On the Ion Implantation Synthesis of Ag-Embedded Over Sr-Substituted Hydroxyapatite on a Nano-Topography Patterned Ti for Application in Acetabular Fracture Sites.

Introduction: There is an ongoing need for improved healing response and expedited osseointegration on the Ti implants in acetabular fracture sites. To achieve adequate bonding and mechanical stability between the implant surface and the acetabular fracture, a new coating technology must be developed to promote bone integration and prevent bacterial growth. Methods: A cylindrical Ti substrate mounted on a rotating specimen holder was used to implant Ca2+, P2+, and Sr2+ ions at energies of 100 KeV, 75 KeV and 180 KeV, respectively, using a low-energy accelerator to synthesize strontium-substituted hydroxyapatite at varying conditions. Ag2+ ions of energy 100 KeV were subsequently implanted on the as-formed surface at the near-surface region to provide anti-bacterial properties to the as-formed specimen. Results: The properties of the as-formed ion-implanted specimen were compared with the SrHA-Ag synthesized specimens by cathodic deposition and low-temperature high-speed collision technique. The adhesion strength of the ion-implanted specimen was 43 ± 2.3 MPa, which is well above the ASTM standard for Ca-P coating on Ti. Live/dead cell analysis showed higher osteoblast activity on the ion-implanted specimen than the other two. Ag in the SrHA implanted Ti by ion implantation process showed superior antibacterial activity. Discussion: In the ion implantation technique, nano-topography patterned surfaces are not concealed after implantation, and their efficacy in interacting with the osteoblasts is retained. Although all three studies examined the antibacterial effects of Ag2+ ions and the ability to promote bone tissue formation by MC3T3-E1 cells on SrHA-Ag/Ti surfaces, ion implantation techniques demonstrated superior ability. The synthesized specimen can be used as an effective implant in acetabular fracture sites based on their mechanical and biological properties.

Control of artificial membrane fusion in physiological ionic solutions beyond the limits of electroformation.

Membrane fusion, merging two lipid bilayers, is crucial for fabricating artificial membrane structures. Over the past 40 years, in contrast to precise and controllable membrane fusion in-vivo through specific molecules such as SNAREs, controlling the fusion in-vitro while fabricating artificial membrane structures in physiological ionic solutions without fusion proteins has been a challenge, becoming a significant obstacle to practical applications. We present an approach consisting of an electric field and a few kPa hydraulic pressure as an additional variable to physically control the fusion, enabling tuning of the shape and size of the 3D freestanding lipid bilayers in physiological ionic solutions. Mechanical model analysis reveals that pressure-induced parallel/normal tensions enhance fusion among membranes in the microwell. In-vitro peptide-membrane assay, mimicking vesicular transport via pressure-assisted fusion, and stability of 38 days with in-chip pressure control via pore size-regulated hydrogel highlight the potential for diverse biological applications.

Uncertainty quantification and sensitivity analysis of neuron models with ion concentration dynamics.

This paper provides a comprehensive and computationally efficient case study for uncertainty quantification (UQ) and global sensitivity analysis (GSA) in a neuron model incorporating ion concentration dynamics. We address how challenges with UQ and GSA in this context can be approached and solved, including challenges related to computational cost, parameters affecting the system's resting state, and the presence of both fast and slow dynamics. Specifically, we analyze the electrodiffusive neuron-extracellular-glia (edNEG) model, which captures electrical potentials, ion concentrations (Na+, K+, Ca2+, and Cl-), and volume changes across six compartments. Our methodology includes a UQ procedure assessing the model's reliability and susceptibility to input uncertainty and a variance-based GSA identifying the most influential input parameters. To mitigate computational costs, we employ surrogate modeling techniques, optimized using efficient numerical integration methods. We propose a strategy for isolating parameters affecting the resting state and analyze the edNEG model dynamics under both physiological and pathological conditions. The influence of uncertain parameters on model outputs, particularly during spiking dynamics, is systematically explored. Rapid dynamics of membrane potentials necessitate a focus on informative spiking features, while slower variations in ion concentrations allow a meaningful study at each time point. Our study offers valuable guidelines for future UQ and GSA investigations on neuron models with ion concentration dynamics, contributing to the broader application of such models in computational neuroscience.

A thiazole-based colorimetric and photoluminescent chemosensors for As3+ ions detection: Density functional theory, test strips, real samples, and bioimaging applications.

A Schiff-base Ethyl (E)-2-(3-((2-carbamothioylhydrazono)methyl)-4-hydroxyphenyl)-4-methylthiazole-5-carboxylate (TZTS) dual functional colorimetric and photoluminescent chemosensor which includes thiazole and thiosemicarbazide has been synthesized to detect arsenic (As3+) ions selectively in DMSO: H2O (7:3, v/v) solvent system. The molecular structure of the probe was characterized via FT-IR, 1H, and 13C NMR & HRMS analysis. Interestingly, the probe exhibits a remarkable and specific colorimetric and photoluminescence response to As3+ ions when exposed to various metal cations. The absorption spectral changes of TZTS were observed upon the addition of As3+ ions, with a naked eye detectable color change from colorless to yellow color. Additionally, the chemosensor (TZTS) exhibited a new absorption band at 412 nm and emission enhancements in photoluminescence at 528 nm after adding As3+ ions. The limit of detection (LOD) for As3+ ions was calculated to be 16.5 and 7.19 × 10-9 M by the UV-visible and photoluminescent titration methods, respectively. The underlying mechanism and experimental observations have been comprehensively elucidated through techniques such as Job's plot, Benesi-Hildebrand studies, and density functional theory (DFT) calculations. For practical application, the efficient determination of As3+ ions were accomplished using a spike and recovery approach applied to real water samples. In addition, the developed probe was successfully employed in test strip applications, allowing for the naked-eye detection of arsenic ions. Moreover, fluorescence imaging experiments of As3+ ions in the breast cancer cell line (MCF-7) demonstrated their practical applications in biological systems. Consequently, these findings highlight the significant potential of the TZTS sensor for detecting As3+ ions in environmental analysis systems.

Colorimetric detection of electrolyte ions in blood based on biphasic microdroplet extraction.

BACKGROUND: Timely diagnosis and prevention of diseases require rapid and sensitive detection of biomarkers from blood samples without external interference. Abnormal electrolyte ion levels in the blood are closely linked to various physiological disorders, including hypertension. Therefore, accurate, interference-free, and precise measurement of electrolyte ion concentrations in the blood is particularly important. RESULTS: In this work, a colorimetric sensor based on a biphasic microdroplet extraction is proposed for the detection of electrolyte ions in the blood. This sensor employs mini-pillar arrays to facilitate contact between adjacent blood microdroplets and organic microdroplets serving as sensing phases, with any color changes being monitored through a smartphone's colorimetric software. The sensor is highly resistant to interference and does not require pre-treatment of the blood samples. Remarkably, the sensor exhibits exceptional reliability and stability, allowing for rapid enrichment and detection of K+, Na+, and Cl- in the blood within 10 s (Cl-), 15 s (K+) and 40 s (Na+) respectively. SIGNIFICANCE: The colorimetric sensor based on biphasic microdroplet extraction offers portability due to its compact size and ease of operation without the need for large instruments. Additionally, it is location-independent, making it a promising tool for real-time biomarker detection in body fluids such as blood.

Fragment ion intensity prediction improves the identification rate of non-tryptic peptides in timsTOF.

Immunopeptidomics is crucial for immunotherapy and vaccine development. Because the generation of immunopeptides from their parent proteins does not adhere to clear-cut rules, rather than being able to use known digestion patterns, every possible protein subsequence within human leukocyte antigen (HLA) class-specific length restrictions needs to be considered during sequence database searching. This leads to an inflation of the search space and results in lower spectrum annotation rates. Peptide-spectrum match (PSM) rescoring is a powerful enhancement of standard searching that boosts the spectrum annotation performance. We analyze 302,105 unique synthesized non-tryptic peptides from the ProteomeTools project on a timsTOF-Pro to generate a ground-truth dataset containing 93,227 MS/MS spectra of 74,847 unique peptides, that is used to fine-tune the deep learning-based fragment ion intensity prediction model Prosit. We demonstrate up to 3-fold improvement in the identification of immunopeptides, as well as increased detection of immunopeptides from low input samples.

Optoelectronic Response to the Fluor Ion Bond on 4-(4,4,5,5-Tetramethyl-1,3,2-dioxoborolan-2-yl)benzaldehyde.

Boronate esters are a class of compounds containing a boron atom bonded to two oxygen atoms in an ester group, often being used as precursors in the synthesis of other materials. The characterization of the structure and properties of esters is usually carried out by UV-visible, infrared, and nuclear magnetic resonance (NMR) spectroscopic techniques. With the aim to better understand our experimental data, in this article, the density functional theory (DFT) is used to analyze the UV-visible and infrared spectra, as well as the isotropic shielding and chemical shifts of the hydrogen atoms 1H, carbon 13C and boron 11B in the compound 4-(4,4,5,5-tetramethyl-1,3,2-dioxoborolan-2-yl)benzaldehyde. Furthermore, this study considers the change in its electronic and spectroscopic properties of this particular ester, when its boron atom is coordinated with a fluoride anion. The calculations were carried out using the LSDA and B3LYP functionals in Gaussian-16, and PBE in CASTEP. The results show that the B3LYP functional gives the best approximation to the experimental data. The formation of a coordinated covalent B-F bond highlights the remarkable sensitivity of the NMR chemical shifts of carbon, oxygen, and boron atoms and their surroundings. Furthermore, this bond also highlights the changes in the electron transitions bands n → π* and π → π* during the absorption and emission of a photon in the UV-vis, and in the stretching bands of the C=C bonds, and bending of BO2 in the infrared spectrum. This study not only contributes to the understanding of the properties of boronate esters but also provides important information on the interactions and responses optoelectronic of the compound when is bonded to a fluorine atom.

Ionic Effect on the Microenvironment of Biomolecular Condensates.

Biomolecules such as proteins and RNA could organize to form condensates with distinct microenvironments through liquid-liquid phase separation (LLPS). Recent works have demonstrated that the microenvironment of biomolecular condensates plays a crucial role in mediating biological activities, such as the partition of biomolecules, and the subphase organization of the multiphasic condensates. Ions could influence the phase transition point of LLPS, following the Hofmeister series. However, the ion-specific effect on the microenvironment of biomolecular condensates remains unknown. In this study, we utilized fluorescence lifetime imaging microscopy (FLIM), fluorescence recovery after photobleaching (FRAP), and microrheology techniques to investigate the ion effect on the microenvironment of condensates. We found that ions significantly affect the microenvironment of biomolecular condensates: salting-in ions increase micropolarity and reduce the microviscosity of the condensate, while salting-out ions induce opposing effects. Furthermore, we manipulate the miscibility and multilayering behavior of condensates through ion-specific effects. In summary, our work provides the first quantitative survey of the microenvironment of protein condensates in the presence of ions from the Hofmeister series, demonstrating how ions impact micropolarity, microviscosity, and viscoelasticity of condensates. Our results bear implications on how membrane-less organelles would exhibit varying microenvironments in the presence of continuously changing cellular conditions.

Ion detection in a DNA nanopore FET device.

An ion detection device that combines a DNA-origami nanopore and a field-effect transistor (FET) was designed and modeled to determine sensitivity of the nanodevice to the local cellular environment. Such devices could be integrated into a live cell, creating an abiotic-biotic interface integrated with semiconductor electronics. A continuum model is used to describe the behavior of ions in an electrolyte solution. The drift-diffusion equations are employed to model the ion distribution, taking into account the electric fields and concentration gradients. This was matched to the results from electric double layer theory to verify applicability of the model to a bio-sensing environment. The FET device combined with the nanopore is shown to have high sensitivity to ion concentration and nanopore geometry, with the electrical double layer behavior governing the device characteristics. A logarithmic relationship was found between ion concentration and a single FET current, generating up to 200 nA of current difference with a small applied bias.

A label-free photoelectrochemical biosensor for silver ions based on Zn-Co doped C and CdS QD nanomaterials.

A sensitive photoelectrochemical (PEC) biosensor for silver ions (Ag+) was developed based on Zn-Co doped C and CdS quantum dot (CdS QD) nanomaterials. Hydrophobic modified sodium alginate (HMA), which could stabilize and improve the PEC performance of CdS QDs, was also used for the construction of PEC sensors. Especially, Zn-Co doped C, CdS QDs and HMA were sequentially modified onto an electrode surface via the drop-coating method, and a C base rich DNA strand was then immobilized onto the modified electrode. As the C base in DNA specifically recognized Ag+, it formed a C-Ag+-C complex in the presence of Ag+, which created a spatial steric hindrance, resulting in a reduced PEC response. The sensing platform is sensitive to Ag+ in the range of 10.0 fM to 0.10 µM, with a limit of detection of 3.99 fM. This work offers an ideal platform to determine trace heavy metal ions in environmental monitoring and bioanalysis.

Fully Integrated Multiplexed Wristwatch for Real-Time Monitoring of Electrolyte Ions in Sweat.

Considerable progress has already been made in sweat sensors based on electrochemical methods to realize real-time monitoring of biomarkers. However, realizing long-term monitoring of multiple targets at the atomic level remains extremely challenging, in terms of designing stable solid contact (SC) interfaces and fully integrating multiple modules for large-scale applications of sweat sensors. Herein, a fully integrated wristwatch was designed using mass-manufactured sensor arrays based on hierarchical multilayer-pore cross-linked N-doped porous carbon coated by reduced graphene oxide (NPCs@rGO-950) microspheres with high hydrophobicity as core SC, and highly selective monitoring simultaneously for K+, Na+, and Ca2+ ions in human sweat was achieved, exhibiting near-Nernst responses almost without forming an interfacial water layer. Combined with computed tomography, solid-solid interface potential diffusion simulation results reveal extremely low interface diffusion potential and high interface capacitance (598 µF), ensuring the excellent potential stability, reversibility, repeatability, and selectivity of sensor arrays. The developed highly integrated-multiplexed wristwatch with multiple modules, including SC, sensor array, microfluidic chip, signal transduction, signal processing, and data visualization, achieved reliable real-time monitoring for K+, Na+, and Ca2+ ion concentrations in sweat. Ingenious material design, scalable sensor fabrication, and electrical integration of multimodule wearables lay the foundation for developing reliable sweat-sensing systems for health monitoring.

Fluorescence Sensors for the Detection of L-Histidine Based on Silver Nanoclusters Modulated by Copper Ions.

In this study, Cu2+ modulated silver nanoclusters were constructed for the turn-on, label-free detection of L-histidine. Six Ag NCs protected by oligonucleotides (DNA-Ag NCs) were tested in a series of experiments. Finally, A-DAN-Ag NCs were chosen as the best candidate due to their excellent fluorescent properties. The fluorescence of A-DAN-Ag NCs was quenched using Cu2+ through energy or electron transfer. However, quenched fluorescence could be restored dramatically in the presence of L-histidine due to Cu2+ liberation from A-DAN-Ag NCs and because of the chelation between the imidazole group of L-histidine and Cu2+. The proposed sensor exhibited high selectivity towards L-histidine over other amino acids, with a limit of detection (LOD) of 0.096 µM ranging from 0 to 8 µM. The proposed sensor succeeded in detecting L-histidine in diluted human urine. Therefore, the sensor has promising practical applications in biological systems.

The Role of the Unbinding Cycle on the Coordination Abilities of the Bi-Cyclopeptides toward Cu(II) Ions.

Bicyclic peptides have attracted the interest of pharmaceutical companies because of their remarkable properties, putting them on a new path in medicine. Their conformational rigidity improves proteolytic stability and leads to rapid penetration into tissues via any possible route of administration. Moreover, elimination of renal metabolism is of great importance, for example, for people with a history of liver diseases. In addition, each ring can function independently, making bicyclic peptides extremely versatile molecules for further optimization. In this paper, we compared the potentiometric and spectroscopic properties studied by UV-vis, MCD, and EPR of four synthetic analogues of the bi-cyclic peptide c(PKKHP-c(CFWKTC)-PKKH) (BCL). In particular, we correlated the structural and spectral properties of complexes with coordinating abilities toward Cu(II) ions of MCL1 (Ac-PKKHPc(CFWKTC)PKKH-NH2) that contains the unbinding cycle and N- and C-terminal linear parts with two histidine residues, one per part; two monocyclic ligands containing one histidine residue, both in the N-terminal position, i.e., MCL2 (Ac-PKKHPc(CFWKTC)PKKS-NH2) and in the C-terminal position, i.e., MCL3 (Ac-PKKSPc(CFWKTC)PKKH-NH2), respectively; and the linear structure LNL (Ac-PKKHPSFWKTSPKKH-NH2). Potentiometric results have shown that the bicyclic structure promotes the involvement of the side chain imidazole donors in Cu(II) binding. On the other hand, the results obtained for the mono-cyclic analogues lead to the conclusion that the coordination of the histidine moiety as an anchoring group is promoted by its location in the peptide sequence further from the nonbinding cycle, strongly influencing the involvement of the amide donors in Cu(II) coordination.

Tandem mass spectrometry of homologous 3-hydroxyfurazan and nitrile amino acids: Analysis of cooperative interactions and fragmentation processes.

The assignment of structure by tandem mass spectrometry (MS/MS) relies on the interpretation of the fragmentation behavior of gas-phase ions. Mass spectra were acquired for a series of heterocyclic mimetics of acidic amino acids and a related series of nitrile amino acids. All amino acids were readily protonated or deprotonated by electrospray ionization (ESI), and distinctive fragmentation processes were observed when the ions were subjected to collision-induced dissociation (CID). The deprotonated heterocycles showed bond cleavages of the 3-hydroxyfurazan ring with formation of oxoisocyanate and the complementary deprotonated nitrile amino acid. Further fragmentation of the deprotonated nitrile amino acids was greatly dependent on the length of the alkyl nitrile side chain. Competing losses of CO2 versus HCN occurred from α-cyanoglycinate (shortest chain), whereas water was lost from 2-amino-5-cyanopentanoate (longest chain). Interestingly, loss of acrylonitrile by a McLafferty-type fragmentation process was detected for 2-amino-4-cyanobutanoate, and several competing processes were observed for ß-cyanoalanate. In one process, cyanide ion was formed either by consecutive losses of ammonia, carbon dioxide, and acetylene or by a one-step decarboxylative elimination. In another, complementary ions were obtained from ß-cyanoalanate by loss of acetonitrile or HN=CHCO2H. Fragmentation of the protonated 3-hydroxyfurazan and nitrile amino acids resulted in the cumulative loss (H2O + CO), a loss that is commonly observed for protonated aliphatic α-amino acids. Overall, the distinct fragmentation behavior of the multifunctional 3-hydroxyfurazan amino acids correlated with the charged site, whereas fragmentations of the deprotonated nitrile amino acids showed cooperative interactions between the nitrile and the carboxylate groups.

Design a Friendly Nanoscale Chemical Sensor Based on Gold Nanoclusters for Detecting Thiocyanate Ions in Food Industry Applications.

The surfactant cetyltrimethylammonium bromide (CTAB) induces the aggregation of gold nanoclusters (GNCs), leading to the development of a proposed fluorometric technique for detecting thiocyanate (SCN-) ions based on an anti-aggregation mechanism. This approach is straightforward to execute, highly sensitive, and selective. A significant quenching effect occurs in fluorescence upon using the aggregation agent CTAB in GNCs synthesis, resulting in a transition from intense red fluorescence to dim red. The decrease in fluorescence intensity of GNCs in the presence of CTAB is caused by the mechanism of fluorescence quenching mediated by aggregation. As the levels of SCN- rise, the fluorescence of CTAB-GNCs increases; this may be detected using spectrofluorometry or by visually inspecting under UV irradiation. The recovery of red fluorescence of CTAB-GNCs in the presence of SCN- enables the precise and discerning identification of SCN- within the concentration range of 2.86-140 nM. The minimum detectable concentration of the SCN- ions was 1 nM. The selectivity of CTAB-GNCs towards SCN- ions was investigated compared to other ions, and it was demonstrated that CTAB-GNCs exhibit exceptional selectivity. Furthermore, we believe that CTAB-GNCs have novel possibilities as favorable sensor candidates for various industrial applications. Our detection technique was validated by analyzing SCN- ions in milk samples, which yielded promising results.

Electrochemical Impedance Spectroscopy for Ion Sensors with Interdigitated Electrodes: Capacitance Calculations, Equivalent Circuit Models and Design Optimizations.

Electrochemical impedance spectroscopy (EIS) is becoming more and more relevant for the characterization of biosensors employing interdigitated electrodes. We compare four different sensor topologies for an exemplary use case of ion sensing to extract recommendations for the design optimizations of impedimetric biosensors. Therefore, we first extract how sensor design parameters affect the sensor capacitance using analytical calculations and finite element (FEM) simulations. Moreover, we develop equivalent circuit models for our sensor topologies and validate them using FEM simulations. As a result, the impedimetric sensor response is better understood, and sensitive and selective frequency ranges can be determined for a given sensor topology. From this, we extract design optimizations for different sensing principles.

Production of levulinic acid from macroalgae by hydrothermal conversion with ionic resin catalyst.

Gracilaria verrucosa is red algae (Rhodophyta) that is particularly significant because of its potential for bioenergy production as a sustainable and environmentally friendly marine bioresource. This study focuses on the production of levulinic acid from G. verrucosa using hydrothermal conversion with an ionic resin Purolite CT269DR as the catalyst. By optimization of the conversion condition, a 30.3 % (22.58 g/L) yield of levulinic acid (LA) (based on carbohydrate content) was obtained at 200 °C for 90 min with 12.5 % biomass and 50 % catalyst loading of biomass quantity. Simultaneously, formic acid yielded 14.0 % (10.42 g/L). The LA yield increased with increasing combined severity (CS) levels under tested ranges. Furthermore, the relationship between CS and LA synthesis was effectively fitted to the nonlinear sigmoidal equation. However, as the yield of sugar decreased, LA yield was linearly increased. Thus, the use of ionic resin as a heterogeneous catalyst presents significant potential for the manufacture of platform chemicals, specifically LA, through the conversion of renewable marine macroalgae.

Fabrication of melamine formaldehyde/graphene oxide composite for efficient static and dynamic adsorption of lead ions from aqueous medium.

The present work discusses the synthesis, characterization, and environmental applications of graphene oxide (GO), melamine formaldehyde resin (MF), and melamine formaldehyde/graphene oxide composite (MGO) for the efficient removal of Pb2+ from aqueous medium via batch and column procedures. TGA, XRD, TEM, zeta potential, nitrogen adsorption/desorption, ATR-FTIR, and other characterization techniques revealed that MGO is characterized by a greater surface area (609 m2/g), total pore volume (1.0106 cm3/g), pHPZC (6.5), and the presence of various surface chemical functional groups. The synthesized solid adsorbents were used in both static and dynamic adsorption processes to remove Pb2+, with varying application parameters such as pH, starting concentration, adsorbent dosage, and shaking time in the case of static adsorption method. While through the column adsorption process the effects of column bed height, flow rate, and starting Pb2+ were taken into consideration. Results of the batch adsorption demonstrated that MGO had the highest Langmuir adsorption capacity (201.5 mg/g), and the adsorption fit the nonlinear Langmuir adsorption model and Elovich kinetic models. The adsorption of Pb2+ onto all prepared solid materials is endothermic, spontaneous, and physical in nature, as demonstrated by thermodynamic studies. Column adsorption of Pb2+ well fitted by Thomas and Yoon Nelson nonlinear adsorption models. MGO showed a maximum column adsorption capacity of 168 mg/g when applying 4 cm, 15 mL/min, and 150 mg/L as bed height, flow rate, and initial Pb2+, respectively. With only a 12.6% reduction in its adsorption capacity, column regeneration showed that MGO exhibited a high degree of reusability even after five cycles of adsorption/desorption studies.

EDTA enables to alleviate impacts of metal ions on conjugative transfer of antibiotic resistance genes.

Various heavy metals are reported to be able to accelerate horizontal transfer of antibiotic resistance genes (ARGs). In real water environmental settings, ubiquitous complexing agents would affect the environmental behaviors of heavy metal ions due to the formation of metal-organic complexes. However, little is known whether the presence of complexing agents would change horizontal gene transfer due to heavy metal exposure. This study aimed to fill this gap by investigating the impacts of a typical complexing agent ethylenediaminetetraacetic acid (EDTA) on the conjugative transfer of plasmid-mediated ARGs induced by a range of heavy metal ions. At the environmentally relevant concentration (0.64 mg L-1) of metal ions, all the tested metal ions (Mg2+, Ca2+, Co2+, Pb2+, Ni2+, Cu2+, and Fe3+) promoted conjugative transfer of ARGs, while an inhibitory effect was observed at a relatively higher concentration (3.20 mg L-1). In contrast, EDTA (0.64 mg L-1) alleviated the effects of metal ions on ARGs conjugation transfer, evidenced by 11 %-66 % reduction in the conjugate transfer frequency. Molecular docking and dynamics simulations disclosed that this is attributed to the stronger binding of metal ions with the lipids in cell membranes. Under metal-EDTA exposure, gene expressions related to oxidative stress response, cell membrane permeability, intercellular contact, energy driving force, mobilization, and channels of plasmid transfer were suppressed compared with the metal ions exposure. This study offers insights into the alleviation mechanisms of complexing agents on ARGs transfer induced by free metal ions.

Structural Elucidation of Ubiquitin via Gas-Phase Ion/Ion Cross-Linking Reactions Using Sodium-Cationized Reagents Coupled with Infrared Multiphoton Dissociation.

Accurate structural determination of proteins is critical to understanding their biological functions and the impact of structural disruption on disease progression. Gas-phase cross-linking mass spectrometry (XL-MS) via ion/ion reactions between multiply charged protein cations and singly charged cross-linker anions has previously been developed to obtain low-resolution structural information on proteins. This method significantly shortens experimental time relative to conventional solution-phase XL-MS but has several technical limitations: (1) the singly deprotonated N-hydroxysulfosuccinimide (sulfo-NHS)-based cross-linker anions are restricted to attachment at neutral amine groups of basic amino acid residues and (2) analyzing terminal cross-linked fragment ions is insufficient to unambiguously localize sites of linker attachment. Herein, we demonstrate enhanced structural information for alcohol-denatured A-state ubiquitin obtained from an alternative gas-phase XL-MS approach. Briefly, singly sodiated ethylene glycol bis(sulfosuccinimidyl succinate) (sulfo-EGS) cross-linker anions enable covalent cross-linking at both ammonium and amine groups. Additionally, covalently modified internal fragment ions, along with terminal b-/y-type counterparts, improve the determination of linker attachment sites. Molecular dynamics simulations validate experimentally obtained gas-phase conformations of denatured ubiquitin. This method has identified four cross-linking sites across 8+ ubiquitin, including two new sites in the N-terminal region of the protein that were originally inaccessible in prior gas-phase XL approaches. The two N-terminal cross-linking sites suggest that the N-terminal half of ubiquitin is more compact in gas-phase conformations. By comparison, the two C-terminal linker sites indicate the signature transformation of this region of the protein from a native to a denatured conformation. Overall, the results suggest that the solution-phase secondary structures of the A-state ubiquitin are conserved in the gas phase. This method also provides sufficient sensitivity to differentiate between two gas-phase conformers of the same charge state with subtle structural variations.