Domain Dynamics Research Articles

Impact of the Lead‐Free Crystal Matrix 0.94NBaTiO3‐0.06SrTiO3 on the Photoluminescence Properties of Eu+3

The investigation reveals that the crystal field environment induces photoluminescence in Eu3+. These synthesized materials hold promise for a wide array of commercial applications, particularly in the light emitting diode industry, representing a significant advancement for the current generation of technology. The lead‐free electroceramics 0.94NB1−xEuxTiO3‐0.06SrTiO3 (x = 0 and x = 0.1) are fabricated using the conventional solid‐state reaction technique. Within these ceramics, both rhombohedral (R3c) and tetragonal (P4mm) structural phases coexist. The structural conformation and fluctuations in average grain size indicate the successful substitution of Eu3+ in 0.94NB1−xTiO3‐0.06SrTiO3 (x = 0). The incorporation of Eu3+ ions into the host matrix induces a long‐range ferroelectric state, marked by a rhombohedral (R3c) distortion, alongside enhanced tetragonal (P4mm) features. This structural modification results from the interaction between the Eu3+ ions and the host lattice, which fosters the emergence of a ferroelectric polarization. The coexistence of rhombohedral and tetragonal symmetries suggests a complex interplay of phases that collectively enhance the material's ferroelectric properties, potentially offering new avenues for applications in electronic and optical devices. Notably, compared to 0.94NB1−xEuxTiO3‐0.06SrTiO3 with (x = 0), the coercive field (Ec) significantly improves, while remanent polarization decreases in the presence of Eu3+. The domain orientation, particularly in Stage‐C, demonstrates a pronounced scaling behavior, which can be attributed to the crystal field surrounding the Eu3+ ions. This interaction influences the material's domain dynamics, enhancing its electromechanical properties. As a result, both of these lead‐free ceramics exhibit considerable potential for future electroceramic applications, offering a promising alternative in environmentally sustainable technologies.

Ferroelectric Domain Modulation with Tip-Poling Engineering in BiFeO3 Films

BiFeO3 (BFO) films with ferroelectricity are the most promising candidates regarding the next generation of storage devices and sensors. The comprehensive understanding of ferroelectric switchable properties is challenging and critical to robust domain wall nanoelectronics. Herein, the domain dynamic was explored in detail under external bias conditions using scanning probe microscopy, which is meaningful for the understanding of domain dynamics and the foundation of ferroelectric devices. The results show that domain reversal occurred under external electric fields with sufficient energy excitation, combined with the existence of a charged domain wall. These findings extend the domain dynamic and current paths in ferroelectric films and shed light on the potential applications for ferroelectric devices.

Interaction Dynamics of Plant-Specific Insert Domains from Cynara cardunculus: A Study of Homo- and Heterodimer Formation.

Plant aspartic proteinases (APs) from Cynara cardunculus feature unique plant-specific insert (PSI) domains, which serve as essential vacuolar sorting determinants, mediating the transport of proteins to the vacuole. Although their role in vacuolar trafficking is well established, the exact molecular mechanisms that regulate PSI interactions and functions remain largely unknown. This study explores the ability of PSI A and PSI B to form homo- and heterodimers using a combination of pull-down assays, the mating-based split-ubiquitin system (mbSUS), and FRET-FLIM analyses. Pull-down assays provided preliminary evidence of potential PSI homo- and heterodimer formation. This was conclusively validated by the more robust in vivo mbSUS and FRET-FLIM assays, which clearly demonstrated the formation of both homo- and heterodimers between PSI A and PSI B within cellular environments. These findings suggest that PSI dimerization is related to their broader functional role, particularly in protein trafficking. Results open new avenues for future research to explore the full extent of PSI dimerization and its implications in plant cellular processes.

Human Vision as A Multi-Circuit Mathematical Model of the Automated Control System

Abstract The paper contains a proposal an original, extended mathematical model of an automatic system of human vision reaction to a forcing light pulse. A comprehensive mathematical model of the vision process was proposed in the form of an equation described in the frequency (dynamics) domain. Mathematical modelling of human senses is very important. It enables better integration of automation systems with a human cooperating with them, also as an automation system. This provides the basis for reasoning based on a mathematical model instead of intuitive reasoning about human reactions to visual stimuli. A block diagram of the proposed system with five human reaction paths is given. The following can be distinguished in the scheme: the main track consisting of: the transport delay of the eye reaction, the transport delay of the afferent nerves, the inertia of the brain with a preemptive action, the transport delay of the centrifugal nerves and the inertial and transport delay of the neuromotor system. In addition, the scheme of the system includes four tracks of negative feedback of motor and force reactions: upper eyelid, lower eyelid, pupil and lens. In the proposed model, the components of each path along with their partial mathematical models are given and discussed. For each reaction path, their overall mathematical models are also given. Taking into account the comprehensive models of all five reaction paths, a complete mathematical model of the automatic system of human reaction to a forcing light impulse is proposed. The proposed mathematical model opens up many possibilities for synchronizing it with mathematical models of many mechatronics and automation systems and their research. Optimizing the parameters of this model and its synchronization with specific models of automation systems is difficult and requires many numerical experiments. This approach enables the design of automation systems that are better synchronized with human reactions to existing stimuli and the selection of optimal parameters of their operation already in the design phase. The proposed model allows, for example, accurate determination of difficulty levels in computer games. Another example of the use of the proposed model is the study of human reactions to various situations generated virtually, for example in flight simulators and other similar ones.

Imaging in-operando LiCoO2 nanocrystallites with Bragg coherent X-ray diffraction

Although the LiCoO2 (LCO) cathode material has been widely used in commercial lithium ion batteries (LIB) and shows high stability, LIB’s improvements have several challenges that still need to be overcome. In this paper, we have studied the in-operando structural properties of LCO within battery cells using Bragg Coherent X-ray Diffraction Imaging to identify ways to optimise the LCO batteries’ cycling. We have successfully reconstructed the X-ray scattering phase variation (a fingerprint of atomic displacement) within a ≈ (1.6 × 1.4 × 1.3) μm3 LCO nanocrystal across a charge/discharge cycle. Reconstructions indicate strained domains forming, expanding, and fragmenting near the surface of the nanocrystal during charging, with a determined maximum relative lattice displacements of 0.467 Å. While discharging, all domains replicate in reverse the effects observed from the charging states, but with a lower maximum relative lattice displacements of 0.226 Å. These findings show the inefficiency-increasing domain dynamics within LCO lattices during cycling.

The Copenhagen School’s widening security theory in relation to cybersecurity. Applicability and Implications

This paper critically examines the relationship between cybersecurity and Copenhagen School’s widening security theory, with the aim of assessing the possibility of applying this theoretical framework to the cyber realm. As cybersecurity is a relatively recent addition to the security discourse, this research explores whether the Copenhagen School’s traditional framework, which was primarily focused on securitisation processes in the five main sectors (military, political, economic, environmental, and societal), adequately encompasses the unique aspects and dynamics of cyber domain. The research question is: Why the cybersecurity field can’t become a separate constructivist sector? The study begins with a detailed overview of both cybersecurity landscape and Copenhagen School’s fundamental principles to provide the context for a comparative analysis of the Copenhagen theory and contemporary cybersecurity literature. In doing so, the research delves into the features of cybersecurity, with a focus on the evolving nature of cyber threats and vulnerabilities. By performing a qualitative analysis of the existing literature, the paper assesses the limitations of integrating these two concepts, ultimately concluding that cybersecurity lacks the distinct characteristics required to be considered a separate sector under the Copenhagen School’s framework. The findings contribute to the ongoing discussions regarding the adaptation of traditional security theories to address contemporary security challenges in the digital age.

Probing ferroelectric phase transitions in barium titanate single crystals via in situ second harmonic generation microscopy

Ferroelectric materials play a crucial role in a broad range of technologies due to their unique properties that are deeply connected to the pattern and behavior of their ferroelectric (FE) domains. Chief among them, barium titanate (BaTiO3; BTO) sees widespread applications such as in electronics but equally is a ferroelectric model system for fundamental research, e.g., to study the interplay of such FE domains, the domain walls (DWs), and their macroscopic properties, owed to BTO’s multiple and experimentally accessible phase transitions. Here, we employ Second Harmonic Generation Microscopy (SHGM) to in situ investigate the cubic-to-tetragonal (at ∼126°C) and the tetragonal-to-orthorhombic (at ∼5°C) phase transition in single-crystalline BTO via three-dimensional (3D) DW mapping. We demonstrate that SHGM imaging provides the direct visualization of FE domain switching as well as the domain dynamics in 3D, shedding light on the interplay of the domain structure and phase transition. These results allow us to extract the different transition temperatures locally, to unveil the hysteresis behavior, and to determine the type of phase transition at play (first/second order) from the recorded SHGM data. The capabilities of SHGM in uncovering these crucial phenomena can easily be applied to other ferroelectrics to provide new possibilities for in situ engineering of advanced ferroic devices.

Domain Dynamics Response to Polarization Switching in Relaxor Ferroelectrics.

Nanoscale polar regions, or nanodomains (NDs), are crucial for understanding the domain structure and high susceptibility of relaxors. However, unveiling the evolution and function of NDs during polarization switching at the microscopic level is of great challenge. The experimental in situ characterization of NDs under electric-field perturbations, and computational accurate prediction of the dipole switching within a sufficiently large supercell, are notoriously tricky and tedious. These difficulties hinder a full understanding of the link between micro domain dynamics and macro polarization switching. Herein, the real-time evolution of NDs at the nanoscale is observed and visualized during polarization switching in an exemplary relaxor system of Bi5- xLaxMg0.5Ti3.5O15. Two fundamentally different domain switching pathways and dynamic characteristics are revealed: one steep, bipolar-like switching between two degenerate polarization states; and another flat, multi-step switching process with a thermodynamically stable non-polar mesophase mediating the degenerate polarization states. The two are determined by the distinct Landau energy landscapes that are strongly dependent on the intrinsic domain configurations and interdomain interactions. This work bridges the gap between micro domain dynamics and macro polarization switching, providing a guiding principle for the strategic design and optimization of relaxors.

Adaptive support constraint based on pixel difference distribution for twin-image removal in in-line holography

A tight support domain can enhance the reconstruction effect of phase retrieval algorithms using a support domain constraint. Hence, an adaptive support method based on pixel difference distribution to calculate a more accurate support domain is proposed in this paper. The support domain is continuously updated at each iteration of the phase retrieval algorithm, resulting in a support domain that closely corresponds to the shape and size of the object. Simulations are conducted to investigate the reconstruction effect of complex-valued objects as well as the influence of varying the binarization threshold and the difference window size on the convergence performance in the absence of noise. The changing dynamics of the support domain during the iterative process are also showcased. The experiments demonstrate that the adaptive support method can improve the reconstruction image quality and image contrast under actual conditions. Both simulations and experiments affirm the feasibility of this approach.

Cooperative dynamics of PARP-1 zinc-finger domains in the detection of DNA single-strand breaks

The DNA single-strand break (SSB) repair pathway is initiated by the multifunctional enzyme PARP-1, which recognizes the broken DNA ends by its two zinc-finger domains, Zn1 and Zn2. Despite a number of experiments performed with different DNA configurations and reduced fragments of PARP-1, many details of this interaction that is crucial to the correct initiation of the repair chain are still unclear. We performed Molecular Dynamics (MD) computer simulations of the interaction between the Zn1/Zn2 domains of PARP-1 and a DNA hairpin including a missing nucleotide to simulate the presence of an SSB, a construct used in recent experiments. The role of Zn1 and Zn2 interacting with the SSB ends is studied in detail, both independently and cooperatively. We also explored, PARP-1 operating as a dimer, with the two Zn-fingers coming from two separate copies of the enzyme. By an extensive set of all-atom molecular simulations employing state-of-the art force fields, assisted by empirical docking and free-energy calculations, we conclude that the particular conformation of the DNA hairpin can indeed spontaneously open up by thermal fluctuations, up to extremely kinked deformations. However, such extreme localized deformations are rarely observed in free, long DNA fragments. Protein side-loops make contact with the DNA hairpin grooves, and help Zn2 to penetrate deep in the SSB gap. In this way, Zn2 can interact with the nucleotides opposite to the missing base. Overall, Zn1 plays a secondary role: the crucial factor for the interaction is rather the relative arrangement of the Zn1/Zn2 couple, and their mutual orientation with respect to the 3′\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$3'$$\\end{document} and 5′\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$5'$$\\end{document} SSB end terminals. This helps to obtain an early interacting configuration, which ultimately leads to molecular PARP-1-DNA structures similar to those observed experimentally. Such findings represent an important step toward defining the detailed function of PARP-1 in the early stages of SSB recognition.

Mental health at the intersections: understanding South Asian Muslim youth mental health in Peel Region, Toronto, Canada

Purpose The purpose of this study was to understand the unique mental health concerns and access barriers experienced by South Asian Muslim youth populations living in the Peel Region of Toronto, Canada. Design/methodology/approach For this qualitative exploratory study, interviews (n = 15) were conducted with mental health professionals, educators and spiritual leaders (n = 11) who work with South Asian Muslim youth living in Peel Region, as well as with South Asian Muslim youth themselves (n = 4, aged 20–23). Interview transcripts were analyzed using reflexive thematic analysis. Findings Four primary themes emerged from the data: challenges and stressors, barriers, facilitators and hope and recovery. South Asian Muslim youth navigate a number of unique stressors related to the domains of culture, religion and family dynamics, as well as the impact of migration. Practical implications The findings stress the necessity of creating culturally safe, multilevel strategies to meet the nuanced challenges and diverse needs of South Asian Muslim youth communities. Originality/value This is one of the few papers to the knowledge that addresses the mental health needs and service access barriers of youth populations at the intersections of South Asian diasporic community belonging and Muslim faith in Canada.

Quantitative Assessment of Conformational Heterogeneity in Apolipoprotein E4 Using Hydrogen-Deuterium Exchange Mass Spectrometry.

Apolipoprotein E4 (apoE4) is the strongest genetic risk factor for Alzheimer's disease (AD). However, structural differences between apoE4 and the AD-neutral isoform, apoE3, still remain unclear. Recent studies suggest that apoE4 harbors intermediates. However, the biophysical properties and isoform specificity of these intermediates are not known. Here, we use the kinetics of hydrogen-deuterium exchange by mass spectrometry (HDX-MS) to examine the conformational heterogeneities in apoE3 and apoE4. First, we use numerical simulations to compute the HDX-mass spectra of a protein following mixed EX1/EX2 kinetics. The results indicate that in the presence of EX1 kinetics, which is an indicator of conformational heterogeneity, time evolution of the standard deviation (σ(t)) of the spectra exhibits a clear peak, which is dependent on the number of residues (NEX1) and the rate constant of EX1 kinetics (kEX1). Then, we performed experiments with several variants of the apoE proteins and compared them with simulation to estimate NEX1 and kEX1. Kinetics of the mean deuteration is found to be faster for apoE4, consistent with its poorer stability than apoE3. Importantly, in the case of apoE4, σ(t) exhibits a clear peak at t ∼ 60 s, but apoE3 shows only a small peak at 1800 s. Therefore, both NEX1 and kEX1 are larger for apoE4, indicating greater conformational heterogeneity. Notably, the partial EX1 kinetics is observed in both the isolated N-terminal fragment and the full-length form of apoE4, although it is more pronounced in the full-length protein. Moreover, it is enhanced at higher pH and in the presence of bis-ANS. Mutations such as R61T and R112I diminish the EX1 kinetics, making apoE4 behave more like apoE3. Thus, the amino acid substitution at position 112 alters the structural dynamics of the N-terminal domain of apoE4; the changes are further propagated and amplified in the full-length protein. We conclude that HDX-MS is a label-free and robust methodology to characterize structural heterogeneities of proteins even under native conditions. This opens opportunities for screening of the "structure corrector" drug molecules that could convert apoE4 to apoE3-like.

Transcribing RNA polymerases: Dynamics of twin supercoiled domains

Gene transcription by an RNA polymerase (RNAP) enzyme requires that double-stranded DNA be locally and transiently opened, which results in an increase of DNA supercoiling downstream of the RNAP and a decrease of supercoiling upstream of it. When the DNA is initially torsionally relaxed and the RNAP experiences sufficiently large rotational drag, these variations lead to positively supercoiled plectonemes ahead of the RNAPs and negatively supercoiled ones behind it, a feature known as “twin supercoiled domain” (TSD). This work aims at deciphering into some more detail the torsional dynamics of circular DNA molecules being transcribed by RNAP enzymes. To this end, we performed Brownian dynamics simulations with a specially designed coarse-grained model. Depending on the superhelical density of the DNA molecule and the ratio of RNAP’s twist injection rate and rotational relaxation speed, simulations reveal a rich panel of behaviors, which sometimes differ markedly from the crude TSD picture. In particular, for sufficiently slow rotational relaxation speed, positively supercoiled plectonemes never form ahead of an RNAP that transcribes a DNA molecule with physiological negative supercoiling. Rather, negatively supercoiled plectonemes form almost periodically at the upstream side of the RNAP and grow up to a certain length before detaching from the RNAP and destabilizing rapidly. The extent to which topological barriers hinder the dynamics of TSDs is also discussed.

Structure and Dynamics of the CCCH-Type Tandem Zinc Finger Domain of POS-1 and Implications for RNA Binding Specificity.

CCCH-type tandem zinc finger (TZF) motifs are found in many RNA-binding proteins involved in regulating mRNA stability, translation, and splicing. In Caenorhabditis elegans, several RNA-binding proteins that regulate embryonic development and cell fate determination contain CCCH TZF domains, including POS-1. Previous biochemical studies have shown that despite high levels of sequence conservation, POS-1 recognizes a broader set of RNA sequences compared to the human homologue tristetraprolin. However, the molecular basis of these differences remains unknown. In this study, we refined the consensus RNA sequence and determined the differing binding specificities of the two zinc fingers of POS-1. We also determined the solution structure and characterized the internal dynamics of the TZF domain of POS-1. From the structure, we identified unique features that define the RNA binding specificity of POS-1. We also observed that the TZF domain of POS-1 is in equilibrium between interconverting conformations. Transitions between these conformations require internal motions involving many residues with correlated dynamics in each ZF. We propose that the correlated dynamics are necessary to allow allosteric communication between the nucleotide-binding pockets observed in the N-terminal ZF. Our study shows that both the structure and conformational plasticity of POS-1 are important in ensuring recognition of its RNA binding targets.

Mimicking Antiferroelectrics with Ferroelectric Superlattices.

Antiferroelectric oxides are promising materials for applications in high-density energy storage, solid-state cooling, and negative capacitance devices. However, the range of oxide antiferroelectrics available today is rather limited. In this work, it is demonstrated that antiferroelectric properties can be electrostatically engineered in artificially layered ferroelectric superlattices. Using a combination of synchrotron X-ray nanodiffraction, scanning transmission electron microscopy, macroscopic electrical measurements, and lateral and vertical piezoresponse force microscopy in parallel-plate capacitor geometry, a highly reversible field-induced transition is observed from a stable in-plane polarized state to a state with in-plane and out-of-plane polarized nanodomains that mimics, at the domain level, the nonpolar to polar transition of traditional antiferroelectrics, with corresponding polarization-voltage double hysteresis and comparable energy storage capacity. Furthermore, it is found that such superlattices exhibit large out-of-plane dielectric responses without involving flux-closure domain dynamics. These results demonstrate that electrostatic and strain engineering in artificially layered materials offers a promising route for the creation of synthetic antiferroelectrics.

Understanding the stability and dynamics of influenza a H5N1 polymerase PB2 CAP-Binding domain in complex with natural compounds for antiviral drug discovery

Influenza A virus, particularly the H5N1 strain, poses a significant threat to public health due to its ability to cause severe respiratory illness and its high mortality rate. Traditional antiviral drugs targeting influenza A virus have faced challenges such as drug resistance and limited efficacy. Therefore, new antiviral compounds are needed to be discovered and developed. This study concentrated on examining the stability and behavior of the H5N1 polymerase PB2 CAP-binding domain when interacting with natural compounds, aiming to identify potential candidates for antiviral drug discovery. Through the virtual screening process, four lead compounds, ZINC000096095464, ZINC000044404209, ZINC000001562130, and ZINC000059779788, were selected, and these compounds showed binding energies −9.6, −9.4, −9.3, and −9.2 kcal/mol, respectively. When complexed with PB2, the ligand showed acceptable binding stability due to significant bond formation. However, during the 200ns MD simulation analysis, three (ZINC000096095464, ZINC000044404209, and ZINC000059779788) showed significant stability, which was proven by the trajectory analysis. The Rg-RMSD-based FEL plot showed significant structural stability due to stable conformers. The free-binding energy calculation also validates the stability of these complexes. This study offers valuable insights into the stability and dynamics of the H5N1 polymerase PB2 CAP-binding domain in complexes with natural compounds. These findings highlight the potential of these natural compounds as antiviral agents against the H5N1 influenza virus. Furthermore, this research contributes to the broader field of influenza virus treatment by demonstrating the effectiveness of computational methods in predicting and evaluating the stability and dynamics of potential drug candidates.

Structural, electrical, and dynamic scaling behavior of Ba0.85Ca0.15Zr0.10Ti0.90O3 nanoceramics synthesized at low temperature by sonochemical method

In contrast to lead-based materials, lead-free ceramics Ba0.85Ca0.15Zr0.10Ti0.90O3 (BCZT) offer outstanding dielectric, ferroelectric, and piezoelectric properties. A novel sonochemical method is employed to synthesize BCZT at low temperatures. The impact of high-energy acoustic waves reduces the calcination temperature to 600 °C, which is 300–400 °C lower than the already reported values. The samples are further sintered at different temperatures. The BCZT shows good dielectric properties (εr ∼3000 and tanδ ∼0.075 at 1 kHz) at room temperature. X-ray diffraction analysis shows the co-existence of tetragonal and orthorhombic phases. Further, the scaling behavior is studied for domain dynamics in the sample. A three-stage polarization reversal mechanism is observed in BCZT ceramics. From the systematic study of the domain reversal mechanism, BCZT appears to be a promising candidate for sensors and actuator applications.

Utilizing biological experimental data and molecular dynamics for the classification of mutational hotspots through machine learning.

Benzo[a]pyrene, a notorious DNA-damaging carcinogen, belongs to the family of polycyclic aromatic hydrocarbons commonly found in tobacco smoke. Surprisingly, nucleotide excision repair (NER) machinery exhibits inefficiency in recognizing specific bulky DNA adducts including Benzo[a]pyrene Diol-Epoxide (BPDE), a Benzo[a]pyrene metabolite. While sequence context is emerging as the leading factor linking the inadequate NER response to BPDE adducts, the precise structural attributes governing these disparities remain inadequately understood. We therefore combined the domains of molecular dynamics and machine learning to conduct a comprehensive assessment of helical distortion caused by BPDE-Guanine adducts in multiple gene contexts. Specifically, we implemented a dual approach involving a random forest classification-based analysis and subsequent feature selection to identify precise topological features that may distinguish adduct sites of variable repair capacity. Our models were trained using helical data extracted from duplexes representing both BPDE hotspot and nonhotspot sites within the TP53 gene, then applied to sites within TP53, cII, and lacZ genes. We show our optimized model consistently achieved exceptional performance, with accuracy, precision, and f1 scores exceeding 91%. Our feature selection approach uncovered that discernible variance in regional base pair rotation played a pivotal role in informing the decisions of our model. Notably, these disparities were highly conserved among TP53 and lacZ duplexes and appeared to be influenced by the regional GC content. As such, our findings suggest that there are indeed conserved topological features distinguishing hotspots and nonhotpot sites, highlighting regional GC content as a potential biomarker for mutation. Code for comparing machine learning classifiers and evaluating their performance is available at https://github.com/jdavies24/ML-Classifier-Comparison, and code for analysing DNA structure with Curves+ and Canal using Random Forest is available at https://github.com/jdavies24/ML-classification-of-DNA-trajectories.

NMR Dynamic View of the Stabilization of the WW4 Domain by Neutral NaCl and Kosmotropic Na2SO4 and NaH2PO4.

The Hofmeister series categorizes ions based on their effects on protein stability, yet the microscopic mechanism remains a mystery. In this series, NaCl is neutral, Na2SO4 and Na2HPO4 are kosmotropic, while GdmCl and NaSCN are chaotropic. This study employs CD and NMR to investigate the effects of NaCl, Na2SO4, and Na2HPO4 on the conformation, stability, binding, and backbone dynamics (ps-ns and µs-ms time scales) of the WW4 domain with a high stability and accessible side chains at concentrations ≤ 200 mM. The results indicated that none of the three salts altered the conformation of WW4 or showed significant binding to the four aliphatic hydrophobic side chains. NaCl had no effect on its thermal stability, while Na2SO4 and Na2HPO4 enhanced the stability by ~5 °C. Interestingly, NaCl only weakly interacted with the Arg27 amide proton, whereas Na2SO4 bound to Arg27 and Phe31 amide protons with Kd of 32.7 and 41.6 mM, respectively. Na2HPO4, however, bound in a non-saturable manner to Trp9, His24, and Asn36 amide protons. While the three salts had negligible effects on ps-ns backbone dynamics, NaCl and Na2SO4 displayed no effect while Na2HPO4 significantly increased the µs-ms backbone dynamics. These findings, combined with our recent results with GdmCl and NaSCN, suggest a microscopic mechanism for the Hofmeister series. Additionally, the data revealed a lack of simple correlation between thermodynamic stability and backbone dynamics, most likely due to enthalpy-entropy compensation. Our study rationalizes the selection of chloride and phosphate as the primary anions in extracellular and intracellular spaces, as well as polyphosphate as a primitive chaperone in certain single-cell organisms.

Membrane-Active Antibiotics Affect Domains in Bacterial Membranes as the First Step of Their Activity.

The need to combat antimicrobial resistance is becoming more and more pressing. Here we investigate the working mechanism of a small cationic agent, N-alkylamide 3d, by conventional and high-speed atomic force microscopy. We show that N-alkylamide 3d interacts with the membrane of Staphylococcus aureus, where it changes the organization and dynamics of lipid domains. After this initial step, supramolecular structures of the antimicrobial agent attach on top of the affected membrane gradually, covering it entirely. These results demonstrate that lateral domains in the bacterial membranes might be affected by small antimicrobial agents more often than anticipated. At the same time, we show a new dual-step activity of N-alkylamide 3d that not only destroys the lateral membrane organization but also effectively covers the whole membrane with aggregates. This final step could render the membrane inaccessible from the outside and possibly prevent signaling and waste disposal of living bacteria.