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At least 1,711 records · Page 95

DNA Binding and Phosphorylation Regulate the Core Structure of the NF-κB p50 Transcription Factor

The NF-κB transcription factors are known to be extensively phosphorylated, with dynamic site-specific modification regulating their ability to dimerize and interact with DNA. p50, the proteolytic product of p105 (NF-κB1), forms homodimers that bind DNA but lack intrinsic transactivation function, functioning as repressors of transcription from κB promoters. Here, we examine the roles of specific phosphorylation events catalysed by either protein kinase A (PKA{sub c}) or Chk1, in regulating the functions of p50 homodimers. LC-MS/MS analysis of proteolysed p50 following in vitro phosphorylation allows us to define Ser328 and Ser337 as PKA{sub c}- and Chk1-mediated modifications, and pinpoint an additional four Chk1 phosphosites: Ser65, Thr152, Ser242 and Ser248. Native mass spectrometry (MS) reveals Chk1- and PKA{sub c}-regulated disruption of p50 homodimer formation through Ser337. Additionally, we characterise the Chk1-mediated phosphosite, Ser242, as a regulator of DNA binding, with a S242D p50 phosphomimetic exhibiting a > 10-fold reduction in DNA binding affinity. Conformational dynamics of phosphomimetic p50 variants, including S242D, are further explored using ion-mobility MS (IM-MS). Finally, comparative theoretical modelling with experimentally observed p50 conformers, in the absence and presence of DNA, reveals that the p50 homodimer undergoes conformational contraction during electrospray ionisation that is stabilised by complex formation with κB DNA. .

74 ATOMIC AND MOLECULAR PHYSICS↗

Gas-solid interfacial modification of oxygen activity in layered oxide cathodes for lithium-ion batteries

Lattice oxygen can play an intriguing role in electrochemical processes, not only maintaining structural stability, but also influencing electron and ion transport properties in high-capacity oxide cathode materials for Li-ion batteries. Here, we report the design of a gas–solid interface reaction to achieve delicate control of oxygen activity through uniformly creating oxygen vacancies without affecting structural integrity of Li-rich layered oxides. Theoretical calculations and experimental characterizations demonstrate that oxygen vacancies provide a favourable ionic diffusion environment in the bulk and significantly suppress gas release from the surface. The target material is achievable in delivering a discharge capacity as high as 301 mAh g –1 with initial Coulombic efficiency of 93.2%. After 100 cycles, a reversible capacity of 300 mAh g –1 still remains without any obvious decay in voltage. Lastly, this study sheds light on the comprehensive design and control of oxygen activity in transition-metal-oxide systems for next-generation Li-ion batteries.

25 ENERGY STORAGE↗

A Printing-Centric Approach to the Electrostatic Modification of Polymer/Clay Composites for Use in 3D Direct-Ink Writing

Polymer/clay composite inks are exceptionally useful materials for fabrication processes based on 3D direct-ink writing, however, there remains an insufficient understanding of how their physiochemical dynamics impact printability. Using a model system, N-isopropylacrylamide/Laponite, the electrostatic interactions between Laponite platelets are modified to tune critical rheological properties in order to improve printability. Rheological measurements and X-ray scattering experiments are carried out to monitor the nano/micro-structural dynamics and complex physicochemical interactions of Laponite as it impacts complex modulus in the linear region, flow behavior, thixotropy, and yield stress of the composite ink. Modification of the electrostatic interactions between platelets reduces the yield stress of the material, while maintaining a complex microstructure that allows for sufficient recovery times upon removal of stress to form stable, and thus printable, filaments. A printing-centric approach is established based on a fundamental understanding of electrostatic inter-particle interactions, harnessing the innate microstructure of Laponite in 3D direct-ink writing of composites.

Rauzan, Brittany M.↗

2'-O-methylation in mRNA disrupts tRNA decoding during translation elongation

Chemical modifications of mRNA may regulate many aspects of mRNA processing and protein synthesis. Recently, 2'-O-methylation of nucleotides was identified as a frequent modification in translated regions of human mRNA, showing enrichment in codons for certain amino acids. Here, using single-molecule, bulk kinetics and structural methods, we show that 2'-O-methylation within coding regions of mRNA disrupts key steps in codon reading during cognate tRNA selection. Our results suggest that 2'-O-methylation sterically perturbs interactions of ribosomal-monitoring bases (G530, A1492 and A1493) with cognate codon–anticodon helices, thereby inhibiting downstream GTP hydrolysis by elongation factor Tu (EF-Tu) and A-site tRNA accommodation, leading to excessive rejection of cognate aminoacylated tRNAs in initial selection and proofreading. In conclusion, our current and prior findings highlight how chemical modifications of mRNA tune the dynamics of protein synthesis at different steps of translation elongation.

59 BASIC BIOLOGICAL SCIENCES↗

Empirical modeling of the storm time innermost magnetosphere using Van Allen Probes and THEMIS data: Eastward and banana currents

Abstract The structure of storm time currents in the inner magnetosphere, including its innermost region inside 4 R E , is studied for the first time using a modification of the empirical geomagnetic field model TS07D and new data from Van Allen Probes and Time History of Events and Macroscale Interactions during Substorms missions. It is shown that the model, which uses basis‐function expansions instead of ad hoc current modules to approximate the magnetic field, consistently improves its resolution and magnetic field reconstruction with the increase of the number of basis functions and resolves the spatial structure and evolution of the innermost eastward current. This includes a connection between the westward ring current flowing largely at and the eastward ring current concentrated at resulting in a vortex current pattern. A similar pattern coined ‘banana current’ was previously inferred from the pressure distributions based on the energetic neutral atom imaging and first‐principles ring current simulations. The morphology of the equatorial currents is dependent on storm phase. During the main phase, it is complex, with several asymmetries forming banana currents. Near SYM ‐ H minimum, the banana current is strongest, is localized in the evening‐midnight sector, and is more structured compared to the main phase. It then weakens during the recovery phase resulting in the equatorial currents to become mostly azimuthally symmetric.

Stephens, G. K.↗

Red-Shifted Absorptions of Cation-Defective and Surface-Functionalized Anatase with Enhanced Photoelectrochemical Properties

Manipulating the atomic structure of semiconductors is a fine way to tune their properties. The rationalization of their modified properties is, however, particularly challenging as defects locally disrupt the long-range structural ordering, and a deeper effort is required to fully describe their structure. In this work, we investigated the photoelectrochemical properties of an anatase-type structure featuring a high content of titanium vacancies stabilized by dual-oxide substitution by fluoride and hydroxide anions. Such atomic modification induces a slight red-shift band gap energy of 0.08 eV as compared to pure TiO 2 , which was assigned to changes in titanium–anion ionocovalent bonding. Under illumination, electron paramagnetic resonance spectroscopy revealed the formation of Ti III and O 2 – radicals which were not detected in defect-free TiO 2 . Consequently, the modified anatase shows higher ability to oxidize water with lower electron–hole recombination rate. To further increase the photoelectrochemical properties, we subsequently modified the compound by a surface functionalization with N-methyl-2-pyrrolidone (NMP). This treatment further modifies the chemical composition, which results in a red shift of the band gap energy to 3.03 eV. Moreover, the interaction of the NMP electron-donating molecules with the surface induces an absorption band in the visible region with an estimated band gap energy of 2.25–2.50 eV. Under illumination, the resulting core–shell structure produces a high concentration of reduced Ti III and O 2 – , suggesting an effective charge carrier separation which is confirmed by high photoelectrochemical properties. This work provides new opportunities to better understand the structural features that affect the photogenerated charge carriers.

74 ATOMIC AND MOLECULAR PHYSICS↗

Improving nanoparticle superlattice stability with deformable polymer gels

The self-assembly of colloidal nanoparticles into ordered superlattices typically uses dynamic interactions to govern particle crystallization, as these non-permanent bonds prevent the formation of kinetically trapped, disordered aggregates. However, while the use of reversible bonding is critical in the formation of highly ordered particle arrangements, dynamic interactions also inherently make the structures more prone to disassembly or disruption when subjected to different environmental stimuli. Thus, there is typically a trade-off between the ability to initially form an ordered colloidal material and the ability of that material to retain its order under different conditions. Here, we present a method for embedding colloidal nanoparticle superlattices into a polymer gel matrix. This encapsulation strategy physically prevents the nanoparticles from dissociating upon heating, drying, or the introduction of chemicals that would normally disrupt the lattice. However, the use of a gel as the embedding medium still permits further modification of the colloidal nanoparticle lattice by introducing stimuli that deform the gel network (as this deformation in turn alters the nanoparticle lattice structure in a predictable manner). Moreover, encapsulation of the lattice within a gel permits further stabilization into fully solid materials by removing the solvent from the gel or by replacing the solvent with a liquid monomer that can be photopolymerized. This embedding method therefore makes it possible to incorporate ordered colloidal arrays into a polymer matrix as either dynamic or static structures, expanding their potential for use in responsive materials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Alkaline salt-promoted construction of hydrophilic and nitrogen deficient graphitic carbon nitride with highly improved photocatalytic efficiency

Graphitic carbon nitride (g-C 3 N 4 ) possesses fascinating merits, but its practical applications are limited by the inferior properties of limited visible-light sorption, rapid recombination of photo-excited charge carriers and low electrical conductivity. Introduction of N-defects is an efficient approach to tune its optical properties, but strategies capable of creating abundant vacancies and simultaneously maintaining the highly crystalline architecture are still limited and highly desired. In this work, a facile construction methodology was demonstrated to afford g-C 3 N 4 with abundant N vacancies, high crystallinity, a hydrophilic surface structure, a small particle size, and an increased surface area under neat and mild conditions. Furthermore, the essence of our approach lies in the treatment of the bulk g-C 3 N 4 precursor with an alkaline salt (LiN(SiMe 3 ) 2 ) with a low melting point, moderate nucleophilicity, and easy removal procedures. The unique structural properties of the afforded ND-g-C 3 N 4 allow for a significantly redshifted absorption edge and enhanced charge carrier separation, leading to superior photocatalytic hydrogen evolution performance three times that obtained by pristine g-C 3 N 4 . The modification strategy developed herein sheds light on the fabrication of g-C 3 N 4 -based materials with improved photocatalytic efficiency via efficient introduction of N defects, variation of the surface structure, and retention of the high crystallinity.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Structural evolution in crystalline MoO{sub 3} nanoparticles with tunable size

In this study MoO{sub 3} nanoparticles were prepared in porous Vycor glass by impregnation-decomposition cycles (IDC) with molybdenum(VI) 2-ethylhexanoate. X-ray diffraction data show that the nanoparticles are crystalline and are in the orthorhombic {alpha}-MoO{sub 3} phase. Raman spectroscopy data also indicate the formation of this phase. The profiles in the Raman spectra changed with the number of IDC, indicating a structural evolution of the MoO{sub 3} nanoparticles. The IDC methodology promoted a linear mass increase and allowed tuning the nanoparticle size. Analysis of HRTEM images revealed that for 3, 5 and 7 IDC, the MoO{sub 3} nanoparticle average diameters are 3.2, 3.6 and 4.2 nm. Diffuse reflectance spectroscopy indicates a consistent red shift in the band gap from 3.35 to 3.29 eV as the size increases from 3.2 to 4.2 nm. This observed red shift in the band gap of the MoO{sub 3} nanoparticles is presumably due to quantum confinement effects. - Graphical abstract: Modification of profile Raman spectra for crystalline MoO{sub 3} nanoparticles in function of the particle size. Highlights: Black-Right-Pointing-Pointer Structural evolution of the MoO{sub 3} nanoparticles as a function of the crystallite size. Black-Right-Pointing-Pointer Tunable optical properties by controlling the MoO{sub 3} nanoparticle size. Black-Right-Pointing-Pointer The impregnation-decomposition methodology allowed tuning the nanoparticle size. Black-Right-Pointing-Pointer The red shift in the band gap of the MoO{sub 3} nanoparticles is due to quantum size effect. Black-Right-Pointing-Pointer The short-distance order in MoO{sub 3} nanoparticle is function to area/volume ratio.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Enriched immersed finite element and isogeometric analysis: algorithms and data structures

Immersed finite element methods provide a convenient analysis framework for problems involving geometrically complex domains, such as those found in topology optimization and microstructures for engineered materials. However, their implementation remains a major challenge due to, among other things, the need to apply nontrivial stabilization schemes and generate custom quadrature rules. This article introduces the robust and computationally efficient algorithms and data structures comprising an immersed finite element preprocessing framework. The input to the preprocessor consists of a background mesh and one or more geometries defined on its domain. The output is structured into groups of elements with custom quadrature rules formatted such that common finite element assembly routines may be used without or with only minimal modifications. The key to the preprocessing framework is the construction of material topology information, concurrently with the generation of a quadrature rule, which is then used to perform enrichment and generate stabilization rules. While the algorithmic framework applies to a wide range of immersed finite element methods using different types of meshes, integration, and stabilization schemes, the preprocessor is presented within the context of the extended isogeometric analysis. This method utilizes a structured B-spline mesh, a generalized Heaviside enrichment strategy considering the material layout within individual basis functions’ supports, and face-oriented ghost stabilization. Using a set of examples, the effectiveness of the enrichment and stabilization strategies is demonstrated alongside the preprocessor’s robustness in geometric edge cases. Additionally, the performance and parallel scalability of the implementation are evaluated.

Computer implementation↗

Influence of the hyperfine structure of the atomic states on the collective effects in the Rb{sub 2} quasi-molecule

A consistent quantum approach is used to study the influence of intraatomic spin–orbit and hyperfine interactions on the character of a resonance dipole–dipole interatomic interaction and, hence, collective effects. For this purpose, the collective spontaneous decay of excited states and the spectral dependence of the total scattering cross section of a monochromatic light wave are analyzed in the system consisting of two rubidium-87 atoms. The modification of the radiation properties and the interaction of the atoms with external radiation are studied as functions of the interatomic distance. The presence of a complex structure of the sublevels of both the ground and excited states is shown to modify the collective effects substantially as compared to the case when this structure is absent.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

A Trichomonas vaginalis C2-XYPPX-repeat protein with a structured C2 domain displaying dampened flexibility upon binding calcium

C2 domains are ubiquitous membrane-binding modules of ∼130 residues in eukaryotes that are often associated with proteins involved in membrane trafficking and lipid modification. The genome of Trichomonas vaginalis, the most common, non-viral, sexually transmitted human pathogen, encodes eight genes that contain a N-terminal C2 module linked to a XYPPX-repeat domain of more than four XYPPX repeats (C2-XYPPX). While the function of the XYPPX-repeat domain remains unknown, its multiple association with C2 domains in T. vaginalis suggests it is important. Here, the C2 domain from one of these C2-XYPPX-repeat proteins, Tv-C2-1, was structurally and physically characterized using X-ray crystallography and NMR spectroscopy. The crystal structure for Tv-C2-1 shows that this domain shares a fold common to all C2 domains, a compact Greek-key motif composed of eight anti-parallel β-strands in the type-2 topology. An NMR chemical shift perturbation study with Ca 2+ showed that Tv-C2-1 bound two Ca 2+ atoms primarily via two loops (loop-1 and loop-3) on the predicted calcium binding face of the protein with K d s of 58.0 ± 0.1 μM and 232 ± 6 μM. Estimations of the overall rotational correlation time, τ c , in the apo (11.1 ns) and Ca 2+ -bound (9.2 ns) state suggests the protein becomes more compact upon Ca 2+ binding, consistent with a decrease in dynamics in loop-3 and marginally in loop-1 suggested by amide 15 N heteronuclear steady-state { 1 H}- 15 N NOEs. Showing Tv-C2-1 binds calcium and adopts a compact Greek-key motif structure, two primary features of C2 domains, suggests understanding the function of the XYPPX-repeat domain may be warranted.

NMR spectroscopy↗

Surface Induced Dissociation Coupled with High Resolution Mass Spectrometry Unveils Heterogeneity of a 211 kDa Multicopper Oxidase Protein Complex

Manganese oxidation is an important biogeochemical process that is largely regulated by bacteria through enzymatic reactions. However, the detailed mechanism is poorly understood due to challenges in isolating and characterizing these unknown enzymes. A manganese oxidase, Mnx, from Bacillus sp. PL-12 has been successfully overexpressed in active form as a protein complex with a molecular mass of 211 kDa. We have recently used surface induced dissociation (SID) and ion mobility-mass spectrometry (IM-MS) to release and detect folded subcomplexes for determining subunit connectivity and quaternary structure. The data from the native mass spectrometry experiments led to a plausible structural model of this multicopper oxidase, which has been difficult to study by conventional structural biology methods. It was also revealed that each Mnx subunit binds a variable number of copper ions. Becasue of the heterogeneity of the protein and limited mass resolution, ambiguities in assigning some of the observed peaks remained as a barrier to fully understanding the role of metals and potential unknown ligands in Mnx. In this study, we performed SID in a modified Fourier transform-ion cyclotron resonance (FTICR) mass spectrometer. The high mass accuracy and resolution offered by FTICR unveiled unexpected artificial modifications on the protein that had been previously thought to be iron bound species based on lower resolution spectra. Additionally, isotopically resolved spectra of the released subcomplexes revealed the metal binding stoichiometry at different structural levels. This method holds great potential for in-depth characterization of metalloproteins and protein–ligand complexes. .

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Comparative transcriptomics of CAZy enzymes in white- and brown-rot agaricomycetes: Evolutionary insights into lignocellulose degradation and the relevance of GH16 glycoside hydrolase functional divergence

White-rot and brown-rot fungi (WRF and BRF, respectively) decompose lignocellulose, the main structural component of plant biomass, through distinct mechanisms. This study examines the transcriptomic responses of three WRF species (Pleurotus ostreatus, Phanerochaete chrysosporium, and Heterobasidion irregulare) and two BRF species (Fomitopsis schrenkii and Rhodonia placenta) grown on poplar wood (W) and glucose (G) as sole carbon sources. RNA-seq analysis revealed upregulation of carbohydrate-active enzymes (CAZymes) linked to lignocellulose degradation. WRF displayed a broader enzymatic repertoire, whereas BRF employed a more selective approach. Among these responses, GH16 glycoside hydrolases were consistently upregulated across all species, including BRF. Since GH16 enzymes are involved in both plant hemicellulose modification and cell wall remodeling, their wood-induced expression may reflect multiple processes rather than a single conserved wood-decay mechanism. Structural and phylogenetic analyses revealed species-specific divergence, consistent with potential functional specialization. These findings broaden our understanding of fungal enzymatic strategies and highlight GH16 enzymes as candidates for further study. Beyond the immediate context of wood decay, this work has broader implications for fungal ecology, evolutionary biology, and biotechnological applications such as biomass conversion and sustainable bioenergy.

Fungal ecological strategies↗

Improved electrochemical and thermal performances of layered Li[Li 0.2 Ni 0.17 Co 0.07 Mn 0.56 ]O 2 via Li 2 ZrO 3 surface modification

We successfully coated a conductive Li 2 ZrO 3 layer on the surface of Li-rich layered cathode Li[Li 0.2 Ni 0.17 Co 0.07 Mn 0.56 ]O 2 in order to enhance its electrochemical performances. For the crystal structures, electrochemical properties and thermal stabilities of the bare and coated materials are studied by X-ray diffraction (XRD), field emission scanning electron microscopy (FESEM), high resolution transmission electron microscopy (HRTEM), electron diffraction spectroscopy (EDS), inductively coupled plasma (ICP), galvanostatic cycling, cyclic voltammetry (CV), electrochemical impedance spectroscopy (EIS), Fourier transform infrared spectroscopy (FTIR) and differential scanning calorimetry (DSC). We found that the electrochemical performances of Li-rich cathode material are obviously improved by Li 2 ZrO 3 surface modification. Especially, the 1 wt.% Li 2 ZrO 3 -coated material demonstrates the best cycling performance, with capacity retention of 89% after 50 cycles, much better than that of the pristine one, 64%. Intensive explorations indicate that the improved electrochemical properties can be attributed to the Li 2 ZrO 3 surface layer, which not only stabilizes the cathode structure by decreasing the loss of oxygen, but also protects the Li-rich cathode material from side reaction(s) with the electrolyte and thus suppressing the fast growth of solid electrolyte interface (SEI) film on the surface of oxide particles.

25 ENERGY STORAGE↗

On the structural affinity of macromolecules with different biological properties: Molecular dynamics simulations of a series of TEM-1 mutants

Highlights: •We have performed molecular dynamics simulations of TEM-1 mutants. •Mutations effects on the mechanical properties are considered. •Mutants do not significantly alter the average enzymes structure. •Mutants produce sharp alterations in enzyme conformational repertoire. •Mutants also produce changes in the active site volume. -- Abstract: Molecular Dynamics simulations have been carried out in order to provide a molecular rationalization of the biological and thermodynamic differences observed for a class of TEM β-lactamases. In particular we have considered the TEM-1(wt), the single point mutants TEM-40 and TEM-19 representative of IRT and ESBL classes respectively, and TEM-1 mutant M182T, TEM-32 and TEM-20 which differ from the first three for the additional of M182T mutation. Results indicate that most of the thermodynamic, and probably biological behaviour of these systems arise from subtle effects which, starting from the alterations of the local interactions, produce drastic modifications of the conformational space spanned by the enzymes. The present study suggests that systems showing essentially the same secondary and tertiary structure may differentiate their chemical–biological activity essentially (and probably exclusively) on the basis of the thermal fluctuations occurring in their physiological environment.

60 APPLIED LIFE SCIENCES↗

Bottom-Up Meets Top-Down: The Crossroads of Multiscale Chromatin Modeling

Chromatin can be viewed as a hierarchically structured fiber that regulates gene expression. It consists of a complex network of DNA and proteins whose characteristic dynamical modes facilitate compaction and rearrangement in the cell nucleus. These modes stem from chromatin's fundamental unit, the nucleosome, and their effects are propagated across length scales. Understanding the effects of nucleosome dynamics on the chromatin fiber, primarily through post-translational modifications that occur on the histones, is of central importance to epigenetics. Within the last decade, imaging and chromosome conformation capture techniques have revealed a number of structural and statistical features of the packaged chromatin fiber at a hitherto unavailable level of resolution. Such experiments have led to increased efforts to develop polymer models that aim to reproduce, explain, and predict the contact probability scaling and density heterogeneity. At nanometer scales, available models have focused on the role of the nucleosome and epigenetic marks on local chromatin structure. At micrometer scales, existing models have sought to explain scaling laws and density heterogeneity. Less work, however, has been done to reconcile these two approaches: bottom-up and top-down models of chromatin. Here, we highlight the multiscale simulation models that are driving toward an understanding of chromatin structure and function, from the nanometer to the micron scale, and we highlight areas of opportunity and some of the prospects for new frameworks that bridge these two scales. Taken together, experimental and modeling advances over the last few years have established a robust platform for the study of chromatin fiber structure and dynamics, which will be of considerable use to the chromatin community in developing an understanding of the interplay between epigenomic regulation and molecular structure.

59 BASIC BIOLOGICAL SCIENCES↗

Reconfigurable Pinwheel Artificial-Spin-Ice and Superconductor Hybrid Device

The ability to control the potential landscape in a medium of interacting particles could lead to intriguing collective behavior and innovative functionalities. In this work, we utilize spatially reconfigurable magnetic potentials of a pinwheel artificial-spin-ice (ASI) structure to tailor the motion of superconducting vortices. The reconstituted chain structures of the magnetic charges in the pinwheel ASI and the strong interaction between magnetic charges and superconducting vortices allow significant modification of the transport properties of the underlying superconducting thin film, resulting in a reprogrammable resistance state that enables a reversible and switchable vortex Hall effect. Our results highlight an effective and simple method of using ASI as an in situ reconfigurable nanoscale energy landscape to design reprogrammable superconducting electronics, which could also be applied to the in situ control of properties and functionalities in other magnetic particle systems, such as magnetic skyrmions.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗