The removal of per- and polyfluoroalkyl substances (PFAS) is a rapidly growing research area, yet key knowledge gaps remain in understanding adsorption mechanisms. To advance adsorbent design, the adsorption of a mixture of 22 PFAS species on pristine SBA-15 silica were examined, aminoethyl-grafted SBA (SBA-NH), and diethylenetriamine-terminated SBA (SBA-TA). Adsorption pathways were investigated using liquid-state ¹⁹F NMR and LC-MS/MS. SBA-TA achieved the highest PFAS removal (79% in methanol:water (50:50) and 93% in 3% aqueous film-forming foam), followed by SBA-NH (78% and 69%) and pristine SBA (36% and 66%). Pristine SBA showed notable adsorption in methanol:water (~70mg/g dry weight), attributed to its linear micropores matching PFAS cross-sectional dimensions. Functionalization with ammonium groups greatly enhanced capacity (~150mg/g), with SBA-TA outperforming SBA-NH, underscoring the role of ion–ion interactions in PFAS retention. These results were validated using groundwater from the Hovgården landfill site in Sweden.

Polyoxometalates (POMs) represent well-defined molecular models for metal oxide nanoparticles and provide valuable insight into their interactions with biomolecules. Here, we investigate the interaction of Keggin-type phosphotungstic (H3PW12O40) and silicotungstic (H4SiW12O40) acids with RNA-derived nucleosides cytidine and guanosine, showing for the first time that these POMs can act as catalysts for the deglycosylation of nucleosides and provide a possible molecular mechanism that facilitates this process. These systems provide useful molecular-level models for metal oxide nanoparticle-biomolecule interactions and potential RNA deglycosylation pathways. Six crystalline complexes were obtained and structurally characterized by single-crystal X-ray diffraction, revealing extensive hydrogen bonding networks and pronounced interactions between nucleobases and the POM surfaces associated with charge transfer. In several cases, catalytic deglycosylation of nucleosides occurred during crystallization, yielding nucleobase-POM complexes and providing direct structural evidence of nucleoside cleavage. Complementary solution studies performed by 1H NMR demonstrated rapid and selective catalytic deglycosylation of guanosine by silicotungstate under acidic near-boiling conditions, following apparent first-order kinetics (k = 0.399 min-1), whereas cytidine reacted rather slowly, yielding only trace amounts of cytosine complexes. Phosphotungstate anions revealed analogous but slower reactivity. Control experiments showed no comparable catalytic activity for TiO2 nanoparticle models (TiBALDH) under identical conditions. The results highlight pronounced differences in reactivity between purine and pyrimidine nucleosides and emphasize the role of charge-transfer and hydrogen-bonding interactions in POM-mediated catalysis. These findings provide molecular-level insight into metal oxide-biomolecule interactions and support the use of POMs as tunable models for understanding potential RNA degradation pathways induced by metal oxide nanoparticles.

Mucosa-associated lymphoid tissue lymphoma translocation protein 1 (MALT1) is a central regulator of immune signalling, yet how its conformational dynamics govern activation remains poorly understood. Here, we integrate NMR relaxation measurements, molecular dynamics simulations, and ensemble modelling to characterise the solution-state behaviour of the catalytic core MALT1(PCASP-Ig3)339-719 under different ionic conditions. Under low-salt conditions, all simulations converge to a dominant inactive ensemble characterised by inward rotation of residue W580 and coordinated rearrangements of regulatory loops, indicating that the inactive state is energetically favoured in solution. At intermediate ionic strength, reversible loop motions permit transient access to active-like conformations, whereas high-salt conditions suppress loop dynamics and trap the protein in its functional starting conformational basin. Comparison with experimental NMR relaxation data identifies the low-salt inactive ensemble as the best representation of solution-state dynamics, revealing stable hydrophobic cores and loop-localised conformational plasticity. Together, these results support ionic strength as a key determinant for MALT1 conformational equilibria in solution and suggest how coordinated loop dynamics regulate access to catalytically competent states. This provides a dynamic framework for future structure-based modulation of MALT1 activity.

Abstract Tryptophan (Trp) oxidation is a key biochemical process influencing plant development and numerous biomedical pathways. Here, we investigate how manganese doping modulates the catalytic behavior of titanium dioxide nanoparticles toward selective Trp oxidation. Mn-doped TiO2 nanoparticles containing 5%, 10%, and 20% Mn were systematically examined, while structurally related metal oxides (pristine TiO2, MnO2, MnFe2O4, maghemite (γ-Fe2O3), and industrial Fe3O4) were included as reference materials to establish catalytic benchmarks. Whereas the reference oxides predominantly promoted nonspecific reactive oxygen species (ROS) generation or exhibited lower catalytic efficiency, Mn-doped TiO2 displayed highly tunable reactivity. Specifically, 5% Mn doping favored broad-spectrum photocatalytic ROS production, whereas increasing the Mn content to 20% transformed the material from a conventional photocatalyst into a highly selective nanozyme. The 20% Mn-doped TiO2 exhibited superior biomimetic catalytic activity and was therefore subjected to detailed mechanistic studies. Nuclear magnetic resonance (NMR) spectroscopy and mass spectrometry (MS) revealed highly selective, nanozyme-driven Trp oxidation pathways leading to the formation of auxin-mimicking metabolites. In vivo experiments using Arabidopsis thaliana demonstrated that the resulting metabolite cocktail significantly stimulated lateral root formation, indicating improved nutrient acquisition potential. Collectively, these findings establish Mn-doped TiO2 as a tunable catalytic platform capable of directing amino acid oxidation toward biologically relevant products and highlight its potential applications in agriculture and biomedicine.

The removal of per- and polyfluoroalkyl substances (PFAS) is a rapidly growing research area, yet key knowledge gaps remain in understanding adsorption mechanisms. To advance adsorbent design, the adsorption of a mixture of 22 PFAS species on pristine SBA-15 silica were examined, aminoethyl-grafted SBA (SBA-NH), and diethylenetriamine-terminated SBA (SBA-TA). Adsorption pathways were investigated using liquid-state & sup1; F-9 NMR and LC-MS/MS. SBA-TA achieved the highest PFAS removal (79% in methanol:water (50:50) and 93% in 3% aqueous film-forming foam), followed by SBA-NH (78% and 69%) and pristine SBA (36% and 66%). Pristine SBA showed notable adsorption in methanol:water (similar to 70 mg/g dry weight), attributed to its linear micropores matching PFAS cross-sectional dimensions. Functionalization with ammonium groups greatly enhanced capacity (similar to 150 mg/g), with SBA-TA outperforming SBA-NH, underscoring the role of ion-ion interactions in PFAS retention. These results were validated using groundwater from the Hovg & aring;rden landfill site in Sweden.

Polymerization isomerism for tungsten alkoxides was observed via quick mutual transformation of distinct molecular forms near room temperature.

Mucosa-associated lymphoid tissue lymphoma translocation protein 1 (MALT1) is a central regulator of immune signalling, yet the conformational dynamics governing its activation remain poorly defined. Building on our earlier solution-state analysis of apo MALT1(PCASP-Ig3) 339–719 , which revealed domain flexibility, dynamic autoinhibition, and sensitivity to physiological ionic conditions, we combine NMR relaxation, molecular dynamics simulations, and ensemble modelling to delineate how solution environment reshapes its conformational landscape. Because most structural information derives from dimeric or inhibitor-bound states, the behaviour of monomeric, ligand-free MALT1 in physiological solution has remained unclear. Here, MD simulations show that low-salt conditions drive all trajectories toward a unified inactive-like ensemble, marked by inward rotation of W580 and coordinated rearrangements of Loop 2 and Loop 3, indicating that the inactive state is energetically favoured and its reactivation kinetically suppressed. Physiological ionic strength partially restores access to active-like loop motions, aligning with NMR evidence that sodium modulates catalytic readiness. In contrast, high-salt conditions rigidify the PCASP–Ig3 module, suppressing loop fluctuations and preventing active–inactive transitions, thereby strongly enriching the active-state population. Importantly, the combined MD–NMR analysis demonstrates that the NMR-initiated ensembles provide the most faithful representation of backbone and loop dynamics under low-salt conditions, capturing substrate-independent loop rearrangements, stable hydrophobic-core behaviour, and the intrinsic transitions that shape MALT1’s conformational equilibrium. Together, these findings identify ionic strength as a key regulator of MALT1 conformational equilibria,, highlighting how loop dynamics and domain flexibility tune its proteolytic competence and providing a dynamic framework for future structure-based modulation of MALT1 activity.

The activity of small non-photoactive titania nanoparticles against corona viruses emerges due most probably to direct membrane disruption via complexation with phospholipid molecules and their subsequent removal.

Conformational heterogeneity is essential for protein function, yet validating theoretical molecular dynamics (MD) ensembles remains a significant challenge. In this study, we present an approach that integrates free MD simulations, starting from an AlphaFold-generated structure, with refined experimental NMR-relaxation data to identify biologically relevant holistic time-resolved 4D conformational ensembles. Specifically, we select trajectory segments (RMSD plateaus) consistent with experimental observables. For the extracellular region of Streptococcus pneumoniae PsrSp, we found that only specific segments of the long MD trajectory aligned well with experimental data. The resulting ensembles revealed two regions with increased flexibility, both of which play important functional roles.

The crystal structure of the extracellular region of the second pneumococcal LCP, a polyisoprenyl-teichoic acid-peptidoglycan teichoic acid transferase PsrSp, was determined and refined to 2.15 Å resolution. Despite the low sequence homology with other LCP proteins, the PsrSp maintains the fold of the LCP domain, and the positions of the residues suggested to participate in the transferase function are conserved. The tunnel found in the PsrSp between the central β-sheet and three α-helices is wide enough to accommodate polyisoprenyl-teichoic acid. Comparison of the crystallographic temperature factors of LCP from distinct bacteria demonstrated that the four long loops located close to the teichoic acid and peptidoglycan binding sites have different relative mobilities. To compare the dynamics of the PsrSp in crystalline state and in solution, NMR spectra were recorded, and 88% of the residues were assigned in the 1H-15N TROSY HSQC spectra. Perfect accordance in the secondary structure of the crystal structure of PsrSp with NMR data demonstrated correct assignment. Moreover, the relative mobility of the essential loops estimated from the crystallographic B-factor is in good agreement with order parameter S2, predicted from chemical shift. We hypothesize that the dynamics of these loops are important for the substrate promiscuity of LCP proteins.

Mucosa-associated lymphoid tissue lymphoma-translocation protein 1 (MALT1) is an attractive target for the development of modulatory compounds in the treatment of lymphoma and other cancers. While the three-dimensional structure of MALT1 has been previously determined through X-ray analysis, its dynamic behaviour in solution has remained unexplored. We present here dynamic analyses of the apo MALT1 form along with the E549A mutation. This investigation used NMR 15N relaxation and NOE measurements between side-chain methyl groups. Our findings confirm that MALT1 exists as a monomer in solution, and demonstrate that the domains display semi-independent movements in relation to each other. Our dynamic study, covering multiple time scales, along with the assessment of conformational populations by Molecular Dynamic simulations, Alpha Fold modelling and PCA analysis, put the side chain of residue W580 in an inward position, shedding light at potential mechanisms underlying the allosteric regulation of this enzyme. NMR relaxation and AlphaFold structural ensemble modelling of MALT1 reveals motions between its PCASP and Ig3 domains. This sheds light into the mechanisms of the protein's allosteric regulation.

One of the crucial metabolic processes for both plant and animal kingdoms is the oxidation of the amino acid tryptophan (TRP) that regulates plant growth and controls hunger and sleeping patterns in animals. Here, we report revolutionary insights into how this process can be crucially affected by interactions with metal oxide nanoparticles (NPs), creating a toolbox for a plethora of important biomedical and agricultural applications. Molecular mechanisms in TRP-NP interactions were revealed by NMR and optical spectroscopy for ceria and titania and by X-ray single-crystal study and a computational study of model TRP-polyoxometalate complexes, which permitted the visualization of the oxidation mechanism at an atomic level. Nanozyme activity, involving concerted proton and electron transfer to the NP surface for oxides with a high oxidative potential, like CeO2 or WO3, converted TRP in the first step into a tricyclic organic acid belonging to the family of natural plant hormones, auxins. TiO2, a much poorer oxidant, was strongly binding TRP without concurrent oxidation in the dark but oxidized it nonspecifically via the release of reactive oxygen species (ROS) in daylight.

Per- and polyfluoroalkyl substances (PFAS) are very stable and ubiquitously distributed in terrestrial and aquatic environments, and treatment and remediation techniques for the removal of PFAS are urgently needed. In this study, mesoporous silica matrix SBA-15 grafted with alkyl amino groups was used to remove perfluorooctanoate (PFOA) from aqueous solutions. The amino groups were grafted onto SBA-15 by the condensation of alkyl amino silanes. The synthesized adsorbents were studied by SEM, TEM, IR, low-temperature nitrogen sorption, and XRD. The solid-state and liquid F-19 NMR spectroscopy, EDX, and LC-MS/MS results showed high adsorption efficiency and rapid reaction kinetics. In freshly prepared solutions and on the surface of the sorbents, the presence of PFOA micelles was observed. Furthermore, the introduction of amine-containing groups into the structure of the sorbent allows the sorption of up to 649 mg/g of PFOA from solutions. Results showed that the protonated surface amino groups and PFOA interacted electrostatically. The obtained results open perspectives for producing adsorbents for facile extraction of PFAS.

ABSTRACT Mucosa-associated lymphoid tissue lymphoma-translocation protein 1 (MALT1) has emerged as an attractive target for the development of modulatory compounds, particularly in the treatment of lymphoma and other cancers. While the three-dimensional structure of MALT1(PCASP-Ig3) 339–719 has been previously determined through X-ray analysis, its dynamic behaviour in solution has remained largely unexplored. We present here inaugural dynamic analyses of the apo MALT1(PCASP-Ig3) 339–719 form along with its mutated variant, E549A. This investigation harnessed an array of NMR relaxation techniques, including longitudinal and transverse 15 N auto-relaxation, heteronuclear NOE, transverse cross-correlated relaxation and NOE measurements between side-chain methyl groups. Our findings unequivocally confirm that MALT1(PCASP-Ig3) 339–719 exists solely as a monomer in solution, and demonstrate that the two domains display semi-independent movements in relation to each other. Our extensive dynamic study, covering a range of time scales, along with the assessment of diverse conformational populations for MALT1(PCASP-Ig3) 339–719 , by Molecular Dynamic simulations, Alpha Fold modelling and PCA analysis, shed light at potential mechanisms underlying the allosteric regulation of this enzyme, and the specific importance of interdomain motions.

The nsp1 of SARS-CoV-2 is a multifunctional protein that modifies the intracellular environment for the needs of viral replication. It is responsible for the development of translational shutoff, and its expression alone is sufficient to cause a cytopathic effect (CPE).

The dengue protease NS2B/NS3pro has been reported to adopt either an 'open' or a 'closed' conformation. We have developed a conformational filter that combines NMR with MD simulations to identify conformational ensembles that dominate in solution. Experimental values derived from relaxation parameters for the backbone and methyl side chains were compared with the corresponding back-calculated relaxation parameters of different conformational ensembles obtained from free MD simulations. Our results demonstrate a high prevalence for the 'closed' conformational ensemble while the 'open' conformation is absent, indicating that the latter conformation is most probably due to crystal contacts. Conversely, conformational ensembles in which the positioning of the co-factor NS2B results in a 'partially' open conformation, previously described in both MD simulations and X-ray studies, were identified by our conformational filter. Altogether, we believe that our approach allows for unambiguous identification of true conformational ensembles, an essential step for reliable drug discovery.

Nuclear magnetic resonance (NMR) spectroscopy has become a formidable tool for biochemistry and medicine. Although J-coupling carries essential structural information it may also limit the spectral resolution. Homonuclear decoupling remains a challenging problem. In this work, we introduce a new approach that uses a specific coupling value as prior knowledge, and the Hankel property of the exponential NMR signal to achieve broadband heteronuclear decoupling using the low-rank method. Our results on synthetic and realistic HMQC spectra demonstrate that the proposed method not only effectively enhances resolution by decoupling, but also maintains sensitivity and suppresses spectral artefacts. The approach can be combined with non-uniform sampling, which means that the resolution can be further improved without any extra acquisition time.

Abstract The dengue virus protease NS3pro/NS2B, a key antiviral target for drug development, has been previously reported to adopt either an “open” or a “closed” conformation in an ensemble of crystal structures with different NS2B C-terminus (NS2B) positioning. In this study, in order to unambiguous identify the specific conformational ensembles that dominates in solution we apply a novel strategy, referred to as conformational filter, based on Nuclei Magnetic Resonance (NMR) spectroscopy complemented by Molecular Dynamic (MD) calculations. This was achieved by comparison of the experimental values of the relaxation parameters in the fast dynamic time window of the back bone and methyl side chains with corresponding back calculated relaxation parameters of the different conformational ensembles obtained from free MD simulations. Our analyses of the relaxation data averaged over the ensembles populated indicate that “open” conformation of DENV-2 NS3pro/NS2B registered by X-ray but not in solution is absent or below the detection threshold. Based on this data we claim that the “open” conformation found for this part of the crystal structure of NS3pro/NS2B is probably due to crystal contacts. Importantly that conformational ensembles selected through NOE restrained MD as well as observed in crystallisation where position of co factor NS2B is located in so called “partly” open conformation was in full agreement with the conformational filter: experimental and free MD calculated relaxation parameters showed good agreement. Additionally we unambiguously showed a high probability for the conformational ensemble of the “closed” conformation.

Eutrophication is an important threat to aquatic ecosystems world-wide, and reliable identification of areas vulnerable to phosphorus (P) losses from diffuse sources is essential for high efficiency of mitigation measures. In this three-step study we investigated (i) relationships between the agronomic (Olsen-P and P-AL) and environmental soil P tests (P-CaCl 2 ) with molecular techniques ( 31 P NMR and XANES) followed by (ii) rainfall simulation experiment on topsoil lysimeters and (iii) comparison to long-term field measurements of water quality. Soil samples were collected from seven sites indicated to be vulnerable to nutrient losses due to underlying geology. High P release correlated to standard agronomic P tests (Olsen P, r = 0.67; and P-AL, r = 0.74) and low P sorption capacity (r = − 0.5). High content of iron-bound P compounds indicated more labile P and higher release of dissolved P (r = 0.67). The leaching experiment showed that three out of four soils with high initial soil P status had both higher P leaching concentrations before fertilization (0.83–7.7 mg P l −1 ) compared to soil with low initial soil P status (0.007–0.23 mg P l −1 ), and higher increase in P concentrations after fertilization. Higher soil P sorption capacity reduced P leaching losses. Finally, long-term monitoring data show no significant trends in P losses in a field with low initial P content and moderate P fertilization rates whereas high and over time increasing P losses were recorded in a field with high initial soil P content and repetitively high P fertilization rates.

Mucosa-associated lymphoid tissue protein 1 (MALT1) plays a key role in adaptive immune responses by modulating specific intracellular signalling pathways that control the development and proliferation of both T and B cells. Dysfunction of these pathways is coupled to the progress of highly aggressive lymphoma as well as to potential development of an array of different immune disorders. In contrast to other signalling mediators, MALT1 is not only activated through the formation of the CBM complex together with the proteins CARMA1 and Bcl10, but also by acting as a protease that cleaves multiple substrates to promote lymphocyte proliferation and survival via the NF-κB signalling pathway. Herein, we present the partial 1 H, 13 C Ile/Val/Leu-Methyl resonance assignment of the monomeric apo form of the paracaspase-IgL 3 domain of human MALT1. Our results provide a solid ground for future elucidation of both the three-dimensional structure and the dynamics of MALT1, key for adequate development of inhibitors, and a thorough molecular understanding of its function(s).