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Viscosity, or the "thickness," of aerosols plays a key role in atmospheric processes like ice formation, water absorption, and heterogeneous kinetics. However, the viscosity of sea spray aerosols (SSA) has not been widely studied. This research explored the relationship between particle size and viscosity of authentic SSA particles through particle bounce, atomic force microscopy analysis, and predictive viscosity modeling from molecular composition. The study found that 40 nm SSA particles had estimated viscosities around 10 4 Pa·s and bounce fractions three times higher than 100 and 200 nm particles with less than 10 2 Pa·s at a relative humidity (RH) of 60%. Additional studies revealed the Kelvin effect and particle density, influenced by particle size, have a greater impact on size-dependent bounce fractions than changes in RH across impactor stages. While changes in the level of surfactants can impact particle bounce, the increased viscosity in smaller SSA is attributed to the formation of gel-like phase states caused by cation-organic cross-links between divalent calcium ions and organic anions enriched in the smaller particles. This work shows the smallest gel-like SSA particles observed in the field are highly viscous, which has implications for cloud formation, secondary aerosol growth, and pollutant transport in coastal environments.

Artificial ion channel membranes hold high promise in water treatment, nanofluidics, and energy conversion, but it remains a great challenge to construct such smart membranes with both reversible ion-gating capability and desirable ion selectivity. Herein, we constructed a smart MXene-based membrane via p -phenylenediamine functionalization (MLM-PPD) with highly stable and aligned two-dimensional subnanochannels, which exhibits reversible ion-gating capability and ultrahigh metal ion selectivity similar to biological ion channels. The pH-sensitive groups within the MLM-PPD channel confers excellent reversible Mg 2+ -gating capability with a pH-switching ratio of up to 100. The mono/divalent metal-ion selectivity up to 1243.8 and 400.9 for K + /Mg 2+ and Li + /Mg 2+ , respectively, outperforms other reported membranes. Theoretical calculations combined with experimental results reveal that the steric hindrance and stronger PPD-ion interactions substantially enhance the energy barrier for divalent metal ions passing through the MLM-PPD, and thus leading to ultrahigh mono/divalent metal-ion selectivity. This work provides a new strategy for developing artificial-ion channel membranes with both reversible ion-gating functionality and high-ion selectivity for various applications.

The layered liquid crystalline phases formed by DNA molecules, which include rigid and flexible segments ("gapped DNA"), enable the study of both end-to-end stacking and side-to-side (helix-to-helix) lateral interactions, forming a model system to study such interactions at physiologically relevant DNA and ion concentrations. The observed layer structure exhibits long-range interlayer and in-layer positional correlations. In particular, the in-layer order has implications for DNA condensation, as it reflects whether these normally repulsive interactions become attractive under certain ionic conditions. Using synchrotron small-angle X-ray scattering measurements, we investigate the impact of divalent Mg 2+ cations (in addition to a constant 150 mM Na + ) on the stability of the inter- and in-layer DNA ordering as a function of temperature between 5 and 65 °C. DNA constructs with different terminal base pairings were created to mediate the strength of the attractive end-to-end stacking interactions between the blunt ends of the gapped DNA constructs. We demonstrate that the stabilities at a fixed DNA concentration of both interlayer and in-layer order are significantly enhanced even at a few mM Mg 2+ concentration. The stabilities are even higher at 30 mM Mg 2+ ; however, a marked decrease is observed at 100 mM Mg 2+ , suggesting a change in the nature of side-by-side interactions within this Mg 2+ concentration range. We discuss the implications of these results in terms of counterion-mediated DNA-DNA attraction and DNA condensation.

Manganese oxides can oxidize organic compounds, such as phenols, and may potentially be used in passive water treatment applications. However, the impact of common water constituents, including cations and dissolved organic matter (DOM), on this reaction is poorly understood. For example, the presence of DOM can increase or decrease phenol oxidation rates with manganese oxides. Furthermore, the interactions of DOM and cations and their impact on the phenol oxidation rates have not been examined. Therefore, we investigated the oxidation kinetics of six phenolic contaminants with acid birnessite in ten whole water samples. The oxidation rate constants of 4-chlorophenol, 4- tert -octylphenol, 4-bromophenol, and phenol consistently decreased in all waters relative to buffered ultrapure water, whereas the oxidation rate of bisphenol A and triclosan increased by up to 260% in some waters. Linear regression analyses and targeted experiments demonstrated that the inhibition of phenol oxidation is largely determined by cations. Furthermore, quencher experiments indicated that radical-mediated interactions from oxidized DOM contributed to enhanced oxidation of bisphenol A. The variable changes between compounds and water samples demonstrate the challenge of accurately predicting contaminant transformation rates in environmentally relevant systems based on experiments conducted in the absence of natural water constituents.

Molecular mechanics (MM) simulations have the potential to provide detailed insights into the mechanisms of enzymes that utilize nucleotides as cofactors. In most cases, the activities of these enzymes also require the binding of divalent cations to catalytic sites. However, modeling divalent cations in MM simulations has been challenging. The inclusion of explicit polarization was considered promising, but despite improvements over nonpolarizable force fields and despite the inclusion of "Nonbonded-fix (NB-fix)" corrections, errors in interaction energies of divalent cations with proteins remain large. Importantly, the application of these models fails to reproduce the experimental structural data on Mg 2+ ·Protein·ATP complexes. Focusing on these complexes, here we provide a systematic assessment of the polarizable AMOEBA model and recommend critical changes that substantially improve its predictive performance. Our key results are as follows. We first show that our recent revision of the AMOEBA protein model (AMOEBABIO18-HFC), which contains high field corrections (HFCs) to induced dipoles, dramatically improves Mg 2+ -protein interaction energies, reducing the mean absolute error (MAE) from 17 to 10 kcal/mol. This further supports the general applicability of AMOEBABIO18-HFC. The inclusion of many-body NB-fix corrections further reduces MAE to 6 kcal/mol, which amounts to less than 2% error. The errors are estimated with respect to vdW-inclusive density functional theory that we benchmark against CCSD(T) calculations and experiments. We also present a new model of ATP with revised polarization parameters to better capture its high field response, as well as new vdW and dihedral parameters. The ATP model accurately predicts experimental Mg 2+ -ATP binding free energy in the aqueous phase and provides new insights into how Mg 2+ associates with ATP. Finally, we show that molecular dynamics (MD) simulations of Mg 2+ ·Kinase·ATP complexes carried out with these improvements lead to a better agreement in global and local catalytic site structures between MD and X-ray crystallography.

The effects of CaCl 2 and MgCl 2 on the cloud point temperature of two different elastin-like polypeptides (ELPs) were studied using a combination of cloud point measurements, molecular dynamics simulations, and infrared spectroscopy. Changes in the cloud point for the ELPs in aqueous divalent metal cation solutions were primarily governed by two competing interactions: the cation-amide oxygen electrostatic interaction and the hydration of the cation. In particular, Ca 2+ cations can more readily shed their hydration shells and directly contact two amide oxygens by the formation of ion bridges. By contrast, Mg 2+ cations were more strongly hydrated and preferred to partition toward the amide oxygens along with their hydration shells. In fact, although hydrophilic ELP V 5 A 2 G 3 was salted-out at low concentrations of MgCl 2 , it was salted-in at higher salt concentrations. By contrast, CaCl 2 salted the ELP sharply out of solution at higher salt concentrations because of the bridging effect.

The denaturation of DNA is a critical process in biology and has many biotechnological applications. We investigated the compaction of locally denatured DNA by a chemical denaturation agent, dimethyl sulfoxide (DMSO), using magnetic tweezers (MTs), atomic force microscopy (AFM), and dynamic light scattering (DLS). Our results show that DMSO not only is capable of denaturing DNA but also able to compact DNA directly. When the DMSO concentration is above 10%, DNA condensation occurs due to the reduction in the persistence length of DNA and excluded volume interactions. Meanwhile, locally denatured DNA is easily condensed by divalent cations, such as magnesium ions (Mg 2+ ), contrasting with no native DNA condensation by the classical divalent cations. Specifically, the addition of more than 3 mM Mg 2+ to a 5% DMSO solution leads to DNA condensation. The critical condensing force ( F C ) increases from 6.4 to 9.5 pN when the Mg 2+ concentration grows from 3 to 10 mM. However, F C decreases gradually with a further increase in Mg 2+ concentration. For 3% DMSO solution, above 30 mM Mg 2+ is needed to compact DNA and a weaker condensing force was measured. With increasing Mg 2+ concentration, the morphology of the DMSO partially denatured DNA complex changes from loosely random coils to a dense network structure, even forming a spherical condensation nucleus, and finally to a partially disintegrated network. These findings show that the elasticity of DNA plays an important role in its denaturation and condensation behavior.

Understanding the fundamental reactivity of polymetallic complexes is challenging due to the complexity of their structures with many possible bond breaking and forming processes. Here, we apply ion mobility mass spectrometry coupled with density functional theory to investigate the disassembly mechanisms and energetics of a family of heterometallic rings and rotaxanes with the general formula [NH 2 RR'][Cr 7 MF 8 (O 2 C t Bu) 16 ] with M = Mn II , Fe II , Co II , Ni II , Cu II , Zn II , Cd II . Our results show that their stability can be tuned both by altering the d-metal composition in the macrocycle and by the end groups of the secondary ammonium cation [NH 2 RR'] + . Ion mobility probes the conformational landscape of the disassembly process from intact complex to structurally distinct isobaric fragments, providing unique insights to how a given divalent metal tunes the structural dynamics.

Colloidal single-walled carbon nanotubes (SWCNTs) offer a promising platform for the nanoscale engineering of molecular recognition. Optical sensors have been recently designed through the modification of noncovalent corona phases (CPs) of SWCNTs through a phenomenon known as corona phase molecular recognition (CoPhMoRe). In CoPhMoRe constructs, DNA CPs are of great interest due to the breadth of the design space and our ability to control these molecules with sequence specificity at scale. Utilizing these constructs for metal ion sensing is a natural extension of this technology due to DNA's well-known coordination chemistry. Additionally, understanding metal ion interactions of these constructs allows for improved sensor design for use in complex aqueous environments. In this work, we study the interactions between a panel of 9 dilute divalent metal cations and 35 DNA CPs under the most controlled experimental conditions for SWCNT optical sensing to date. We found that best practices for the study of colloidal SWCNT analyte responses involve mitigating the effects of ionic strength, dilution kinetics, laser power, and analyte response kinetics. We also discover that SWCNT with DNA CPs generally offers two unique sensing states at pH 6 and 8. The combined set of sensors in this work allowed for the differentiation of Hg 2+ , Pb 2+ , Cr 2+ , and Mn 2+ . Finally, we implemented Hg 2+ sensing in the context of portable detection within fish tissue extract, demonstrating nanomolar level detection.

The glyoxalase gene family consists of six structurally and functionally diverse enzymes with broad roles in metabolism. The common feature that defines this family is based on structural motifs that coordinate divalent cations which are required for activity. These family members have been implicated in a variety of physiological processes, including amino-acid metabolism (4-hydroxyphenylpyruvate dioxygenase; HPD ), primary metabolism (methylmalonyl-CoA epimerase; MCEE ), and aldehyde detoxication (glyoxalase 1; GLO1 ) and therefore have significant associations with disease. A central function of this family is the detoxification of reactive dicarbonyls (e.g., methylglyoxal), which react with cellular nucleophiles, resulting in the modification of lipids, proteins, and DNA. These damaging modifications activate canonical stress responses such as heat shock, unfolded protein, antioxidant, and DNA damage responses. Thus, glyoxalases serve an important role in homeostasis, preventing the pathogenesis of metabolic disease states, including obesity, diabetes, cardiovascular disease, renal failure, and aging. This review presents a thorough overview of the literature surrounding this diverse enzyme class. Although extensive literature exists for some members of this family (e.g., GLO1 ), little is known about the physiological role of glyoxalase domain-containing protein 4 ( GLOD4 ) and 5 ( GLOD5 ), paving the way for exciting avenues for future research.

Nanofiltration (NF), highly prospective for drinking water treatment, faces a challenge in simultaneously removing emerging contaminants while maintaining mineral salts, particularly divalent cations. To overcome this challenge, NF membranes possessing small pores concomitant with highly negatively charged surfaces were synthesized via a two-step fabrication strategy. The key is to generate a polyamide active layer having a loose and carboxyl group-abundant segment on top and a dense barrier segment underneath. This was achieved by restrained interfacial polymerization between trimesoyl chloride and partly protonated piperazine to form a highly depth-heterogeneous polyamide network, followed by second amidation in an organic environment to remove untethered polyamide fragments and associate malonyl chlorides with reserved amine groups to introduce more negative charges. Most importantly, on first-principle engineering the spatial architecture of the polyamide layer, amplifying asymmetric charge distribution was paired with the thinning of the vertical structure. The optimized membrane exhibits high salt/organic rejection selectivity and water permeance superior to most NF membranes reported previously. The rejections of eight emerging contaminants were in the range of 66.0-94.4%, much higher than the MgCl 2 rejection of 41.1%. This new fabrication strategy, suitable for various diacyl chlorides, along with the new membranes so produced, offers a novel option for NF in potable water systems.

Probing the protein surface accessibility of different residues is a powerful way of characterizing the overall conformation of intrinsically disordered proteins (IDPs). We present a two-dimensional (2D) time-resolved photo-CIDNP (TR-CIDNP) experiment suitable for IDP analysis. Pulse stretching of high-power laser pulses, band-selective decoupling of 13 C α , and simultaneous application of radiofrequency and laser pulses were implemented to quantitatively analyze the IDP surface at ultrahigh resolution. Comparative analysis with other methods that measure protein surface accessibility validated the newly developed method and emphasized the importance of dye charge in photo-CIDNP. Using the neutral riboflavin dye, surface accessibilities were measured to be nearly identical for the four Tyr residues of α-synuclein (α-Syn), whose 1 H α - 13 C α correlations were well-resolved in the 2D TR-CIDNP spectrum. Having confirmed the similarity between the time-resolved and steady-state photo-CIDNP results for α-Syn, we used the more sensitive latter method to show that divalent cations induce compaction of the C-terminal region and release of the N-terminal region of α-Syn. The photo-CIDNP method presented herein can be used as an orthogonal and independent method for investigating important biological processes associated with changes in the overall IDP conformation.

To enhance the use of nanofiltration in the production of quality drinking water, particularly through the efficient removal of micropollutants yet still preserving essential minerals, the targeted nanofiltration membranes (NFMs) are required to have small pore dimensions coupled with a high, net-negative charge density. Herein, after the formation of a separation layer using piperazine interfacially polymerized with trimesoyl chloride, the exploitation of residual amine groups was systematically investigated by different diacyl chlorides in an organic milieu, which caused the upper part of the final separation layer to be denser and highly negatively charged. Hence, this protocol offers a novel means to fabricate NFMs simultaneously endowed with a low molecular cutoff (MWCO) of 145-238 Da and a reduced rejection of MgCl 2 (48%-80%) as well as a competitive water permeance. Those features are ideally applicable to the goal of removing small micropollutants while preserving mineral ions, as needed for the energy-efficient production of safe, quality drinking water. Furthermore, an attempt was made to correlate MWCO with MgCl 2 rejection, which provides some insights on the nexus of the electrostatic effects constrained by size exclusion. The significance of residual amine groups and the modification environment was unveiled, and this method paves a new avenue for designing functional NFMs.

Transition metals such as zinc and copper are essential in numerous life processes, and both deficiency and toxic overload of these metals are associated with various diseases. Fluorescent metal sensors are powerful tools for studying the roles of metal ions in the physiology and pathology of biological systems. Green fluorescent protein (GFP) and its derivatives are highly utilized for protein-based sensor design, but application to anaerobic systems is limited because these proteins require oxygen to become fluorescent. Bacteriophytochrome-based monomeric near-infrared fluorescent proteins (miRFPs) covalently bind a bilin cofactor, which can be added exogenously for anaerobic cells. miRFPs can also have emission wavelengths extending to >700 nm, which is valuable for imaging applications. Here, we evaluated the suitability of miRFP670 and miRFP709 as platforms for single fluorescent protein metal ion sensors. We found that divalent metal ions like Zn 2+ , Co 2+ , Ni 2+ , and Cu 2+ can quench from ∼6-20% (Zn 2+ , Co 2+ , and Ni 2+ ) and up to nearly 90% (Cu 2+ ) of the fluorescence intensity of pure miRFPs and have similar impacts in live Escherichia coli cells expressing miRFPs. The presence of a 6× histidine tag for purification influences metal quenching, but significant Cu 2+ -induced quenching and a picomolar binding affinity are retained in the absence of the His 6 tag in both cuvettes and live bacterial cells. By comparing the Cu 2+ and Cu + -induced quenching results for miRFP670 and miRFP709 and through examining absorption spectra and previously reported crystal structures, we propose a surface metal binding site near the biliverdin IXα chromophore.

Metal processing using microorganisms has many advantages including the potential for reduced environmental impacts as compared to conventional technologies. Acidithiobacillus ferrooxidans is an iron- and sulfur-oxidizing chemolithoautotroph that is known to participate in metal bioleaching, and its metabolic capabilities have been exploited for industrial-scale copper and gold biomining. In addition to bioleaching, microorganisms could also be engineered for selective metal binding, enabling new opportunities for metal bioseparation and recovery. Here, we explored the ability of polyhistidine (polyHis) tags appended to two recombinantly expressed endogenous proteins to enhance the metal binding capacity of A. ferrooxidans . The genetically engineered cells achieved enhanced cobalt and copper binding capacities, and the Langmuir isotherm captures their interaction behavior with these divalent metals. Additionally, the cellular localization of the recombinant proteins correlated with kinetic modeling of the binding interactions, where the outer membrane-associated polyHis-tagged licanantase peptide bound the metals faster than the periplasmically expressed polyHis-tagged rusticyanin protein. The selectivity of the polyHis sequences for cobalt over copper from mixed metal solutions suggests potential utility in practical applications, and further engineering could be used to create metal-selective bioleaching microorganisms.

The interactions of DNA molecules and metal ions lead to changes in their configuration and conformation, which in turn influence the current characteristics of the solution as DNA molecules are translocated through a micro/nanofluidic channel and ultimately cause serious impacts on the practical applications of DNA/gene chips for precisely manipulating and studying the molecular properties of single DNA molecules. In this study, the current characteristics of λ-DNA solutions without or with metal ions (i.e., K + , Na + , Mg 2+ , and Ca 2+ ) were experimentally investigated when they were transported through a 5 μm microcapillary under an external electric field with asymmetric electrodes. Experimental data indicated some meaningful results. First, the current-voltage relations of the metal ion solutions were all linear, while those of λ-DNA solutions without or with metal ions were all nonlinear and followed power functions, of which the indices were related to the type, valence, and mobility of ions. Furthermore, as the concentrations of metal ions increased, the power indices of the λ-DNA solutions with monovalent metal ions increased, while those of the λ-DNA solutions with divalent ions decreased. Finally, the main reasons for the current characteristics were theoretically attributed to two possible mechanisms: the polarizations on the asymmetric electrodes and the interactions between λ-DNA and metal ions. These findings are helpful for the design of new biomedical micro/nanofluidic sensors and labs on a chip for accurately manipulating single DNA molecules.

Fibrinogen nanofibers are very attractive biomaterials to mimic the native blood clot architecture. Previously, we reported the self-assembly of fibrinogen nanofibers in the presence of monovalent salts and have now studied how divalent salts influence fibrinogen precipitation. Although the secondary fibrinogen structure was significantly altered with divalent metal ions, morphological analysis revealed exclusively smooth fibrinogen precipitates. In situ monitoring of the surface roughness facilitated predicting the tendency of various salts to form fibrinogen fibers or smooth films. Analysis of the chemical composition revealed that divalent salts were removed from smooth fibrinogen films upon rinsing while monovalent Na + species were still present in fibrinogen fibers. Therefore, we assume that the decisive factor controlling the morphology of fibrinogen precipitates is direct ion-protein contact, which requires disruption of the ion-surrounding hydration shells. We conclude that in fibrinogen aggregates, this mechanism is effective only for monovalent ions, whereas divalent ions are limited to indirect fibrinogen adsorption.

Divalent calcium ion (Ca 2+ ) plays an indispensable role as a second messenger in a myriad of signal transduction processes. Of utmost importance for the faultless functioning of calcium-modulated signaling proteins is their binding selectivity of the native metal cation over rival biogenic/abiogenic metal ion contenders in the intra/extracellular fluids. In this Perspective, we summarize recent findings on the competition between the cognate Ca 2+ and other biogenic or abiogenic divalent cations for binding to Ca 2+ -signaling proteins or organic cofactors. We describe the competition between the two most abundant intracellular biogenic metal ions (Mg 2+ and Ca 2+ ) for Ca 2+ -binding sites in signaling proteins, followed by the rivalry between native Ca 2+ and "therapeutic" Li + as well as "toxic" Pb 2+ . We delineate the key factors governing the rivalry between the native and non-native cations in proteins and highlight key implications for the biological performance of the respective proteins/organic cofactors.

Divalent cations, especially Ca 2+ and Mg 2+ , play a vital role in the function of biomolecules and making them important to be constituents in samples for in vitro biophysical and biochemical characterizations. Although lipid nanodiscs are becoming valuable tools for structural biology studies on membrane proteins and for drug delivery, most types of nanodiscs used in these studies are unstable in the presence of divalent metal ions. To avoid the interaction of divalent metal ions with the belt of the nanodiscs, synthetic polymers have been designed and demonstrated to form stable lipid nanodiscs under such unstable conditions. Such polymer-based nanodiscs have been shown to provide an ideal platform for structural studies using both solid-state and solution NMR spectroscopies because of the near-native cell-membrane environment they provide and the unique magnetic-alignment behavior of large-size nanodiscs. In this study, we report an investigation probing the effects of Ca 2+ and Mg 2+ ions on the formation of polymer-based lipid nanodiscs and the magnetic-alignment properties using a synthetic polymer, styrene maleimide quaternary ammonium (SMA-QA), and 1,2-dimyristoyl- sn -glycero-3-phosphocholine (DMPC) lipids. Phosphorus-31 NMR experiments were used to evaluate the stability of the magnetic-alignment behavior of the nanodiscs for varying concentrations of Ca 2+ or Mg 2+ at different temperatures. It is remarkable that the interaction of divalent cations with lipid headgroups promotes the stacking up of nanodiscs that results in the enhanced magnetic alignment of nanodiscs. Interestingly, the reported results show that both the temperature and the concentration of divalent metal ions can be optimized to achieve the optimal alignment of nanodiscs in the presence of an applied magnetic field. We expect the reported results to be useful in the design of nanodisc-based nanoparticles for various applications in addition to atomic-resolution structural and dynamics studies using NMR and other biophysical techniques.

Self-assembled monolayers are attractive for surface modification due to their ease of synthesis and the range of chemical functionality that can be applied. Metal-phosphonate monolayer properties can be controlled through the metal ions that can be used in their formation. The organization and fluid properties of these monolayers can be understood in the context of their thermodynamic properties and the association and dissociation kinetics that proceed at the metal-phosphonate complex. In this work, four different M(II)-phosphonate monolayers were synthesized and the diffusional behavior of free and tethered chromophores was evaluated using fluorescence recovery after photobleaching measurements. The ω-terminal group identity of the metal-phosphonate monolayer was varied to determine its effect on monolayer dynamics.

In several neurodegenerative diseases, cell toxicity can emerge from damage produced by amyloid aggregates to lipid membranes. The details accounting for this damage are poorly understood including how individual amyloid peptides interact with phospholipid membranes before aggregation. Here, we use all-atom molecular dynamics simulations to investigate the molecular mechanisms accounting for amyloid-membrane interactions and the role played by calcium ions in this interaction. Model peptides known to self-assemble into amyloid fibrils and bilayer made from zwitterionic and anionic lipids are used in this study. We find that both electrostatic and hydrophobic interactions contribute to peptide-bilayer binding. In particular, the attraction of peptides to lipid bilayers is dominated by electrostatic interactions between positive residues and negative phosphate moieties of lipid head groups. This attraction is stronger for anionic bilayers than for zwitterionic ones. Hydrophobicity drives the burial of nonpolar residues into the interior of the bilayer producing strong binding in our simulations. Moreover, we observe that the attraction of peptides to the bilayer is significantly reduced in the presence of calcium ions. This is due to the binding of calcium ions to negative phosphate moieties of lipid head groups, which leaves phospholipid bilayers with a net positive charge. Strong binding of the peptide to the membrane occurs less frequently in the presence of calcium ions and involves the formation of a "Ca 2+ bridge".

We demonstrate the remarkable ability of surface-enhanced Raman spectroscopy (SERS) to track the allosteric changes in restriction endonuclease KpnI (R.KpnI) caused by metal ions. R.KpnI binds and promiscuously cleaves DNA upon activation by Mg 2+ ions. However, the divalent ion Ca 2+ induces high fidelity cleavage, which can be overcome by higher concentrations of Mg 2+ ions. In the absence of any 3D crystal structure, for the first time, we have elucidated the structural underpinnings of such a differential effect of divalent ions on the endonuclease activity. A combined SERS and molecular dynamics (MD) approach showed that Ca 2+ ion activates an enzymatic switch in the active site, which is responsible for the high fidelity activity of the enzyme. Thus, SERS in combination with MD simulations provides a powerful tool for probing the link between the structure and activity of enzyme molecules that play vital roles in DNA transactions.

The emergence of new pathogens and multidrug resistant bacteria is an important public health issue that requires the development of novel classes of antibiotics. Antimicrobial peptides (AMPs) are a promising platform with great potential for the identification of new lead compounds that can combat the aforementioned pathogens due to their broad-spectrum antimicrobial activity and relatively low rate of resistance emergence. AMPs of multicellular organisms made their debut four decades ago thanks to ingenious researchers who asked simple questions about the resistance to bacterial infections of insects. Questions such as "Do fruit flies ever get sick?", combined with pioneering studies, have led to an understanding of AMPs as universal weapons of the immune system. This review focuses on a subclass of AMPs that feature a metal binding motif known as the amino terminal copper and nickel (ATCUN) motif. One of the metal-based strategies of hosts facing a pathogen, it includes wielding the inherent toxicity of copper and deliberately trafficking this metal ion into sites of infection. The sudden increase in the concentration of copper ions in the presence of ATCUN-containing AMPs (ATCUN-AMPs) likely results in a synergistic interaction. Herein, we examine common structural features in ATCUN-AMPs that exist across species, and we highlight unique features that deserve additional attention. We also present the current state of knowledge about the molecular mechanisms behind their antimicrobial activity and the methods available to study this promising class of AMPs.

Although molecular dynamics simulations allow for the study of interactions among virtually all biomolecular entities, metal ions still pose significant challenges in achieving an accurate structural and dynamical description of many biological assemblies, particularly to coarse-grained (CG) models. Although the reduced computational cost of CG methods often makes them the technique of choice for the study of large biomolecular systems, the parameterization of metal ions is still very crude or not available for the vast majority of CG force fields. Here, we show that incorporating statistical data retrieved from the Protein Data Bank (PDB) to set specific Lennard-Jones interactions can produce structurally accurate CG molecular dynamics simulations using the SIRAH force field. We provide a set of interaction parameters for calcium, magnesium, and zinc ions, which cover more than 80% of the metal-bound structures reported in the PDB. Simulations performed on several proteins and DNA systems show that it is possible to preclude the use of topological constraints by modifying specific Lennard-Jones interactions.

Zwitterionic peptides are great candidates as antifouling coating materials in many biomedical applications. We investigated the structure and antifouling properties of surface-tethered zwitterionic peptide monolayers with different peptide chain lengths and charge distributions using a combination of surface plasma resonance, atomic force microscopy, and all atomistic molecular dynamics (MD) simulation techniques. Our results demonstrate that zwitterionic peptides with more zwitterionic lysine (K) and glutamic acid (E) repeating units exhibit better antifouling performance. The block charge distributions of the positive and negative charges in the peptides (having multiple positive charges next to the same amount of negative charges), although affecting the structure of the peptide molecules, do not significantly change the antifouling properties of the peptide monolayers in the solutions containing monovalent ions. However, divalent cations, Ca 2+ and Mg 2+ , in solution can significantly alter the structure and lower the antifouling performance of the zwitterionic peptide monolayers, especially with the sequences of block charges. All atomistic MD simulations quantitatively reveal that the divalent cations in solution lead to more interchain electrostatic cross-links between peptide chains, especially for peptides with block charges, which causes dehydration of the zwitterionic peptides and diminishes their antifouling performances.

Divalent cations are often required to fold RNA, which is a highly charged polyanion. Condensation of ions, such as Mg 2+ or Ca 2+ , in the vicinity of RNA renormalizes the effective charges on the phosphate groups, thus minimizing the intra RNA electrostatic repulsion. The prevailing view is that divalent ions bind diffusively in a nonspecific manner. In sharp contrast, we arrive at the exact opposite conclusion using a theory for the interaction of ions with the phosphate groups using RISM theory in conjunction with simulations based on an accurate three-interaction-site RNA model. The divalent ions bind in a nucleotide-specific manner using either the inner (partially dehydrated) or outer (fully hydrated) shell coordination. The high charge density Mg 2+ ion has a preference to bind to the outer shell, whereas the opposite is the case for Ca 2+ . Surprisingly, we find that bridging interactions, involving ions that are coordinated to two or more phosphate groups, play a crucial role in maintaining the integrity of the folded state. Their importance could become increasingly prominent as the size of the RNA increases. Because the modes of interaction of divalent ions with DNA are likely to be similar, we propose that specific inner and outer shell coordination could play a role in DNA condensation, and perhaps genome organization as well.

Although two-dimensional titanium carbide (Ti 3 C 2 T x MXene) has emerged as a shining star material in various communities, its environmental behaviors and fate remain unknown. Herein, the colloidal properties and stability of Ti 3 C 2 T x MXene are explored in aquatic systems for the first time, considering the roles of solution chemistry conditions (e.g., pH, ionic types, and strength). It was found that pH had no effect on the stability of Ti 3 C 2 T x in the range of 5.0-11.0, whereas ionic valence and concentrations displayed significant effects on the aggregation behavior of Ti 3 C 2 T x . By employing time-resolved dynamic light scattering measurements, the critical coagulation concentration (CCC) value of Ti 3 C 2 T x was determined to be 12 mM for NaCl. The divalent cations Ca 2+ and Mg 2+ exhibited higher destabilizing capacity to Ti 3 C 2 T x , as evidenced by the lower CCC values (0.3 and 0.4 mM for CaCl 2 and MgCl 2 , respectively) and faster coagulation rates. Long-term stability studies implied that Ti 3 C 2 T x MXene was less likely to be transported over long distances in the synthetic or natural waters. These findings provided significant insights into the fate and transport of Ti 3 C 2 T x in the aquatic environment.

Knowledge of the nature of exchangeable (labile) intracellular Zn(II) is increasingly important for biomedical research. The detection and quantitative determination of Zn(II) ions is usually performed by using Zn(II)-specific fluorescent sensors, among which 2-[2-[2-[2-[bis(carboxylatomethyl)amino]-5-methoxyphenoxy]ethoxy]-4-(2,7-difluoro-3-oxido-6-oxo-4a,9a-dihydroxanthen-9-yl)anilino]acetate (FluoZin-3) has been used most widely. Selectivity of this sensor for Zn(II) over other divalent cations was demonstrated, but possible interference in its performance by other compounds has not been investigated. Many potential low molecular weight ligands for Zn(II) ions (LMWLs) are abundant in the cell. In this study we demonstrate that FluoZin-3 is susceptible to competition for Zn(II) from LMWLs and also forms strong ternary complexes with some of them. We determined the set of conditional stability constants C K tern for ternary Zn(FluoZin-3)(LMWL) complexes using fluorescence titrations and applied it to model the response of exchangeable zinc to FluoZin-3. We found that competition and formation of ternary complexes with LMWLs together strongly affect (net reduce) the Zn(FluoZin-3) fluorescence. This effect may cause a significant underestimation of exchangeable Zn(II). We also demonstrated a strong pH dependence of this effect. Reduced glutathione (GSH) emerged as the most important Zn(II) partner among the LMWLs, characterized with K tern = 2.8 ± 0.2 × 10 6 M -1 . Our experiments and calculations suggest that Zn(LMWL) complexes contribute to the exchangeable cellular zinc pool.

Herein, new near-infrared (NIR) luminescent ruthenium complexes were prepared for detecting Cu 2+ ions. Then, ruthenium complex hybrid nanomaterials (Ru-LPMSNs) were fabricated successfully by imbedding the ruthenium complex into mesoporous silica nanoparticles. Benefiting from the novel large-pore mesoporous structure and good adsorbility of LPMSNs, Ru-LPMSN hybrid materials showed a significantly enhanced fluorescence intensity and stability. NIR fluorescence of Ru-LPMSNs was rapidly quenched by Cu 2+ ions. Ru-LPMSNs also showed high Cu 2+ ion selectivity and sensitivity as a sensor. The detection limit of Cu 2+ ions was 10 nM with a wide linear relationship between the fluorescence intensity of Ru-LPMSNs and the concentration of Cu 2+ ions. The mechanism of fluorescence quenching might be that the combination of the ruthenium complex and Cu 2+ ions constrained the photoinduced electron-transfer process. Furthermore, Ru-LPMSNs dramatically increased the fluorescence signals in cells and achieved Cu 2+ -ion detection. Ru-LPMSNs had different tissue affinities and could monitor distribution of exogenous Cu 2+ ions in vivo. Moreover, Ru-LPMSNs realized direct and rapid detection of Cu 2+ -ion content in serum. These results indicated the potential applications of the prepared nanomaterials as Cu 2+ detection agents.

The fluorescent probe for the detection of calcium ions is an indispensable tool in the biomedical field. The millimolar order of Ca(II) ions is associated with many physiological processes and diseases, such as hypercalcemia, soft tissue calcification, and bone microcracks. However, the conventional fluorescent probes are only suitable for imaging Ca(II) ions in the nanomolar to micromolar range, which can be because of their high affinities toward Ca(II) ions and aggregation-caused quenching drawbacks. To tackle this challenge, we herein develop an aggregation-induced emission (AIE) probe SA-4CO 2 Na for selective and light-up detection of Ca(II) ions in the millimolar range (0.6-3.0 mM), which can efficiently distinguish between hypercalcemic (1.4-3.0 mM) and normal (1.0-1.4 mM) Ca 2+ ion levels. The formation of fibrillar aggregates between SA-4CO 2 Na and Ca(II) ions was clearly verified by fluorescence, scanning electron microscopy, and transmission electron analysis. Moreover, this AIE-active probe can be used for wash-free and light-up imaging of a high concentration of Ca(II) ions even in the solid analytes, including calcium deposits in psammomatous meningioma slice, microcracks on bovine bone surface, and microdefects on hydroxyapatite-based scaffold. It is thus expected that this AIE-active probe would have broad biomedical applications through light-up imaging and sensing of Ca(II) ions at the millimolar level.

A highly selective two-point separation strategy was designed based on a cross-like all-in-one lab-on-paper analytical device. The stable and cleavable enzyme-coated reduced graphene oxide (rGO)-PdAu probe was fabricated as the signal reporter to enable the visualization and electrochemiluminescence (ECL) dual-mode sensing of Pb 2+ . Concretely, the experimental workflow consists of the following process: (i) fabrication of the lab-on-paper device and growth of Au nanoparticles on ECL detection zone, (ii) immobilization of Pb 2+ -specific DNAzyme, and (iii) hybridization between DNAzyme and rGO-PdAu-glucose oxidase (GOx) labeled oligonucleotide to form the double-stranded DNA. Upon addition of Pb 2+ into the prepared system, the double-helix structure of the DNA was destroyed, resulting in the release of cleaved rGO-PdAu-GOx probe to visualization bar to promote the effective oxidation and color change of 3,3',5,5'-tetramethylbenzidine. As a consequence, the color change can be recognized by naked eye, meanwhile GOx on an uncleaved signal probe can oxidize glucose along with the H 2 O 2 production. As a co-reaction reagent for luminol ECL system, the concentration of H 2 O 2 is proportional to the ECL intensity, which constitutes a new mechanism for colorimetric and ECL dual mode to detect Pb 2+ . With the method developed here, the concentration of Pb 2+ could be easily determined by the naked eye within a linear range from 5 to 2000 nM, as well as by monitoring the decreased ECL intensity of luminol in a linear range of 0.5-2000 nM. This work not only constructs a simple and versatile platform for on-site visible monitoring of Pb 2+ in tap water and river water but also furnishes a strategy for designing a dual-mode sensing toward different heavy metal ions based on specific DNAzyme in the fields of environmental monitoring-related technologies.

The development of an inorganic-organic hybrid probe to more accurately detect ions in living systems is very challenging but highly desirable. Here we combined upconversion nanoparticles with the electrically active ferrocene group to detect Cu 2+ in living cells. The as-prepared probe displays three different signal changes in absorption, emission, and electrochemical behavior, respectively, during Cu 2+ ion detection. Moreover, this new probe has been demonstrated to show high stability and adaptability. In addition, bioimaging testing reveals that this probe is suitable for detecting and visualizing Cu 2+ in A549 cells with low cytotoxicity.

Experimental and theoretical studies on ion-lipid interactions predict that binding of calcium ions to cell membranes leads to macroscopic mechanical effects and membrane remodeling. Herein, we provide experimental evidence that a point source of Ca 2+ acting upon a negatively charged membrane generates spontaneous curvature and triggers the formation of tubular protrusions that point away from the ion source. This behavior is rationalized by strong binding of the divalent cations to the surface of the charged bilayer, which effectively neutralizes the surface charge density of outer leaflet of the bilayer. The mismatch in the surface charge density of the two leaflets leads to nonzero spontaneous curvature. We probe this mismatch through the use of molecular dynamics simulations and validate that calcium ion binding to a lipid membrane is sufficient to generate inward spontaneous curvature, bending the membrane. Additionally, we demonstrate that the formed tubular protrusions can be translated along the vesicle surface in a controlled manner by repositioning the site of localized Ca 2+ exposure. The findings demonstrate lipid membrane remodeling in response to local chemical gradients and offer potential insights into the cell membrane behavior under conditions of varying calcium ion concentrations.

We atomistically compute the change in free energy upon binding of the globular domain of the complement protein C1q to carbon nanotubes (CNTs) and graphene in solution. Our modeling results imply that C1q is able to disaggregate and disperse bundles of large diameter multiwalled CNTs but not those of thin single-walled CNTs, and we validate this prediction with experimental observations. The results support the view of a strong binding with potential implications for the understanding of the immune response and biomedical applications of graphitic nanomaterials.

Most RNA-cleaving DNAzymes require a metal ion to interact with the scissile phosphate for activity. Therefore, few unmodified DNAzymes work with thiophilic metals because of their low affinity for phosphate. Recently, an Ag + -specific Ag10c DNAzyme was reported via in vitro selection. Herein, Ag10c is characterized to rationalize the role of the strongly thiophilic Ag + . Systematic mutation studies indicate that Ag10c is a highly conserved DNAzyme and its Ag + binding is unrelated to C-Ag + -C interaction. Its activity is enhanced by increasing Na + concentrations in buffer. At the same metal concentration, activity decreases in the following order: Li + > Na + > K + . Ag10c binds one Na + ion and two Ag + ions for catalysis. The pH-rate profile has a slope of ∼1, indicating a single deprotonation step. Phosphorothioate substitution at the scissile phosphate suggests that Na + interacts with the pro-R p oxygen of the phosphate, and dimethyl sulfate footprinting indicates that the DNAzyme loop is a silver aptamer binding two Ag + ions. Therefore, Ag + exerts its function allosterically, while the scissile phosphate interacts with Na + , Li + , Na + , or Mg 2+ . This work suggests the possibility of isolating thiophilic metal aptamers based on DNAzyme selection, and it also demonstrates a new Ag + aptamer.

In the following, molecular simulations are used to reveal unexpected behavior within bacterial membranes. We show that lipopolysaccharide molecules found in these membranes form viscous amorphous solids when they are interlinked with monovalent and divalent cations. The bilayers exhibit both liquid and glassy characteristics, due to the coexistence of both liquid and crystalline domains in the bilayer. Polymyxin B1, a potent antimicrobial peptide, is shown to increase order within the lipopolysaccharide bilayers by inducing the formation of crystalline patches. Crucially we are able to decompose the energetics of insertion into their enthalpic and entropic components. The present coarse-grain molecular dynamics study provides unprecedented insights into the antibacterial action of antimicrobial peptides, thus paving the way for development of novel therapeutic agents to treat multiple drug resistant Gram-negative bacteria.

Zinc-finger proteins are regulators of critical signaling pathways for various cellular functions, including apoptosis and oncogenesis. Here, we investigate how binding site protonation states and zinc coordination influence protein structure, dynamics, and ultimately function, as these pivotal regulatory proteins are increasingly important for protein engineering and therapeutic discovery. To better understand the thermodynamics and dynamics of the zinc finger of NEMO (NF-κB essential modulator), as well as the role of zinc, we present results of 20 μs molecular dynamics trajectories, 5 μs for each of four active site configurations. Consistent with experimental evidence, the zinc ion is essential for mechanical stabilization of the functional, folded conformation. Hydrogen bond motifs are unique for deprotonated configurations yet overlap in protonated cases. Correlated motions and principal component analysis corroborate the similarity of the protonated configurations and highlight unique relationships of the zinc-bound configuration. We hypothesize a potential mechanism for zinc binding from results of the thiol configurations. The deprotonated, zinc-bound configuration alone predominantly maintains its tertiary structure throughout all 5 μs and alludes rare conformations potentially important for (im)proper zinc-finger-related protein-protein or protein-DNA interactions.

The EutT enzyme from Salmonella enterica, a member of the family of ATP:cobalt(I) corrinoid adenosyltransferase (ACAT) enzymes, requires a divalent transition metal ion for catalysis, with Fe(II) yielding the highest activity. EutT contains a unique cysteine-rich HX 11 CCX 2 C(83) motif (where H and the last C occupy the 67th and 83rd positions, respectively, in the amino acid sequence) not found in other ACATs and employs an unprecedented mechanism for the formation of adenosylcobalamin. Recent kinetic and spectroscopic studies of this enzyme revealed that residues in the HX 11 CCX 2 C(83) motif are required for the tight binding of the divalent metal ion and are critical for the formation of a four-coordinate (4c) cob(II)alamin [Co(II)Cbl] intermediate in the catalytic cycle. However, it remained unknown which, if any, of the residues in the HX 11 CCX 2 C(83) motif bind the divalent metal ion. To address this issue, we have characterized Co(II)-substituted wild-type EutT (EutT WT /Co) by using electronic absorption, electron paramagnetic resonance, and magnetic circular dichroism (MCD) spectroscopies. Our results indicate that the reduced catalytic activity of EutT WT /Co relative to that of the Fe(II)-containing enzyme arises from the incomplete incorporation of Co(II) ions and, thus, a decrease in the relative population of 4c Co(II)Cbl. Our MCD data for EutT WT /Co also reveal that the Co(II) ions reside in a distorted tetrahedral coordination environment with direct cysteine sulfur ligation. Additional spectroscopic studies of EutT/Co variants possessing a single alanine substitution of either His67, His75, Cys79, Cys80, or Cys83 indicate that Cys80 coordinates to the Co(II) ion, while the additional residues are important for maintaining the structural integrity and/or high affinity of the metal binding site.