Microscopic insight to specificity of metal ion cofactor in DNA cleavage by restriction endonuclease EcoRV.

Restriction endonucleases protect bacterial cells against bacteriophage infection by cleaving the incoming foreign DNA into fragments. In presence of Mg2+ ions, EcoRV is able to cleave the DNA but not in presence of Ca2+ , although the protein binds to DNA in presence of both metal ions. We make an attempt to understand this difference using conformational thermodynamics. We calculate the changes in conformational free energy and entropy of conformational degrees of freedom, like DNA base pair steps and dihedral angles of protein residues in Mg2+ (A)-EcoRV-DNA complex compared to Ca2+ (S)-EcoRV-DNA complex using all-atom molecular dynamics (MD) trajectories of the complexes. We find that despite conformational stability and order in both complexes, the individual degrees of freedom behave differently in the presence of two different metal ions. The base pairs in cleavage region are highly disordered in Ca2+ (S)-EcoRV-DNA compared to Mg2+ (A)-EcoRV-DNA. One of the acidic residues ASP90, coordinating to the metal ion in the vicinity of the cleavage site, is conformationally destabilized and disordered, while basic residue LYS92 gets conformational stability and order in Ca2+ (S) bound complex than in Mg2+ (A) bound complex. The enhanced fluctuations hinder placement of the metal ion in the vicinity of the scissile phosphate of DNA. Similar loss of conformational stability and order in the cleavage region is observed by the replacement of the metal ion. Considering the placement of the metal ion near scissile phosphate as requirement for cleavage action, our results suggest that the changes in conformational stability and order of the base pair steps and the protein residues lead to cofactor sensitivity of the enzyme. Our method based on fluctuations of microscopic conformational variables can be applied to understand enzyme activities in other protein-DNA systems.

Molecular mechanism of water reorientational slowing down in concentrated ionic solutions.

Water dynamics in concentrated ionic solutions plays an important role in a number of material and energy conversion processes such as the charge transfer at the electrolyte-electrode interface in aqueous rechargeable ion batteries. One long-standing puzzle is that all electrolytes, regardless of their "structure-making/breaking" nature, make water rotate slower at high concentrations. To understand this effect, we present a theoretical simulation study of the reorientational motion of water molecules in different ionic solutions. Using an extended Ivanov model, water rotation is decomposed into contributions from large-amplitude angular jumps and a slower frame motion which was studied in a coarse-grained manner. Bearing a certain resemblance to water rotation near large biological molecules, the general deceleration is found to be largely due to the coupling of the slow, collective component of water rotation with the motion of large hydrated ion clusters ubiquitously existing in the concentrated ionic solutions. This finding is at variance with the intuitive expectation that the slowing down is caused by the change in fast, single-molecular water hydrogen bond switching adjacent to the ions.

Ion Selectivity in Nonpolymeric Thermosensitive Systems Induced by Water-Attenuated Supramolecular Recognition.

The chemistry of aqueous salt solutions is rich with ambiguities, especially in stimuli-responsive supramolecular systems. Rational use of ion specificity to design supramolecular responsive materials, however, remains a challenging task. In this work, a low-molecular-weight supramolecular system was developed that was used to reveal the underlying systematic relationship between ions, water, and solutes. By utilizing these water-attenuated supramolecular forces (with Ka only ca. 30 m-1 ), an alternative concept for fabricating an aqueous responsive system in ionic medium was demonstrated. This work not only provides mechanistic insight into the underdeveloped role of topology in ion specificity upon noncharged polar surfaces, but also demonstrates the feasibility of utilizing weak supramolecular approaches to control the thermoresponsiveness.

Ion Specificity on Electric Energy Generated by Flowing Water Droplets.

The development of energy-conversion devices using water movement has actively progressed. Ionovoltaic devices, which are driven by ion dynamics, show ion specificity by which different ions with identical charges show different output performance. However, the ion specificity remains poorly understood because the influence of the ion species on generated electric signals is not elucidated. The ion specificity in electric signals induced by flowing water droplet was investigated in terms of its relationship with the potential profile across the solid-liquid interface.

Sodium recognition by the Na+/Ca2+ exchanger in the outward-facing conformation.

Na(+)/Ca(2+) exchangers (NCXs) are ubiquitous membrane transporters with a key role in Ca(2+) homeostasis and signaling. NCXs mediate the bidirectional translocation of either Na(+) or Ca(2+), and thus can catalyze uphill Ca(2+) transport driven by a Na(+) gradient, or vice versa. In a major breakthrough, a prokaryotic NCX homolog (NCX_Mj) was recently isolated and its crystal structure determined at atomic resolution. The structure revealed an intriguing architecture consisting of two inverted-topology repeats, each comprising five transmembrane helices. These repeats adopt asymmetric conformations, yielding an outward-facing occluded state. The crystal structure also revealed four putative ion-binding sites, but the occupancy and specificity thereof could not be conclusively established. Here, we use molecular-dynamics simulations and free-energy calculations to identify the ion configuration that best corresponds to the crystallographic data and that is also thermodynamically optimal. In this most probable configuration, three Na(+) ions occupy the so-called Sext, SCa, and Sint sites, whereas the Smid site is occupied by one water molecule and one H(+), which protonates an adjacent aspartate side chain (D240). Experimental measurements of Na(+)/Ca(2+) and Ca(2+)/Ca(2+) exchange by wild-type and mutagenized NCX_Mj confirm that transport of both Na(+) and Ca(2+) requires protonation of D240, and that this side chain does not coordinate either ion at Smid. These results imply that the ion exchange stoichiometry of NCX_Mj is 3:1 and that translocation of Na(+) across the membrane is electrogenic, whereas transport of Ca(2+) is not. Altogether, these findings provide the basis for further experimental and computational studies of the conformational mechanism of this exchanger.

Cation-Selective Channel Regulated by Anions According to Their Hofmeister Ranking.

Specificity of small ions, the Hofmeister ranking, is long-known and has many applications including medicine. Yet it evades consistent theoretical description. Here we study the effect of Hofmeister anions on gramicidin A channels in lipid membranes. Counterintuitively, we find that conductance of this perfectly cation-selective channel increases about two-fold in the H2 PO4-

Electrolyte-induced aggregation of zein protein nanoparticles in aqueous dispersions.

Ion specific effects on the charging and aggregation features of zein nanoparticles (ZNP) were studied in aqueous suspensions by electrophoretic and time-resolved dynamic light scattering techniques. The influence of mono- and multivalent counterions on the colloidal stability was investigated for positively and negatively charged particles at pH values below and above the isoelectric point, respectively. The sequence of the destabilization power of monovalent salts followed the prediction of the indirect Hofmeister series for positively charged particles, while the direct Hofmeister series for negatively charged ones assumed a hydrophobic character for their surface. The multivalent ions destabilized the oppositely charged ZNPs more effectively and the aggregation process followed the Schulze-Hardy rule. For some multivalent ions, strong adsorption led to charge reversal resulting in restabilization of the suspensions. The experimental critical coagulation concentrations (CCCs) could be well-predicted with the theory developed by Derjaguin, Landau, Verwey and Overbeek indicating that the aggregation processes were mainly driven by electrical double layer repulsion and van der Waals attraction. The ion specific dependence of the CCCs is owing to the modification of the surface charge through ion adsorption at different extents. These results are crucial for drug delivery applications, where inorganic electrolytes are present in ZNP samples.

Cd(II) adsorption on earth-abundant serpentine in aqueous environment: Role of interfacial ion specificity.

Adsorption of heavy metal ions (e.g., Cd(II)) on clay minerals significantly affects their transport and fate in natural and engineered waterbodies. To date, the role of interfacial ion specificity in the adsorption of Cd(II) on earth-abundant serpentine remains elusive. In this work, the adsorption of Cd(II) on serpentine at typical environment conditions (pH 4.5-5.0), particularly under the complex influence of common environmental anions (e.g., NO3-, SO42-) and cations (e.g., K+, Ca2+, Fe3+, Al3+) was systemically investigated. It was found that the adsorption of Cd(II) on serpentine surface due to the inner-sphere complexation could be negligibly affected by the anion type, yet the cations specifically modulated the Cd(II) adsorption. The presence of mono- and divalent cations moderately enhanced the Cd(II) adsorption by weakening the electrostatic double layer (EDL) repulsion between Cd(II) and Mg-O plane of serpentine, while trivalent cations significantly suppressed the adsorption of Cd(II) due to the competitive adsorption. Based on the spectroscopy analysis, Fe3+ and Al3+ were found to robustly bind the surface active sites of serpentine, thereby preventing the inner-sphere adsorption of Cd(II). The density functional theory (DFT) calculation indicated that Fe(III) and Al(III) exhibited the larger adsorption energy (Ead = -146.1 and -516.1 kcal mol-1, respectively) and stronger electron transfer capacity with serpentine compared to Cd(II) (Ead = -118.1 kcal mol-1), thus resulting in the formation of more stable Fe(III)-O and Al(III)-O inner-sphere complexes. This study provides valuable insights into the influence of interfacial ion specificity on the Cd(II) adsorption in terrestrial and aquatic environments.

SARS-CoV-2 Fusion Peptide has a Greater Membrane Perturbating Effect than SARS-CoV with Highly Specific Dependence on Ca2.

Coronaviruses are a major infectious disease threat, and include the zoonotic-origin human pathogens SARS-CoV-2, SARS-CoV, and MERS-CoV (SARS-2, SARS-1, and MERS). Entry of coronaviruses into host cells is mediated by the spike (S) protein. In our previous ESR studies, the local membrane ordering effect of the fusion peptide (FP) of various viral glycoproteins including the S of SARS-1 and MERS has been consistently observed. We previously determined that the sequence immediately downstream from the S2' cleavage site is the bona fide SARS-1 FP. In this study, we used sequence alignment to identify the SARS-2 FP, and studied its membrane ordering effect. Although there are only three residue differences, SARS-2 FP induces even greater membrane ordering than SARS-1 FP, possibly due to its greater hydrophobicity. This may be a reason that SARS-2 is better able to infect host cells. In addition, the membrane binding enthalpy for SARS-2 is greater. Both the membrane ordering of SARS-2 and SARS-1 FPs are dependent on Ca2+, but that of SARS-2 shows a greater response to the presence of Ca2+. Both FPs bind two Ca2+ ions as does SARS-1 FP, but the two Ca2+ binding sites of SARS-2 exhibit greater cooperativity. This Ca2+ dependence by the SARS-2 FP is very ion-specific. These results show that Ca2+ is an important regulator that interacts with the SARS-2 FP and thus plays a significant role in SARS-2 viral entry. This could lead to therapeutic solutions that either target the FP-calcium interaction or block the Ca2+ channel.

The Dynamic Ion Motive Force Powering the Bacterial Flagellar Motor.

The bacterial flagellar motor (BFM) is a rotary molecular motor embedded in the cell membrane of numerous bacteria. It turns a flagellum which acts as a propeller, enabling bacterial motility and chemotaxis. The BFM is rotated by stator units, inner membrane protein complexes that stochastically associate to and dissociate from individual motors at a rate which depends on the mechanical and electrochemical environment. Stator units consume the ion motive force (IMF), the electrochemical gradient across the inner membrane that results from cellular respiration, converting the electrochemical energy of translocated ions into mechanical energy, imparted to the rotor. Here, we review some of the main results that form the base of our current understanding of the relationship between the IMF and the functioning of the flagellar motor. We examine a series of studies that establish a linear proportionality between IMF and motor speed, and we discuss more recent evidence that the stator units sense the IMF, altering their rates of dynamic assembly. This, in turn, raises the question of to what degree the classical dependence of motor speed on IMF is due to stator dynamics vs. the rate of ion flow through the stators. Finally, while long assumed to be static and homogeneous, there is mounting evidence that the IMF is dynamic, and that its fluctuations control important phenomena such as cell-to-cell signaling and mechanotransduction. Within the growing toolbox of single cell bacterial electrophysiology, one of the best tools to probe IMF fluctuations may, ironically, be the motor that consumes it. Perfecting our incomplete understanding of how the BFM employs the energy of ion flow will help decipher the dynamical behavior of the bacterial IMF.

Interfacial ion specificity modulates hydrophobic interaction.

HYPOTHESIS: Ion specificity is crucial in assembly and aggregation of polymers in water driven by hydrophobic interaction. An increasing number of studies have suggested that specific ion adsorption and consequent impact on interfacial water molecules should play an important role in modulating hydrophobic interaction. EXPERIMENTS: Here, bubble probe atomic force microscopy (AFM) combined with theoretical modeling analysis was applied to quantify hydrophobic interactions involving three model polymers in solutions containing different ions. FINDINGS: For polystyrene, the hydrophobic interaction's decay length D0 was reduced from 0.75 nm to 0.60 nm by introducing weakly hydrated cations (e.g., K+ and NH4+), while varying anion type had little effect. For poly(methyl methacrylate) and polydimethylsiloxane, anion specificity was demonstrated more evident in shortening the hydrophobic interaction range, with D0 decreasing from 0.63 nm to 0.50 nm and from 0.72 nm to 0.58 nm respectively when strongly hydrated F- or Cl- was replaced by weakly hydrated I-. Such results could arise from specific ion adsorption at water/polymer interface which disrupts the water structuring effect. From the nanomechanical perspective, this work has revealed the importance of interfacial ion specificity in modulating hydrophobic interaction, which offers novel implications for tuning assembly behavior of macromolecules in relevant engineering applications such as micelle formation and foam stabilization.

Ion specific hydration in nano-confined electrical double layers.

We probe counter-ion specific effects in nano-confined electrical-double-layers (EDLs) by means of direct force measurements across a model slit pore in the extended surface forces apparatus. By variation of solution composition, we compare four different counter-ions with dissimilar hydration properties, namely Na+, K+, Cs+ as well as H3O+, all confined between (001) mica surfaces. We discuss the results in terms of a recently proposed π-transition model, evoking hydrated ion layering as the recurrent structural element in highly confined EDLs. We demonstrate that the π-transition essentially proceeds in multiple steps in coherence with the event of single- or multiple- hydrated-ion layering.

Incorporation of ion and solvent structure into mean-field modeling of the electric double layer.

An electric double layer forms when the small mobile ions of an electrolyte interact with an extended charged object, a macroion. The competition between electrostatic attraction and translational entropy loss of the small ions results in a diffuse layer of partially immobilized ions in the vicinity of the macroion. Modeling structure and energy of the electric double layer has a long history that has lead to the classical Poisson-Boltzmann theory and numerous extensions that account for ion-ion correlations and structural ion and solvent properties. The present review focuses on approaches that instead of going beyond the mean-field character of Poisson-Boltzmann theory introduce structural details of the ions and the solvent into the Poisson-Boltzmann modeling framework. The former include not only excluded volume effects but also the presence of charge distributions on individual ions, spatially extended ions, and internal ionic degrees of freedom. The latter treat the solvent either explicitly as interacting Langevin dipoles or in the form of effective non-electrostatic interactions, in particular Yukawa interactions, that are added to the Coulomb potential. We discuss how various theoretical models predict structural properties of the electric double layer such as the differential capacitance and compare some of these predictions with computer simulations.

Investigating the influence of histidine residues on the metal ion binding ability of the wheat metallothionein γ-Ec-1 domain.

While Zn(II) and Cd(II) have similar geochemical and environmental properties, their biological properties are distinctively different as Cd(II) ions have very limited metabolic significance and are mostly even toxic, while Zn(II) ions belong to the most essential micronutrients. One of the key proteins involved in intracellular Zn(II) and Cd(II) binding are metallothioneins (MTs), small cysteine-rich proteins ubiquitously found in many different organisms. In the past two decades, also MT sequences from diverse species that contain histidine residues have been found, and His-metal ion coordination has been shown. It is not clear, however, why in some MTs parts of the Cys residues are replaced by His, while most other MTs only contain Cys residues for metal ion binding. To address this question, we used the γ-domain of the early-cysteine labeled (Ec-1) metallothionein from common wheat as a model system because its enclosed M2Cys6 cluster represents the smallest metal-thiolate cluster possible with divalent metal ions. Based on the known three-dimensional structure of the γ-domain we set about to investigate the influence of a single Cys-to-His mutation on the structure and metal ion binding abilities of this domain. Combined data obtained by mass spectrometry, UV, as well as NMR spectroscopy suggest a preference for Zn(II) versus Cd(II) ions in the histidine containing binding site.