Search Results (213)

As the demand for sustainable and bio-based alternatives to petroleum-derived membranes grows, polysaccharides have emerged as promising candidates. In this study, we fabricated free-standing membranes from konjac glucomannan (KGM), a neutral polysaccharide, using a simple base-induced insolubilization process. Fourier transform infrared spectroscopy revealed that the deacetylation of KGM chains promotes extensive intermolecular hydrogen bonding, creating a robust and stable three-dimensional network without the need for chemical cross-linkers. The resulting KGM free-standing membranes exhibited excellent mechanical properties, characterized by high tensile strength in the dry state and remarkable flexibility when hydrated. Furthermore, the membranes demonstrated superior chemical resistance to organic solvents such as acetone and n-hexane. Transport studies showed that the membranes possess a highly dense structure with no detectable pressure-driven pure-water permeation up to 0.25 MPa. Solute permeation experiments using eight model molecules (molecular weight = 144–14,600 Da) indicated that transport behavior is consistent with diffusion through a hydrated polymer network. The effective diffusion coefficient D_eff showed a strong correlation with molecular weight M, following the relationship D_eff ∝ M^−1.7. Furthermore, the permeation behavior remained stable across a wide pH range (2–12), and, within the investigated range of monovalent solutes, D_eff was insensitive to solute charge, indicating that mass transport is dominated by size-based diffusion rather than electrostatic interactions. These findings suggest that KGM free-standing membranes enable reliable molecular fractionation based on size-dependent diffusion within a stable, neutral matrix, offering significant potential for sustainable separation technologies and biomedical applications. Full article

Non-metallic hydride donors have emerged as an interesting, highly tunable class of compounds capable of CO₂ reduction, with benzimidazoles being simple, yet efficient and regenerable, representatives. In this work, the role of superbases as auxiliary groups attached to the benzimidazole framework was investigated using the CPCM(CH₃CN)/ωB97xD/aug-cc-pVTZ//CPCM(CH₃CN)/ωB97xD/6-31+G(d,p) approach. Three modes of operation were assessed through hydricity calculations and the modeling of two different CO₂ reduction mechanisms. Among the superbases considered, phosphazene substituents yielded the largest increase in the hydride donation ability, lowering hydricity by 6 kcal mol⁻¹ relative to 2-methylbenzimidazole, with the α-substitution exerting a stronger effect than β-substitution. For most systems, changes in hydricity correlate with changes in aromaticity, except in systems where steric congestion limits optimal substituent alignment. CO₂ activation pathways encompassing guanidine/CO₂ hydrogen bonding and guanidinium carboxamidine formation were modeled. In the former, transition state structures were significantly stabilized, and the overall exergonicity of the reduction is enhanced. Also, utilizing the longer and more flexible linker additionally decreases the barrier for the reaction. The carboxamidine pathway is disfavored because of the high stability of the carboxamidine intermediate and low barrier for the C–N bond cleavage, which reverses the mechanism to the reduction of isolated CO₂. Full article

Pseudomonas aeruginosa causes severe healthcare-associated infections, yet no vaccine has been licenced. To circumvent the antigenic variability of classical surface antigens, we evaluated LolB—an essential outer-membrane lipoprotein whose periplasmic orientation favours T-cell-dominant mechanisms with potential antibody access via outer-membrane vesicles (OMVs) or bacteriolysis. An integrative in silico pipeline combined multi-strain conservation (20 isolates), epitope discovery (B- and T-cell), safety filters, physicochemical profiling, de novo/refined 3D modelling, molecular dynamics (MD), and docking to TLR4/MD-2. LolB was highly conserved (95–100% identity) under strong purifying selection (dN/dS = 0.15). A conformational B-cell hotspot centred on Q72 mapped to a solvent-accessible flexible loop. Two class II epitopes—LAAQNSPLT and FLGSAAAVS—showed predicted high affinity (IC₅₀ < 10 nM), non-toxicity, and broad coverage, with the pooled set achieving 98.6% global HLA coverage in silico. The final 119-aa construct (N-terminal hBD-3 adjuvant; GPGPG linkers) was compact and tractable (MW = 12.7 kDa; instability index < 40; near-neutral GRAVY) and scored higher for antigenicity than native LolB (VaxiJen 0.82 vs. 0.41). MD supported thermal stability up to 350 K, linker RMSF < 1.5 Å, and a stable 18.2 ± 2.8 Å interdomain spacing. Docking predicted a 1420 Ų interface and ΔG = −10.2 kcal·mol⁻¹ (Kd = 28 nM) with reproducible polar contacts, suggesting productive TLR4/MD-2 engagement. A conservative R42A/K variant is proposed to temper IFN-γ bias. This work therefore suggests an essentiality-anchored LolB-derived multi-epitope construct as a computational vaccine candidate against multidrug-resistant P. aaeruginosa and defines specific experimentally testable hypotheses for future in vitro/in vivo assessment. Essentiality-anchored epitope selection plus adjuvant-surface engineering yielded a structurally coherent, immunologically rational LolB-derived multi-epitope vaccine warranting experimental validation. Full article

Tuberculosis, caused by Mycobacterium tuberculosis, remains a global health challenge, particularly due to multidrug-resistant strains. Photodynamic therapy using porphyrin-based photosensitizers offers a promising alternative by targeting the trehalose-rich cell wall of the bacillus. Motivated by prior experimental observations that shorter linkers improve efficacy, this study probes the molecular basis of linker-length-dependent activity in trehalose–porphyrin glycoconjugates. Here, we show that shorter linker lengths are consistent with improved activity in vitro and, in an Ag85B docking model, constrain conformational flexibility, reduce solvent exposure, and promote tighter packing consistent with stronger predicted interactions. Using computational docking, we analyzed binding scores, RMSD variability, steric clashes, and protein–ligand interactions for conjugates docked into Ag85B, a key enzyme in cell wall synthesis. Shorter linkers (0–2 carbons) were found to exhibit superior binding scores, lower RMSD variability, and stronger interactions with residues such as ARG 43, including unique π–cation interactions. In contrast, longer linkers displayed increased flexibility, reduced binding specificity, and greater solvent exposure. These findings, which support our experimental observations, suggest a molecular basis for linker-dependent efficacy and provide a framework for designing next-generation porphyrin-based therapeutics for tuberculosis treatment. Full article

Hydrogels have attracted significant interest in multifunctional applications. Among them, self-healing hydrogel stands out for its ability to autonomously repair damage through reversible interactions, yet achieving both rapid self-healing and superior mechanical strength remains challenging. In this study, we report the fabrication of a dual cross-linked hydrogel (PAA-Alg-B) prepared via free radical polymerization of acrylic acid and alginic acid, employing N,N′-methylenebisacrylamide, or vinyl-modified nanocellulose as primary cross-linker, with Fe³⁺ or borax serving as an additional dynamic cross-linker. The resulting borax based hydrogel (PAA-Alg-B) exhibits remarkable fast self-healing efficiency enabled by reversible borate ester bonds and hydrogen bonding. It demonstrates tunable mechanical strength with toughness of 137 kJ/m³ and elongation at break up to 1117%, alongside exceptional swelling capacity (448 g/g). The adsorption studies reveal high removal efficiencies for heavy metals, with maximum capacities of 87.57 mg/g (Cr³⁺), 114.02 mg/g (Ni²⁺), and 99.42 mg/g (Cu²⁺), governed by chemisorption kinetics. The PAA-Alg-B can also be used as a promising solid-state electrolyte and separator for flexible supercapacitors. Protonic modulation via H₂SO₄ soaking significantly enhances ionic conductivity, electrochemical performance, and cycling stability. These findings highlight the potential of natural polymer-based, mechanically robust, self-healing hydrogels for sustainable wastewater treatment and advanced energy storage applications. Full article

The onset of proteolysis targeting chimeras (PROTACs) has reshaped the entire context of targeted cancer therapy by offering a novel approach for the selective degradation of disease-causing proteins, overcoming the limitations of traditional occupancy-driven inhibition. This heterobifunctional technology recruits endogenous E3 ubiquitin ligases to mark proteins of interest (POI) for proteosomal degradation via the ubiquitin-proteasome system (UPS). Unlike conventional inhibitors, PROTACs function catalytically and can target previously “undruggable proteins”, such as transcription factors, scaffold proteins, and non-enzymatic regulators, offering potential to overcome acquired resistance and achieve potent efficacy at sub-stoichiometric doses. The review explores the latest innovations in PROTAC design, including E3 ligase selection, linker chemistry, and ligand optimization, while highlighting promising preclinical and clinical candidates against oncogenic drivers, anti-apoptotic factors (BCL-xL), and nuclear hormone receptors. Furthermore, we critically examine key translational challenges, such as pharmacokinetics, off-target effects, and resistance mechanisms, and discuss viable solutions, including dual E3 ligase engagement, novel modalities like AUTACs/ATTECs, LYTACs, and AI-driven design. As the field rapidly evolves from foundational to clinical application, PROTACs are redefining therapeutic possibilities, offering a robust, flexible, and scalable framework for the future of precision oncology. Full article

Therapeutic proteins face a critical pharmacokinetic challenge: rapid clearance from circulation limits their clinical efficacy. Albumin-binding domains (ABDs) offer an elegant solution by enabling therapeutic proteins to “hitchhike” on serum albumin’s favorable 19-day half-life through FcRn-mediated recycling. Clinical validation through approved therapeutics like ozoralizumab demonstrates the success of this approach, with preclinical studies showing fusion to an ABD extended half-life to 18 days. This review provides an analysis of ABD-fusion protein design, integrating structural biology, computational prediction, and rational engineering principles. We catalog the major classes of albumin-binding modalities, including bacterial three-helix bundle domains, engineered peptides, antibody-derived binders, and alternative scaffolds, comparing their binding properties, size contributions, cross-species reactivity, and production cost. Critical examination of linker architectures reveals that flexible glycine-serine linkers (particularly the widely successful (GGGGS)₃ motif) provide optimal balance between domain independence and molecular economy, though linker choice profoundly influences not only spatial separation but also binding affinity, folding, stability, and pharmacokinetics. We evaluate the utility and limitations of the structure prediction tools for ABD-fusion design. We establish practical guidelines for integrating computational screening with experimental validation. This review provides protein engineers and synthetic biologists with a comprehensive framework for rational design of albumin-binding therapeutics, emphasizing the synergistic integration of structural insight, computational prediction, and systematic experimental validation to accelerate development of next-generation long-acting biotherapeutics. Full article

Background: CD25, the α-chain of the interleukin-2 (IL-2) receptor, is highly expressed on malignant cells and tumor-infiltrating regulatory T-cells (Tregs) in hematologic malignancies, making it an attractive therapeutic target for tumor elimination and immunomodulation. Methods: We developed a CD25-specific aptamer–drug conjugate (CD25-ApDC) by linking a CD25 aptamer to monomethyl auristatin E via a cathepsin B-cleavable Val-Cit linker. Results: The aptamer exhibited high affinity for CD25 (Kd = 16.4 ± 0.29 nM), rapid receptor-mediated uptake (half-time = 9.6 min), and selective inhibition of IL-2 signaling in CD25^high cells, with no activity in CD25^low cells. In vitro, CD25-ApDC induced selective cytotoxicity, confirmed by apoptosis and G2/M arrest in CD25-positive cancer cells while having no effect on CD25-negative cells. Co-culture studies confirmed selective depletion of CD25^high Treg-like cells, suggesting potential to relieve immune suppression within the tumor microenvironment. In vivo, CD25-ApDC achieved complete tumor remission in xenograft and disseminated models with optimized dosing, showing efficacy and tolerability comparable to Brentuximab vedotin. Increasing drug-to-aptamer ratios further enhanced outcomes, supporting flexible dosing strategies. Conclusions: These findings highlight CD25-ApDC as a promising therapeutic modality for hematologic malignancies, offering advantages in specificity, tissue penetration, and manufacturability over conventional antibody-based therapies. Full article

Gas sensors are essential in areas such as environmental monitoring, industrial safety, and healthcare, where the accurate detection of hazardous and volatile gases is crucial for ensuring safety and well-being. Metal–organic frameworks (MOFs), which are crystalline porous materials composed of metal nodes and organic linkers, have recently emerged as a versatile platform for gas sensing due to their adjustable porosity, high surface area, and diverse chemical functionality. This review provides a detailed overview of MOF-based gas sensors, beginning with the fundamental sensing mechanisms of physisorption, chemisorption, and charge transfer interactions with gas molecules. We explore design strategies, including functionalization and the use of composites, which improve sensitivity, selectivity, response speed, and durability. Particular attention is given to the influence of MOF morphology, pore size engineering, and framework flexibility on adsorption behavior. Recent developments are showcased across various applications, including the detection of volatile organic compounds (VOCs), greenhouse gases, toxic industrial chemicals, and biomedical markers. Finally, we address practical challenges such as humidity interference, scalability, and integration into portable platforms, while outlining future opportunities for real-world deployment of MOF-based sensors in environmental, industrial, and medical fields. This review highlights the potential of MOFs to transform next-generation gas sensing technology by integrating foundational material design with real-world applications. Full article

The flavivirus NS1 protein is a component of the viral replication complex and plays diverse, yet poorly understood, roles in the viral life cycle. To enable real-time visualization of the developing replication organelle and biochemical analysis of tagged NS1 and its interacting partners, we engineered a replication-competent yellow fever virus (YFV) replicon encoding a C-terminal fusion of NS1 with green fluorescent protein (NS1-GFP). The initial variant was non-viable in the absence of trans-complementation with wild-type NS1; however, viability was partially restored through the introduction of co-adaptive mutations in GFP (Q204R/A206V) and NS4A (M108L). Subsequent cell culture adaptation generated a 17-nucleotide frameshift within the NS1-GFP linker, resulting in a more flexible and less hydrophobic linker sequence. The optimized genome, in the form of a replicon, replicates in packaging cells that produce YFV structural proteins, as well as in naive BHK-21 cells. In the packaging cells, the adapted NS1-GFP replicon produces titers of infectious particles of approximately 10⁶ FFU/mL and is genetically stable over five passages. The expressed NS1-GFP fusion protein localizes to the endoplasmic reticulum and co-fractionates with detergent-resistant heavy membranes, a hallmark of flavivirus replication organelles. This NS1-GFP replicon provides a novel platform for studying NS1 functions and can be further adapted for proximity-labeling strategies aimed at identifying the still-unknown protease responsible for NS1-NS2A cleavage. Full article

Intrinsically disordered regions enable transcription factors (TFs) to undergo structural changes upon ligand binding, facilitating the transduction of environmental signals into gene expression. In this study, we applied molecular modeling methods to explore the hypothesis that unstructured inter-domain and subdomain linkers in bacterial TFs can function as sensors for carbohydrate signaling molecules. We combined molecular dynamics simulations and carbohydrate docking to analyze six repressors with GntR-type DNA-binding domains, including UxuR, GntR and FarR from Escherichia coli, as well as AraR, NagR and YydK from Bacillus subtilis. Protein models obtained from different time points of the dynamic simulations were subjected to sequential carbohydrate docking. We found that the inter-domain linker of the UxuR monomer binds D-fructuronate, D-galacturonate, D-glucose, and D-glucuronate with an affinity comparable to nonspecific interactions. However, these ligands formed multimolecular clusters, a feature absent in the UxuR dimer, suggesting that protein dimerization may depend on linker occupancy by cellular carbohydrates. D-glucose interacted with linkers connecting subdomains of the LacI/GalR-type E-domains in GntR and AraR, forming hydrogen bonds that connected distant structural modules of the proteins, while in NagR, FarR and YydK, it bridged the inter-domain linkers and a β-sheet within the HutC-type E-domains. Hence, our results establish flexible linkers as pivotal metabolic sensors that directly integrate nutritional cues to alter gene expression in bacteria. Full article

Vascular endothelial growth factor 165 (VEGF₁₆₅) stands out as a pivotal isoform of the VEGF-A protein and is critically involved in various angiogenesis-related diseases. Consequently, it has emerged as a promising target for diagnosing and treating such conditions. Structurally, VEGF₁₆₅ forms a homodimer, and each of its constituting monomers comprises a receptor-binding domain (RBD) and a heparin-binding domain (HBD). These two domains are linked by a flexible linker, and thus the overall structure of VEGF₁₆₅ remains incompletely understood. Aptamers are known as potent drugs that interact with VEGF₁₆₅, and dimeric aptamers that can simultaneously interact with two distant domains are frequently adopted to improve the potency. However, designing such aptamer dimers faces challenges in regard to determining the appropriate length of the linker connecting the two aptamer fragments. To gain insight into this distance information, we here employ biased molecular dynamics (MD) simulations with the umbrella sampling method, with the distance between the two HBDs serving as a reaction coordinate. Our simulations reveal an overall preference for compact conformations with HBD-HBD distances below 3 nm, with the minimum of the potential of mean force located at 1.1 nm. We find that VEGF₁₆₅ with the optimal HBD-HBD distance forms hydrogen bonds with its receptor VEGFR-2 that well match experimentally known key hydrogen bonds. We then try to computationally design aptamer homodimers consisting of two del5-1 aptamers connected by various linker lengths to target VEGF₁₆₅. Collectively, our findings may provide quantitative guidelines for rationally designing high-affinity aptamers for targeting VEGF₁₆₅. Full article

A conjugated helical cage, comprising two 1,3,5-tris(phenylethynyl)benzene units connected by diyne linkers, was successfully synthesized. X-ray crystallography revealed helical molecular structures with large twisted angles and a 1:1 mixture of P- and M-enantiomers. Variable-temperature-NMR measurement indicated the racemization process between the enantiomers occurs rapidly on the NMR timescale. The rapid interconversion is attributed to the flexible diyne linkages, even though they were believed to be rigid. Full article

Four new porous homochiral metal–organic frameworks (MOFs), [M₂(camph)₂(bpa)]∙Solv (M = Co(II), Ni(II), Cu(II) and Zn(II)), based on (+)-camphoric acid (H₂camph) and 1,2-bis(4-pyridyl)ethane (bpa) were synthesized and characterized. The crystal structures of [Ni₂(camph)₂(bpa)] and [Zn₂(camph)₂(bpa)] were established by single-crystal X-ray diffraction analysis. Powder X-ray data prove the phase purity and isostructural nature of all four compounds. The thermal stability of [M₂(camph)₂(bpa)] was found to depend on the electronic configuration, as well as on the redox properties of the metal cation, and varied from 225 °C (M = Zn²⁺) to 375 °C (M = Ni²⁺). The reversible, solvent-induced sponge-like dynamics of the coordination frameworks was thoroughly investigated. Changes in the positions of reflexes, related to the length of the flexible bpa linker, were observed by powder XRD, pointing to transitions between an open-framework phase and a squeezed, non-porous phase in a crystal-to-crystal manner, while the integrity and connectivity of the coordination network were maintained. Size-selective adsorption from a benzene–cyclohexane 1:1 mixture on [Zn₂(camph)₂(bpa)] was studied by ¹H NMR analysis. The benzene-favorable composition of guest molecules (C₆H₆:C₆H₁₂ = 5:1) occluded within the host crystalline sponge revealed a preferable adsorption affinity towards smaller benzene compared with larger cyclohexane. High framework stability in various solvents, as well as successful molecular separation in the liquid state, validates the potential utilization of chiral porous metal(II) camphorate MOFs in important stereoselective applications. Full article

Tricopeptide repeats refer to 30 or more amino acid (aa) repeats, of which the best studied ones are 34-aa and 35-aa long, named Tetratricopeptide and Pentatricopeptide repeats, respectively, and abbreviated as TPR and PPR. Recently, 37-aa and 38-aa repeats (Heptatricopeptide, HPR; Octatricopeptide, OPR) have been reported, but 36-aa repeats or repeats outside the 34–38 range (such as 33-aa or 39-aa) are apparently missing. This review is an analytical discourse of the structural and functional commonalities as well as differences among all tricopeptide repeats. In structure, the use of Artificial Intelligence (AI)-based prediction and experimental 3D structures revealed that regardless of the number of amino acids, these repeats are all alpha-helical in nature, whereby the tandem helices are joined by relatively flexible linkers or spacers to form a superhelix. In function, many tricopeptide repeats bind specific RNA, thus playing important roles in RNA processing and stability. The specificity is determined by the interaction between specific amino acid residues with the nucleotides in the RNA, while the helices offer a scaffold that holds the interacting residues in position. Detailed analysis of various known TPR and PPR revealed conserved amino acids at specific positions, such that they serve as signature motifs. Moreover, extra helices upstream or downstream of the repeat domains often maintain the continuum of the superhelical vortex. Evidently, the overall helicity and the presence of critical amino acid residues in strategic places are more important for the biological function of the tricopeptide repeats than the exact amino acid length of the repeat. Full article