Oligomeric Structure Research Articles

Complement activation by IgG subclasses is governed by their ability to oligomerize upon antigen binding.

Complement activation through antibody-antigen complexes is crucial in various pathophysiological processes and utilized in immunotherapies to eliminate infectious agents, regulatory immune cells, or cancer cells. The tertiary structures of the four IgG antibody subclasses are largely comparable, with the most prominent difference being the hinge regions connecting the Fab and Fc domains, providing them with unique structural flexibility. Complement recruitment and activation depend strongly on IgG subclass, which is commonly rationalized by differences in hinge flexibility and the respective affinities for C1, the first component of the classical complement pathway. However, a unifying mechanism of how these different IgG subclass properties combine to modulate C1 activation has not yet been proposed. We here demonstrate that complement activation is determined by their varying ability to form IgG oligomers on antigenic surfaces large enough to multivalently bind and activate C1. We directly visualize the resulting IgG oligomer structures and characterize their distribution by means of high-speed atomic force microscopy, quantify their complement recruitment efficiency from quartz crystal microbalance experiments, and characterize their ability to activate complement on tumor cell lines as well as in vesicle-based complement lysis assays. We present a mechanistic model of the multivalent interactions that govern C1 binding to IgG oligomers and use it to extract kinetic rate constants from real-time interaction data from which we further calculate equilibrium dissociation constants. Together, we provide a comprehensive view on the parameters that govern complement activation by the different IgG subclasses, which may inform the design of future antibody therapies.

Phosphorus and nitrogen-rich oligomeric structures as durable, antibacterial and formaldehyde-free flame retardants for cotton fabrics

Phosphorus and nitrogen-rich oligomeric structures as durable, antibacterial and formaldehyde-free flame retardants for cotton fabrics

An Accurate and Fast 31P qNMR Assay Method for Oligonucleotide Therapeutics.

Chemically modified nucleic acid molecules have been developed as oligonucleotide therapeutics, and its assay is critical in quality assurance. The common DNA/RNA quantification method using UV-260 nm can lack accuracy because of structure modifications and the possible formation of higher-order structure (HOS). Additionally, process-associated water and counterions affect the accuracy in gravimetric analysis. Thus, to improve accuracy, efficiency, and flexibility, in this work a fast (<1 h) externally referenced 31P quantitative-NMR (qNMR) method was developed. The qNMR assay results agreed within 1-5% of the UV-260 nm results for the single-stranded DNA standards, confirming the method accuracy. Next, an NMR and UV comparison study was performed on intact oligonucleotide drug products. The 31P qNMR method showed 7 ± 2%, 8 ± 1%, and 12 ± 1% lower concentration values compared with drug product labels for eteplirsen, inotersen, and inclisiran, respectively. Meanwhile the UV-260 nm results showed 28 ± 3%, 10 ± 3%, and 10 ± 1% lower concentrations than the label for the same three drugs. The agreement between NMR and UV for phosphorothioate (PS)-based inotersen and mostly phosphodiester (PO)-based inclisiran suggest that the labeled concentration may have been obtained using different extinction coefficients. The underestimate of UV results for eteplirsen, which has a phosphorodiamidate morpholino oligomer (PMO) structure, suggests that the UV-260 nm extinction coefficient may need to be re-established for the PMO based oligonucleotide. Therefore, the 31P qNMR method could be a primary assay method for the oligonucleotide drug and reference standard.

Simulation-Guided Molecular Modeling of Nisin and Lipid II Assembly and Membrane Pore Formation.

The lantibiotic pore-forming peptide nisin is a promising candidate in the fight against multidrug-resistant bacteria due to its unique structure, which allows it to disrupt bacteria in two distinct ways─Lipid II trafficking and transmembrane pore formation. However, exactly how nisin and Lipid II assemble into oligomeric pore structures in the bacterial membrane is not known. Spontaneous peptide assembly into pores is difficult to observe in even the very long-time scale molecular dynamics (MD) simulations. In this study, we adopted an MD-guided modeling approach to investigate the nisin-nisin and nisin-Lipid II associations in the membrane environment. Through extensive microsecond-time scale all-atom MD simulations, we established that nisin monomers dimerize by forming β-sheets in a POPE:POPG lipid bilayer and oligomerize further to form stable transmembrane channels. We determined that these nisin dimers use Lipid II as a dimer interface to incur enhanced stability. Our results provide a clearer understanding of the self-assembly of nisin monomers within the membrane and insights into the role of Lipid II in the structural integrity of oligomeric structures.

Non-linear disulphide-centred S-shaped oligomers containing inner and outer spacers with lateral Schiff base: synthesis and mesomorphic properties

ABSTRACT A new series of non-linear S-shaped oligomers [bis-6-(2-((4-methoxyphenyl-imino)methyl)-5-(4’-hexyloxy-4-biphenyloxycarbonyl)-phenoxy)alkyl]disulphide have been synthesised and characterised. The present oligomers consist of a central disulphide (S-S) linkage, Schiff base, outer alkyl spacer (n 1 = six carbons) and inner alkyl spacer (n 2 = six to eleven carbons). Upon cooling, all the oligomers show monotropic nematic phase. The odd–even effect was found at the transition temperature of Cr-I (TCr-I) and temperature range from isotropization to crystallisation (∆TI-Cr). However, the odd–even effect was not observed at the transition temperatures of I-N and N-Cr as the values decrease when n 2 increases. The representative oligomer with n 2 = 7 undergone photoisomerisation behaviour and completed the conversion from trans to cis within a duration of 13 mins and vice versa (up to 1200 min). Optimized molecular structures of oligomers with n 2 = 6 and 7 were obtained from TMoleX, and their length-to-breadth ratio can be reasonably employed to explain the odd–even effect in TCr-I, ∆TI-Cr and the reduction of its values in entropy change (∆SI-N/R).

Exploring the Kinetics and Thermodynamics of a Novel Histidine Ammonia-Lyase from Geobacillus kaustophilus.

Histidine ammonia-lyase (HAL) plays a pivotal role in the non-oxidative deamination of L-histidine to produce trans-urocanic, a crucial process in amino acid metabolism. This study examines the cloning, purification, and biochemical characterization of a novel HAL from Geobacillus kaustophilus (GkHAL) and eight active site mutants to assess their effects on substrate binding, catalysis, thermostability, and secondary structure. The GkHAL enzyme was successfully overexpressed and purified to homogeneity. Its primary sequence displayed 40.7% to 43.7% similarity with other known HALs and shared the same oligomeric structure in solution. Kinetic assays showed that GkHAL has optimal activity at 85 °C and pH 8.5, with high thermal stability even after preincubation at high temperatures. Mutations at Y52, H82, N194, and E411 resulted in a complete loss of catalytic activity, underscoring their essential role in enzyme function, while mutations at residues Q274, R280, and F325 did not abolish activity but did reduce catalytic efficiency. Notably, mutants R280K and F325Y displayed novel activity with L-histidinamide, expanding the substrate specificity of HAL enzymes. Circular dichroism (CD) analysis showed minor secondary structure changes in the mutants but no significant effect on global GkHAL folding. These findings suggest that GkHAL could be a promising candidate for potential biotechnological applications.

Caveolin assemblies displace one bilayer leaflet to organize and bend membranes.

Caveolin is a monotopic integral membrane protein, widely expressed in metazoa and responsible for constructing enigmatic membrane invaginations known as caveolae. Recently, the high-resolution structure of a purified human caveolin assembly, the CAV1-8S complex, revealed a unique organization of 11 protomers arranged in a tightly packed, radially symmetric spiral disc. One face and the outer rim of this disc are highly hydrophobic, suggesting that the complex incorporates into membranes by displacing hundreds of lipids from one leaflet. The feasibility of this unique molecular architecture and its biophysical and functional consequences are currently unknown. Using Langmuir film balance measurements, we find that CAV1-8S is highly surface active and intercalates into lipid monolayers. Molecular simulations of biomimetic bilayers support this 'leaflet replacement' model and reveal that while CAV1-8S effectively displaces phospholipids from one bilayer leaflet, it accumulates 40-70 cholesterol molecules into a disordered monolayer between the complex and its distal lipid leaflet. We find that CAV1-8S preferentially associates with positively curved membrane surfaces due to its influence on the conformations of distal leaflet lipids, and that these effects laterally sort lipids of the distal leaflet. Large-scale simulations of multiple caveolin assemblies confirmed their association with large, positively curved membrane morphologies, consistent with the shape of caveolae. Further, association with curved membranes regulates the exposure of caveolin residues implicated in protein-protein interactions. Altogether, the unique structure of CAV1-8S imparts unusual modes of membrane interaction with implications for membrane organization, morphology, and physiology.

Oligomeric State and Drug Binding of the SARS-CoV-2 Envelope Protein Are Sensitive to the Ectodomain.

The envelope (E) protein of SARS-CoV-2 is the smallest of the three structural membrane proteins of the virus. E mediates budding of the progeny virus in the endoplasmic reticulum Golgi intermediate compartment of the cell. It also conducts ions, and this channel activity is associated with the pathogenicity of SARS-CoV-2. The structural basis for these functions is still poorly understood. Biochemical studies of E in detergent micelles found a variety of oligomeric states, but recent 19F solid-state NMR data indicated that the transmembrane domain (ETM, residues 8-38) forms pentamers in lipid bilayers. Hexamethylene amiloride (HMA), an E inhibitor, binds the pentameric ETM at the lipid-exposed helix-helix interface. Here, we investigate the oligomeric structure and drug interaction of an ectodomain-containing E construct, ENTM (residues 1-41). Unexpectedly, 19F spin diffusion NMR data reveal that ENTM adopts an average oligomeric state of dimers instead of pentamers in lipid bilayers. A new amiloride inhibitor, AV-352, shows stronger inhibitory activity than HMA in virus-like particle assays. Distance measurements between 13C-labeled protein and a trifluoromethyl group of AV-352 indicate that the drug binds ENTM with a higher stoichiometry than ETM. We measured protein-drug contacts using a sensitivity-enhanced two-dimensional 13C-19F distance NMR technique. The results indicate that AV-352 binds the C-terminal half of the TM domain, similar to the binding region of HMA. These data provide evidence for the existence of multiple oligomeric states of E in lipid bilayers, which may carry out distinct functions and may be differentially targeted by antiviral drugs.

Nanoscale Structural Characterization of Amyloid β 1-42 Oligomers and Fibrils Grown in the Presence of Fatty Acids.

Mono- and polyunsaturated fatty acids (FAs) are broadly used as food supplements. However, their effect on the aggregation of amyloidogenic proteins remains unclear. In this study, we investigated the effect of a large number of mono- and polyunsaturated, as well as fully saturated FAs on the aggregation of amyloid β1-42 (Aβ1-42) peptide. A progressive aggregation of this peptide is the expected molecular cause of Alzheimer's disease (AD), one of the most common neurodegenerative pathologies in the world. We found that arachidonic and stearic acids delayed the aggregation of Aβ1-42. Using Nano-Infrared spectroscopy, we found that FAs caused very little if any changes in the secondary structure of Aβ1-42 oligomers and fibrils formed at different stages of protein aggregation. However, the analyzed mono- and polyunsaturated, as well as fully saturated FAs uniquely altered the toxicity of Aβ1-42 fibrils. We found a direct relationship between the degree of FAs unsaturation and toxicity of Aβ1-42 fibrils formed in their presence. Specifically, with an increase in the degree of unsaturation, the toxicity Aβ1-42/FA fibrils increased. These results indicate that fully saturated or monounsaturated FAs could be used to decrease the toxicity of amyloid aggregates and, consequently, decelerate the development of AD.

Supramolecular structure of epoxy oligomers

AbstractBased on the generalized results of experimental methods for studying the viscosity of oligomers—DSC, electron microscopy, NMR spin echo, x‐ray diffraction analysis, edge wetting angles, laser microinterference, atomic force microscopy, dynamic light scattering, plastic flow—an analysis of the features of the supramolecular organization of melts and solutions of epoxy oligomers was carried out. In terms of thermofluctuation approach, a qualitative assessment of the structural elements forming a macroscopic polymer body is given, and direct morphological evidence of their structure, thermodynamic stability, size evolution with temperature changes and elastic‐strain effects is presented. A mathematical apparatus has been developed to describe the destruction of domains in solutions and melts of oligomers. Analytical equations have been proposed for calculating the time of thermofluctuation relaxation of domains. Based on the analysis of the supramolecular structure of dian epoxy oligomers by transmission electron microscopy and translational mobility of oligomer macromolecules in the high temperature region (Tg + 150°C), it has been suggested that a structure such as “flickering clusters” of free volume elements is formed in the oligomer melts.Highlights Phase diagrams of aromatic and aliphatic epoxy oligomers have been constructed. The influence of molecular weight on the activation energy of diffusion of viscous flow is estimated. It has been shown that the supramolecular structure of epoxy oligomers in the melt contains “flickering clusters.” The lifetime of density fluctuations of epoxy oligomers domains in melts has been calculated.

GSH Oligomer-Directed Chiral Au-Helicoid Nanoparticles for Discriminating Penicillamine Enantiomers.

Preparing chiral plasmonic nanoparticles (NPs) with strong chiroptical responses is crucial in numerous fields including constructing optical materials, chiral sensing, and chiral-dependent biological processes. However, precise regulation over the chiral optical activity and chiral configuration of plasmonic NPs is still a challenge. In this work, we report Au helicoid NPs with different chiral structures and reversal chirality directed by the oligomeric structure of inducer glutathione (GSH). By precisely controlling the oligomeric structure of GSH and other synthetic parameters, we successfully prepared chiral Au helicoid NPs with a high anisotropy factor of 0.03. The obtained chiral Au NPs demonstrated an excellent performance in discriminating penicillamine (Pen) enantiomers. Our findings provide a construction strategy for chiral Au NPs and contribute insight into the regulation effect of chiral inducers on the growth of chiral metal NPs.

Exploring Electrochemical Sensing for Fungicide Detection: Utilization of Newly Synthesized Oligomers.

The determination of thiabendazole is crucial for ensuring food safety, environmental protection, and compliance with regulatory standards. Accurate detection helps prevent harmful exposure, ensuring the safety of agricultural products and safeguarding public health. Therefore, this study investigates the electrochemical sensing capabilities of newly synthesized oligo 3-amino-5-mercapto-1,2,4-triazole (oligo AMTa) using hydrogen tetrachloroaurate (III) (HAuCl4) as an oxidizing agent at room temperature for thiabendazole (TBZ) detection, employing a simple electrode fabrication process. The prepared oligo AMTa was thoroughly characterized using UV-visible spectroscopy, scanning electron microscopy (SEM), Energy Dispersive X-ray Analysis (EDAX), X-ray diffraction (XRD), X-ray photoelectron spectroscopy (XPS), high-resolution mass spectroscopy (HR-MS), and Fourier-transform infrared spectroscopy (FT-IR) to confirm its oligomerization structure and properties. The IR spectrum of oligo AMTa reveals a new peak at 1449 cm-1, indicating the conversion of -NH2 groups to -N=N- groups during oligomerization, unlike AMTa. Additionally, the disappearance of the -SH group peak at 2615 cm-1 in oligo AMTa suggests an S-S linkage involvement in the oligomerization process. In the oligo AMTa XPS spectrum, the presence of C=N is displayed by a small peak at 287.3 eV, and oligomerization via -NH and N=N is confirmed by the lack of a 284.0 eV peak for C-C or C=C. Gold nanoparticle formation is not demonstrated by the 84.8 eV peak, which implies that the gold atom is not in the Au0 state. The HR-MS spectrum of oligo AMTa shows a peak at m/z 564.08, indicating a chain of five monomers, and another peak at m/z 435.03, confirming the presence of a tetrameric form of AMTa. After that, the GC electrode was directly linked to the oligo AMTa by the potentiodynamic method. SEM, electrochemical impedance spectroscopy (EIS), and cyclic voltammetry (CV) were all employed to confirm the fabrication of oligo AMTa. The SEM image illustrates the formation of a particlelike structure with a uniform size of the oligomer after cycling in 0.1 M H2SO4. After electrocycling, the size of the oligomer was reduced from 2.6 μm to 30 nm. The oligo AMTa-modified electrode possesses the highest electroactive surface area and electrical conductivity due to several key factors. First, the presence of amino (-NH2) and thiol (-SH) functional groups in AMTa enhances the surface coverage and density of electroactive sites, increasing the electroactive surface area. Additionally, the conjugated structure of AMTa facilitates efficient electron transfer, resulting in enhanced electrical conductivity compared to unmodified electrodes. Eventually, the electrochemical oxidation of TBZ occurred using the fabricated electrodes. The GC/oligo AMTa electrode exhibited a four-fold increase in oxidation current for TBZ compared to unmodified GC electrodes. This enhancement is due to the improved surface properties from the oligo AMTa modification, which significantly boosts TBZ adsorption through strong interactions like hydrogen bonding and π-π stacking. These interactions, along with the increased surface area and catalytic properties, facilitate effective electron transfer, resulting in a higher oxidation current. As an outcome, the film was employed to determine the sensitivity level of TBZ, and a LOD of 1.8 × 10-11 M (S/N = 3) was found. The straightforward method's practical utility was proven by measuring TBZ in tap water, water spinach, and pear juice samples. The comprehensive characterization of oligo AMTa provided insights into its interaction mechanisms with thiabendazole, contributing to the development of a reliable, cost-effective, and efficient sensor.

Unraveling the Molecular Complexity of N-Terminus Huntingtin Oligomers: Insights into Polymorphic Structures.

Huntington's disease (HD) is a fatal neurodegenerative disorder resulting from an abnormal expansion of polyglutamine (polyQ) repeats in the N-terminus of the huntingtin protein. When the polyQ tract surpasses 35 repeats, the mutated protein undergoes misfolding, culminating in the formation of intracellular aggregates. Research in mouse models suggests that HD pathogenesis involves the aggregation of N-terminal fragments of the huntingtin protein (htt). These early oligomeric assemblies of htt, exhibiting diverse characteristics during aggregation, are implicated as potential toxic entities in HD. However, a consensus on their specific structures remains elusive. Understanding the heterogeneous nature of htt oligomers provides crucial insights into disease mechanisms, emphasizing the need to identify various oligomeric conformations as potential therapeutic targets. Employing coarse-grained molecular dynamics, our study aims to elucidate the mechanisms governing the aggregation process and resultant aggregate architectures of htt. The polyQ tract within htt is flanked by two regions: an N-terminal domain (N17) and a short C-terminal proline-rich segment. We conducted self-assembly simulations involving five distinct N17 + polyQ systems with polyQ lengths ranging from 7 to 45, utilizing the ProMPT force field. Prolongation of the polyQ domain correlates with an increase in β-sheet-rich structures. Longer polyQ lengths favor intramolecular β-sheets over intermolecular interactions due to the folding of the elongated polyQ domain into hairpin-rich conformations. Importantly, variations in polyQ length significantly influence resulting oligomeric structures. Shorter polyQ domains lead to N17 domain aggregation, forming a hydrophobic core, while longer polyQ lengths introduce a competition between N17 hydrophobic interactions and polyQ polar interactions, resulting in densely packed polyQ cores with outwardly distributed N17 domains. Additionally, at extended polyQ lengths, we observe distinct oligomeric conformations with varying degrees of N17 bundling. These findings can help explain the toxic gain-of-function that htt with expanded polyQ acquires.

PROTIC POLYMERIC IONIC LIQUID OF A BLOCK OLIGOMERIC STRUCTURE WITH IONIC BONDS IN THE MAIN CHAIN

A method for the synthesis of protic polymeric ionic liquid (PIL) of a block oligomeric structure with ionic bonds in the main chain, which turns into a liquid state at temperatures below 50 °C, was developed. Ionic bonding was used to form a polymer chain. It was formed as a result of neutralization reaction between oligomers of telechelic structure with terminal acidic and basic groups. A new linear oligomer containing basic tertiary nitrogen atoms at the ends of the oligoether chain (PEO-2NEt2) was obtained by reaction of α,ω-diglycidyl ether of polyethylene glycol MW 1000 with N,N-diethylamine. A linear oligomer with terminal sulfonic acid groups (PEO-2SO3H), which is a product of the interaction of polyethylene glycol (MW 1000) with the cyclic anhydride of 2-sulfobenzoic acid, was used as an acidic linear oligomer. The synthesis of PIL [PEO-2H-2NEt2]2+ [PEO-2SO3]2- was carried out by neutralization of basic oligomer PEO-2NEt2 with the acidic oligomer PEO-2SO3H in their molar ratio of 1:1. The structure of the obtained compound was characterized by the methods of FTIR and 1H NMR spectroscopy. According to the DSC data, the synthesized PIL contains an amorphous phase with a glass transition temperature of -49.7 °С and a crystalline phase with a melting temperature of 34.5 °С. The decomposition onset temperature corresponding to 5% weight loss is 271 °C according to the TGA. The ionic conductivity of PIL studied by dielectric relaxation spectroscopy under anhydrous conditions in the range from 40 °C to 100 °C increases with increase in temperature and reaches 2.7·10-4 S/cm. The resulting compound is promising as a proton-conducting medium for various electrochemical devices.

Molecular Insights into Adhesion at Interface of Geopolymer Binder and Cement Mortar.

The degradation of concrete and reinforced concrete structures is a significant technical and economic challenge, requiring continuous repair and rehabilitation throughout their service life. Geopolymers (GPs), known for their high mechanical strength, low shrinkage, and durability, are being increasingly considered as alternatives to traditional repair materials. However, there is currently a lack of understanding regarding the interface bond properties between new geopolymer layers and old concrete substrates. In this paper, using advanced computational techniques, including quantum mechanical calculations and stochastic modeling, we explored the adsorption behavior and interaction mechanism of aluminosilicate oligomers with different Si/Al ratios forming the geopolymer gel structure and calcium silicate hydrate as the substrate at the interface bond region. We analyzed the electron density distributions of the highest occupied and lowest unoccupied molecular orbitals, examined the reactivity indices based on electron density functional theory, performed Mulliken charge population analysis, and evaluated global reactivity descriptors for the considered oligomers. The results elucidate the mechanisms of local and global reactivity of the oligomers, the equilibrium low-energy configurations of the oligomer structures adsorbed on the surface of C-(A)-S-H(I) (100), and their adsorption energies. These findings contribute to a better understanding of the adhesion properties of geopolymers and their potential as effective repair materials.

Strong yet Tough Catalyst-Free Transesterification Vitrimer with Excellent Fire-Retardancy, Durability, and Closed-Loop Recyclability.

Despite great advances in vitrimer, it remains highly challenging to achieve a property portfolio of excellent mechanical properties, desired durability, and high fire safety. Thus, a catalyst-free, closed-loop recyclable transesterification vitrimer (TPN1.50) with superior mechanical properties, durability, and fire retardancy is developed by introducing a rationally designed tertiary amine/phosphorus-containing reactive oligomer (TPN) into epoxy resin (EP). Because of strong covalent interactions between TPN and EP and its linear oligomer structure, as-prepared TPN1.50 achieves a tensile strength of 86.2MPa and a toughness of 6.8MJm-3, superior to previous vitrimer counterparts. TPN1.50 containing 1.50 wt% phosphorus shows desirable fire retardancy, including a limiting oxygen index of 35.2% and a vertical burning (UL-94) V-0 classification. TPN1.50 features great durability and can maintain its structure integrity in 1M HCl or NaOH solution for 100 days. This is because the tertiary amines are anchored within the cross-linked network and blocked by rigid P-containing groups, thus effectively suppressing the transesterification. Owing to its good chemical recovery, TPN1.50 can be used as a promising resin for creating recyclable carbon fiber-reinforced polymer composites. This work offers a promising integrated method for creating robust durable fire-safe vitrimers which facilitate the sustainable development of high-performance polymer composites.

COSMOPharm: Drug-Polymer Compatibility of Pharmaceutical Amorphous Solid Dispersions from COSMO-SAC.

The quantum mechanics-aided COSMO-SAC activity coefficient model is applied and systematically examined for predicting the thermodynamic compatibility of drugs and polymers. The drug-polymer compatibility is a key aspect in the rational selection of optimal polymeric carriers for pharmaceutical amorphous solid dispersions (ASD) that enhance drug bioavailability. The drug-polymer compatibility is evaluated in terms of both solubility and miscibility, calculated using standard thermodynamic equilibrium relations based on the activity coefficients predicted by COSMO-SAC. As inherent to COSMO-SAC, our approach relies only on quantum-mechanically derived σ-profiles of the considered molecular species and involves no parameter fitting to experimental data. All σ-profiles used were determined in this work, with those of the polymers being derived from their shorter oligomers by replicating the properties of their central monomer unit(s). Quantitatively, COSMO-SAC achieved an overall average absolute deviation of 13% in weight fraction drug solubility predictions compared to experimental data. Qualitatively, COSMO-SAC correctly categorized different polymer types in terms of their compatibility with drugs and provided meaningful estimations of the amorphous-amorphous phase separation. Furthermore, we analyzed the sensitivity of the COSMO-SAC results for ASD to different model configurations and σ-profiles of polymers. In general, while the free volume and dispersion terms exerted a limited effect on predictions, the structures of oligomers used to produce σ-profiles of polymers appeared to be more important, especially in the case of strongly interacting polymers. Explanations for these observations are provided. COSMO-SAC proved to be an efficient method for compatibility prediction and polymer screening in ASD, particularly in terms of its performance-cost ratio, as it relies only on first-principles calculations for the considered molecular species. The open-source nature of both COSMO-SAC and the Python-based tool COSMOPharm, developed in this work for predicting the API-polymer thermodynamic compatibility, invites interested readers to explore and utilize this method for further research or assistance in the design of pharmaceutical formulations.

Mechanistic insights from the atomic-level quaternary structure of short-lived GPCR oligomers in live cells.

The functional significance of the interactions between proteins in living cells to form short-lived quaternary structures cannot be overemphasized. Yet, quaternary structure information is not captured by current methods, neither can those methods determine structure within living cells. The dynamic versatility, abundance, and functional diversity of G protein-coupled receptors (GPCRs) pose myriad challenges to existing technologies but also present these proteins as the ideal testbed for new technologies to investigate the complex inter-regulation of receptor-ligand, receptor-receptor, and receptor-downstream effector interfaces in living cells. Here, we present development and use of a novel method capable of overcoming existing challenges by combining distributions (or spectrograms) of FRET efficiencies from populations of fluorescently tagged proteins associating into oligomeric complexes in live cells with diffusion-like trajectories of FRET donors and acceptors obtained from molecular dynamics (MD) simulations. Our approach provides an atom-level picture of the binding interfaces within oligomers of the human secretin receptor (hSecR) in live cells and allows for extraction of mechanistic insights into the function of GPCRs oligomerization. This FRET-MD spectrometry approach is a robust platform for investigating protein-protein binding mechanisms and opens a new avenue for investigating stable as well as fleeting quaternary structures of any membrane proteins in living cells.

Structural insights into rapamycin-induced oligomerization of a FRB-FKBP fusion protein.

Inducible dimerization systems, such as rapamycin-induced dimerization of FK506 binding protein (FKBP) and FKBP-rapamycin binding (FRB) domain, are widely employed chemical biology tools to manipulate cellular functions. We previously advanced an inducible dimerization system into an inducible oligomerization system by developing a bivalent fusion protein, FRB-FKBP, which forms large oligomers upon rapamycin addition and can be used to manipulate cells. However, the oligomeric structure of FRB-FKBP remains unclear. Here, we report that FRB-FKBP forms a rotationally symmetric trimer in crystals, but a larger oligomer in solution, primarily tetramers and pentamers, which maintain similar inter-subunit contacts as in the crystal trimer. These findings expand the applications of the FRB-FKBP oligomerization system in diverse biological events.

Chemical and Solvent‐Based Recycling of High‐Performance Epoxy Thermoset Utilizing Imine‐Containing Secondary Amine Hardener

AbstractEpoxy thermosets are indispensable in various industrial applications due to their exceptional material properties. However, their limited recyclability poses a significant challenge for sustainability. To address this issue, integrating recyclable imine moieties into epoxy systems has emerged as a promising strategy. Despite recent advancements, challenges persist concerning the hydrolytic stability of imine‐based epoxy thermosets and the formation of irregular oligomeric structures upon depolymerization. In this study, these shortcomings are solved by designing a liquid imine monomer with secondary amine functionalities, which is subsequently reacted with commercially available epoxy monomers to produce high‐performance epoxy thermosets. Remarkably, the developed imine‐based epoxy system shows no sign of hydrolysis even under high‐temperature aqueous conditions, underscoring its potential for various industrial applications. Only the treatment with aqueous HCl results in the selective formation of exclusively well‐defined molecules, in high isolated yields after depolymerization. Crosslinking these building blocks once again yields recycled polymers with properties identical to pristine material. Moreover, it is discovered that, despite the crosslinked nature of the epoxy thermoset, the complete dissolution of the intact polymer in dichloromethane allowed for simple solvent‐based recycling. Through design on the molecular level, the recycling of imine‐based epoxy polymers is achieved via chemical and solvent‐based techniques.