Search Results (84)

G protein-coupled receptors (GPCRs) transmit through G proteins upon agonist activation, followed by phosphorylation by GPCR kinases (GRKs) to initiate β-arrestin signaling. However, the molecular mechanisms underlying GPCR signaling regulation by distinct agonists, GRK subtypes, and phosphorylation patterns remain poorly understood. The angiotensin II (AngII) type 1 receptor (AT1R), a prototypical GPCR, serves as an ideal model for studying biased ligands and signaling. Here, we investigated the wild-type (WT) AT1R and mutants of three potential phosphorylation motifs at its C-terminus (Motif I: S326/S328/S331, Motif II: T332/S335/T336/S338, and Motif III: S346/S347/S348/T349) using unbiased agonist AngII, β-arrestin-biased agonist TRV026, and G protein-biased agonist TRV056, along with GRK2/3/5/6 subtypes. We employed phosphorylation assays, β-arrestin pull-down experiments, molecular dynamics simulations, and AlphaFold3 predictions to dissect these mechanisms. Our results reveal that GRK2-mediated AT1R phosphorylation is abolished by mutations in Motifs I and II, with Motif II exhibiting a more pronounced effect. This phosphorylation was enhanced by Gβγ subunits. In contrast, GRK3-mediated phosphorylation remained unaffected by any mutations. GRK5 specifically phosphorylated Motif II, while GRK6 phosphorylated Motif II with the unbiased agonist AngII and both Motifs I and II with biased agonists TRV026 and TRV056. Notably, Motif II mutations reduced β-arrestin1/2 recruitment by GRK5/6 but not GRK2/3. Molecular dynamics simulations demonstrated that Motif II phosphorylation minimized steric hindrance, facilitating stable β-arrestin interactions, whereas Motif I phosphorylation increased intramolecular contacts that potentially impede recruitment. AlphaFold3 models provided detailed insights into the interactions between Motif II and β-arrestin1/2. Collectively, our findings elucidate diverse AT1R phosphorylation patterns driven by different agonists and GRK subtypes, offering a framework for developing signaling-biased AT1R therapeutics by decoding GRK-specific phosphorylation barcodes. Full article

Through-space charge transfer (TSCT) between spatially adjacent donor and acceptor units has garnered considerable attention as a promising design principle for optoelectronic materials. While TSCT systems incorporating rigid spacers have been extensively studied to enhance through-space interactions, transition metal complexes connected by flexible linkers remain underexplored, despite increasing interest in their potential TSCT behavior. Herein, we report the design and synthesis of a donor–acceptor–donor (D-A-D)-type complex (1), in which a central naphthalenediimide (NDI) electron acceptor is linked to 2-phenylpyridinato(salicylaldiminato)platinum(II) complexes via flexible alkyl linkers. By systematically varying the linker length (n = 3, 4, 5, 6; 1a–d), we achieved precise control over the spatial arrangement between the NDI core and the platinum moieties in solution. Notably, compound 1a (n = 3) adopts an S-shaped conformation in solution, giving rise to a distinct TSCT absorption band. The structural and photophysical properties were thoroughly investigated using single-crystal X-ray diffraction, ¹H NMR, NOESY analysis, and DFT calculations, which collectively support the existence of the folded conformation and associated TSCT behavior. These findings highlight that TSCT can be effectively induced in flexible molecular systems by exploiting intramolecular spatial proximity and non-covalent interactions, thereby offering new avenues for the design of responsive optoelectronic materials. Full article

The homozygous Leu100Pro amino acid substitution in SPRED2, a protein negatively controlling RAS function, has recently been identified to be causally linked to a recessive form of Noonan syndrome. The amino acid substitution was documented to affect protein stability and cause a decreased and/or less stable interaction with neurofibromin, a RAS-specific GTPase activating protein negatively regulating RAS function. To further investigate the structural and functional impact of Leu100Pro, we structurally characterized the consequences of this change on the interaction of SPRED2 with neurofibromin, by 1 µn-long molecular dynamics (MD) simulations. Our analyses failed in identifying local perturbations predicted to disrupt or dramatically affect SPRED2 binding to neurofibromin, though a rearrangement of their interaction was observed. On the other hand, MD simulations also identified long-range structural rearrangements of the SPRED2 EVH-1 domain, which might be relevant for an aberrant folding of the mutant driving the previously documented accelerated degradation. Overall, the performed MD simulations suggest the occurrence of multiple intramolecular and intermolecular structural perturbations driven by the Leu100Pro change that likely contribute to its LoF behavior. Full article

Mus m 1 lipocalin is the cause of mouse allergy in sensitized individuals. The production of a soluble, stable, and immunogenic isoform of Mus m 1 is essential for developing new diagnostic tools and immunotherapeutic protocols for treating allergic symptoms. To that end, using molecular dynamics (MD), we explored the impact of substitutions at positions 120 and 138 on the structure and dynamics of the allergic isoform Mus m 1.0102. HINT-based analysis of the MD trajectories, obtained for the mutants Y120F, Y120A, C138S, and C138A, allowed the assessment of the mutations’ impact on the network of intramolecular interactions, providing insights into the mechanisms underlying protein stability, dynamics, and allergenic reactivity. The C138A mutant revealed a reduction in the solvent-accessible surface area in the region of the mutated residue, of the radius of gyration, and of the α-helix displacement from the β-barrel, features that correlate with an increase in folding stability and a satisfactory allergenic potential. We consider C138A a good candidate to be exploited for diagnostic and vaccine purposes. Full article

In this study, we developed a novel one-pot synthesis method to fabricate well-defined single-chain polymeric nanoparticles (SCNPs) integrated with interpenetrating polymer network (IPN) systems. The synthesis process involved an initial intramolecular crosslinking of poly(methyl methacrylate-co-glycidyl methacrylate) to form SCNP followed by intermolecular crosslinking to produce single-chain nanogel (SCNG) structures. In addition, the achieved single-chain polymeric nanoparticle was subsequently incorporated into an IPN structure through urethane bond formation and a Diels–Alder click reaction involving furfuryl methacrylate (FMA) and bismaleimide (BMI). The thermal properties, swelling behaviors, and morphologies of the resulting SCNP-IPN systems were investigated. This work presents a novel strategy that integrates the single-chain folding concept with IPN systems, providing a promising platform for the development of robust and functional polymeric materials with potential applications in advanced materials science. Full article

Glutathione (GSH) plays a crucial role in various physiological processes and its imbalances are closely related to various pathological conditions. Probes for detection and imaging of GSH are not only useful for understanding GSH chemical biology but are also important for exploring potential theranostic agents. Herein, we report a fast intramolecular thiol-activated arylselenoamides (FITA)-based fluorescent probe using 2,4-dinitrophenyl alkylthioether as a sulfydryl-selective receptor for the first time. The fluorescence of the probe was low due to the double effects of PET, while the probe exhibits an 86-fold fluorescence enhancement at 460 nm after GSH activation and a detection limit of 0.95 μM. Furthermore, the probe is low-toxic and capable of imaging cellular GSH. This work further expands the design and applicability of the FITA-based platform, offering a new thiol-deprotection strategy for development of fluorescent probes. Full article

Aggregation is intricately linked to protein folding, necessitating a precise understanding of their relationship. Traditionally, aggregation has been viewed primarily as a sequential consequence of protein folding and misfolding. However, this conventional paradigm is inherently incomplete and can be deeply misleading. Remarkably, it fails to adequately explain how intrinsic and extrinsic factors, such as charges and cellular macromolecules, prevent intermolecular aggregation independently of intramolecular protein folding and structure. The pervasive inconsistencies between protein folding and aggregation call for a new framework. In all combined reactions of molecules, both intramolecular and intermolecular rate (or equilibrium) constants are mutually independent; accordingly, intrinsic and extrinsic factors independently affect both rate constants. This universal principle, when applied to protein folding and aggregation, indicates that they should be treated as two independent yet interconnected processes. Based on this principle, a new framework provides groundbreaking insights into misfolding, Anfinsen’s thermodynamic hypothesis, molecular chaperones, intrinsic chaperone-like activities of cellular macromolecules, intermolecular repulsive force-driven aggregation inhibition, proteome solubility maintenance, and proteinopathies. Consequently, this paradigm shift not only refines our current understanding but also offers a more comprehensive view of how aggregation is coupled to protein folding in the complex cellular milieu. Full article

Bgl2p is a major, conservative, constitutive glucanosyltransglycosylase of the yeast cell wall (CW) with amyloid amino acid sequences, strongly non-covalently anchored in CW, but is able to leave it. In the environment, Bgl2p can form fibrils and/or participate in biofilm formation. Despite a long study, the question of how Bgl2p is anchored in CW remains unclear. Earlier, it was demonstrated that Bgl2p lost the ability to attach in CW and to fibrillate after the deletion of nine amino acids in its C-terminal region (CTR). Here, we demonstrated that a Bgl2p anchoring is weakened by substitution Glu-233/Ala in the active center. Using AlphaFold and molecular modeling approach, we demonstrated the role of CTR on Bgl2p attachment and supposed the conformational possibilities determined by the presence or absence of an intramolecular disulfide bond, forming by Cys-310, leading to accessibility of amyloid sequence and β-turns localized in CTR of Bgl2p for protein interactions. We hypothesized the mode of Bgl2p attachment in CW. Using atomic force microscopy, we investigated fibrillar structures formed by peptide V187MANAFSYWQ196 and suggested that it can serve as a factor leading to the induction of amyloid formation during interaction of Bgl2p with other proteins and is of medical interest being located close to the surface of the molecule. Full article

Antimony (Sb) is currently a widespread element with key roles in telecommunication, sustainable energy, and military industries, among others. Its significant toxicity determines the need to realize sensors for water, air, and soil and the industrial process monitoring of Sb species. Unfortunately, no antimony sensors exist so far, and just laboratory analysis methods are in use. We aimed to contribute to the development of optical sensors for the metalloid by tailoring, for the first time, luminescent Ru(II) and Re(I) polypyridyl complexes to probe and quantify the presence of Sb(III). The molecular design of the complexes includes the multifunctional Sb-binding 2-(2,2′-bithien-5-yl)-1H-imidazo[4,5-f]-1,10-phenanthroline (btip) ligand that ensures the molecular binding of Sb(III) in organic media. The Ru(II)-btip complex is additionally endowed with one 2,2′-bipyrazine (bpz) or two 1,4,5,8-tetraazaphenanthrene (tap) ligands, namely [Ru(bpz)(btip)₂]²⁺ and [Ru(tap)₂(btip)]²⁺, that boost the excited state oxidation potential of the probe, leading to an intramolecular photoinduced electron transfer from btip to the Ru(II) core. The latter is suppressed upon interaction with Sb(III), leading to an 11-fold increase in both the luminescence intensity and lifetime of [Ru(bpz)(btip)₂]²⁺ in the presence of ca. 50 μmol L⁻¹ of SbCl₃ in organic medium. The fluorescence intensity of [Re(CO)₃(H₂O)(btip)]⁺ also increases upon interaction with Sb(III) but to a much lesser extent due to the intraligand π*→π nature of its emission compared to the Ru(II) ligand-to-metal excited state deactivation. However, the weak π*→d emission band in the red spectral region of the former is quenched by the semimetallic element. The sensing mechanisms of the Ru(II)- and Re(I)-btip probes that allow luminescence intensity (Ru, Re), ratiometric (Ru), and lifetime measurements (Ru) are compared and discussed in this initial solution sensing study. Full article

A tetraphenylethylene (TPE) derivative, TPEPhDAT, modified by diaminotriazine (DAT), was prepared by successive Suzuki–Miyaura coupling and ring-closing reactions. This compound exhibits aggregation-induced emission enhancement (AIEE) properties in the DMSO/MeOH system, with a fluorescence emission intensity in the aggregated state that is 5-fold higher than that of its counterpart in a dilute solution. Moreover, the DAT structure of the molecule is a good acceptor of protons; thus, the TPEPhDAT molecule exhibits acid-responsive fluorescence. TPEPhDAT was protonated by trifluoroacetic acid (TFA), leading to fluorescence quenching, which was reversibly restored by treatment with ammonia (on–off switch). Time-dependent density functional theory (TDDFT) computational studies have shown that protonation enhances the electron-withdrawing capacity of the triazine nucleus and reduces the bandgap. The protonated TPEPhDAT conformation became more distorted, and the fluorescence lifetime was attenuated, which may have produced a twisted intramolecular charge transfer (TICT) effect, leading to fluorescence redshift and quenching. MeOH can easily remove the protonated TPEPhDAT, and this acid-induced discoloration and erasable property can be applied in anti-counterfeiting. Full article

Biochar materials have garnered attention as potential catalysts for peroxymonosulfate (PMS) activation due to their cost-effectiveness, notable specific surface area, and advantageous structural properties. In this study, a suite of plantain-derived biochar (MBB-400, MBB-600, and MBB-800), possessing a well-defined pore structure and a substantial number of uniformly distributed active sites (oxygen vacancy, OVs), was synthesized through a facile calcination process at varying temperatures (400, 600, and 800 °C). These materials were designed for the activation of PMS in the degradation of sulfamethoxazole (SMX). Experimental investigations revealed that OVs not only functioned as enriched sites for pollutants, enhancing the opportunities for free radicals (^•OH/SO₄^•−) and surface-bound radicals (SBRs) to attack pollutants, but also served as channels for intramolecular charge transfer leaps. This role contributed to a reduction in interfacial charge transfer resistance, expediting electron transfer rates with PMS, thereby accelerating the decomposition of pollutants. Capitalizing on these merits, the MBB-800/PMS system displayed a 61-fold enhancement in the conversion rate for SMX degradation compared to inactivated MBB/PMS system. Furthermore, the MBB-800 exhibited less cytotoxicity towards rat pheochromocytoma (PC12) cells. Hence, the straightforward calcination synthesis of MBB-800 emerges as a promising biochar catalyst with vast potential for sustainable and efficient wastewater treatment and environmental remediation. Full article

The molecular structure of a van der Waals-bonded complex involving 2,6-di-tert-butylphenol and a single argon atom has been determined through rotational spectroscopy. The experimentally derived structural parameters were compared to the outcomes of quantum chemical calculations that can accurately account for dispersive interactions in the cluster. The findings revealed a π-bound configuration for the complex, with the argon atom engaging the aromatic ring. The microwave spectrum reveals both fine and hyperfine tunneling components. The main spectral doubling is evident as two distinct clusters of lines, with an approximate separation of 179 MHz, attributed to the torsional motion associated with the hydroxyl group. Additionally, each component of this doublet further splits into three components, each with separations measuring less than 1 MHz. Investigation into intramolecular dynamics using a one-dimensional flexible model suggests that the main tunneling phenomenon originates from equivalent positions of the hydroxyl group. A double-minimum potential function with a barrier of 1000 (100) cm⁻¹ effectively describes this extensive amplitude motion. However, the three-fold fine structure, potentially linked to internal motions within the tert-butyl group, requires additional scrutiny for a comprehensive understanding. Full article

Simvastatin (SIM) is a potent lipid-lowering drug used to control hyper-cholesterolemia and prevent cardiovascular diseases. SIM presents low oral bioavailability (5%) because of its low aqueous solubility. In this work, polyelectrolyte complexes (PEC) are developed with different chitosan (CS) and carboxymethylcellulose (CMC) ratios that will allow for an increase in the SIM dissolution rate (2.54-fold) in simulated intestinal medium (pH 4.5). Scanning Electron Microscopy (SEM) images revealed highly porous structures. The changes between both complexes, PEC-SIM:CS:CMC (1:1:2) and (1:2:1), were related to the relaxation of the polymer chains upon absorption of the dissolution medium. Fourier-transform infrared spectroscopy (FTIR), differential scanning calorimetry (DSC) and powder X-ray diffraction (XRPD) studies were used to evaluate the polymer/polymer and drug/polymer interactions on the different PEC-SIM:CS:CMC ratios. In addition, the PEC-SIM:CS:CMC (1:2:1) complex exhibited a high ratio of protonated amino groups (NH₃⁺) and an increase in intramolecular hydrogen bonds, which were correlated with a high expansion of the interpolymer chains and an increase in the SIM dissolution rate. Different kinetic models such as zero-order, first-order, Higuchi and Korsmeyer–Peppas were studied to evaluate the influence of CS/CMC ionic interactions on the ability to improve the release rate of poorly soluble drugs. Full article

The CCT/TRiC complex is a type II chaperonin that undergoes ATP-driven conformational changes during its functional cycle. Structural studies have provided valuable insights into the mechanism of this process, but real-time dynamics analyses of mammalian type II chaperonins are still scarce. We used diffracted X-ray tracking (DXT) to investigate the intramolecular dynamics of the CCT complex. We focused on three surface-exposed loop regions of the CCT1 subunit: the loop regions of the equatorial domain (E domain), the E and intermediate domain (I domain) juncture near the ATP-binding region, and the apical domain (A domain). Our results showed that the CCT1 subunit predominantly displayed rotational motion, with larger mean square displacement (MSD) values for twist (χ) angles compared with tilt (θ) angles. Nucleotide binding had a significant impact on the dynamics. In the absence of nucleotides, the region between the E and I domain juncture could act as a pivotal axis, allowing for greater motion of the E domain and A domain. In the presence of nucleotides, the nucleotides could wedge into the ATP-binding region, weakening the role of the region between the E and I domain juncture as the rotational axis and causing the CCT complex to adopt a more compact structure. This led to less expanded MSD curves for the E domain and A domain compared with nucleotide-absent conditions. This change may help to stabilize the functional conformation during substrate binding. This study is the first to use DXT to probe the real-time molecular dynamics of mammalian type II chaperonins at the millisecond level. Our findings provide new insights into the complex dynamics of chaperonins and their role in the functional folding cycle. Full article

Receptor tyrosine kinase (RTK) KIT is key regulator of cellular signalling, and its deregulation contributes to the development and progression of many serious diseases. Several mutations lead to the constitutive activation of the cytoplasmic domain of KIT, causing the aberrant intracellular signalling observed in malignant tumours. Elucidating the molecular basis of mutation-induced effects at the atomistic level is absolutely required. We report the first dynamic 3D model (DYNASOME) of the full-length cytoplasmic domain of the oncogenic mutant KIT^D816V generated through unbiased long-timescale MD simulations under conditions mimicking the natural environment of KIT. The comparison of the structural and dynamical properties of multidomain KIT^D816V with those of wild type KIT (KIT^WT) allowed us to evaluate the impact of the D816V mutation on each protein domain, including multifunctional well-ordered and intrinsically disordered (ID) regions. The two proteins were compared in terms of free energy landscape and intramolecular coupling. The increased intrinsic disorder and gain of coupling within each domain and between distant domains in KIT^D816V demonstrate its inherent self-regulated constitutive activation. The search for pockets revealed novel allosteric pockets (POCKETOME) in each protein, KIT^D816V and KIT^WT. These pockets open an avenue for the development of new highly selective allosteric modulators specific to KIT^D816V. Full article