Exploring the application of piezoelectric ceramics in bone regeneration

Piezoelectric ceramics are piezoelectric materials with polycrystalline structure and have been widely used in many fields such as medical imaging and sound sensors. As knowledge about this kind of material develops, researchers find piezoelectric ceramics possess favorable piezoelectricity, biocompatibility, mechanical properties, porous structure and antibacterial effect and endeavor to apply piezoelectric ceramics to the field of bone tissue engineering. However, clinically no piezoelectric ceramics have been exercised so far. Therefore, in this paper we present a comprehensive review of the research and development of various piezoelectric ceramics including barium titanate, potassium sodium niobate and zinc oxide ceramics and aims to explore the application of piezoelectric ceramics in bone regeneration by providing a detailed overview of the current knowledge and research of piezoelectric ceramics in bone tissue regeneration.

In-silico design, pharmacophore-based screening, and molecular docking studies reveal that benzimidazole-1,2,3-triazole hybrids as novel EGFR inhibitors targeting lung cancer

Lung cancer is a complex and heterogeneous disease, which has been associated with various molecular alterations, including the overexpression and mutations of the epidermal growth factor receptor (EGFR). In this study, designed a library of 1843 benzimidazole-1,2,3-triazole hybrids and carried out pharmacophore-based screening to identify potential EGFR inhibitors. The 164 compounds were further evaluated using molecular docking and molecular dynamics simulations to understand the binding interactions between the compounds and the receptor. In-si-lico ADME and toxicity studies were also conducted to assess the drug-likeness and safety of the identified compounds. The results of this study indicate that benzimidazole-1,2,3-triazole hybrids BENZI-0660, BENZI-0125, BENZI-0279, BENZI-0415, BENZI-0437, and BENZI-1110 exhibit dock scores of -9.7, -9.6, -9.6, -9.6, -9.6, -9.6 while referencing molecule -7.9 kcal/mol for EGFR (PDB ID: 4HJO), respectively. The molecular docking and molecular dynamics simulations revealed that the identified compounds formed stable interactions with the active site of EGFR, indicating their potential as inhibitors. The in-silico ADME and toxicity studies showed that the compounds had favorable drug-likeness properties and low toxicity, further supporting their potential as therapeutic agents. Finally, performed DFT studies on the best-selected ligands to gain further insights into their electronic properties. The findings of this study provide important insights into the potential of benzimidazole-1,2,3-triazole hybrids as promising EGFR inhibitors for the treatment of lung cancer. This research opens up a new avenue for the discovery and development of potent and selective EGFR inhibitors for the treatment of lung cancer.Communicated by Ramaswamy H. Sarma.

Partitioning of an Enzyme-Polymer Surfactant Nanocomplex into Lipid-Rich Cellular Compartments Drives In Situ Hydrolysis of Organophosphates

Most organophosphates (OPs) are hydrophobic, and after exposure, can sequester into lipophilic regions within the body, such as adipose tissue, resulting in long term chronic effects. Consequently, there is an urgent need for therapeutic agents that can decontaminate OPs in these hydrophobic regions. Accordingly, an enzyme-polymer surfactant nanocomplex is designed and tested comprising chemically supercharged phosphotriesterase (Agrobacterium radiobacter; arPTE) electrostatically conjugated to amphiphilic polymer surfactant chains ([cat.arPTE][S-]). Experimentally-derived structural data are combined with molecular dynamics (MD) simulations to provide atomic level detail on conformational ensembles of the nanocomplex using dielectric constants relevant to aqueous and lipidic microenvironments. These show the formation of a compact admicelle pseudophase surfactant corona under aqueous conditions, which reconfigures to yield an extended conformation at a low dielectric constant, providing insight into the mechanism underpinning cell membrane binding. Significantly, it demonstrated that [cat.arPTE][S-] spontaneously binds to human mesenchymal stem cell membranes (hMSCs), resulting in on-cell OP hydrolysis. Moreover, the nanoconstruct can endocytose and partition into the intracellular fatty vacuoles of adipocytes and hydrolyze sequestered OP.

Molecular motion behaviors of starch affect starch-polyphenol inclusion complex and digestibility among different stilbenes polyphenol structures

Starch-polyphenol V-type inclusion complex has become a hot topic due to its anti-digestibility and nutritional function. This paper aimed to explore the molecular motion behavior of starch affects starch-polyphenol inclusion complex and digestibility among different stilbene polyphenol structures (resveratrol (RA), pterostilbene (PB) and polydatin (PD) via the high-pressure homogenization (HPH) and heat moisture treatment (HMT) processes), which represented the fully extended and limited molecular motion behavior of starch, respectively. These results revealed distinct trends in complex formation among different stilbenes polyphenol structures, highlighting RA as particularly conducive to increasing single helix and V-type crystalline structures with the highest resistant starch (RS) content of 28.11 % due to its smaller steric hindrance. Novelty, in HPH environments with extended molecular motion behavior, the steric hindrance and hydrophobicity/CH-π interactions of polyphenols influence complex formation in the order of RA > PB > PD. Conversely, in HMT systems with limited molecular motion behavior, the limited movement of molecules emphasized the importance of hydrogen bond interactions between polyphenols and starch. Thus, the glucoside in PD enhanced its interaction with starch compared to methoxy-modified PB, leading to increased formation of inclusion complex with RS content of 18.61 %. Overall, these findings deepen the understanding of starch-polyphenol interactions.

Phosphorylation of cytosolic hPGK1 affects protein stability and ligand binding: implications for its subcellular targeting in cancer

Human phosphoglycerate kinase 1(hPGK1) is a key glycolytic enzyme that regulates the balance between ADP and ATP concentrations inside the cell. Phosphorylation of hPGK1 at S203 and S256 has been associated with enzyme import from the cytosol to the mitochondria and the nucleus respectively. These changes in subcellular locations drive tumorigenesis and are likely associated with site-specific changes in protein stability. In this work, we investigate the effects of site-specific phosphorylation on thermal and kinetic stability and protein structural dynamics by hydrogen-deuterium exchange (HDX) and molecular dynamics (MD) simulations. We also investigate the binding of 3-phosphoglycerate and Mg-ADP using these approaches. We show that the phosphomimetic mutation S256D reduces hPGK1 kinetic stability by 50-fold, with no effect of the mutation S203D. Calorimetric studies of ligand binding show a large decrease in affinity for Mg-ADP in the S256D variant, whereas Mg-ADP binding to the WT and S203D can be accurately investigated using protein kinetic stability and binding thermodynamic models. HDX and MD simulations confirmed the destabilization caused by the mutation S256D (with some long-range effects on stability) and its reduced affinity for Mg-ADP due to the strong destabilization of its binding site (particularly in the apo-state). Our research provides evidence suggesting that modifications in protein stability could potentially enhance the translocation of hPGK1 to the nucleus in cancer. While the structural and energetic basis of its mitochondrial import remain unknown.

Mechanistic insights into uptake, transfer and exchange of metal ions by the three-metal clusters of a metalloprotein

Metallothioneins (MTs) are small proteins that coordinate d-block metal ions in sulfur-metal clusters to control metal ion concentrations within the cell. Here we study metal cluster formation in the MT of the periwinkle Littorina littorea (LlMT) by nuclear magnetic resonance (NMR). We demonstrate that the three Cd2+ ions in each domain are taken up highly cooperatively, that is, in an all-or-none fashion, with a four- to six-fold higher affinity for the C-terminal domain. During the transfer of metal ions from Cd2+-loaded MT to apo MT, Cd2+ is most efficiently transferred from the metalated protein to the apo C-terminal domain. This behavior might be connected to unique structural motifs in the C-terminal domain, such as two double-CXC motifs and an increased proportion of positively charged residues. In Cd2+/Zn2+ metal exchange experiments, the N-terminal domain displayed the most efficient inter-molecular metal exchange. Amide hydrogen exchange reveals fewer protected amides for the N-terminal domain, suggesting the structure might more easily "open up" to facilitate metal exchange. Experiments with a physical separation of donor and acceptor species demonstrate that metal exchange and transfer require protein-protein contacts. These findings provide insights into the mechanism of metal uptake and metal transfer, which are important processes during metal detoxification in snail MTs.

Targeting RNA with small molecules, from RNA structures to precision medicines: IUPHAR review: 40

RNA plays important roles in regulating both health and disease biology in all kingdoms of life. Notably, RNA can form intricate three-dimensional structures, and their biological functions are dependent on these structures. Targeting the structured regions of RNA with small molecules has gained increasing attention over the past decade, because it provides both chemical probes to study fundamental biology processes and lead medicines for diseases with unmet medical needs. Recent advances in RNA structure prediction and determination and RNA biology have accelerated the rational design and development of RNA-targeted small molecules to modulate disease pathology. However, challenges remain in advancing RNA-targeted small molecules towards clinical applications. This review summarizes strategies to study RNA structures, to identify small molecules recognizing these structures, and to augment the functionality of RNA-binding small molecules. We focus on recent advances in developing RNA-targeted small molecules as potential therapeutics in a variety of diseases, encompassing different modes of actions and targeting strategies. Furthermore, we present the current gaps between early-stage discovery of RNA-binding small molecules and their clinical applications, as well as a roadmap to overcome these challenges in the near future.

Insights into the Hierarchical Assembly of a Chemically Diverse Peptide Hydrogel Derived from Human Semenogelin I

A peptide corresponding to a 13-residue segment of the human protein semenogelin I has been shown to generate a hydrogel consisting of amyloid-like fibrils. The relative chemical diversity (compared to synthetic de novo sequences) with 11 distinct amino acids makes this peptide (P0) an ideal candidate for investigating the role of individual residues in gelation. Herein, the N-terminal residues have been sequentially removed to furnish a series of truncated peptides, P1-P10, ranging from 12 to 3 residues in length. FTIR spectroscopy investigations reveal that P0-P6 forms a β-sheet secondary structure while shorter sequences do not self-assemble. Site-specific isotope labeling of the amide backbone of P0-P2 with the IR-sensitive vibrational probe 13C═O yields FTIR spectra indicative of the initial formation of a kinetic product that slowly transforms into a structurally different thermodynamic product. The effects of the isotopic labels on the IR spectra facilitate the assignment of parallel and antiparallel structures, which are sometimes coexistent. Additional IR studies of three PheCN-labeled P0 sequences are consistent with an H-bonded β-sheet amide core, spanning the 7 central residues. The macromolecular assembly of peptides that form β-sheets was assessed by cryo-TEM, SAXS/WAXS, and rheology. Cryo-TEM images of peptides P1-P6 display μm-long nanofibrils. Peptides P0-P3 generate homogeneous hydrogels composed of colloidally stable nanofibrils, and P4-P6 undergo phase separation due to the accumulation of attractive interfibrillar interactions. Three amino acid residues, Ser39, Phe40, and Gln43, were identified to be of particular interest in the truncated peptide series as the removal of any one of them, as the sequence shortens, leads to a major change in material properties.

From straight to curved: A historical perspective of DNA shape

DNA is the macromolecule responsible for storing the genetic information of a cell and it has intrinsic properties such as deformability, stability and curvature. DNA Curvature plays an important role in gene transcription and, consequently, in the subsequent production of proteins, a fundamental process of cells. With recent advances in bioinformatics and theoretical biology, it became possible to analyze and understand the involvement of DNA Curvature as a discriminatory characteristic of gene-promoting regions. These regions act as sites where RNAp (ribonucleic acid-polymerase) binds to initiate transcription. This review aims to describe the formation of Curvature, as well as highlight its importance in predicting promoters. Furthermore, this article provides the potential of DNA Curvature as a distinguishing feature for promoter prediction tools, as well as outlining the calculation procedures that have been described by other researchers. This work may support further studies directed towards the enhancement of promoter prediction software.

Ion-mediated condensation controls the mechanics of mitotic chromosomes

During mitosis in eukaryotic cells, mechanical forces generated by the mitotic spindle pull the sister chromatids into the nascent daughter cells. How do mitotic chromosomes achieve the necessary mechanical stiffness and stability to maintain their integrity under these forces? Here we use optical tweezers to show that ions involved in physiological chromosome condensation are crucial for chromosomal stability, stiffness and viscous dissipation. We combine these experiments with high-salt histone depletion and theory to show that chromosomal elasticity originates from the chromatin fibre behaving as a flexible polymer, whereas energy dissipation can be explained by modelling chromatin loops as an entangled polymer solution. Taken together, we show how collective properties of mitotic chromosomes, a biomaterial of incredible complexity, emerge from molecular properties, and how they are controlled by the physico-chemical environment.

A Live-Cell Epigenome Manipulation by Photo-Stimuli-Responsive Histone Methyltransferase Inhibitor

Post-translational modifications on the histone H3 tail regulate chromatin structure, impact epigenetics, and hence the gene expressions. Current chemical modulation tools, such as unnatural amino acid incorporation, protein splicing, and sortase-based editing, have allowed for the modification of histones with various PTMs in cellular contexts, but are not applicable for editing native chromatin. The use of small organic molecules to manipulate histone-modifying enzymes alters endogenous histone PTMs but lacks precise temporal and spatial control. To date, there has been no achievement in modulating histone methylation in living cells with spatiotemporal resolution. In this study, a new method is presented for temporally manipulating histone dimethylation H3K9me2 using a photo-responsive inhibitor that specifically targets the methyltransferase G9a on demand. The photo-caged molecule is stable under physiological conditions and cellular environments, but rapidly activated upon exposure to light, releasing the bioactive component that can immediately inhibit the catalytic ability of the G9a in vitro. Besides, this masked compound could also efficiently reactivate the inhibition of methyltransferase activity in living cells, subsequently suppress H3K9me2, a mark that regulates various chromatin functions. Therefore, the chemical system will be a valuable tool for manipulating the epigenome for therapeutic purposes and furthering the understanding of epigenetic mechanisms.

An escape from ESKAPE pathogens: A comprehensive review on current and emerging therapeutics against antibiotic resistance

The rise of antimicrobial resistance has positioned ESKAPE pathogens as a serious global health threat, primarily due to the limitations and frequent failures of current treatment options. This growing risk has spurred the scientific community to seek innovative antibiotic therapies and improved oversight strategies. This review aims to provide a comprehensive overview of the origins and resistance mechanisms of ESKAPE pathogens, while also exploring next-generation treatment strategies for these infections. In addition, it will address both traditional and novel approaches to combating antibiotic resistance, offering insights into potential new therapeutic avenues. Emerging research underscores the urgency of developing new antimicrobial agents and strategies to overcome resistance, highlighting the need for novel drug classes and combination therapies. Advances in genomic technologies and a deeper understanding of microbial pathogenesis are crucial in identifying effective treatments. Integrating precision medicine and personalized approaches could enhance therapeutic efficacy. The review also emphasizes the importance of global collaboration in surveillance and stewardship, as well as policy reforms, enhanced diagnostic tools, and public awareness initiatives, to address resistance on a worldwide scale.

Tracing troubles: Unveiling the hidden impact of inorganic contamination on juvenile green sea turtle

Human activities and climate change have negatively affected the world's oceans, leading to a decline of 30 to 60 % in coastal ecosystems' biodiversity and habitats. The projected increase in the human population to 9.7 billion by 2050 raises concerns about the sustainability of marine ecosystem conservation and exploitation. Marine turtles, as sentinel species, accumulate contaminants, including trace elements, due to their extensive migration and long-life span. However, there is a lack of data on the degree of contamination and their effects on marine turtles' health. This study focuses on assessing in-situ inorganic contamination in juvenile green sea turtles from La Réunion Island and its short-term impact on individual health, using conventional biomarkers and proteomics. The goals include examining contamination patterns in different tissues and identifying potential new biomarkers for long-term monitoring and conservation efforts. The study identified differential metal contamination between blood and scute samples, which could help illuminate temporal exposure to trace elements in turtle individuals. We also found that some conventional biomarkers were related to trace element exposure, while the proteome responded differently to various contaminant mixtures. Immune processes, cellular organization, and metabolism were impacted, indicating that contaminant mixtures in the wild would have an effect on turtle's health. Fifteen biomarker candidates associated with strong molecular responses of sea turtle to trace element contamination are proposed for future long-term monitoring. The findings emphasize the importance of using proteomic approaches to detect subtle physiological responses to contaminants in the wild and support the need for non-targeted analysis of trace elements in the biomonitoring of sea turtle health.

Leishmania protein KMP-11 modulates cholesterol transport and membrane fluidity to facilitate host cell invasion

The first step of successful infection by any intracellular pathogen relies on its ability to invade its host cell membrane. However, the detailed structural and molecular understanding underlying lipid membrane modification during pathogenic invasion remains unclear. In this study, we show that a specific Leishmania donovani (LD) protein, KMP-11, forms oligomers that bridge LD and host macrophage (MΦ) membranes. This KMP-11 induced interaction between LD and MΦ depends on the variations in cholesterol (CHOL) and ergosterol (ERG) contents in their respective membranes. These variations are crucial for the subsequent steps of invasion, including (a) the initial attachment, (b) CHOL transport from MΦ to LD, and (c) detachment of LD from the initial point of contact through a liquid ordered (Lo) to liquid disordered (Ld) membrane-phase transition. To validate the importance of KMP-11, we generate KMP-11 depleted LD, which failed to attach and invade host MΦ. Through tryptophan-scanning mutagenesis and synthesized peptides, we develop a generalized mathematical model, which demonstrates that the hydrophobic moment and the symmetry sequence code at the membrane interacting protein domain are key factors in facilitating the membrane phase transition and, consequently, the host cell infection process by Leishmania parasites.

Multiconfigurational Excitonic Couplings in Homo- and Heterodimer Stacks of Azobenzene-Derived Dyes

Molecular excitons play a major role within dye aggregates and hold significant potential for (opto)electronic and photovoltaic applications. Numerous studies have documented alterations in the spectral properties of dye homoaggregates, but only limited work has been reported for heteroaggregates. In this article, dimeric dye stacks were constructed from azobenzene-like dyes with identical or distinct structures, and their excitonic features were computationally investigated. Our results show that strong exciton coupling is not limited to identical chromophores, as often assumed, based on a recently made available Frenkel Exciton Hamiltonian and multiconfigurational plus second-order perturbation theory energetics methodology. Heteroaggregate stacks were found to exhibit different absorption features from the corresponding interacting monomers, indicating considerable coupling interactions between units. We analyzed how such coupling may vary according to various aspects, such as the relative positions of the interacting monomers or the differences in their energetics. Such qualitative and semiquantitative analyses allow the evaluation of the excitonic behavior of these dye aggregates to encourage further efforts toward a deeper understanding of the excitonic properties of tailored dye heteroaggregate systems.

Rapidly Screening the Correlation between the Rotational Mobility and the Hydrogen Bonding Strength of Confined Water

Automated Deuterium Relaxation-Ordered SpectroscopY in solution (ADROSYS), an automated two-dimensional deuterium NMR methodology, discriminates between D2O populations (as well as deuterium-labeled alcohol groups) whose properties differ as a result of being confined inside nanoscale volumes. In this contribution, a proof-of-principle demonstration on reverse micelles (RMs) yields the insight that as the length scale of the confinement decreases from several nanometers down to less than a nanometer, the position of the signal peak migrates through the two-dimensional (2D) spectrum, tracing out a distinctive path in the 2D space (of relaxation time vs chemical shift). The signals typically follow a relatively gentle linear path for water confined on the scale of several nanometers, before curving once the surfactants confine the water molecules to length scales smaller than 1-2 nm. The qualitative shape of this path, especially in the regime of strong confinement, can change with different choices of surfactants, i.e., a different choice of chemistry at the edges of the confining environment. An important facet of this research was to demonstrate the relatively wide applicability of these techniques by showing that both: (1) Standard modern NMR instrumentation is capable of deploying an automated measurement, even though the choice of a deuterium nucleus is nonstandard and frequently requires companion proton spectra in order to reference the chemical shifts; and (2) well-established (though underutilized) modern techniques can process the resulting signal even though it involves the somewhat unusual combination of chemical shifts along one dimension and a distribution of relaxation times along another dimension. In addition to demonstrating that this technique can be deployed across many samples of interest, detailed facts pertaining to the broadening or shifting of resulting signals upon inclusion of various guest molecules are also discussed.

Conductance Channels in a Single-Entity Enzyme

For a long time, the prevailing view in the scientific community was that proteins, being complex macromolecules composed of amino acid chains linked by peptide bonds, adopt folded structure with insulating or semiconducting properties, with high bandgaps. However, recent discoveries of unexpectedly high conductance levels, reaching values in the range of dozens of nanosiemens (nS) in proteins, have challenged this conventional understanding. In this study, we used scanning tunneling microscopy (STM) to explore the single-entity conductance properties of enzymatic channels, focusing on bilirubin oxidase (BOD) as a model metalloprotein. By immobilizing BOD on a conductive carbon surface, we discern its preferred orientation, facilitating the formation of electronic and ionic channels. These channels show efficient electron transport (ETp), with apparent conductance up to the 15 nS range. Notably, these conductance pathways are localized, minimizing electron transport barriers due to solvents and ions, underscoring BOD's redox versatility. Furthermore, electron transfer (ET) within the BOD occurs via preferential pathways. The alignment of the conductance channels with hydrophilicity maps, molecular vacancies, and regions accessible to electrolytes explains the observed conductance values. Additionally, BOD exhibits redox activity, with its active center playing a critical role in the ETp process. These findings significantly advance our understanding of the intricate mechanisms that govern ETp processes in proteins, offering new insights into the conductance of metalloproteins.

Deciphering Spectroscopic Signatures of Competing Ca2+ - Peptide Interactions

Calcium-protein interactions are of paramount importance in biochemistry. They are a key element in a number of biological processes, such as neuronal signaling. Therefore, an understanding of the interaction at the molecular level is highly desirable. Here, we study the zwitterionic model peptide l-alanyl-l-alanine (2Ala), which has two distinct and competing binding sites for Ca2+: The carbonyl of the peptide bond and the C-terminus, the carboxylate group. We perform linear and two-dimensional IR spectroscopy experiments and find that the spectroscopic signatures of both moieties in the IR spectra change in amplitude and peak position upon the addition of CaCl2: A blueshift of the asymmetric carboxylate band and a redshift for the amide I mode. Ab initio molecular dynamics simulations confirm the direct interaction of the Ca2+ ion at both the carboxylate and the amide CO site leading to different spectral responses. The blueshift of the asymmetric carboxylate band is caused by a localization of the charge, leading to a decoupling of the CO stretching modes of the carboxylate group. The slight redshift of the amide I mode of 2Ala upon the addition of CaCl2 contrasts the blueshift that has been observed for isolated amide motifs, such as N-methylacetamide (NMA). This difference is caused by the smaller number of water molecules being replaced by the Ca2+ ion for 2Ala's amide compared to less sterically hindered, isolated amide carbonyls, in conjunction with vibrational Stark effects. Our results highlight the importance of considering potential competing binding sites, such as the amide CO backbone, the termini and residues, as well as the nature of the hydration of both peptide and ion, when exploring ions' interacting with small peptides and larger proteins.

Insights into the Role of Side-Chain Team Work in nDsbDOx/Red Proteins: Mechanism of Substrate Binding

N-terminal disulfide bond oxidoreductase (nDsbDOx/Red) proteins display divergent substrate binding mechanisms depending on the conformational changes to the Phe70 cap, which is also dependent on the disulfide redox state. In nDsbDOx, the cap dynamics is complex (shows both open/closed Phe70 cap conformations), resulting in an active site that is highly flexible. So the system's active site is conformationally selective (the active site adapts before substrate binding) toward its substrate. In nDsbDRed, the cap is generally closed, resulting in induced fit-type binding (adapts after substrate approach). Recent studies predict Tyr40 and Tyr42 residues to act as internal nucleophiles (Tyr40/42O-) for disulfide association/dissociation in nDsbDOx/Red, supplementing the electron transfer channel. From this perspective, we investigate the cap dynamics and the subsequent substrate binding modes in these proteins. Our molecular dynamics simulations show that the cap opening eliminates Tyr42O- electrostatic interactions irrespective of the disulfide redox state. The active site becomes highly flexible, and the conformational selection mechanism governs. However, Tyr40O- formation does not alter the chemical environment; the cap remains mostly closed and plausibly follows the induced fit mechanism. Thus, it is apparent that mostly Tyr42O- facilitates the internal nucleophile-mediated self-preparation of nDsbDOx/Red proteins for binding.

Segregative phase separation of strong polyelectrolyte complexes at high salt and high polymer concentrations

The phase behavior of polyelectrolyte complexes and coacervates (PECs) at low salt concentrations has been well characterized, but their behavior at concentrations well above the binodal is not well understood. Here, we investigate the phase behavior of stoichiometric poly(styrene sulfonate)/poly(diallyldimethylammonium) mixtures at high salt and high polymer concentrations. Samples were prepared by direct mixing of PSS/PDADMA PECs, water, and salt (KBr). Phase separation was observed at salt concentrations approximately 1 M above the binodal. Characterization by thermogravimetric analysis, FTIR, and NMR revealed that both phases contained significant amounts of polymer, and that the polymer-rich phase was enriched in PSS, while the polymer-poor phase was enriched in PDADMA. These results suggest that high salt concentrations drive salting out of the more hydrophobic polyelectrolyte (PSS), consistent with behavior observed in weak polyelectrolyte systems. Interestingly, at the highest salt and polymer concentrations studied, the polymer-rich phase contained both PSS and PDADMA, suggesting that high salt concentrations can drive salting out of partially-neutralized complexes as well. Characterization of the behavior of PECs in the high concentration limit appears to be a fruitful avenue for deepening fundamental understanding of the molecular-scale factors driving phase separation in these systems.

The replicative helicase CMG is required for the divergence of cell fates during asymmetric cell division in vivo

We report that the eukaryotic replicative helicase CMG (Cdc45-MCM-GINS) is required for differential gene expression in cells produced by asymmetric cell divisions in C. elegans. We found that the C. elegans CMG component, PSF-2 GINS2, is necessary for transcriptional upregulation of the pro-apoptotic gene egl-1 BH3-only that occurs in cells programmed to die after they are produced through asymmetric cell divisions. We propose that CMG's histone chaperone activity causes epigenetic changes at the egl-1 locus during replication in mother cells, and that these changes are required for egl-1 upregulation in cells programmed to die. We find that PSF-2 is also required for the divergence of other cell fates during C. elegans development, suggesting that this function is not unique to egl-1 expression. Our work uncovers an unexpected role of CMG in cell fate decisions and an intrinsic mechanism for gene expression plasticity in the context of asymmetric cell division.

Mechanisms underlying the changes in the structural, physicochemical, and emulsification properties of porcine myofibrillar proteins induced by prolonged pulsed electric field treatment

This study aimed to explore how pulsed electric field (PEF) treatment affects the structural, physicochemical, and emulsification properties of porcine-derived myofibrillar proteins (MPs). Increasing PEF treatment induced partial polarization and protein unfolding, resulting in notable denaturation that affected both the secondary and tertiary structures. PEF treatment also improved the solubility and emulsification ability of MPs by reducing their pH and surface hydrophobicity. Confocal laser scanning microscopy confirmed the effective adsorption of MPs and PEF-treated MPs at the oil/water interface, resulting in well-fabricated Pickering emulsions. A weak particle network increased the apparent viscosity in short-term PEF-treated Pickering emulsions. Conversely, in emulsions with long-term PEF-treated MP, rheological variables decreased, and dispersion stability increased. These results endorse the potential application of PEF-treated porcine-derived MPs as efficient Pickering stabilizers, offering valuable insights into the creative use of PEF for enhancing high-quality meat products, meeting the increasing demand for clean-label choices.

Ultrasensitive detection of a responsive fluorescent thymidine analogue in DNA via pulse-shaped two-photon excitation

Fluorescent base analogues (FBAs) are versatile nucleic acid labels that can replace a native nucleobase, while maintaining base pairing and secondary structure. Following the recent demonstration that free FBAs can be detected at the single-molecule level, the next goal is to achieve this level of detection sensitivity in oligonucleotides. Due to the short-wavelength absorption of most FBAs, multiphoton microscopy has emerged as a promising approach to single-molecule detection. We report the multiphoton-induced fluorescence of 5-(5-(4-methoxyphenyl)thiophen-2-yl)-6-aza-uridine (MeOthaU), a polarity-sensitive fluorescent thymidine analogue, as a nucleoside, and in two single-stranded deoxyribo-oligonucleotides, with and without their complementary strands. Ensemble steady-state and time-resolved measurements in dioxane, following one-photon and two-photon excitation, reveals both strongly and weakly emissive species, assigned as rotamers, while in Tris buffer there are additional non-emissive states, which are attributed to tautomeric forms populated in aqueous environments. The two-photon (2P) brightness for MeOthaU is highest as the free nucleoside in dioxane (10 GM) and lowest as the free nucleoside in Tris buffer (0.05 GM). The species-averaged 2P brightness values in DNA are higher for the single strands (0.66 and 0.82 GM for sequence context AXA and AXT, respectively, where X is MeOthaU) than in the duplex (0.31 and 0.25 GM for AXA and AXT, respectively). Using 2P microscopy with pulse-shaped broadband excitation, we were able to detect single- and double-stranded oligos with a molecular brightness of 0.8-0.9 kHz per molecule. This allowed the detection of as few as 7 DNA molecules in the focus, making it the brightest responsive FBA in an oligonucleotide reported to date.

The dual role of mannosylerythritol lipid-A: Improving gelling property and exerting antibacterial activity in chicken and beef gel

Gel meat products are important in the meat market. To develop high-quality meat gel products, mannosylerythritol lipid-A (MEL-A) was added to chicken and beef gels, and their physicochemical and biological properties of the composite gel formed by heating were determined in this study. The results of texture analysis showed that MEL-A could significantly improve the hardness, gumminess and chewiness of meat gels and reduce water loss (P < 0.05). In addition, rheological and differential scanning calorimetry (DSC) analysis showed that MEL-A not only improved the rheological properties of meat gel, but also improved its thermal stability. The results of dynamic rheological analysis also showed that MEL-A improved the gel strength of meat gel, and the gel strength of chicken was the highest after adding 1.5 % MEL-A while the gel strength of beef was the highest after adding 2 % MEL-A. The image of scanning electron microscopy (SEM) and protein molecular weight distribution measurement indicated that MEL-A induced protein aggregation, resulting in fewer pores in the meat gels and a more compact network structure. These results suggest that different meat gels show good gel properties, so MEL-A has a lot of potential for gel product development.

Stress sharing as cognitive glue for collective intelligences: A computational model of stress as a coordinator for morphogenesis

Individual cells have numerous competencies in physiological and metabolic spaces. However, multicellular collectives can reliably navigate anatomical morphospace towards much larger, reliable endpoints. Understanding the robustness and control properties of this process is critical for evolutionary developmental biology, bioengineering, and regenerative medicine. One mechanism that has been proposed for enabling individual cells to coordinate toward specific morphological outcomes is the sharing of stress (where stress is a physiological parameter that reflects the current amount of error in the context of a homeostatic loop). Here, we construct and analyze a multiscale agent-based model of morphogenesis in which we quantitatively examine the impact of stress sharing on the ability to reach target morphology. We found that stress sharing improves the morphogenetic efficiency of multicellular collectives; populations with stress sharing reached anatomical targets faster. Moreover, stress sharing influenced the future fate of distant cells in the multi-cellular collective, enhancing cells' movement and their radius of influence, consistent with the hypothesis that stress sharing works to increase cohesiveness of collectives. During development, anatomical goal states could not be inferred from observation of stress states, revealing the limitations of knowledge of goals by an extern observer outside the system itself. Taken together, our analyses support an important role for stress sharing in natural and engineered systems that seek robust large-scale behaviors to emerge from the activity of their competent components.

Effective drug design screening in bacterial glycolytic enzymes via targeting alternative allosteric sites

Three glycolytic enzymes phosphofructokinase (PFK), glyceraldehyde-3-phosphate dehydrogenase (GADPH) and pyruvate kinase (PK) that belong to Staphylococcus aureus were used as targets for screening a dataset composed of 7229 compounds of which 1416 were FDA-approved. Instead of catalytic sites, evolutionarily less conserved allosteric sites were targeted to identify compounds that would selectively bind the bacteria's glycolytic enzymes instead of the human host. Seven different allosteric sites provided by three enzymes were used in independent screening experiments via docking. For each of the seven sites, a total of 723 compounds were selected as the top 10 % which displayed the highest binding affinities. All compounds were then united to yield the top 54 drug candidates shared by all seven sites. Next, 17 out of 54 were selected and subjected to in vitro experiments for testing their inhibition capability for antibacterial growth and enzymatic activity. Accordingly, four compounds displaying antibacterial growth inhibition above 40 % were determined as Candesartan cilexetil, Montelukast (sodium), Dronedarone (hydrochloride) and Thonzonium (bromide). In a second round of experiment, Candesartan cilexetil and Thonzonium displayed exceptionally high killing efficiencies on two bacterial strains of S.aureus (methicillin-sensitive and methicillin-resistant) with concentrations as low as 4 μg/mL and 0.5 μg/mL. Yet, their enzymatic assays were not in accordance with their killing effectiveness. Different inhibitory effects was observed for each compound in each enzymatic assay. A more effective target strategy would be to screen for drug compounds that woud inhibit a combination of glycolytic enzymes observed in the glycolytic pathway.

Unveiling the impact of low-frequency electrical stimulation on network synchronization and learning behavior in cultured hippocampal neural networks

Understanding the dynamics of neural networks and their response to external stimuli is crucial for unraveling the mechanisms associated with learning processes. In this study, we hypothesized that electrical stimulation (ES) would lead to significant alterations in the activity patterns of hippocampal neuronal networks and investigated the effects of low-frequency ES on hippocampal neuronal populations using the microelectrode arrays (MEAs). Our findings revealed significant alterations in the activity of hippocampal neuronal networks following low-frequency ES trainings. Post-stimulation, the neural activity exhibited an organized burst firing pattern characterized by increased spike and burst firings, increased synchronization, and enhanced learning behaviors. Analysis of peri-stimulus time histograms (PSTHs) further revealed that low-frequency ES (1Hz) significantly enhanced neural plasticity, thereby facilitating the learning process of cultured neurons, whereas high-frequency ES (>10Hz) impeded this process. Moreover, we observed a substantial increase in correlations and connectivity within neuronal networks following ES trainings. These alterations in network properties indicated enhanced synaptic plasticity and emphasized the positive impact of low-frequency ES on hippocampal neural activities, contributing to the brain's capacity for learning and memory.

An isochoric optical platform for interrogation of aqueous glass formation processes

Aqueous vitrification (glass formation) processes are integral to modern cryopreservation, but experimental methods by which to study them are limited, particularly at the mL volume scales relevant to many biomedical applications. Here, we introduce an inexpensive custom optical platform, the isochoric vitrification cryo-macroscope (or "isovitriscope"), to supplement standard techniques with new qualitative and quantitative data streams. The platform consists of an LED light source, a isochoric (constant-volume) chamber with sapphire optical windows, and a camera, which can operate in two modes. One mode enables sharp visual observation of the glass transition and other low-temperature physical processes, including cracking, annealing, ice and hydrate crystallization, cavity formation, melting, etc. The other mode enables tracking of the optical temperature-evolution of the system via recorded light intensity, which we demonstrate may be used to measure the onset glass transition temperature with accuracy similar to differential scanning calorimetry (DSC), and to identify the temperature coordinates of other phase change events. The isovitriscope thus offers a single device combining the phenomenological insight of conventional visual inspection with the quantitative insight of techniques like calorimetry, at the >1 mL volume scales increasingly relevant to cryopreservation applications. To demonstrate uses of the isochoric optical platform, we herein conduct a series of observational studies examining the rich multi-phase phenomena at play during isochoric vitrification of binary cryoprotectant solutions; the effect of surface wettabilities on crack formation in the glassy state; the analogy between differential calorimetric and optical analysis; and more. In summary, the isochoric vitrification cryo-macroscope, or isovitriscope, adds a valuable new tool for the study of aqueous vitrification processes.

Cryo-EM structure of the zinc-activated channel (ZAC) in the Cys-loop receptor superfamily

Cys-loop receptors are a large superfamily of pentameric ligand-gated ion channels with various physiological roles, especially in neurotransmission in the central nervous system. Among them, zinc-activated channel (ZAC) is a Zn2+-activated ion channel that is widely expressed in the human body and is conserved among eukaryotes. Due to its gating by extracellular Zn2+, ZAC has been considered a Zn2+ sensor, but it has undergone minimal structural and functional characterization since its molecular cloning. Among the families in the Cys-loop receptor superfamily, only the structure of ZAC has yet to be determined. Here, we determined the cryo-EM structure of ZAC in the apo state and performed structure-based mutation analyses. We identified a few residues in the extracellular domain whose mutations had a mild impact on Zn2+ sensitivity. The constriction site in the ion-conducting pore differs from the one in other Cys-loop receptor structures, and further mutational analysis identified a key residue that is important for ion selectivity. In summary, our work provides a structural framework for understanding the ion-conducting mechanism of ZAC.

Nanoplasmonic microarray-based solid-phase amplification for highly sensitive and multiplexed molecular diagnostics: application for detecting SARS-CoV-2

A novel approach is introduced using nanoplasmonic microarray-based solid-phase recombinase polymerase amplification (RPA) that offers high sensitivity and multiplexing capabilities for gene detection. Nanoplasmonic microarrays were developed through one-step immobilization of streptavidin/biotin primers and fine-tuning the amplicon size to achieve high plasmon-enhanced fluorescence (PEF) on the nanoplasmonic substrate, thereby improving sensitivity. The specificity and sensitivity of solid-phase RPA on nanoplasmonic microarrays was evaluated in detecting E, N, and RdRP genes of SARS-CoV-2. High specificity was achieved by minimizing primer-dimer formation and employing a stringent washing process and high sensitivity obtained with a limit of detection of four copies per reaction within 30 min. In clinical testing with nasopharyngeal swab samples (n = 30), the nanoplasmonic microarrays demonstrated a 100% consistency with the PCR results for detecting SARS-CoV-2, including differentiation of Omicron mutations BA.1 and BA.2. This approach overcomes the sensitivity issue of solid-phase amplification, as well as offers rapidity, high multiplexing capabilities, and simplified equipment by using isothermal reaction, making it a valuable tool for on-site molecular diagnostics.

Selective Inhibition of hsp90 Paralogs: Uncovering the Role of Helix 1 in Grp94-Selective Ligand Binding

Grp94 is the endoplasmic reticulum paralog of the hsp90 family of chaperones, which have been targeted for therapeutic intervention via their highly conserved ATP binding sites. The design of paralog-selective inhibitors relies on understanding the protein structural elements that drive higher affinity in selective inhibitors. Here, we determined the structures of Grp94 and Hsp90 in complex with the Grp94-selective inhibitor PU-H36, and of Grp94 with the non-selective inhibitor PU-H71. In Grp94, PU-H36 derives its higher affinity by utilizing Site 2, a Grp94-specific side pocket adjoining the ATP binding cavity, but in Hsp90 PU-H36 occupies Site 1, a side pocket that is accessible in all paralogs with which it makes lower affinity interactions. The structure of Grp94 in complex with PU-H71 shows only Site 1 binding. While changes in the conformation of helices 4 and 5 in the N-terminal domain occur when ligands bind to Site 1 of both Hsp90 and Grp94, large conformational shifts that also involve helix 1 are associated with the engagement of the Site 2 pocket in Grp94 only. Site 2 in Hsp90 is blocked and its helix 1 conformation is insensitive to ligand binding. To understand the role of helix 1 in ligand selectivity, we tested the binding of PU-H36 and other Grp94-selective ligands to chimeric Grp94/Hsp90 constructs. These studies show that helix 1 is the major determinant of selectivity for Site 2 targeted ligands and also influences the rate of ATPase activity in Hsp90 paralogs.

Lipid Compositions of Liquid-Ordered and Liquid-Disordered Phases in Ternary Membranes of Sphingomyelin, Cholesterol, and Dioleoylphosphatidylcholine Determined by 2H NMR: Stearoyl-Sphingomyelin Compared with Its Palmitoyl Counterpart

Sphingomyelin (SM) and cholesterol are the major lipids in the signaling platforms of cell membranes, known as lipid rafts. In particular, SM with a stearoyl chain (C18-SM) is abundant in specific tissues such as the brain, the most cholesterol-rich organ, whereas the distribution of palmitoyl (C16)-SM is ubiquitous. Here, we reveal the differences between palmitoyl- and stearoyl-SM in lipid-lipid interactions based on the tie lines obtained from the 2H solid-state NMR spectra of bilayer systems composed of SM/dioleoylphosphatidylcholine/cholesterol 33:33:33 and 40:40:20. Lipid probes carrying position-selective deuterations, 10',10'-d2-SM, 24-d1-cholesterol, and 6″,6″-d2-dioleoyl-phosphatidylcholine, were incorporated into the membranes. 2H NMR peaks from these probes in the membranes directly provide the lipid compositions of the liquid-ordered (Lo) and liquid-disordered (Ld) regions. Without using bulky fluorescent groups, these probes allow us to obtain the end points of the tie lines in a ternary phase diagram based on the lever rule. Consequently, the tie lines of the stearoyl-SM membranes were steeper than those of the palmitoyl-SM membranes, indicating that cholesterol content was higher in the Lo domains of stearoyl-SM, regardless of the total concentration of unsaturated phospholipids. When comparing the content of unsaturated lipids in the Lo domain, the stearoyl-SM membranes had a higher content than palmitoyl-SM membranes. These results revealed that stearoyl-SM is suitable for stabilizing biologically functional microdomains in cholesterol-rich organs, whereas palmitoyl-SM may be better suited for stabilizing domains in tissue membranes with normal cholesterol content. The small but significant differences in the lipid interactions between stearoyl-SM and palmitoyl-SM may be related to the spatiotemporal formation of functional domains in biological environments.

Comparison of Methodologies for Absolute Binding Free Energy Calculations of Ligands to Intrinsically Disordered Proteins

Modulating the function of Intrinsically Disordered Proteins (IDPs) with small molecules is of considerable importance given the crucial roles of IDPs in the pathophysiology of numerous diseases. Reported binding affinities for ligands to diverse IDPs vary broadly, and little is known about the detailed molecular mechanisms that underpin ligand efficacy. Molecular simulations of IDP ligand binding mechanisms can help us understand the mode of action of small molecule inhibitors of IDP function, but it is still unclear how binding energies can be modeled rigorously for such a flexible class of proteins. Here, we compare alchemical absolute binding free energy calculations (ABFE) and Markov-State Modeling (MSM) protocols to model the binding of the small molecule 10058-F4 to a disordered peptide extracted from a segment of the oncoprotein c-Myc. The ABFE results produce binding energy estimates that are sensitive to the choice of reference structure. In contrast, the MSM results produce more reproducible binding energy estimates consistent with weak mM binding affinities and transient intermolecular contacts reported in the literature.

Phosphorylation of P-stalk proteins defines the ribosomal state for interaction with auxiliary protein factors

Ribosomal action is facilitated by the orchestrated work of trans-acting factors and ribosomal elements, which are subject to regulatory events, often involving phosphorylation. One such element is the ribosomal P-stalk, which plays a dual function: it activates translational GTPases, which support basic ribosomal functions, and interacts with the Gcn2 kinase, linking the ribosomes to the ISR pathway. We show that P-stalk proteins, which form a pentamer, exist in the cell exclusively in a phosphorylated state at five C-terminal domains (CTDs), ensuring optimal translation (speed and accuracy) and may play a role in the timely regulation of the Gcn2-dependent stress response. Phosphorylation of the CTD induces a structural transition from a collapsed to a coil-like structure, and the CTD gains conformational freedom, allowing specific but transient binding to various protein partners, optimizing the ribosome action. The report reveals a unique feature of the P-stalk proteins, indicating that, unlike most ribosomal proteins, which are regulated by phosphorylation in an on/off manner, the P-stalk proteins exist in a constantly phosphorylated state, which optimizes their interaction with auxiliary factors.

Investigating pH-induced conformational switch in PIM-1: An integrated multi spectroscopic and MD simulation study

PIM-1 is a Ser/Thr kinase, which has been extensively studied as a potential target for cancer therapy due to its significant roles in various cancers, including prostate and breast cancers. Given its importance in cancer, researchers are investigating the structure of PIM-1 for pharmacological inhibition to discover therapeutic intervention. This study examines structural and conformational changes in PIM-1 across different pH using various spectroscopic and computational techniques. Spectroscopic results indicate that PIM-1 maintains its secondary and tertiary structure within the pH range of 7.0-9.0. However, protein aggregation occurs in the acidic pH range of 5.0-6.0. Additionally, kinase assays suggested that PIM-1 activity is optimal within the pH range of 7.0-9.0. Subsequently, we performed a 100 ns all-atom molecular dynamics (MD) simulation to see the effect of pH on PIM-1 structural stability at the molecular level. MD simulation analysis revealed that PIM-1 retains its native conformation in alkaline conditions, with some residual fluctuations in acidic conditions as well. A strong correlation was observed between our MD simulation, spectroscopic, and enzymatic activity studies. Understanding the pH-dependent structural changes of PIM-1 can provide insights into its role in disease conditions and cellular homeostasis, particularly regarding protein function under varying pH conditions.

Amphiphilic shuttle peptide delivers base editor ribonucleoprotein to correct the CFTR R553X mutation in well-differentiated airway epithelial cells

Base editing could correct nonsense mutations that cause cystic fibrosis (CF), but clinical development is limited by the lack of delivery methods that efficiently breach the barriers presented by airway epithelia. Here, we present a novel amphiphilic shuttle peptide based on the previously reported S10 peptide that substantially improved base editor ribonucleoprotein (RNP) delivery. Studies of the S10 secondary structure revealed that the alpha-helix formed by the endosomal leakage domain (ELD), but not the cell penetrating peptide (CPP), was functionally important for delivery. By isolating and extending the ELD, we created a novel shuttle peptide, termed S237. While S237 achieved lower delivery of green fluorescent protein, it outperformed S10 at Cas9 RNP delivery to cultured human airway epithelial cells and to pig airway epithelia in vivo, possibly due to its lower net charge. In well-differentiated primary human airway epithelial cell cultures, S237 achieved a 4.6-fold increase in base editor RNP delivery, correcting up to 9.4% of the cystic fibrosis transmembrane conductance regulator (CFTR) R553X allele and restoring CFTR channel function close to non-CF levels. These findings deepen the understanding of peptide-mediated delivery and offer a translational approach for base editor RNP delivery for CF airway disease.

Understanding Cu+2 binding with DNA: A molecular dynamics study comparing Cu2+ and Mg2+ binding to the Dickerson DNA

Cu2+ ions led DNA damage by reactive oxygen species (ROS) is widely known biological phenomena. The ionic radii of Cu2+ and Mg2+ being similar, the binding of Cu2+ ions to DNA is expected to be similar to that of the Mg2+ ions. However, little is known how Cu2+ ions bind in different parts (phosphate, major and minor grooves) of a double-strand (ds) DNA, especially at atomic level. In the present study, we employ molecular dynamic (MD) simulations to investigate the binding of Cu2+ ions with the Dickerson DNA, a B-type dodecamer double stranded (ds) DNA. The binding characteristics of Cu2+ and Mg2+ ions with this dsDNA are compared to get an insight into the differences and similarities in binding behavior of both ions. Unlike Mg2+ ions, the first hydration shell of Cu2+ is found to be labile, thus it shows both direct and indirect binding with the dsDNA, i.e., binding through displacement of water from the hydration shell or through the hydration shell. Though the binding propensity of Cu2+ ions with dsDNA is observed relatively stronger, the binding order to phosphates, major groove, and minor groove is found qualitatively similar (phosphates > major groove > minor groove) for both ions. The study gives a deep understanding of Cu2+ binding to DNA, which could be helpful in rationalizing the Cu2+ led ROS-mediated DNA damage.

Tutorial Review on the Set-Up and Running of Quantum Mechanical Cluster Models for Enzymatic Reaction Mechanisms

Enzymes turnover substrates into products with amazing efficiency and selectivity and as such have great potential for use in biotechnology and pharmaceutical applications. However, details of their catalytic cycles and the origins surrounding the regio- and chemoselectivity of enzymatic reaction processes remain unknown, which makes the engineering of enzymes and their use in biotechnology challenging. Computational modelling can assist experimental work in the field and establish the factors that influence the reaction rates and the product distributions. A popular approach in modelling is the use of quantum mechanical cluster models of enzymes that take the first- and second coordination sphere of the enzyme active site into consideration. These QM cluster models are widely applied but often the results obtained are dependent on model choice and model selection. Herein, we show that QM cluster models can give highly accurate results that reproduce experimental product distributions and free energies of activation within several kcal mol-1, regarded that large cluster models with >300 atoms are used that include key hydrogen bonding interactions and charged residues. In this tutorial review, we give general guidelines on the set-up and applications of the QM cluster method and discuss its accuracy and reproducibility. Finally, several representative QM cluster model examples on metal-containing enzymes are presented, which highlight the strength of the approach.

Hierarchical ion interactions in the direct air capture of CO2 at air/aqueous interfaces

The direct air capture (DAC) of CO2 using aqueous solvents is plagued by slow kinetics and interfacial barriers that limit effectiveness in combating climate change. Functionalizing air/aqueous surfaces with charged amphiphiles shows promise in accelerating DAC; however, insight into these interfaces and how they evolve in time remains poorly understood. Specifically, competitive ion interactions between DAC reagents and reaction products feedback onto the interfacial structure, thereby modulating interfacial chemical composition and overall function. In this work, we probe the role of glycine amino acid anions (Gly-), an effective CO2 capture reagent, that promotes the organization of cationic oligomers at air/aqueous interfaces. These surfaces are probed with vibrational sum frequency generation spectroscopy and molecular dynamics simulations. Our findings demonstrate that the competition for surface sites between Gly- and captured carbonaceous anions (HCO3-, CO32-, carbamates) drives changes in surface hydration, which in turn tunes oligomer ordering. This phenomenon is related to a hierarchical ordering of anions at the surface that are electrostatically attracted to the surface and their ability to compete for interfacial water. These results point to new ways to tune interfaces for DAC via stratification of ions based on relative surface propensities and specific ion effects.

The small molecule ZPD-2 inhibits the aggregation and seeded polymerisation of C-terminally truncated α-Synuclein

Protein aggregation, particularly the formation of amyloid fibrils, is associated with numerous human disorders, including Parkinson's disease. This neurodegenerative condition is characterised by the accumulation of α-Synuclein amyloid fibrils within intraneuronal deposits known as Lewy bodies or neurites. C-terminally truncated forms of α-Synuclein are frequently observed in these inclusions in the brains of patients, and their increased aggregation propensity suggests a role in the disease's pathogenesis. This study demonstrates that the small molecule ZPD-2 acts as a potent inhibitor of both the spontaneous and seeded amyloid polimerisation of C-terminally truncated α-Synuclein by interfering with early aggregation intermediates. This dual activity positions this molecule as a promising candidate for therapeutic development in treating synucleinopathies.

Stacking correlation length in single-stranded DNA

Base stacking is crucial in nucleic acid stabilization, from DNA duplex hybridization to single-stranded DNA (ssDNA) protein binding. While stacking energies are tiny in ssDNA, they are inextricably mixed with hydrogen bonding in DNA base pairing, making their measurement challenging. We conduct unzipping experiments with optical tweezers of short poly-purine (dA and alternating dG and dA) sequences of 20-40 bases. We introduce a helix-coil model of the stacking-unstacking transition that includes finite length effects and reproduces the force-extension curves. Fitting the model to the experimental data, we derive the stacking energy per base, finding the salt-independent value $\Delta G_0^{ST}=0.14(3)$ kcal/mol for poly-dA and $\Delta G_0^{ST}=0.07(3)$ kcal/mol for poly-dGdA. Stacking in these polymeric sequences is predominantly cooperative with a correlation length of ∼4 bases at zero force . The correlation length reaches a maximum of ∼10 and 5 bases at the stacking-unstacking transition force of ∼10 and 20 pN for poly-dA and poly-dGdA, respectively. The salt dependencies of the cooperativity parameter in ssDNA and the energy of DNA hybridization are in agreement, suggesting that double-helix stability is primarily due to stacking. Analysis of poly-rA and poly-rC RNA sequences shows a larger stacking stability but a lower stacking correlation length of ∼2 bases.

Piezoelectricity and flexoelectricity in biological cells: the role of cell structure and organelles

Living tissues experience various external forces on cells, influencing their behaviour, physiology, shape, gene expression, and destiny through interactions with their environment. Despite much research done in this area, challenges remain in our better understanding of the behaviour of the cell in response to external stimuli, including the arrangement, quantity, and shape of organelles within the cell. This study explores the electromechanical behaviour of biological cells, including organelles like microtubules, mitochondria, nuclei, and cell membranes. A two-dimensional bio-electromechanical model for two distinct cell structures has been developed to analyze the behavior of the biological cell to the external electrical and mechanical responses. The piezoelectric and flexoelectric effects have been included via multiphysics coupling for the biological cell. All the governing equations have been discretized and solved by the finite element method. It is found that the longitudinal stress is absent and only the transverse stress plays a crucial role when the mechanical load is imposed on the top side of the cell through compressive displacement. The impact of flexoelectricity is elucidated by introducing a new parameter called the maximum electric potential ratio ( V R , max ). It has been found that V R , max depends upon the orientation angle and shape of the microtubules. The magnitude of V R , max exhibit huge change when we change the shape and orientation of the organelles, which in some cases (boundary condition (BC)-3) can reach to three times of regular shape organelles. Further, the study reveals that the number of microtubules significantly impacts effective elastic and piezoelectric coefficients, affecting cell behavior based on structure, microtubule orientation, and mechanical stress direction. The insight obtained from the current study can assist in advancements in medical therapies such as tissue engineering and regenerative medicine.

Dynamic sampling of a surveillance state enables DNA proofreading by Cas9

CRISPR-Cas9 has revolutionized genome engineering applications by programming its single-guide RNA, where high specificity is required. However, the precise molecular mechanism underscoring discrimination between on/off-target DNA sequences, relative to the guide RNA template, remains elusive. Here, using methyl-based NMR to study multiple holoenzymes assembled in vitro, we elucidate a discrete protein conformational state which enables recognition of DNA mismatches at the protospacer adjacent motif (PAM)-distal end. Our results delineate an allosteric pathway connecting a dynamic conformational switch at the REC3 domain, with the sampling of a catalytically competent state by the HNH domain. Our NMR data show that HiFi Cas9 (R691A) increases the fidelity of DNA recognition by stabilizing this "surveillance state" for mismatched substrates, shifting the Cas9 conformational equilibrium away from the active state. These results establish a paradigm of substrate recognition through an allosteric protein-based switch, providing unique insights into the molecular mechanism which governs Cas9 selectivity.

FRAP analysis of peptide diffusion in extracellular matrix mimetic hydrogels as an in vitro model for subcutaneous injection

Subcutaneous (SC) injection is a common route of administration for drug compounds with poor oral bioavailability. However, bioavailability is often variable and incomplete, and there is as yet no standard accepted medium for simulation of the human SC environment. In this work we evaluate a FRAP based method for quantitative determination of local self-diffusion coefficients within extracellular matrix (ECM) mimetic hydrogels, potentially useful as in vitro models for drug transport in the ECM after SC injection. Gels were made consisting of either agarose, cross-linked collagen (COL) and hyaluronic acid (HA) or cross-linked HA. The diffusivities of uncharged FITC-dextran (FD4), the highly charged poly-lysine (PLK20) and poly-glutamic acid (PLE20) as well as the GLP-1 analogue exenatide were determined within the gels using FRAP. The diffusion coefficients in uncharged agarose gels were in the range of free diffusion in PBS. The diffusivity of cationic PLK20 in gels containing anionic HA was substantially decreased due to strong electrostatic interactions. Peptide aggregation could be observed as immobile fractions in experiments with exenatide. We conclude that the FRAP method provides useful information of peptides' interactions and transport properties in hydrogel networks, giving insight into the mechanisms affecting absorption of drug compounds after subcutaneous injection.

A TLR7 Agonist Conjugated to a Nanofibrous Peptide Hydrogel as a Potent Vaccine Adjuvant

Toll-like receptors (TLRs) recognize pathogen- and damage-associated molecular patterns and, in turn, trigger the release of cytokines and other immunostimulatory molecules. As a result, TLR agonists are increasingly being investigated as vaccine adjuvants. Many of these agonists are small molecules that quickly diffuse away from the vaccination site, limiting their co-localization with antigens and, thus, their effect. Here, the small-molecule TLR7 agonist 1V209 is conjugated to a positively-charged multidomain peptide (MDP) hydrogel, K2, which was previously shown to act as an adjuvant promoting humoral immunity. Mixing the 1V209-conjugated K2 50:50 with the unfunctionalized K2 produces hydrogels that retain the shear-thinning and self-healing physical properties of the original MDP while improving the solubility of 1V209 more than 200-fold compared to the unconjugated molecule. When co-delivered with ovalbumin as a model antigen, 1V209-functionalized K2 produces a robust Th2 immune response and an antigen-specific Th1 immune response superior to alum, a widely used vaccine adjuvant. Together, these results suggest that K2 MDP hydrogels functionalized with 1V209 are a promising adjuvant for vaccines against infectious diseases, especially those benefiting from a combined Th1 and Th2 immune response.

Morphological and Molecular Profiling of Amyloid-β Species in Alzheimer's Pathogenesis

Alzheimer's disease (AD) is the most common form of dementia around the world (~ 65%). Here, we portray the neuropathology of AD, biomarkers, and classification of amyloid plaques (diffuse, non-cored, dense core, compact). Tau pathology and its involvement with Aβ plaques and cell death are discussed. Amyloid cascade hypotheses, aggregation mechanisms, and molecular species formed in vitro and in vivo (on- and off-pathways) are described. Aβ42/Aβ40 monomers, dimers, trimers, Aβ-derived diffusible ligands, globulomers, dodecamers, amylospheroids, amorphous aggregates, protofibrils, fibrils, and plaques are characterized (structure, size, morphology, solubility, toxicity, mechanistic steps). An update on AD-approved drugs by regulatory agencies, along with new Aβ-based therapies, is presented. Beyond prescribing Aβ plaque disruptors, cholinergic agonists, or NMDA receptor antagonists, other therapeutic strategies (RNAi, glutaminyl cyclase inhibitors, monoclonal antibodies, secretase modulators, Aβ aggregation inhibitors, and anti-amyloid vaccines) are already under clinical trials. New drug discovery approaches based on "designed multiple ligands", "hybrid molecules", or "multitarget-directed ligands" are also being put forward and may contribute to tackling this highly debilitating and fatal form of human dementia.

Structural and functional studies of the EGF20-27 region reveal new features of the human Notch receptor important for optimal activation

The Notch receptor is activated by the Delta/Serrate/Lag-2 (DSL) family of ligands. The organization of the extracellular signaling complex is unknown, although structures of Notch/ligand complexes comprising the ligand-binding region (LBR), and negative regulatory region (NRR) region, have been solved. Here, we investigate the human Notch-1 epidermal growth factor-like (EGF) 20-27 region, located between the LBR and NRR, and incorporating the Abruptex (Ax) region, associated with distinctive Drosophila phenotypes. Our analyses, using crystallography, NMR and small angle X-ray scattering (SAXS), support a rigid, elongated organization for EGF20-27 with the EGF20-21 linkage showing Ca2+-dependent flexibility. In functional assays, Notch-1 variants containing Ax substitutions result in reduced ligand-dependent trans-activation. When cis-JAG1 was expressed, Notch activity differences between WT and Ca2+-binding Ax variants were less marked than seen in the trans-activation assays alone, consistent with disruption of cis-inhibition. These data indicate the importance of Ca2+-stabilized structure and suggest the balance of cis- and trans-interactions explains the effects of Drosophila Ax mutations.

Spike by spike frequency analysis of amperometry traces provides statistical validation of observations in the time domain

Amperometry is a commonly used electrochemical method for studying the process of exocytosis in real-time. Given the high precision of recording that amperometry procedures offer, the volume of data generated can span over several hundreds of megabytes to a few gigabytes and therefore necessitates systematic and reproducible methods for analysis. Though the spike characteristics of amperometry traces in the time domain hold information about the dynamics of exocytosis, these biochemical signals are, more often than not, characterized by time-varying signal properties. Such signals with time-variant properties may occur at different frequencies and therefore analyzing them in the frequency domain may provide statistical validation for observations already established in the time domain. This necessitates the use of time-variant, frequency-selective signal processing methods as well, which can adeptly quantify the dominant or mean frequencies in the signal. The Fast Fourier Transform (FFT) is a well-established computational tool that is commonly used to find the frequency components of a signal buried in noise. In this work, we outline a method for spike-based frequency analysis of amperometry traces using FFT that also provides statistical validation of observations on spike characteristics in the time domain. We demonstrate the method by utilizing simulated signals and by subsequently testing it on diverse amperometry datasets generated from different experiments with various chemical stimulations. To our knowledge, this is the first fully automated open-source tool available dedicated to the analysis of spikes extracted from amperometry signals in the frequency domain.

Effect of Internal and Bulge Loops on the Thermal Stability of Small DNA Duplexes

The thermal stabilities of DNA duplexes analogous to the let-7 microRNA:lin-41 mRNA complex from Caenorhabditis elegans have been measured by free solution capillary electrophoresis. DNA duplexes with the same stems but different types of internal or bulge loops and a control with no loop have also been studied. The melting temperatures of the DNA derivatives increased linearly with the logarithm of the Na+ or K+ ion concentration in the solution. Peaks in the electropherograms corresponding to duplexes with internal or bulge loops exhibited extensive tailing at high temperatures, suggesting that denaturation occurred by slow exchange between the duplexes and their component single strands. The single strands did not separate completely from the duplexes in aqueous solutions; instead, they appeared as small subpeaks on the tails of the duplex peaks. However, complete separation of the duplexes from their component single strands was observed at 20 °C in solutions containing 300 mM tetrapropylammonium ions. In addition, counterion condensation appears to be significantly reduced in DNA duplexes containing internal or bulge loops.