding to the 13-26-α-helix, suggesting a relevant role for this segment in melittin imprinting and recognition. Our findings provide insightful information to assist the computational design of molecularly imprinted materials with a validated protocol that can be easily extended to other templates.

Relationship between the polymerization distance of monowave and polywave light-curing units and the irradiance and physical properties of dental resin-based composites.

PURPOSE: To evaluate the influence of the polymerization distance of monowave and polywave light curing units (LCUs) on the measured irradiance relative to the value reported by the manufacturer in relation to the physical properties of resin-based composites (RBCs). METHODS: Four LCUs were used: one monowave and three polywave. The irradiance was measured with a digital radiometer. Depth of cure (DC) and flexural strength (FS) tests were performed according to ISO 4049:2019 at polymerization distances of 0 mm and 5 mm. RESULTS: The irradiance of all LCUs was higher than that reported by the manufacturer (>25-64%). The irradiance of the four LCUs was reduced when polymerization was performed at between 0 to 5 mm (paired t-test, P < 0.001). The DC at 0 mm was similar in all groups but was significantly decreased at 5 mm distance (ANOVA P < 0.001). FS showed differences among the LCUs at 0 mm (ANOVA P < 0.001) and was affected by the polymerization distance. The elastic modulus was unaffected by the LCU used or the distance (ANOVA P > 0.001). CONCLUSIONS: The LCU must be positioned as near as possible to RBCs during the polymerization process, as increased distance negatively affects the depth of cure and flexural strength.

Regulation of Precise DNA Repair by Nuclear Actin Polymerization: A Chance for Improving Gene Therapy?

Although more difficult to detect than in the cytoplasm, it is now clear that actin polymerization occurs in the nucleus and that it plays a role in the specific processes of the nucleus such as transcription, replication, and DNA repair. A number of studies suggest that nuclear actin polymerization is promoting precise DNA repair by homologous recombination, which could potentially be of help for precise genome editing and gene therapy. This review summarizes the findings and describes the challenges and chances in the field.

In vitro antifungal and physicochemical properties of polymerized acrylic resin containing strontium-modified phosphate-based glass.

Acrylic resins are widely used as the main components in removable orthodontic appliances. However, poor oral hygiene and maintenance of orthodontic appliances provide a suitable environment for the growth of pathogenic microorganisms. In this study, strontium-modified phosphate-based glass (Sr-PBG) was added to orthodontic acrylic resin at 0% (control), 3.75%, 7.5%, and 15% by weight to evaluate the surface and physicochemical properties of the novel material and its in vitro antifungal effect against Candida albicans (C. albicans). Surface microhardness and contact angle did not vary between the control and 3.75% Sr-PBG groups (p > 0.05), and the flexural strength was lower in the experimental groups than in the control group (p < 0.05), but no difference was found with Sr-PBG content (p > 0.05). All experimental groups showed an antifungal effect at 24 and 48 h compared to that in the control group (p < 0.05). This study demonstrated that 3.75% Sr-PBG exhibits antifungal effects against C. albicans along with suitable physicochemical properties, which may help to minimize the risk of adverse effects associated with harmful microbial living on removable orthodontic appliances and promote the use of various materials.

Polymerization of ZBTB transcription factors regulates chromatin occupancy.

BCL6, an oncogenic transcription factor (TF), forms polymers in the presence of a small-molecule molecular glue that stabilizes a complementary interface between homodimers of BCL6's broad-complex, tramtrack, and bric-à-brac (BTB) domain. The BTB domains of other proteins, including a large class of TFs, have similar architectures and symmetries, raising the possibility that additional BTB proteins self-assemble into higher-order structures. Here, we surveyed 189 human BTB proteins with a cellular fluorescent reporter assay and identified 18 ZBTB TFs that show evidence of polymerization. Through biochemical and cryoelectron microscopy (cryo-EM) studies, we demonstrate that these ZBTB TFs polymerize into filaments. We found that BTB-domain-mediated polymerization of ZBTB TFs enhances chromatin occupancy within regions containing homotypic clusters of TF binding sites, leading to repression of target genes. Our results reveal a role of higher-order structures in regulating ZBTB TFs and suggest an underappreciated role for TF polymerization in modulating gene expression.

Point mutations at specific sites of the nsp12-nsp8 interface dramatically affect the RNA polymerization activity of SARS-CoV-2.

In a recent characterization of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) variability present in 30 diagnostic samples from patients of the first COVID-19 pandemic wave, 41 amino acid substitutions were documented in the RNA-dependent RNA polymerase (RdRp) nsp12. Eight substitutions were selected in this work to determine whether they had an impact on the RdRp activity of the SARS-CoV-2 nsp12-nsp8-nsp7 replication complex. Three of these substitutions were found around the polymerase central cavity, in the template entry channel (D499G and M668V), and within the motif B (V560A), and they showed polymerization rates similar to the wild type RdRp. The remaining five mutations (P323L, L372F, L372P, V373A, and L527H) were placed near the nsp12-nsp8F contact surface; residues L372, V373, and L527 participated in a large hydrophobic cluster involving contacts between two helices in the nsp12 fingers and the long α-helix of nsp8F. The presence of any of these five amino acid substitutions resulted in important alterations in the RNA polymerization activity. Comparative primer elongation assays showed different behavior depending on the hydrophobicity of their side chains. The substitution of L by the bulkier F side chain at position 372 slightly promoted RdRp activity. However, this activity was dramatically reduced with the L372P, and L527H mutations, and to a lesser extent with V373A, all of which weaken the hydrophobic interactions within the cluster. Additional mutations, specifically designed to disrupt the nsp12-nsp8F interactions (nsp12-V330S, nsp12-V341S, and nsp8-R111A/D112A), also resulted in an impaired RdRp activity, further illustrating the importance of this contact interface in the regulation of RNA synthesis.

Ultrasensitive electrochemical microRNA-21 detection based on MXene and ATRP photocatalytic strategy.

A Ti3C2TxMXene-based biosensor has been developed and the photocatalytic atom transfer radical polymerization (photo ATRP) amplification strategy applied to detect target miRNA-21 (tRNA). Initially, Ti3C2TxMXene nanosheets were synthesized from the Ti3AlC2 MAX precursor via selective aluminum etching. Then, functionalization of Ti3C2TxMXene nanosheets with 3-aminopropyl triethoxysilane (APTES) via silylation reactions to facilitate covalent bonding with hairpin DNA biomolecules specifically designed for tRNA detection. Upon binding with the tRNA, the hairpin DNA liberated the azide (N3) group, initiating a click reaction to affix to the photo ATRP initiator. Through the ATRP photoreaction, facilitated by an organic photoredox catalyst and light, a significant amount of ferrocenyl methyl methacrylate (FMMA) monomer was immobilized on the electrode. Therefore, the electrochemical signal is amplified. The electrochemical efficacy of the biosensor was assessed using square wave voltammetry (SWV). Under optimized conditions, the biosensor demonstrated remarkable sensitivity in detecting tRNA, with a linear detection range from 0.01 fM to 10 pM and a detection limit of 2.81 aM. The findings elucidate that the developed biosensor, in conjunction with the photo ATRP strategy, offers reproducibility, stability, and increased sensitivity, underscoring its potential applications within the experimental medical sector of the biomolecular industry.

[Study on the mesoscopic dynamic effects of tumor treating fields on cell tubulin].

Tumor treatment fields (TTFields) can effectively inhibit the proliferation of tumor cells, but its mechanism remains exclusive. The destruction of cellular microtubule structure caused by TTFields through electric field force is considered to be the main reason for inhibiting tumor cell proliferation. However, the validity of this hypothesis still lacks exploration at the mesoscopic level. Therefore, in this study, we built force models for tubulins subjected to TTFields, based on the physical and electrical properties of tubulin molecules. We theoretically analyzed and simulated the dynamic effects of electric field force and torque on tubulin monomer polymerization, as well as the alignment and orientation of α/ß tubulin heterodimer, respectively. Research results indicate that the interference of electric field force induced by TTFields on tubulin monomer is notably weaker than the inherent electrostatic binding force among tubulin monomers. Additionally, the electric field torque generated by the TTFileds on α/ß tubulin dimers is also difficult to affect their random alignment. Therefore, at the mesoscale, our study affirms that TTFields are improbable to destabilize cellular microtubule structures via electric field dynamics effects. These results challenge the traditional view that TTFields destroy the microtubule structure of cells through TTFields electric field force, and proposes a new approach that should pay more attention to the "non-mechanical" effects of TTFields in the study of TTFields mechanism. This study can provide reliable theoretical basis and inspire new research directions for revealing the mesoscopic bioelectrical mechanism of TTFields.

Master corepressor inactivation through multivalent SLiM-induced polymerization mediated by the oncogene suppressor RAI2.

While the elucidation of regulatory mechanisms of folded proteins is facilitated due to their amenability to high-resolution structural characterization, investigation of these mechanisms in disordered proteins is more challenging due to their structural heterogeneity, which can be captured by a variety of biophysical approaches. Here, we used the transcriptional master corepressor CtBP, which binds the putative metastasis suppressor RAI2 through repetitive SLiMs, as a model system. Using cryo-electron microscopy embedded in an integrative structural biology approach, we show that RAI2 unexpectedly induces CtBP polymerization through filaments of stacked tetrameric CtBP layers. These filaments lead to RAI2-mediated CtBP nuclear foci and relieve its corepressor function in RAI2-expressing cancer cells. The impact of RAI2-mediated CtBP loss-of-function is illustrated by the analysis of a diverse cohort of prostate cancer patients, which reveals a substantial decrease in RAI2 in advanced treatment-resistant cancer subtypes. As RAI2-like SLiM motifs are found in a wide range of organisms, including pathogenic viruses, our findings serve as a paradigm for diverse functional effects through multivalent interaction-mediated polymerization by disordered proteins in healthy and diseased conditions.

Development of functionalized poly(lactide) films with chitosan via SI-SARA ATRP as scaffolds for neuronal cell growth.

Polylactic acid (PLA), a polymer derived from renewable resources, is gaining increasing attention in the development of biomedical devices due to its cost-effectiveness, low immunogenicity, and biodegradability. However, its inherent hydrophobicity remains a problem, leading to poor cell adhesion features. On this basis, the aim of this work was to develop a method for functionalizing the surface of PLA films with a biopolymer, chitosan (CH), which was proved to be a material with intrinsic cell adhesive properties, but whose mechanical properties are insufficient to be used alone. The combination of the two polymers, PLA as a bulk scaffold and CH as a coating, could be a promising combination to develop a scaffold for cell growth. The modification of PLA films involved several steps: aminolysis followed by bromination to graft amino and then bromide groups, poly(glycidyl methacrylate) (PGMA) grafting by surface-initiated supplemental activator and reducing agent atom transfer radical polymerization (SI-SARA ATRP) and finally the CH grafting. To prove the effective adhesive properties, conjugated and non-conjugated films were tested in vitro as substrates for neuronal cell growth using differentiated neurons from human induced pluripotent stem cells. The results demonstrated enhanced cell growth in the presence of CH.

Organic solvents-free and ambient-pressure drying melamine formaldehyde resin aerogels with homogeneous structures, outstanding mechanical strength and flame retardancy.

Atmospheric drying method for fabricating aerogels is considered the most promising way for casting aerogels on a large scale. However, the organic solvent exchange, remaining environmental pollution risk, is a crucial step in mitigating the impact of surface tension during the atmospheric drying process, especially for wet gel formed through the alkoxy-derived sol-gel process, such as melamine-formaldehyde resin (MF) aerogel. Herein, a tough polymer-assisted in situ polymerization was proposed to fabricate MF resin aerogel with a combination of mechanical toughness and strength, enabling it to withstand the capillary force during water evaporation. The monolithic MF resin aerogel through the sol-gel method can be directly prepared without additional network strengthening or organic solvent exchange. The resulting MF resin aerogel exhibits a homogeneous as well as hierarchical structure with macropores and mesopores (~6 µm and ~5 nm), high compressive modulus of 31.8 MPa, self-extinguishing property, and high-temperature thermal insulation with 97 % heat decrease for butane flame combustion. This work presents a straightforward and environmentally friendly method for fabricating MF resin aerogels with nanostructures and excellent performance in open conditions, exhibiting various applications.

The improvement of flame retardancy and compatibility of PBAT/PLLA via a hybrid polyurethane.

Poly (butylene adipate-co-terephthalate)/poly (L-lactic acid) (PBAT/PLLA) is one of the most important biodegradable polymer combinations; however, they are flammable with heavy melt dripping and incompatible. To achieve the objective of flame retardation and compatibility, a hybrid polyurethane (PU) with multiple flame retardation elements is synthesized via a new ring-opening polymerization (ROP) method and integrated into PBAT/PLLA film. The PU not only dissolves in different organic solvents at mild temperature but also improves the compatibility of PBAT/PLLA. As PU with respect to PBAT/PLLA is 20 wt%, the limiting oxygen index (LOI) and UL-94 reach 25.5 % and V-0 rating, respectively. In cone calorimeter test, the peak heat release rate (pHRR) of PU/PBAT/PLLA is ahead of PBAT/PLLA, and the total heat release (THR) decreases to 25.85 MJ/m2. The fire safety is achieved successfully. The initial pyrolysis of PU promotes the formation of a seed carbon layer; it continuously breaks down into a series of phosphorus­oxygen radicals and generates different inert gases, while the pyrolytic solid products accelerate the carbonization to form the carbon/silicon composite layer. Then the polymeric combustion is braked completely. Besides, the PU can also tune the mechanical properties of PBAT/PLLA film and enhance its hydrophobicity. This work opens a new window for developing multifunctional flame retardant and paves the way for the richening engineering application of PBAT/PLLA.

Prebiotic saccharides polymerization improves the encapsulation efficiency, stability, bioaccessibility and gut microbiota modulation of urolithin A liposomes.

This work was to investigate the effect of four prebiotic saccharides gum arabic (GA), fructooligosaccharide (FOS), konjac glucomannan (KGM), and inulin (INU) incorporation on the encapsulation efficiency (EE), physicochemical stability, and in vitro digestion of urolithin A-loaded liposomes (UroA-LPs). The regulation of liposomes on gut microbiota was also investigated by in vitro colonic fermentation. Results indicated that liposomes coated with GA showed the best EE, bioaccessibility, storage and thermal stability, the bioaccessibility was 1.67 times of that of UroA-LPs. The UroA-LPs coated with FOS showed the best freeze-thaw stability and transformation. Meanwhile, saccharides addition remarkably improved the relative abundance of Bacteroidota, reduced the abundances of Proteobacteria and Actinobacteria. The UroA-LPs coated with FOS, INU, and GA exhibited the highest beneficial bacteria abundance of Parabacteroides, Monoglobus, and Phascolarctobacterium, respectively. FOS could also decrease the abundance of harmful bacteria Collinsella and Enterococcus, and increase the levels of acetic acid, butyric acid and iso-butyric acid. Consequently, prebiotic saccharides can improve the EE, physicochemical stability, gut microbiota regulation of UroA-LPs, and promote the bioaccessibility of UroA, but the efficiency varied based on saccharides types, which can lay a foundation for the application of UroA in foods industry and for the enhancement of its bio-activities.

Semiarbitrary qPCR for Sensitive Detection of Circulating miRNA via Terminal Deoxynucleotidyl Transferase-Assisted RNA-Primed DNA Polymerization.

Circulating microRNAs (miRNAs) have recently emerged as noninvasive disease biomarkers. Quantitative detection of circulating miRNAs could offer significant information for clinical diagnosis due to its significance in the development of biological processes. In response to the current challenges of circulating miRNA detection, we introduce a sensitive, selective, and versatile circulating miRNA detection strategy using terminal deoxynucleotidyl transferase (TdT)-catalyzed RNA-primed DNA polymerization (TCRDP) coupled with semiarbitrary qPCR (SAPCR). Semiarbitrary qPCR was first developed here to detect long fragment targets with only a short-known sequence or to detect a short fragment target after extension with terminal transferase. Besides, the subsequent results show that TdT has a preference for RNA, particularly for extending RNAs with purine-rich and unstructured ends. Consequently, utilizing this assay, we have successfully applied it to the quantitative analysis of circulating miR-122 in animal models, a sensitive and informative biomarker for drug-induced liver injury, and as low as 200 zmol of the target is detected with desirable specificity and sensitivity, indicating that the TCRDP-SAPCR can offer a promising platform for nucleic acids analysis.

Programmable DNA Nanomachine Integrated with Electrochemically Controlled Atom Transfer Radical Polymerization for Antibody Detection at Picomolar Level.

The quantitative detection of antibodies is crucial for the diagnosis of infectious and autoimmune diseases, while the traditional methods experience high background signal noise and restricted signal gain. In this work, we have developed a highly efficient electrochemical biosensor by constructing a programmable DNA nanomachine integrated with electrochemically controlled atom transfer radical polymerization (eATRP). The sensor works by binding the target antidigoxin antibody (anti-Dig) to the epitope of the recognization probe, which then initiates the cascaded strand displacement reaction on a magnetic bead, leading to the capture of cupric oxide (CuO) nanoparticles through magnetic separation. After CuO was dissolved, the eATRP initiators were attached to the electrode based on the CuΙ-catalyzed azide-alkyne cycloaddition. The subsequent eATRP reaction results in the formation of long electroactive polymers (poly-FcMMA), producing an amplified current response for sensitive detection of anti-Dig. This method achieved a detection limit at clinically relevant picomolar concentration in human serum, offering a sensitive, convenient, and cost-effective tool for detecting various biomarkers in a wide range of applications.