Deciphering Glycan Dynamics through Nonlinear Correlation Analysis.

Glycans, as one of the fundamental biomolecules alongside nucleic acids and proteins, play critical roles in biological processes, including glycoprotein folding, transport, degradation, and cell-cell interactions. Despite their biological importance, the structural analysis of glycans remains challenging due to their high flexibility and complex branched structures. This study addresses these challenges by combining molecular dynamics (MD) simulations and NMR spectroscopy to obtain dynamic conformational ensembles of glycans.

Central memory T cells with key TCR repertoires and gene expression profiles dominate influenza CD8+ T cell pools across the human lifespan.

Central memory CD8 T cells (T) represent the prominent memory T cell subset in human blood, yet the persistence of T cell receptor (TCR) clonotypic and transcriptional features of epitope-specific T pools across the human lifespan remains unknown. We analyzed T CD8 T cells specific for HLA-A*02:01-M1 (A2/M1; a prominent influenza epitope) in newborns, children, adults, and older adults directly ex vivo. Our data provide evidence that epitope-specific T CD8 pools dominate influenza-specific memory A2/M1CD8 T cell responses from the early childhood until old age.

Exploring the Efficacy of Background Removal with SOM-RPM in Mass Spectrometry Imaging.

Image segmentation is a critical yet fundamental aspect of interpreting the spatio-spectral information contained in complex, high-dimensional mass spectrometry imaging (MSI) data. Clustering methods are commonly employed to group similar pixels to form segmentation maps that describe different spatial features or regions of interest found in material samples. In this study, we initially assessed three clustering methods, -means, DBSCAN, and SOM-RPM, for their ability to identify both intercluster and intracluster variability on a simple bivariate synthetic data set.

A Visible-Light-Responsive Octahedral Cage for Efficient and Selective Cross-[2 + 2] Cycloadditions.

Host-guest complexation enhances or even alters photoreaction selectivity by preorganizing substrates within the host's confined cavities. Since most previous hosts exhibited no visible-light absorption, at least one of the reactants needed to be an aromatic compound with UV-light absorption. Here, we developed a visible-light-responsive ML octahedral cage that retains the encapsulation ability of standard ML cages by simply replacing the photoinert metal unit at every vertex with a photoactive cyclometalated Pt(II) unit.

Expanding the Chemical Space of Antimicrobial Peptides via Enzymatic Prenylation.

Antimicrobial peptides act primarily at the bacterial membrane interface. We report a biocatalytic strategy that enhances their potency by up to 18-fold. The improvement results from the enzymatic installation of bulky isoprenoid chains, which strengthens peptide-membrane interactions and promotes membrane destabilization.

Short-Term Probiotic Colonization Alters Molecular Dynamics of 3D Oral Biofilms.

Three-dimensional (3D) scaffold systems have proven instrumental in advancing our understanding of polymicrobial biofilm dynamics and probiotic interactions within the oral environment. Among oral probiotics, K12 () has shown considerable promise in modulating microbial homeostasis; however, its long-term therapeutic benefits are contingent upon successful and sustained colonization of the oral mucosa. Despite its clinical relevance, the molecular mechanisms underlying the adhesion, persistence, and integration of Ssk12 into the native oral microbiome/biofilm remain inadequately characterized.

Deciphering thermal degradation pathways of metal halide perovskite thin films under ambient conditions.

Understanding the dynamic lattice collapse pathways under thermal stress is pivotal for designing stable perovskite and improving the power conversion efficiency (PCE) of perovskite solar cells (PSCs). However, the lack of dynamic molecular-level characterization techniques has limited a comprehensive understanding of the degradation pathways involved. In this study, we use temperature-dependent Raman spectroscopy (25-375 °C) coupled with multimodal characterization to investigate A-site cation-dependent degradation pathways in mixed-halide perovskites, specifically FACsPbI (FACs) and FAMAPbI (FAMA).

Antisymmetry rules of response properties in certain chemical spaces.

Understanding chemical compound space (CCS), a set of molecules and materials, is crucial for the rational discovery of molecules and materials. Concepts of symmetry have recently been introduced into CCS to account for near degeneracies and differences in electronic energies between iso-electronic materials. In this work, we present approximate relationships of response properties based on a first-principles view of CCS.

Direct observation of long-lived radical pair between flavin and guanine in single- and double-stranded DNA-oligomers.

The mechanism by which cryptochrome (CRY) proteins are capable of sensing weak magnetic fields (e.g., the geomagnetic field: ~50 μT) was suggested to be mediated by spin-correlated radical pairs (SCRPs) comprising a flavin adenine dinucleotide (FAD) radical and a tryptophan (Trp) radical which are formed simultaneously by light-induced electron transfer (ET).

Quantum-chemical molecular dynamics study of polaron formation in perovskite NaTaO as a water-splitting photocatalyst.

The water splitting reaction mediated by photocatalysts is attracting much interest in the context of solar energy utilization. However, our understanding of the charge carrier dynamics underlying the photocatalytic water splitting reaction is still limited. Here, focusing on the perovskite-type oxide NaTaO, which is an archetypical heterogeneous photocatalyst for the water splitting reaction, the charge carrier dynamics were investigated by a computational approach, , molecular dynamics simulations based on quantum chemical calculations.

Genome-wide association study of the taste and hedonic ratings of the low-calorie sweetener acesulfame potassium.

Acesulfame potassium (Ace-K) is a low-calorie sweetener (LCS) widely used as an ingredient in foods and beverages and an excipient in pediatric medicines. While prior candidate gene studies have established that genetic variants in bitter taste receptor (TAS2R) genes are associated with variation in the taste of Ace-K, we sought to identify genetic contributions to its taste using a genome-wide association study (GWAS) of 141 adult panelists who rated the taste of an aqueous solution of Ace-K using the general labelled magnitude scale (gLMS) and its palatability using the hedonic gLMS. To determine whether GWAS-identified associations with Ace-K generalized to a more complex stimulus, panelists also rated the taste of a pediatric medicine that contains Ace-K as an excipient (Children's Motrin™).

Oligomerization Mechanism of Amyloid- Peptides at Hydrophobic Interfaces Revealed by Molecular Dynamics Simulations.

Molecular dynamics simulations of Amyloid-β (Aβ) peptides in water were conducted to calculate the free energy profiles of their dissociation in bulk water and at a hydrophobic interface, as well as their transfer from the bulk to the interface, in order to discuss the thermodynamic cycle of oligomerization. The air/water interface was introduced as a typical hydrophobic interface, and the free energy associated with the process in which two Aβ monomers associate to form a dimer in bulk water, either directly or via the interface, was analyzed. The results show that the Aβ monomer is stabilized at the interface by 6.

Characterisation of an influenza B virus-derived peptide presented by HLA-B*18:01.

The influenza B virus (IBV) can pose a significant threat to global health. Despite this, IBV is understudied compared with influenza A virus (IAV). CD8+ T cells have proven highly effective in reducing influenza disease severity.

Investigation of Proteome-Tetrazine Reactivity for a Highly Selective Tetrazine Ligation in Live Cells.

Tetrazine has been widely used in bio-orthogonal click chemistry for diverse biological applications due to its short reaction time and excellent bio-orthogonality. For efficient click reaction, the stability of tetrazine in physiological conditions is one of the key issues in biological applications. However, the reactions between tetrazine and biomolecules have barely been studied.

Synthesis, Structures, and Properties of Dehydrobiphenyleno[12]Annulenes: Carbon-Rich Compounds Comprising Two Different Antiaromatic Units.

In this work we report the synthesis, structure, and electronic properties of carbon-rich compounds dehydrobiphenyleno[12]annulenes (DBP[12]As) comprising antiaromatic four-membered rings (4MR) and 12-membered ring (12MR). Ultraviolet-visible absorption spectra and electrochemical behaviors of DBP[12]As confirmed their relatively narrow highest occupied molecular orbital (HOMO)-lowest unoccupied molecular orbital (LUMO) gap values and high HOMO energy levels, which were supported by density functional theory simulations. Parent DBP[12]A adopts a slipped herringbone structure in a crystalline state, with the molecules forming 1D stacks via π-π interactions.

Rotation-Direction-Dependent Mechanism of the Inhibitor Protein IF for Mitochondrial ATP Synthase from Atomistic Simulations.

ATPase inhibitory factor 1 (IF) is an endogenous regulatory protein for mitochondrial FF-ATP synthase. It blocks the catalysis and rotation of the F part by deeply inserting itself into the rotor-stator interface. Recent single-molecule manipulation experiments have elucidated that forcible rotations only in the ATP-synthesis direction eject IF, rescuing F from the IF-inhibited state.

Micro Crystalline Sponge Method Combined with Small-Wedge Synchrotron Crystallography for Nanogram Scale Molecular Structure Elucidation.

The crystalline sponge (CS) method enables X-ray structural analysis without the requirement of crystallization of the target compound. However, several technical and crystallographic challenges, such as low guest occupancy, static disorder, and crystal degradation, continue to limit both the accuracy and the success rate of the method. In this study, we explored the downsizing of CS crystals to the range of 1-10 μm to improve data quality and reduce the amount of sample required.

Integrated / Uncertainty Quantification Method for Protein Crystallization Models.

The complexity of protein crystallization and modeling challenges process intensification and the wider adoption of crystallization in biomanufacturing. For computational models to support and replace extensive experiments, they must accurately reflect experiments. However, parameter estimation can be ineffective due to the highly nonlinear model structure and inaccurate online process analytical technology, which must be addressed.

Design, Synthesis, Theoretical Study, and Antioxidant Activity of Aromaticity-Extended Resveratrol Derivatives Incorporating Chalcogen.

Naturally occurring antioxidants have attracted significant research interest, owing to their radical scavenging ability that can be improved via structural modifications. In this study, aromaticity-extended resveratrol analogues (-) containing chalcogens were designed and synthesized using ring closure and Horner-Wadsworth-Emmons reactions. The antioxidant activities of the derivatives were evaluated using 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) (ABST) assay.

Single-Molecule Phosphorescence and Intersystem Crossing in a Coupled Exciton Plasmon System.

Scanning the sharp metal tip of a scanning tunneling microscope (STM) over a molecule allows for tuning the coupling between the tip plasmon and a molecular fluorescence emitter. This allows access to local variations in fluorescence field enhancement and wavelength shifts, which are central parameters for characterizing the plasmon-exciton coupling. Performing the same for phosphorescence with molecular-scale resolution remains a significant challenge.

Synthesis, structure, and properties of twisted π-conjugated molecules featuring three-dimensional π-π interactions in solid states.

Thiophene-containing twisted π-conjugated molecules were synthesized by introducing methyl groups to sterically hindered positions. Three-dimensional π-π stacking was observed in the solid state, and the hole-transporting ability up to 1.85 × 10 cm V s was confirmed by constructing field effect transistor devices.

Microgravity-Assisted Exploration of the Conformational Space of Amyloid β Affected by Tottori-Type Familial Mutation D7N.

The amyloid β (Aβ) Tottori variant (D7N) exhibits unique aggregation behaviors and altered fibril formation, posing challenges for structural characterization. To overcome this, the microgravity environment on the International Space Station was employed to study Tottori-type Aβ40 fibril formation and structure. Under Earth gravity, Tottori-type Aβ40 primarily formed nonfibrillar aggregates, hindering detailed structural analysis.

In Vitro Live Cell Imaging Reveals Nuclear Dynamics and Role of the Cytoskeleton During Asymmetric Division of Pollen Mitosis I in Nicotiana Benthamiana.

Pollen is a male gametophyte of angiosperms. Following meiosis, the microspore undergoes an asymmetric division called pollen mitosis I (PMI), which produces two cells of different sizes: a large vegetative cell and a small generative cell. Polarized nuclear migration and positioning during PMI are important for successful pollen development and cell differentiation.

Trinuclear rare earth pyridyl-β-diketonate complexes: developing new methods towards finding lost toroidal spin states.

A series of rare earth (RE) 'triangles' have been synthesised to investigate the low energy excitations of toroic molecules using inelastic neutron scattering (INS) experiments. β-Diketonate, 1-(2-pyridinyl)-1,3-butandione (-pbdH) has been employed to synthesise [{Ho(O)(-pbd)Cl(HO)}]·8Cl·3HO·0.5EtOH (1) and [{Dy(O)(-pbd)Cl(HO)}]·6Cl·2EtOH·2hexane (2).