Effect Of Ion Binding Research Articles

Comparative analysis of the physical properties of murine and human S100A7: Insight into why zinc piracy is mediated by human but not murine S100A7

S100 proteins are a subfamily of EF-hand calcium-binding proteins found primarily in vertebrate animals. They are distinguished by binding of transition metals and functioning in both the intracellular and extracellular milieu. S100A7 functions in the protection of the skin and mucous membranes and is a biomarker in inflammatory skin disease. A recent study of Neisseria gonorrhoeae infection revealed that human but not murine S100A7 could be used to evade host nutritional immunity. To understand the molecular basis for this difference, we carried out a comparative analysis of the physical and structural properties of human and murine S100A7. The X-ray crystal structure of Ca2+-loaded mouse S100A7 (mS100A7) was determined to 1.69Å resolution, and Ca2+-induced conformational changes were assessed by NMR. Unlike human S100A7 (hS100A7), which exhibits conformational changes in response to binding of Ca2+, no significant changes in mS100A7 were detected. Dynamic light scattering, circular dichroism, and a competition chelator assay were used to compare the Zn2+ affinity and the effects of ion binding on mS100A7 versus hS100A7. Alignment of their sequences revealed a substantial difference in the C-terminal region, which is an important mediator of protein-protein interactions, suggesting a rationale for the specificity of N.gonorrhoeae for hS100A7. These data, along with more detailed analysis of S100A7 sequence conservation across different species, support the proposal that, although hS100A7 is highly conserved in many mammals, the murine protein is a distinct ortholog. Our results highlight the potential limitations of using mouse models for studying bacterial infections in humans.

Probing ion-binding at a protein interface: Modulation of protein properties by ionic liquids

Ions are important to modulate protein properties, including solubility and stability, through specific ion effects. Ionic liquids (ILs) are designer salts with versatile ion combinations with great potential to control protein properties. Although protein-ion binding of common metals is well-known, the IL effect on proteins is not well understood. Here, we employ the model protein lysozyme in dilute and concentrated IL solutions to determine the specific ion binding effect on protein phase behaviour, activity, size and conformational change, aggregation and intermolecular interactions. A combination of spectroscopic techniques, activity assays, small-angle X-ray scattering, and crystallography highlights that ILs, particularly their anions, bind to specific sites in the protein hydration layer via polar contacts on charged, polar and aromatic residues. The specific ion binding can induce more flexible loop regions in lysozyme, while the ion binding in the bulk phase can be more dynamic in solution. Overall, the protein behaviour in ILs depends on the net effect of nonspecific interactions and specific ion binding. Compared to formate, the nitrate anion induced high protein solubility, low activity, elongated shape and aggregation, which is largely owing to its higher propensity for ion binding. These findings provide new insights into protein-IL binding interactions and using ILs to modulate protein properties.

How a highly acidic SH3 domain folds in the absence of its charged peptide target.

Charged residues on the surface of proteins are critical for both protein stability and interactions. However, many proteins contain binding regions with a high net charge that may destabilize the protein but are useful for binding to oppositely charged targets. We hypothesized that these domains would be marginally stable, as electrostatic repulsion would compete with favorable hydrophobic collapse during folding. Furthermore, by increasing the salt concentration, we predict that these protein folds would be stabilized by mimicking some of the favorable electrostatic interactions that take place during target binding. We varied the salt and urea concentrations to probe the contributions of electrostatic and hydrophobic interactions for the folding of the yeast SH3 domain found in Abp1p. The SH3 domain was significantly stabilized with increased salt concentrations due to Debye-Huckel screening and a nonspecific territorial ion-binding effect. Molecular dynamics and NMR show that sodium ions interact with all 15 acidic residues but do little to change backbone dynamics or overall structure. Folding kinetics experiments show that the addition of urea or salt primarily affects the folding rate, indicating that almost all the hydrophobic collapse and electrostatic repulsion occur in the transition state. After the transition state formation, modest yet favorable short-range salt bridges are formed along with hydrogen bonds, as the native state fully folds. Thus, hydrophobic collapse offsets electrostatic repulsion to ensure this highly charged binding domain can still fold and be ready to bind to its charged peptide targets, a property that is likely evolutionarily conserved over 1 billion years.

Measuring Zn2+ binding to DNA and corresponding structural changes using circular dichroism and ICP-OES.

Zinc is the second most abundant transition metal on the body. While the nature of zinc binding to DNA remains unclear it is known that zinc binding causes measureable structural changes. It is not established whether the divalent zinc ions are specifically bound to a particular site within DNA or diffusively bound. By combining CD (circular dichroism) spectroscopy measurements of DNA with ICP-OES (Inductively coupled plasma optical emission spectroscopy) measurements of ions binding to DNA, changes caused by the zinc binding can be monitored. CD spectroscopy measurements oversee changes in the DNA structure, while ICP-OES can quantify the amount of zinc ions bound to the phosphate groups of DNA. This will provide important insight on the effects of transition metal divalent ion binding on DNA structure.

Inclusion of High-Field Target Data in AMOEBA's Calibration Improves Predictions of Protein-Ion Interactions.

The reliability of molecular mechanics simulations to predict effects of ion binding to proteins depends on their ability to simultaneously describe ion-protein, ion-water, and protein-water interactions. Force fields (FFs) to describe protein-water and ion-water interactions have been constructed carefully and have also been refined routinely to improve accuracy. Descriptions for ion-protein interactions have also been refined, although in an a posteriori manner through the use of "nonbonded-fix (NB-fix)" approaches in which parameters from default Lennard-Jones mixing rules are replaced with those optimized against some reference data. However, even after NB-fix corrections, there remains a significant need for improvement. This is also true for polarizable FFs that include self-consistent inducible moments. Our recent studies on the polarizable AMOEBA FF suggested that the problem associated with modeling ion-protein interactions could be alleviated by recalibrating polarization models of cation-coordinating functional groups so that they respond better to the high electric fields present near ions. Here, we present such a recalibration of carbonyls, carboxylates, and hydroxyls in the AMOEBA protein FF and report that it does improve predictions substantially─mean absolute errors in Na+-protein and K+-protein interaction energies decrease from 8.7 to 5.3 and 9.6 to 6.3 kcal/mol, respectively. Errors are computed with respect to estimates from van der Waals-inclusive density functional theory benchmarked against high-level quantum mechanical calculations and experiments. While recalibration does improve ion-protein interaction energies, they still remain underestimated, suggesting that further improvements can be made in a systematic manner through modifications in classical formalism. Nevertheless, we show that by applying our many-body NB-fix correction to Lennard-Jones components, these errors are further reduced to 2.7 and 2.6 kcal/mol, respectively, for Na+ and K+ ions. Finally, we show that the recalibrated AMOEBA protein FF retains its intrinsic reliability in predicting protein structure and dynamics in the condensed phase.

Analyzing the effect of ion binding to the membrane-surface on regulating the light-induced transthylakoid electric potential (ΔΨm).

The transthylakoid membrane potential (ΔΨm) is essential because it can drive the ATP synthesis through the CF0–CF1 type of ATP-synthase in chloroplasts as an energetic equivalent similar to ΔpH. In addition, a high fraction of proton motive force (PMF) stored as the ΔΨm component is physiologically important in the acclimation of photosynthesis to environmental stresses. It has been shown that ΔΨm is the sum of the Donnan potential difference (ΔΨdn) and the diffusion potential difference (ΔΨd). Specifically, ΔΨdn, ΔΨd, and ΔΨm are strongly associated with the ionic activities near the membrane surface, particularly, the extent of ion binding to the charged/neutral sites adjacent to the membrane surface. However, an in-depth analysis of the effect of altered cationic binding to the membrane surface on adjusting the transthylakoid electric potentials (ΔΨdn, ΔΨd, and ΔΨm) is still missing. This lack of a mechanistic understanding is due to the experimental difficulty of closely observing cations binding to the membrane surface in vivo. In this work, a computer model was proposed to investigate the transthylakoid electric phenomena in the chloroplast focusing on the interaction between cations and the negative charges close to the membrane surface. By employing the model, we simulated the membrane potential and consequently, the measured ECS traces, proxing the ΔΨm, were well described by the computing results on continuous illumination followed by a dark-adapted period. Moreover, the computing data clarified the components of transthylakoid membrane potential, unraveled the functional consequences of altered cationic attachment to the membrane surface on adjusting the transthylakoid electric potential, and further revealed the key role played by Donnan potential in regulating the energization of the thylakoid membrane. The current model for calculating electric potentials can function as a preliminary network for the further development into a more detailed theoretical model by which multiple important variables involved in photosynthesis can be explored.

Durability Performance of Concrete with Fly Ash as Fine Aggregate Eroded by Chloride Salt

The aim of this study is to investigate the durability of concrete with fly ash as a fine aggregate (CFA) in chloride salt environments. The natural diffusion method is used to analyze the concrete strength, chloride ion concentration, and diffusion coefficient after chloride salt erosion in a laboratory environment. In addition, scanning electron microscopy, X-ray diffraction, and Mercury intrusion porosimetry are performed to clarify the deterioration mechanism of concrete in chloride salt environments. The results indicate that owing to the chloride ion binding effect, the concrete porosity decreases and the concrete strength increases after chloride salt immersion. The decreased porosity caused by delayed hydration is primarily due to Friedel’s salt and CaCO3 produced during chloride ion erosion. CFA has a lower chloride diffusion coefficient and lower chloride concentration compared with ordinary concrete at all depths. In general, CFA exhibits excellent resistance to chloride salt erosion.

Chloride ion binding effect and corrosion resistance of geopolymer materials prepared with seawater and coral sand

In this work, the chloride binding capacities and chloride diffusion resistance of alkali-activated fly ash and slag powder geopolymer systems prepared with seawater and coral sand are investigated. Through the macro tests (e.g., chloride ion binding ratio, electric flux, etc.), stripping C-S-H, C/N-A-S-H from anhydrous particles and a variety of microscopic tests (e.g., MIP, XRD, SEM-EDS), the chloride binding mechanism of ordinary Portland cement (OPC) and geopolymer are analyzed and compared. The result shows that the chloride binding capacity of geopolymer samples under standard curing is better than that of OPC samples under the same condition (for instance, the 28-day chloride binding coefficient of geopolymer (FS1): 83.372%, OPC (R1): 73.223%). And the binding of chloride ion can be improved to a certain extent by increasing the initial chloride concentration. Geopolymer bounds the chloride ions through physical absorption or chemical reaction with cement compositions. The porous structure of C/N-(A)-S-H gel and high content of Al element promote the chloride binding capacity. The additional porous coral sand can reduce the chloride resistance capacity of specimens. But with slag proportion increasing, the geopolymer shows better chloride resistance capacity (for example the chloride diffusion coefficient decreases by 98% from 152.61 m2/s to 2.86 m2/s when slag proportion increased from 10% to 90%). The chloride diffusivity of geopolymers measured by the electric flux method has a large deviation, which is not suitable for direct evaluating of resistance to chloride penetration of geopolymer system.

Molecular Structure of the Surface-Immobilized Super Uranyl Binding Protein

Recently, a super uranyl binding protein (SUP) was developed, which exhibits excellent sensitivity/selectivity to bind uranyl ions. It can be immobilized onto a surface in sensing devices to detect uranyl ions. Here, sum frequency generation (SFG) vibrational spectroscopy was applied to probe the interfacial structures of surface-immobilized SUP. The collected SFG spectra were compared to the calculated orientation-dependent SUP SFG spectra using a one-excitonic Hamiltonian approach based on the SUP crystal structures to deduce the most likely surface-immobilized SUP orientation(s). Furthermore, discrete molecular dynamics (DMD) simulation was applied to refine the surface-immobilized SUP conformations and orientations. The immobilized SUP structures calculated from DMD simulations confirmed the SUP orientations obtained from SFG data analyzed based on the crystal structures and were then used for a new round of SFG orientation analysis to more accurately determine the interfacial orientations and conformations of immobilized SUP before and after uranyl ion binding, providing an in-depth understanding of molecular interactions between SUP and the surface and the effect of uranyl ion binding on the SUP interfacial structures. We believe that the developed method of combining SFG measurements, DMD simulation, and Hamiltonian data analysis approach is widely applicable to study biomolecules at solid/liquid interfaces.

Aggregation of poly(N-isopropylacrylamide) homopolymer by Cu2+ and Zn2+: Significance for ratiometric metal ion indicators

Aqueous transition metal dications Cu2+ and Zn2+ bind to the amide groups of the responsive polymer poly(N-isopropylacrylamide) (PNIPAm). Ratiometric detection by the response of PNIPAm is based on the effect of metal ion binding to ligands that are copolymerized into PNIPAm. Metal ions bound to copolymerized ligands cause a polarity change that shifts the ratio of coil and globule polymer phases, whereby the coil:globule state is monitored by the FRET process of a pair of fluorophores distributed throughout the polymer. This work shows that aqueous Cu2+ or Zn2+ ([M2+] = 2.5 × 10−2 M to 2.5 × 10−4 M) cause aggregation of the PNIPAm homopolymer (Mn = 8400 and 10,300) in the globule phase above 32 °C, as determined by second-order and dynamic light-scattering. Conditional formation constants (pH 6.3) for Cu2+ binding PNIPAm were measured as log Kc = 2.64 ± 0.07 and 4.02 ± 0.05 for PNIPAm concentrations of 1 mg/mL and 0.05 mg/mL, respectively. The interaction of Cu2+ and Zn2+ with PNIPAm is therefore in competition with the copolymerized ligands and when detecting millimolar to high micromolar concentrations, this interaction poses a potential interference to metal ion detection. Several aggregation processes are implicated based on Cu2+ or Zn2+ from 8 × 10−5 to 2.5 × 10−2 M. These processes are fully reversible by reducing the sample temperature.

Effect of monovalent ion binding on molecular dynamics of the S100-family calcium-binding protein calbindin D9k.

Calbindin D9k is a member of the S100 subfamily of EF-hand calcium binding proteins, and has served as an important model system for biophysical studies. The fast timescale dynamics of the calcium-free (apo) state is characterized using molecular dynamics simulations. Order parameters for the backbone NH bond vectors are determined from the simulations and compared with experimentally derived values, with a focus on the dynamics of calcium-binding site I. There is a significant discrepancy between simulated and experimental order parameters for site I residues in the case of no ion bound in site I. However, it was found in the simulations that a Na+ ion can bind in site I, and the resulting order parameters determined from the simulations are in excellent agreement with experiment. Comparisons are made to X-ray structures of other S100 family members in which Na+ ions were observed or suggested to be bound in site I. © 2019 Wiley Periodicals, Inc.

Y2SK2 and SK3 type dehydrins from Agapanthus praecox can improve plant stress tolerance and act as multifunctional protectants

Two dehydrins from Agapanthus praecox (ApY2SK2 and ApSK3) show important protective effects under complex stresses. Both ApY2SK2 and ApSK3 contain one intron and consist of a full-length cDNA of 981 bp and 1057 bp encoding 186 and 215 amino acids, respectively. ApY2SK2 and ApSK3 transgenic Arabidopsis thaliana show reduced plasma membrane damage and ROS levels and higher antioxidant activity and photosynthesis capability under salt, osmotic, cold and drought stresses compared with the wild-type. ApY2SK2 and ApSK3 are mainly located in the cytoplasm and cell membrane, and ApY2SK2 can even localize in the nucleus. In vitro tests indicate that ApY2SK2 and ApSK3 can effectively protect enzyme activity during the freeze-thaw process, and ApY2SK2 also exhibits this function during desiccation treatment. Furthermore, ApY2SK2 and ApSK3 can significantly inhibit hydroxyl radical generation. These two dehydrins can bind metal ions with a binding affinity of Co2+> Ni2+> Cu2+> Fe3+; the binding affinity of ApSK3 is higher than that of ApY2SK2. Thus, ApY2SK2 has a better protective effect on enzyme activity, and ApSK3 has stronger metal ion binding function and effect on ROS metabolism. Moreover, plant cryopreservation evaluation tests indicate that ApY2SK2 and ApSK3 transformation can enhance the seedling survival ratio from 23% to 47% and 55%, respectively; the addition of recombinant ApY2SK2 and ApSK3 to plant vitrification solution may increase the survival ratio of wild-type A. thaliana seedlings from 24% to 50% and 46%, respectively. These findings suggest that ApY2SK2 and ApSK3 can effectively improve cell stress tolerance and have great potential for in vivo or in vitro applications.

Nonlinear Porous Diffusion Modeling of Hydrophilic Ionic Agrochemicals in Astomatous Plant Cuticle Aqueous Pores: A Mechanistic Approach.

The agricultural industry requires improved efficacy of sprays being applied to crops and weeds in order to reduce their environmental impact and deliver improved financial returns. Enhanced foliar uptake is one means of improving efficacy. The plant leaf cuticle is known to be the main barrier to diffusion of agrochemicals within the leaf. The usefulness of a mathematical model to simulate uptake of agrochemicals in plant cuticles has been noted previously in the literature, as the results of each uptake experiment are specific to each formulation of active ingredient, plant species and environmental conditions. In this work we develop a mathematical model and numerical simulation for the uptake of hydrophilic ionic agrochemicals through aqueous pores in plant cuticles. We propose a novel, nonlinear, porous diffusion model for ionic agrochemicals in isolated cuticles, which extends simple diffusion through the incorporation of parameters capable of simulating: plant species variations, evaporation of surface droplet solutions, ion binding effects on the cuticle surface and swelling of the aqueous pores with water. We validate our theoretical results against appropriate experimental data, discuss the key sensitivities in the model and relate theoretical predictions to appropriate physical mechanisms. Major influencing factors have been found to be cuticle structure, including tortuosity and density of the aqueous pores, and to a lesser extent humidity and cuticle surface ion binding effects.

Effect of Sodium and Chloride Binding on a Lecithin Bilayer. A Molecular Dynamics Study.

The effect of ion binding on the structural, mechanical, dynamic and electrostatic properties of a 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) bilayer in a 0.5 M aqueous NaCl solution is investigated using classical atomistic molecular dynamics simulation with different force-field descriptions for ion-ion and ion-lipid interactions. Most importantly, the repulsive Lennard–Jones parameters for the latter were modified, such that approximately similar binding of cations and anions to the lipid membrane is achieved. This was done to qualitatively improve the apparent ion-lipid binding constants obtained from simulations with the original force field (Berger lipids and GROMOS87 ions in combination with the SPC water model) in comparison to experimental data. Furthermore, various parameters characterizing membrane structure, elasticity, order and dynamics are analyzed. It is found that ion binding as observed in simulations involving the modified in comparison to the original force-field description leads to: (i) a smaller salt-induced change in the area per lipid, which is in closer agreement with the experiment; (ii) a decrease in the area compressibility and bilayer thickness to values comparable to a bilayer in pure water; (iii) lipid deuterium order parameters and lipid diffusion coefficients on nanosecond timescales that are very similar to the values for a membrane in pure water. In general, salt effects on the structural properties of a POPC bilayer in an aqueous sodium-chloride solution appear to be reproduced reasonably well by the new force-field description. An analysis of membrane-membrane disjoining pressure suggests that the smaller salt-induced change in area per lipid induced by the new force-field description is not due to the alteration of membrane-associated net charge, but must rather be understood as a consequence of ion-specific effects on the arrangement of lipid molecules.

The Influence of Metal Ion Binding on the IR Spectra of Nitrogen-Containing PAHs.

Astronomical IR emission spectra form the basis for the now widely accepted abundant presence of polycyclic aromatic hydrocarbons (PAHs) in inter- and circumstellar environments. A small but consistent frequency mismatch is found between the astronomically observed emission band near 6.2 μm and typical CC-stretching vibrations of PAHs measured in laboratory spectra near 6.3-6.4 μm. The shift of the band has been tentatively attributed to a variety of effects, among which the inclusion of heteroatoms, in particular nitrogen, in the PAH skeleton (PANH) as well as to metal ion binding to the PAH molecule. Here we experimentally investigate the combined effect of nitrogen-inclusion and metal ion binding on the IR spectra. In particular, infrared multiple-photon dissociation (IRMPD) spectra are recorded for coordination complexes of Cu+ with one or two quinoline, isoquinoline, and acridine ligands; complexes of the form Cu+(PANH) (MeCN), where the MeCN (acetonitrile) ligand acts as a relatively weakly bound "messenger" are also recorded to qualitatively verify that potential frequency shifts induced by IRMPD are minimal. The experimental IR spectra document the accuracy of IR spectral predictions by density functional theory calculations performed at the B3LYP/6-311+G(2df,2p) level and confirm that a σ-bond is formed between the copper ion and the exoskeletal N atom. The experimental spectra suggest that the CNC stretching mode undergoes a small red shift of up to 20 cm-1, with respect to the band position in the uncomplexed PANH molecule, away from the 6.2 μm interstellar position.

All-Atom Molecular Dynamics Reveals Mechanism of Zinc Complexation with Therapeutic F10.

Advancing the use of therapeutic nucleic acids requires understanding the chemical and structural properties that allow these polymers to promote the death of malignant cells. Here we explore Zn2+ complexation by the fluoropyrimidine polymer F10, which has strong activities in multiple preclinical models of cancer. Delivery of fluoropyrimidine FdUMP in the 10-residue polymer F10 rather than the nucleobase (5-fluorouracil) allows consideration of metal ion binding effects on drug delivery. The differences in metal ion interactions with fluoropyrimidine compared to normal DNA results in conformation changes that affect protein binding, cell uptake, and codelivery of metals such as zinc, and the cytoxicity thereof. Microsecond-time-scale, all-atom simulations of F10 predict that zinc selectively stabilizes the polymer via interactions with backbone phosphate groups and suggest a mechanism of complexation for the zinc-base interactions shown in previous experimental work. The positive zinc ions are attracted to the negatively charged phosphate groups. Once the Zn2+ ions are near F10, they cause the base's N3 nitrogen to deprotonate. Subsequently, magnesium atoms displace zinc from their interactions with phosphate, freeing the zinc ions to interact with the FdU bases by forming weak interactions with the O4 oxygen and the fluorine attached to C5. These interactions of magnesium with phosphate groups and zinc with nucleobases agree with previous experimental results and are seen in MD simulations only when magnesium is introduced after N3 deprotonation, indicating a specific order of metal binding events. Additionally, we predict interactions between zinc and F10's O2 atoms, which were not previously observed. By comparison to 10mers of polyU and polydT, we also predict that the presence of fluorine increases the binding affinity of zinc to F10 relative to analogous strands of RNA and DNA consisting of only native nucleotides.

Effects of Chloride Ion Binding on Microstructure of Cement Pastes

AbstractThe corrosion of steel caused by chloride ions is considered to be the main durability problem of reinforced concrete structures. This paper investigates the total chloride ion content, free chloride concentration in expressed pore solution, Friedel’s salt content, and porosity of portland cement (PC) and PC/fly ash (FA) combination pastes after 7 days of water curing followed by 28 or 150 days immersion in water or 0.3, 0.7, 1.0, and 2.0 mol/L sodium chloride solutions. Results showed that the chloride ion binding capacities of the pastes increased with increase of free chloride ion concentration. The relationship between bound and free chloride ion contents could be described by Langmuir’s equation. The addition of fly ash decreased the bound chloride content and showed negative influences on Friedel’s salt formation due to low activity. Porosity of cement paste decreased as the concentration of soaking chloride ion increased, and was inversely proportional to the amount of Friedel’s salt formed.

Crystal structures of the ligand-binding region of uPARAP: effect of calcium ion binding.

The proteins of the mannose receptor (MR) family share a common domain organization and have a broad range of biological functions. Urokinase plasminogen activator receptor-associated protein (uPARAP) (or Endo180) is a member of this family and plays an important role in extracellular matrix remodelling through interaction with its ligands, including collagens and urokinase plasminogen activator receptor (uPAR). We report the crystal structures of the first four domains of uPARAP (also named the ligand-binding region, LBR) at pH7.4 in Ca(2+)-bound and Ca(2+)-free forms. The first domain (cysteine-rich or CysR domain) folds into a new and unique conformation different from the β-trefoil fold of typical CysR domains. The so-called long loop regions (LLRs) of the C-type lectin-like domain (CTLD) 1 and 2 (the third and fourth domain) mediate the direct contacts between these domains. These LLRs undergo a Ca(2+)-dependent conformational change, and this is likely to be the key structural determinant affecting the overall conformation of uPARAP. Our results provide a molecular mechanism to support the structural flexibility of uPARAP, and shed light on the structural flexibility of other members of the MR family.

Effect of ionic strength on the interfacial viscoelasticity and stability of silk fibroin at the oil/water interface.

The amphiphilic character and surface activity endows silk fibroin with the ability to reside at fluid interfaces and effectively stabilize emulsions. However, the influence of relevant factors and their actual effect on the interfacial viscoelasticity and stability of silk fibroin at the oil/water interface has received less attention. In the present study, the effect of ionic strength on the interfacial viscoelasticity, emulsification effectiveness and stability of silk fibroin at the oil/water interface was investigated in detail. A higher ion concentration facilitates greater adsorption, stronger molecular interaction and faster structure reorganization of silk fibroin at the oil/water interface, thus causing quicker interfacial saturation adsorption, greater interfacial strength and lower interfacial structural fracture on large deformation. However, the presence of concentrated ions screens the charges in silk fibroin molecules and the zeta potential decreases as a result of electrostatic screening and ion-binding effects, which may result in emulsion droplet coalescence and a decrease in emulsion stability. The positively-charged ions significantly affect the interfacial elasticity and stability of silk fibroin layers at the oil/water interface as a result of the strong electrostatic interactions between counter-ions and the negatively-charged groups of silk fibroin. © 2016 Society of Chemical Industry.

Molecular Dynamics Simulation of DNA Capture and Transport in Heated Nanopores.

The integration of local heat sources with solid-state nanopores offers new means for controlling the transmembrane transport of charged biomacromolecules. In the case of electrophoretic transport of DNA, recent experimental studies revealed unexpected temperature dependences of the DNA capture rate, the DNA translocation velocity, and the ionic current blockades produced by the presence of DNA in the nanopore. Here, we report the results of all-atom molecular dynamics simulations that elucidated the effect of temperature on the key microscopic processes governing electric field-driven transport of DNA through nanopores. Mimicking the experimental setup, we simulated the capture and subsequent translocation of short DNA duplexes through a locally heated nanopore at several temperatures and electrolyte conditions. The temperature dependence of ion mobility at the DNA surface was found to cause the dependence of the relative conductance blockades on temperature. To the first order, the effective force on DNA in the nanopore was found to be independent of temperature, despite a considerable reduction of solution viscosity. The temperature dependence of the solution viscosity was found to make DNA translocations faster for a uniformly heated system but not in the case of local heating that does not affect viscosity of solution surrounding the untranslocated part of the molecule. Increasing solution temperature was also found to reduce the lifetime of bonds formed between cations and DNA. Using a flow suppression algorithm, we were able to separate the effects of electro-osmotic flow and direct ion binding, finding the reduced durations of DNA–ion bonds to increase, albeit weakly, the effective force experienced by DNA in an electric field. Unexpectedly, our simulations revealed a considerable temperature dependence of solvent velocity at the DNA surface—slip velocity, an effect that can alter hydrodynamic coupling between the motion of DNA and the surrounding fluid.