Orange luminescence of α-Al2O3 related to clusters consisting of F centers and divalent cations.

The orange luminescence of α-Al2O3 under UV excitation is characterized by a 2.07-eV orange broadband emission that has not yet been elucidated. This emission is present in natural and synthetic crystals and powders, as well as in Be-treated samples. All orange-luminescent materials have low Fe concentration (mostly <1000 ppm) with traces of divalent cations, mostly Mg, or Be in Be-diffused material (dozens of ppm). Mg2+, Mn2+, and Be2+ cations substitute for trivalent Al. To accommodate the charge deficit, several defects are created, including oxygen vacancies also called F centers. Indeed, our excitation spectra revealed the presence of several different F centers (F, F+, and clustered F2, F2 +, F2 2+) in those samples. However, the thermal stability and the measured luminescence lifetimes do not match with previously reported characteristics of isolated F centers. Based on our experiments, we suggest that a complex aggregate of two F centers (F2 2+) trapped at divalent cations is a major cause of this uncommon microsecond lifetime emission, even if a variety of other defects, including Cr3+, V3+, or interstitial Al3+, are present.

Effects of monovalent and divalent cations on the rheology of entangled DNA.

In this paper we investigate the effects of varying cation valency and concentration on the rheology of entangled λDNA solutions. We show that monovalent cations moderately increase the viscoelasticty of the solutions mainly by stabilising linear concatenation of λDNA "monomers" via hybridisation of their sticky ends. On the contrary, divalent cations have a far more complex and dramatic effect on the rheology of the solution and we observe evidence of inter-molecular DNA-DNA bridging by Mg2+. We argue that these results may be interesting in the context of dense solutions of single and double stranded DNA, e.g. in vivo or in biotechnology applications such as DNA origami and DNA hydrogels.

Magnesium alginate as a low-viscosity (intramolecularly cross-linked) system for the sustained and neuroprotective release of magnesium.

The administration of Mg ions is advantageous in pathological scenarios such as pre-enclampsia and forms of neuroinflammation (e.g. stroke or injury); yet, few systems exist for their sustained delivery. Here, we present the (static light scattering and diffusing-wave spectroscopy) characterization of magnesium alginate (MgAlg) as a potentially injectable vehicle ifor the delivery of Mg. Differently from other divalent cations, Mg does not readily induce gelation: it acts within MgAlg coils, making them more rigid and less prone to entangle. As a result, below a threshold concentration (notionally below 0.5 % wt.) MgAlg are inherently less viscous than those of sodium alginate (NaAlg), which is a major advantage for injectables; at higher concentrations, however, (stable, Mg-based) aggregation starts occurring. Importantly, Mg can then be released e.g. in artificial cerebrospinal fluid, via a slow (hours) process of ion exchange. Finally, we here show that MgAlg protects rat neural stem cells from the consequence of an oxidative insult (100 µM H2O2), an effect that we can only ascribe to the sustained liberation of Mg ions, since it was not shown by NaAlg, MgSO4 or the NaAlg/MgSO4 combination. Our results therefore indicate that MgAlg is a promising vehicle for Mg delivery under pathological (inflammatory) conditions.

Theoretical analysis of divalent cation effects on aptamer recognition of neurotransmitter targets.

Aptamer-based sensing of small molecules such as dopamine and serotonin in the brain, requires characterization of the specific aptamer sequences in solutions mimicking the in vivo environment with physiological ionic concentrations. In particular, divalent cations (Mg2+ and Ca2+) present in brain fluid, have been shown to affect the conformational dynamics of aptamers upon target recognition. Thus, for biosensors that transduce aptamer structure switching as the signal response, it is critical to interrogate the influence of divalent cations on each unique aptamer sequence. Herein, we demonstrate the potential of molecular dynamics (MD) simulations to predict the behaviour of dopamine and serotonin aptamers on sensor surfaces. The simulations enable molecular-level visualization of aptamer conformational changes that, in some cases, are significantly influenced by divalent cations. The correlations of theoretical simulations with experimental findings validate the potential for MD simulations to predict aptamer-specific behaviors on biosensors.

Ions-Induced Alginate Gelation According to Elemental Analysis and a Combinatorial Approach.

This study considers the potential of elemental analysis of polysaccharide ionotropic gels in elucidating the junction zones for different divalent cations. The developed algorithm ensures the correct separation of contributions from physically adsorbed and structure-forming ionic compounds, with the obtained results scaled to alginate C12 block. Possible versions of chain association into dimers and their subsequent integration into flat junction zones were analyzed within the framework of the "egg-box" model. The application of combinatorial analysis made it possible to derive theoretical relations to find the probability of various types of egg-box cell occurrences for alginate chains with arbitrary monomeric units ratio µ = M/G, which makes it possible to compare experimental data for alginates of different origins. Based on literature data and obtained chemical formulas, the possible correspondence of concrete biopolymer cells to those most preferable for filling by alkaline earth cations was established. The identified features of elemental composition suggest the formation of composite hydrated complexes with the participation of transition metal cations. The possibility of quantitatively assessing ordered secondary structures formed due to the physical sorption of ions and molecules from environment, correlating with the sorption capabilities of Me2+ alginate, was established.

Free ferrous ions sustain activity of mammalian stearoyl-CoA desaturase-1.

Mammalian stearoyl-CoA desaturase-1 (SCD1) introduces a double-bond to a saturated long-chain fatty acid in a reaction catalyzed by a diiron center. The diiron center is well-coordinated by conserved histidine residues and is thought to remain with the enzyme. However, we find here that SCD1 progressively loses its activity during catalysis and becomes fully inactive after about nine turnovers. Further studies show that the inactivation of SCD1 is due to the loss of an iron (Fe) ion in the diiron center and that the addition of free ferrous ions (Fe2+) sustains the enzymatic activity. Using SCD1 labeled with Fe isotope, we further show that free Fe2+ is incorporated into the diiron center only during catalysis. We also discover that the diiron center in SCD1 has prominent electron paramagnetic resonance signals in its diferric state, indicative of distinct coupling between the two ferric ions. These results reveal that the diiron center in SCD1 is structurally dynamic during catalysis and that labile Fe2+ in cells could regulate SCD1 activity and hence lipid metabolism.

Electrostatic interactions - key determinants of the metal selectivity in La3+ and Ca2+ binding proteins.

Nearly half of all known proteins contain metal co-factors. In the course of evolution two dozen metal cations (mostly monovalent and divalent species) have been selected to participate in processes of vital importance for living organisms. Trivalent metal cations have also been selected, although to a lesser extent as compared with their mono- and divalent counterparts. Notably, factors governing the metal selectivity in trivalent metal centers in proteins are less well understood than those in the respective divalent metal centers. Thus, the source of high La3+/Ca2+ selectivity in lanthanum-binding proteins, as compared with that of calcium-binding proteins (i.e., calmodulin), is still shrouded in mystery. The well-calibrated thermochemical calculations, performed here, reveal the dominating role of electrostatic interactions in shaping the metal selectivity in La3+-binding centers. The calculations also disclose other (second-order) determinants of metal selectivity in these systems, such as the rigidity and extent of solvent exposure of the binding site. All these factors are also implicated in shaping the metal selectivity in Ca2+-binding proteins.

Intricate 3D architecture of a DNA mimic of GFP.

Numerous studies have shown how RNA molecules can adopt elaborate three-dimensional (3D) architectures1-3. By contrast, whether DNA can self-assemble into complex 3D folds capable of sophisticated biochemistry, independent of protein or RNA partners, has remained mysterious. Lettuce is an in vitro-evolved DNA molecule that binds and activates4 conditional fluorophores derived from GFP. To extend previous structural studies5,6 of fluorogenic RNAs, GFP and other fluorescent proteins7 to DNA, we characterize Lettuce-fluorophore complexes by X-ray crystallography and cryogenic electron microscopy. The results reveal that the 53-nucleotide DNA adopts a four-way junction (4WJ) fold. Instead of the canonical L-shaped or H-shaped structures commonly seen8 in 4WJ RNAs, the four stems of Lettuce form two coaxial stacks that pack co-linearly to form a central G-quadruplex in which the fluorophore binds. This fold is stabilized by stacking, extensive nucleobase hydrogen bonding-including through unusual diagonally stacked bases that bridge successive tiers of the main coaxial stacks of the DNA-and coordination of monovalent and divalent cations. Overall, the structure is more compact than many RNAs of comparable size. Lettuce demonstrates how DNA can form elaborate 3D structures without using RNA-like tertiary interactions and suggests that new principles of nucleic acid organization will be forthcoming from the analysis of complex DNAs.

A naphthalimide functionalized fluoran with AIE effect for ratiometric sensing Hg2+ and cell imaging application.

The pollution caused by mercury ions (Hg2+) poses a potential threat to public health. Therefore, monitoring Hg2+ concentration in the environment is necessary and significant. In this work, a naphthalimide functionalized fluoran dye NAF has been prepared, which shows a new red-shift in emission at 550 nm with the maximum intensity in a mixture of water-CH3CN (v/v = 7/3) due to aggregating induced emission (AIE) effect. Meanwhile, NAF can be employed as a Hg2+ ions sensor, which displays a selective and sensitive response to Hg2+ ions by the reduced fluorescence of naphthalimide fluorophore and increased fluorescence of fluoran group, respectively, showing ratiometric fluorescence signal changes with more than 65-fold emission intensity ratio increase and naked eyes visible color change. In addition, the response time is fast (within 1 min) and the sensing can be conducted in a wide pH range (4.0-9.0). Moreover, the detection limit has been evaluated to be 5.5 nM. The sensing mechanism may be attributed to the formation of a π-extended conjugated system due to the Hg2+ ions-induced conversion of spironolactone to the ring-opened form, partially accompanied by the fluorescence resonance energy transfer (FRET) process. Significantly, NAF exhibits suitable cytotoxicity to living HeLa cells, which allows it to be utilized for ratiometric imaging of Hg2+ ions assisted by confocal fluorescence imaging.

Exploring the Influence of Biologically Relevant Ions on the Corrosion Behavior of Biodegradable Zinc in Physiological Fluids.

This work presents a study on the influence of biologically relevant ions on the corrosion of zinc (Zn) in physiological fluids. Electrochemical techniques were used to investigate the degradation of pure Zn exposed to different physiological electrolytes containing chlorides, carbonates, sulfates, and phosphates. The corrosion behavior of Zn in the solutions over a 7-day period was also assessed. SEM, EDS, and FTIR were used to analyze corrosion products. With respect to corrosion, the most aggressive ions are chlorides, which induce localized corrosion, while carbonates and phosphates reduce the corrosive attack of the chloride on Zn while inducing uniform corrosion. Sulfates reduce the corrosion rate by disrupting Zn's passive layer. The overall corrosion rate of Zn changed in each electrolyte depending on the nature of the solution and the corrosion product formed. These findings will be useful in predicting the in-service behavior of future biodegradable Zn medical implants.

Abundant tannic acid modified gelatin/sodium alginate biocomposite hydrogels with high toughness, antifreezing, antioxidant and antibacterial properties.

The acidity of high tannic acid (TA) content solution can destroy the structure of protein, such as gelatin (G). This causes a big challenge to introduce abundant TA into the G-based hydrogels. Here, the G-based hydrogel system with abundant TA as hydrogen bonds provider was constructed by a "protective film" strategy. The protective film around the composite hydrogel was first formed by the chelation of sodium alginate (SA) and Ca2+. Subsequently, abundant TA and Ca2+ were successively introduced into the hydrogel system by immersing method. This strategy effectively protected the structure of the designed hydrogel. After treatment with 0.3 w/v TA and 0.06 w/v Ca2+ solutions, the tensile modulus, elongation at break and toughness of G/SA hydrogel increased about 4-, 2-, and 6-fold, respectively. Besides, G/SA-TA/Ca2+ hydrogels exhibited good water retention, anti-freezing, antioxidant, antibacterial properties and low hemolysis ratio. Cell experiments showed that G/SA-TA/Ca2+ hydrogels possessed good biocompatibility and could promote cell migration. Therefore, G/SA-TA/Ca2+ hydrogels are expected to be used in the field of biomedical engineering. The strategy proposed in this work also provides a new idea for improving the properties of other protein-based hydrogels.

The influence of pH and monovalent/divalent cations on the structural and physicochemical properties of myofibrillar protein from silver carp.

The present study aimed to investigate effects of pH and monovalent (Na+ and K+)/divalent (Ca2+ and Mg2+) cations on the structural and physicochemical properties of myofibrillar protein (MP) from silver carp. MP treated with divalent cation had lesser change for the structure than that treated with monovalent cation. Ca2+-ATPase activity of MP treated with monovalent cation was increased firstly and then decreased, while that treated with divalent cation was decreased with increasing ionic strength. Surface hydrophobicity and Z-average of MP treated with divalent cations was lower than that with monovalent cations, while they decreased and then increased with the pH shifting from 3.0 to 9.0. Zeta potential of MP was increased and then decreased with increasing the pH but decreased and then increased with increasing ionic strength. In general, the pH and monovalent/divalent cations could cause various hydrophobic and electrostatic interactions, resulting in changes of the physicochemical properties of MP.

RNA Captures More Cations than DNA: Insights from Molecular Dynamics Simulations.

The distribution of cations around nucleic acids is essential for a broad variety of processes ranging from DNA condensation and RNA folding to the detection of biomolecules in biosensors. Predicting the exact distribution of ions remains challenging since the distribution and, hence, a broad variety of nucleic acid properties depend on the salt concentration, the valency of the ions, and the ion type. Despite the importance, a general theory to quantify ion-specific effects for highly charged biomolecules is still lacking. Moreover, recent experiments reveal that despite their similar building blocks, DNA and RNA duplexes can react differently to the same ionic conditions. The aim of our current work is to provide a comprehensive set of molecular dynamics simulations using more than 180 µs of simulation time. For the mono- and divalent cations Li+, Na+, K+, Cs+, Ca2+, Sr2+, and Ba2+, the simulations allow us to reveal the ion-specific distributions and binding patterns for DNA and RNA duplexes. The microscopic insights from the simulations display the origin of ion-specificity and shed light on the question of why DNA and RNA show opposing behavior in the same ionic conditions. Finally, the detailed binding patterns from the simulations reveal why RNA can capture more cations than DNA.

Divalent cation induced re-entrant condensation behavior for lipopolysaccharides.

Lipopolysaccharides (LPSs) are negatively charged molecules covering the surface of Gram-negative bacteria (GNB). Adding divalent cations (DCs) is important to stabilize the LPS bilayer. Thus, DCs are always only considered as membrane stabilizing ions. Here, on the basis of a coarse-grained (CG) Martini force field, we conduct molecular dynamic (MD) simulations to study the divalent cation mediated LPS interaction and the stability of the LPS membrane in a wide range of DC concentrations. By measuring the LPS binding free energy and the LPS-LPS aggregate from the association course between two LPS molecules, we find that the initial addition of DCs may significantly facilitate the aggregation of LPSs into a compact structure, while sequentially adding more DCs only unpacks the LPS aggregate and drives the dissolution of LPSs. With an increasing concentration of DCs, we find a gradual replacement of DCs to monovalent cations as condensed counterions on the LPS, which follows a sign change from negative to positive in terms of the LPS effective charge and a switch of LPSs in solution from undergoing precipitation to resolubilization on adding DCs. This interaction change in the level of two LPSs accounts for the structure variation of the LPS assembly on a larger scale, where the LPS packing rigidity in the assembly bilayer is found with a similar nonmonotonic dependence with the DC concentration. Thus, our results demonstrate for the first time the presence of a re-entrant condensation behavior for LPS molecules, which can be exploited for developing novel membrane-perturbing agents based on multivalent ions as efficient GNB antibiotics.

Silica dimerization in the presence of divalent cations.

The presence of monovalent cations and organic tetraalkylammonium ions is known to affect the reaction pathway and chemical kinetics of the silica oligomerization reaction which is important for sol-gel chemistry studies. A detailed theoretical study focusing on the chemical reaction pathway for the dimerisation process in the presence of a divalent cation is presented in this study. Different condensation pathways such as neutral, anionic-I and anionic-II along with their relative possibilities in dimerization have been explored. It has been demonstrated that with an increase in the pH of solution, manifested through the presence of deprotonated ions (as in the anionic cases with or without the presence of divalent cations), the activation activation barrier of the dimerization reaction is lowered. It has also been demonstrated that the addition of divalent cations raises the activation barriers for the reaction and delays the overall dimerisation reaction. The stability and bond characteristics of the bridging Si-OH bond of the resulting dimer products have also been determined. Activation energy barriers for the anionic case have also been observed to vary based upon the dihedral arrangement of the hydroxyl group bonded with the silicon and the orientation of the nucleophilic attack.

Recent Advances in the Structural Biology of Mg2+ Channels and Transporters.

Magnesium ions (Mg2+) are the most abundant divalent cations in living organisms and are essential for various physiological processes, including ATP utilization and the catalytic activity of numerous enzymes. Therefore, the homeostatic mechanisms associated with cellular Mg2+ are crucial for both eukaryotic and prokaryotic organisms and are thus strictly controlled by Mg2+ channels and transporters. Technological advances in structural biology, such as the expression screening of membrane proteins, in meso phase crystallization, and recent cryo-EM techniques, have enabled the structure determination of numerous Mg2+ channels and transporters. In this review article, we provide an overview of the families of Mg2+ channels and transporters (MgtE/SLC41, TRPM6/7, CorA/Mrs2, CorC/CNNM), and discuss the structural biology prospects based on the known structures of MgtE, TRPM7, CorA and CorC.

Consistent Picture of Phosphate-Divalent Cation Binding from Models with Implicit and Explicit Electronic Polarization.

The binding of divalent cations to the ubiquitous phosphate group is essential for a number of key biological processes, such as DNA compaction, RNA folding, or interactions of some proteins with membranes. Yet, probing their binding sites, modes, and associated binding free energy is a challenge for both experiments and simulations. In simulations, standard force fields strongly overestimate the interaction between phosphate groups and divalent cations. Here, we examine how different strategies to include electronic polarization effects in force fields─implicitly, through the use of scaled charges or pair-specific Lennard-Jones parameters, or explicitly, with the polarizable force fields Drude and AMOEBA─capture the interactions of a model phosphate compound, dimethyl phosphate, with calcium and magnesium divalent cations. We show that both implicit and explicit approaches, when carefully parameterized, are successful in capturing the overall binding free energy and that common trends emerge from the comparison of different simulation approaches. Overall, the binding is very moderate, slightly weaker for Ca2+ than Mg2+, and the solvent-shared ion pair is slightly more stable than the contact monodentate ion pair. The bidentate ion pair is higher in energy (or even fully unstable for Mg2+). Our results thus suggest practical ways to capture the divalent cations with biomolecular phosphate groups in complex biochemical systems. In particular, the computational efficiency of implicit models makes them ideally suited for large-scale simulations of biological assemblies, with improved accuracy compared to state-of-the-art fixed-charge force fields.

Reversible, ß-sheet-dependent self-assembly of the phosphoprotein phosvitin is controlled by the concentration and valency of cations.

The hyperphosphorylated protein phosvitin (PV) undergoes a pH-dependent transition between PII- and ß-sheet secondary structures, a process deemed crucial for its role in the promotion of biogenic apatite formation. The transition occurs surprisingly slowly (minutes to hours). This is consistent with a slow aggregation process involving ionic interactions of charged groups on the protein surface. Herein, we determined the associated transition pK values and time constants through matrix least-squares (MLS) global fitting of a series of pH- and time-dependent circular dichroism (CD) spectra recorded in the presence of different mono-, bi- and trivalent cations. Supporting our results with dynamic light scattering data, we clearly identified a close correlation of ß-sheet transition and the formation of small aggregates at low pH. This process is inhibited in the presence of all tested cations with the strongest effects for trivalent cations (Fe3+ and Al3+). In the presence of Ca2+ and Mg2+, larger higher-order particles are formed from PV in the ß-sheet conformation, as identified from the interpretation of differential scattering observed in the CD spectra. Our observations are consistent with the existence of a multi-step equilibrium between aggregated and non-aggregated species of PV. The equilibrium is highly sensitive to the environment pH and salt concentration with exceptional behavior in the presence of divalent cations such as Ca2+ and Mg2+.

A multiparametric fluorescence assay for screening aptamer-protein interactions based on microbeads.

For improving aptamer-ligand binding we have developed a screening system that defines optimal binding buffer composition. Using multiplex assays, one buffer system is needed which guarantees the specific binding of all aptamers. We investigated nine peer-reviewed DNA aptamers. Non-specific binding of aptamers is an obstacle. To address this, we investigated 16 proteins as specificity controls bound covalently to encoded microbeads in a multiplex assay. Increasing the NaCl concentration decreased the binding for all aptamers. Changing pH values by one unit higher or lower did not influence the aptamer binding significantly. However, pH < 5 led to non-specific binding for all aptamers. The PfLDH-aptamer selected in the absence of divalent cations exhibited doubling of its binding signal by the addition of Ca2+ and Mg2+. We confirmed Ca2+ and Mg2+ dependency of the aptamers for streptavidin and thrombin by observing a 90% and 50% binding decrease, respectively. We also achieved a doubling of binding for the streptavidin aptamer when replacing Ca2+ and Mg2+ by Mn2+. A buffer suitable for all aptamers can have considerable variations in pH or ionic strength, but divalent cations (Ca2+, Mg2+, Mn2+) are essential.

Ion-dependent slow protein release from in vivo disintegrating micro-granules.

Through the controlled addition of divalent cations, polyhistidine-tagged proteins can be clustered in form of chemically pure and mechanically stable micron-scale particles. Under physiological conditions, these materials act as self-disintegrating protein depots for the progressive release of the forming polypeptide, with potential applications in protein drug delivery, diagnosis, or theragnosis. Here we have explored the in vivo disintegration pattern of a set of such depots, upon subcutaneous administration in mice. These microparticles were fabricated with cationic forms of either Zn, Ca, Mg, or Mn, which abound in the mammalian body. By using a CXCR4-targeted fluorescent protein as a reporter building block we categorized those cations regarding their ability to persist in the administration site and to sustain a slow release of functional protein. Ca2+ and specially Zn2+ have been observed as particularly good promoters of time-prolonged protein leakage. The released polypeptides result is available for selective molecular interactions, such as specific fluorescent labeling of tumor tissues, in which the protein reaches nearly steady levels.