On the salt-induced stabilization of pair and many-body hydrophobic interactions

Flipping out: role of arginine in hydrophobic interactions and biological formulation design

Arginine has been a mainstay in biological formulation development for decades. To date, the way arginine modulates protein stability has been widely studied and debated. Here, we employed a hydrophobic polymer to decouple hydrophobic effects from other interactions relevant to protein folding. While existing hypotheses for the effects of arginine can generally be categorized as either direct or indirect, our results indicate that direct and indirect mechanisms of arginine co-exist and oppose each other. At low concentrations, arginine was observed to stabilize hydrophobic polymer folding via a sidechain-dominated direct mechanism, while at high concentrations, arginine stabilized polymer folding via a backbone-dominated indirect mechanism. Upon introducing partially charged polymer sites, arginine destabilized polymer folding. Further, we found arginine-induced destabilization of a model virus similar to direct-mechanism destabilization of the charged polymer and concentration-dependent stabilization of a model protein similar to the indirect mechanism of hydrophobic polymer stabilization. These findings highlight the modular nature of the widely used additive arginine, with relevance in the information-driven design of stable biological formulations.

A generic model for pH-sensitive collapse of hydrophobic polymers

The hydrophobic effect is an important contributor to the stability of proteins and may be influenced by many factors including the pH of the solution. To simplify the study of pH effects on proteins, we parameterize biologically motivated titratable monomers which we insert into the sequence of a hydrophobic polymer and study via constant pH molecular dynamics (MD) simulations. We calculate the potential of mean force of the polymer as a function of its radius of gyration at different pH values and observe that the collapsed state of the polymer is destabilized when the titratable monomer is more charged (high pH for an acid and low pH for a base). Further, the extent of the destabilization is influenced by the position of the titratable monomer along the polymer sequence. The pKa value of the titratable monomer is also observed to be sensitive to polymer conformation, in agreement with protein studies. We further study a zwitterionic polymer with an acidic and a basic monomer in the same sequence which presents a pH-dependent hairpin formation. Our model provides a simplified yet powerful framework to study pH effects on the hydrophobic effect, providing insights into mechanisms governing the behavior of intrinsically disordered proteins (IDPs) and pH-sensitive drug delivery, among other applications.

Self-association of cyclodextrin inclusion complexes in a deep eutectic solvent enhances guest solubility

Cyclodextrins are widely used pharmaceutical excipients known to increase the solubility of drug compounds through formation of inclusion complexes. A prominent limitation of common cyclodextrins is their own scarce solubility in water, which renders them unsuitable for many drug formulations. Cyclodextrin solubility can be enhanced in appropriate media such as Deep Eutectic Solvents (DESs). However, DESs can also reduce the equilibrium constant for host-guest complexation, making it challenging to optimize drug solubility using cyclodextrin. To determine the impact and mechanism of cyclodextrin complexation in DES, we tracked changes in the solubility of methyl orange (MO), serving as a hardly soluble model compound, in the presence of β-cyclodextrin (CD) in hydrated urea-choline chloride DES. The highest achievable MO solubility is obtained in concentrated CD-in-DES mixtures at low hydration, resulting from the higher solubility of CD⊃MO complexes in DES compared to water as a solvent. Combining our results with molecular dynamics simulations, we provide evidence that CD⊃MO complexes self-associate into dimers and larger oligomers. This self-association of complexes greatly enhances MO solubilization by CD beyond that expected from the canonical 1:1 binding stoichiometry. This newly unraveled solubilization mechanism via cyclodextrins and its facilitation by DES should aid the design of future drug formulations.

Salting-out effect-mediated size-control of protein nanoparticles towards controllable microstructures for sustained release of eugenol

Size and monodispersity of solid particles are essential to their structuring behaviors at biphasic interfaces. However, delicate control over biomolecular nanoparticle sizes is challenging. In this study, we prepared monodisperse rice protein (RP) nanoparticles by neutralizing RP solutions (pH 12.0) using combined treatments of cationic exchange resins (CERs) and HCl. CERs absorbed Na+ by releasing H+ without producing salt during neutralization. By compromising the usages of CERs and HCl when preparing RPs, the generation of NaCl can be delicately tailored, leading to controllable nanoparticle sizes from 20 nm to 30 nm. By mixing these nanoparticles with eugenol in an aqueous solution, the nanoparticles accommodated eugenol in their cores due to inward diffusion. Furthermore, such eugenol-contained nanoparticles with different sizes demonstrated tunable releases of eugenol due to size-dependent capillary forces, which can be harnessed for suppression of microbial growth on fruit with prolonged effective eugenol concentration.

1H-NMR studies on the volume phase transition of DNA-modified pNipmam microgels

DNA functionalized pNipmam microgels, which have recently been introduced, are examined at different concentrations of sodium chloride and in PBS solutions via temperature dependent 1H-NMR measurements and are compared to pure pNipmam microgels. We show that the DNA modification shifts the volume phase transition temperature towards lower temperatures and the addition of salt and PBS further supports this effect in both materials. Thermodynamic values, i.e. enthalpy, entropy and Gibbs free energy, are determined via a non-linear fit which can be applied directly to the measurement data without further linearization.

Pseudo-Isolated α-Helix Platform for the Recognition of Deep and Narrow Targets

Although interest in stabilized α-helical peptides as next-generation therapeutics for modulating biomolecular interfaces is increasing, peptides have limited functionality and stability due to their small size. In comparison, α-helical ligands based on proteins can make steric clash with targets due to their large size. Here, we report the design of a monomeric pseudo-isolated α-helix (mPIH) system in which proteins behave as if they are peptides. The designed proteins contain α-helix ligands that do not require any covalent chemical modification, do not have frayed ends, and importantly can make sterically favorable interactions similar to isolated peptides. An optimal mPIH showed a more than 100-fold increase in target selectivity, which might be related to the advantages in conformational selection due to the absence of frayed ends. The α-helical ligand in the mPIH displayed high thermal stability well above human body temperature and showed reversible and rapid folding/unfolding transitions. Thus, mPIH can become a promising protein-based platform for developing stabilized α-helix pharmaceuticals.

Theory of Gas Solubility and Hydrophobic Interaction in Aqueous Electrolyte Solutions

Ion-specific effects on the solubility of nonpolar solutes and on the solute-solute hydrophobic interaction in aqueous electrolyte solutions are studied on the basis of a continuum theory that incorporates the excluded volume of the molecules using the four-component (water, cations, anions, and solutes) Boublı́k-Mansoori-Carnahan-Starling-Leland model and ion hydration (electrostriction) using the Born model. We examine how the ordering of ions in the salt effect on the solubility as measured by the Sechenov coefficient K_S changes with varying sizes of ions and solutes. Our calculation reproduces the general trend of experimentally measured K_S and also provides insight into the irregular behavior of K_S for lithium ion. The correlation between K_S and the salt effect on the hydrophobic interaction that has been pointed out earlier is accounted for by an explicit connection between K_S and the salt-enhanced-association coefficient C_I in the expansion of the second osmotic virial coefficient B(n_s) = B(0) - C_In_s + ··· in powers of the salt density n_s at fixed pressure and temperature. The quadratic relation CI≈KS2/4 is derived for ions and solutes that are not very large.

Molecular interaction of nitrate transporter proteins with recombinant glycinebetaine results in efficient nitrate uptake in the cyanobacterium Anabaena PCC 7120

Nitrate transport in cyanobacteria is mediated by ABC-transporter, which consists of a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). Under salt stress, recombinant glycinebetaine (GB) not only protected the rate of nitrate transport in transgenic Anabaena PCC 7120, rather stimulated the rate by interacting with the ABC-transporter proteins. In silico analyses revealed that nrtA protein consisted of 427 amino acids, the majority of which were hydrophobic and contained a Tat (twin-arginine translocation) signal profile of 34 amino acids (1-34). The nrtC subunit of 657 amino acids contained two hydrophobic distinct domains; the N-terminal (5-228 amino acids), which was 59% identical to nrtD (the ATP-binding subunit) and the C-terminal (268-591), 28.2% identical to nrtA, suggesting C-terminal as a solute binding domain and N-terminal as ATP binding domain. Subunit nrtD consisted of 277 amino acids and its N-terminal (21-254) was an ATP binding motif. Phylogenetic analysis revealed that nitrate-ABC-transporter proteins are highly conserved among the cyanobacterial species, though variation existed in sequences resulting in several subclades. Nostoc PCC 7120 was very close to Anabaena variabilis ATCC 29413, Anabaena sp. 4-3 and Anabaena sp. CA = ATCC 33047. On the other, Nostoc spp. NIES-3756 and PCC 7524 were often found in the same subclade suggesting more work before referring it to Anabaena PCC 7120 or Nostoc PCC 7120. The molecular interaction of nitrate with nrtA was hydrophilic, while hydrophobic with nrtC and nrtD. GB interaction with nrtACD was hydrophobic and showed higher affinity compared to nitrate.

Molecular interaction of nitrate transporter proteins with recombinant glycinebetaine results in efficient nitrate uptake in the cyanobacterium Anabaena PCC 7120

Nitrate transport in cyanobacteria is mediated by ABC-transporter, which consists of a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). Under salt stress, recombinant glycinebetaine (GB) not only protected the rate of nitrate transport in transgenic Anabaena PCC 7120, rather stimulated the rate by interacting with the ABC-transporter proteins. In silico analyses revealed that nrtA protein consisted of 427 amino acids, the majority of which were hydrophobic and contained a Tat (twin-arginine translocation) signal profile of 34 amino acids (1–34). The nrtC subunit of 657 amino acids contained two hydrophobic distinct domains; the N-terminal (5–228 amino acids), which was 59% identical to nrtD (the ATP-binding subunit) and the C-terminal (268–591), 28.2% identical to nrtA, suggesting C-terminal as a solute binding domain and N-terminal as ATP binding domain. Subunit nrtD consisted of 277 amino acids and its N-terminal (21–254) was an ATP binding motif. Phylogenetic analysis revealed that nitrate-ABC-transporter proteins are highly conserved among the cyanobacterial species, though variation existed in sequences resulting in several subclades. Nostoc PCC 7120 was very close to Anabaena variabilis ATCC 29413, Anabaena sp. 4–3 and Anabaena sp. CA = ATCC 33047. On the other, Nostoc spp. NIES-3756 and PCC 7524 were often found in the same subclade suggesting more work before referring it to Anabaena PCC 7120 or Nostoc PCC 7120. The molecular interaction of nitrate with nrtA was hydrophilic, while hydrophobic with nrtC and nrtD. GB interaction with nrtACD was hydrophobic and showed higher affinity compared to nitrate.

The driving force for co-translational protein folding is weaker in the ribosome vestibule due to greater water ordering

Interactions between the ribosome and nascent chain can destabilize folded domains in the ribosome exit tunnel's vestibule, the last 3 nm of the exit tunnel where tertiary folding can occur. Here, we test if a contribution to this destabilization is a weakening of hydrophobic association, the driving force for protein folding. Using all-atom molecular dynamics simulations, we calculate the potential-of-mean force between two methane molecules along the center line of the ribosome exit tunnel and in bulk solution. Associated methanes, we find, are half as stable in the ribosome's vestibule as compared to bulk solution, demonstrating that the hydrophobic effect is weakened by the presence of the ribosome. This decreased stability arises from a decrease in the amount of water entropy gained upon the association of the methanes. And this decreased entropy gain originates from water molecules being more ordered in the vestibule as compared to bulk solution. Therefore, the hydrophobic effect is weaker in the vestibule because waters released from the first solvation shell of methanes upon association do not gain as much entropy in the vestibule as they do upon release in bulk solution. These findings mean that nascent proteins pass through a ribosome vestibule environment that can destabilize folded structures, which has the potential to influence co-translational protein folding pathways, energetics, and kinetics.

Effect of salinity on the zinc(II) binding efficiency of siderophore functional groups and implications for salinity tolerance mechanisms in barley

Bacteria, fungi and grasses use siderophores to access micronutrients. Hence, the metal binding efficiency of siderophores is directly related to ecosystem productivity. Salinization of natural solutions, linked to climate change induced sea level rise and changing precipitation patterns, is a serious ecological threat. In this study, we investigate the impact of salinization on the zinc(II) binding efficiency of the major siderophore functional groups, namely the catecholate (for bacterial siderophores), α-hydroxycarboxylate (for plant siderophores; phytosiderophores) and hydroxamate (for fungal siderophores) bidentate motifs. Our analysis suggests that the order of increasing susceptibility of siderophore classes to salinity in terms of their zinc(II) chelating ability is: hydroxamate < catecholate < α-hydroxycarboxylate. Based on this ordering, we predict that plant productivity is more sensitive to salinization than either bacterial or fungal productivity. Finally, we show that previously observed increases in phytosiderophore release by barley plants grown under salt stress in a medium without initial micronutrient deficiencies, are in line with the reduced zinc(II) binding efficiency of the α-hydroxycarboxylate ligand and hence important for the salinity tolerance of whole-plant zinc(II) status.

Liquid-Liquid Phase Separation of Tau Driven by Hydrophobic Interaction Facilitates Fibrillization of Tau

Amyloid aggregation of tau protein is implicated in neurodegenerative diseases, yet its facilitating factors are poorly understood. Recently, tau has been shown to undergo liquid liquid phase separation (LLPS) both in vivo and in vitro. LLPS was shown to facilitate tau amyloid aggregation in certain cases, while being independent of aggregation in other cases. It is therefore important to understand the differentiating properties that resolve this apparent conflict. We report on a model system of hydrophobically driven LLPS induced by high salt concentration (LLPS-HS), and compare it to electrostatically driven LLPS represented by tau-RNA/heparin complex coacervation (LLPS-ED). We show that LLPS-HS promotes tau protein dehydration, undergoes maturation and directly leads to canonical tau fibrils, while LLPS-ED is reversible, remains hydrated and does not promote amyloid aggregation. We show that the nature of the interaction driving tau condensation is a differentiating factor between aggregation-prone and aggregation-independent LLPS.

Influence of Ionic Strength on Hydrophobic Interactions in Water: Dependence on Solute Size and Shape

Hydrophobicity is a phenomenon of great importance in biology, chemistry, and biochemistry. It is defined as the interaction between nonpolar molecules or groups in water and their low solubility. Hydrophobic interactions affect many processes in water, for example, complexation, surfactant aggregation, and coagulation. These interactions play a pivotal role in the formation and stability of proteins or biological membranes. In the present study, we assessed the effect of ionic strength, solute size, and shape on hydrophobic interactions between pairs of nonpolar particles. Pairs of methane, neopentane, adamantane, fullerene, ethane, propane, butane, hexane, octane, and decane were simulated by molecular dynamics in AMBER 16.0 force field. As a solvent, TIP3P and TIP4PEW water models were used. Potential of mean force (PMF) plots of these dimers were determined at four values of ionic strength, 0, 0.04, 0.08, and 0.40 mol/dm³, to observe its impact on hydrophobic interactions. The characteristic shape of PMFs with three extrema (contact minimum, solvent-separated minimum, and desolvation maximum) was observed for most of the compounds for hydrophobic interactions. Ionic strength affected hydrophobic interactions. We observed a tendency to deepen contact minima with an increase in ionic strength value in the case of spherical and spheroidal molecules. Additionally, two-dimensional distribution functions describing water density and average number of hydrogen bonds between water molecules were calculated in both water models for adamantane and hexane. It was observed that the density of water did not significantly change with the increase in ionic strength, but the average number of hydrogen bonds changed. The latter tendency strongly depends on the water model used for simulations.

Exploring the role of hydrophilic amino acids in unfolding of protein in aqueous ethanol solution

Hydrophobic association is the key contributor behind the formation of well packed core of a protein which is often believed to be an important step for folding from an unfolded chain to its compact functional form. While most of the protein folding/unfolding studies have evaluated the changes in the hydrophobic interactions during chemical denaturation, the role of hydrophilic amino acids in such processes are not discussed in detail. Here we report the role of the hydrophilic amino acids behind ethanol induced unfolding of protein. Using free energy simulations, we show that chicken villin head piece (HP-36) protein unfolds gradually in presence of water-ethanol binary mixture with increasing composition of ethanol. However, upon mutation of hydrophilic amino acids by glycine while keeping the hydrophobic amino acids intact, the compact state of the protein is found to be stable at all compositions with gradual flattening of the free energy landscape upon increasing compositions. The local environment around the protein in terms of ethanol/water number significantly differs in wild type protein compared to the mutated protein. The calculated Wyman-Tanford preferential binding coefficient of ethanol for wild type protein reveals that a greater number of cosolutes (here ethanol) bind to the unfolded state compared to its folded state. However, no significant increase in binding coefficient of ethanol at the unfolded state is found for mutated protein. Local-bulk partition coefficient calculation also suggests similar scenarios. Our results reveal that the weakening of hydrophobic interactions in aqueous ethanol solution along with larger preferential binding of ethanol to the unfolded state mediated by hydrophilic amino acids combinedly helps unfolding of protein in aqueous ethanol solution.

A molecular dynamics approach towards evaluating osmotic and thermal stress in the extracellular environment

OBJECTIVE

A molecular dynamics approach to understanding fundamental mechanisms of combined thermal and osmotic stress induced by thermochemical ablation (TCA) is presented.

METHODS

Structural models of fibronectin and fibronectin bound to its integrin receptor provide idealized models for the effects of thermal and osmotic stress in the extracellular matrix. Fibronectin binding to integrin is known to facilitate cell survival. The extracellular environment produced by TCA at the lesion boundary was modelled at 37 °C and 43 °C with added sodium chloride (NaCl) concentrations (0, 40, 80, 160, and 320 mM). Atomistic simulations of solvated proteins were performed using the GROMOS96 force field and TIP3P water model. Computational results were compared with the results of viability studies of human hepatocellular carcinoma (HCC) cell lines HepG2 and Hep3B under matching thermal and osmotic experimental conditions.

RESULTS

Cell viability was inversely correlated with hyperthermal and hyperosmotic stresses. Added NaCl concentrations were correlated with a root mean square fluctuation increase of the fibronectin arginylglycylaspartic acid (RGD) binding domain. Computed interaction coefficients demonstrate preferential hydration of the protein model and are correlated with salt-induced strengthening of hydrophobic interactions. Under the combined hyperthermal and hyperosmotic stress conditions (43 °C and 320 mM added NaCl), the free energy change required for fibronectin binding to integrin was less favorable than that for binding under control conditions (37 °C and 0 mM added NaCl).

CONCLUSION

Results quantify multiple measures of structural changes as a function of temperature increase and addition of NaCl to the solution. Correlations between cell viability and stability measures suggest that protein aggregates, non-functional proteins, and less favorable cell attachment conditions have a role in TCA-induced cell stress.

Hydrophobic Hydration and the Effect of NaCl Salt in the Adsorption of Hydrocarbons and Surfactants on Clathrate Hydrates

Adsorption of functional molecules on the surface of hydrates is key in the understanding of hydrate inhibitors. We investigate the adsorption of a hydrocarbon chain, nonionic and ionic surfactants, and ions at the hydrate-aqueous interface. Our results suggest a strong connection between the water ordering around solutes in bulk and the affinity for the hydrates surface. We distinguish two types of water ordering around solutes: (i) hydrophobic hydration where water molecules form a hydrogen bond network similar to clathrate hydrates, and (ii) ionic hydration where water molecules align according to the polarity of an ionic group. The nonionic surfactant and the hydrocarbon chain induce hydrophobic hydration and are favorably adsorbed on the hydrate surface. Adsorption of ions and the ionic headgroups on the hydrate surface is not favorable because ionic hydration and the hydrogen bond structure of hydrates are incompatible. The nonionic surfactant is adsorbed by the headgroup and tail while adsorption of the ionic surfactants is not favorable through the head. Water ordering is analyzed using the hydrogen bond and tetrahedral density profiles as a function of the distance to the chemical groups. The adsorption of solutes is studied through the free energy profiles as a function of the distance to the hydrate surface. Salt lowers the melting temperature of hydrates, disrupts hydrophobic hydration, reduces the solubility of solutes in the aqueous solution, and increases the propensity of solutes to be adsorbed on hydrate surfaces. Our studies are performed by the unbiased and steered molecular dynamics simulations. The results are in line with experiments on the effect of salt and alkanes in hydrate antiagglomeration.

Hydrophobicity Varying with Temperature, Pressure, and Salt Concentration

Temperature-, pressure-, and salt-concentration-induced variations in the solubility of small nonpolar solutes in aqueous solution and the corresponding variations in the solvent-induced pair attraction between such solute molecules are investigated. The variations in the solvation free energy of a solute and those in the solvent-induced pair attraction are well reproduced by a mean-field approximation in which the repulsive cores of solute molecules are treated as hard spheres and the mean-field energy of a solute molecule is taken to be the average potential energy that the solute molecule feels in solution. The mechanisms of variation in the solvation free energy and those of variation in the solvent-induced pair potential, with increasing temperature, pressure, and salt concentration, are clarified. Correlations between the solvation free energy and the solvent-induced pair potential at a contact distance in temperature, pressure, and salt concentration variations are near linear in any mode of variation, but the slope of the linear relation is dependent on the mode of variation and is determined by a ratio of the solvation thermodynamic quantities characteristic of each mode of variation.

Optimized solubilization of TRIzol-precipitated protein permits Western blotting analysis to maximize data available from brain tissue

BACKGROUND

Techniques simultaneously assessing multiple levels of molecular processing are appealing because molecular signaling underlying complex neural phenomena occurs at complementary levels. The TRIzol method isolates RNA and DNA, but protein retrieval is difficult due to inefficient solubilization of precipitated protein pellets.

NEW METHOD

We optimized a buffer for the efficient solubilization of protein from TRIzol-precipitated brain tissue for Western blotting analysis, which was also more effective at directly homogenizing brain tissue than RIPA buffer.

RESULTS

Protein yield during solubilization, in addition to protein yield via direct homogenization, is increased by optimizing concentrations of chemicals in a standard lysis buffer. Effective incubation parameters for both total protein yield and the analysis of post-translational modifications is remarkably flexible. Importantly, different neural cell types and protein classes are represented in solubilized protein samples. Moreover, we used dissociated mouse brain tissue to isolate microglia from other cell types and successfully resolved cell type-specific proteins from these small and difficult to attain samples.

COMPARISON WITH EXISTING METHOD(S)

Solubilization buffers to date have been comprised primarily of SDS or urea; the data herein demonstrate that components common to lysis buffers can also enhance protein solubilization both after direct homogenization and after precipitation.

CONCLUSIONS

This method is suitable for assessing gene and protein expression from a single brain sample, allowing for a more comprehensive evaluation of neural phenomena while minimizing the number of subjects.

Effect of salt valency and concentration on structure and thermodynamic behavior of anionic polyelectrolyte Na+-polyethacrylate aqueous solution

The intermolecular structure and solvation enthalpy of anionic polyelectrolyte atactic Na⁺-polyethacrylate (PEA) in aqueous solution, as a function of added salt concentration C _s (dilute to concentrated) and valency (NaCl versus CaCl₂), were investigated via molecular dynamics simulations with explicit-ion-solvent and atomistic polymer description. An increase in C _s leads to a decrease in α, which stabilizes to a constant value beyond critical C _s. A significant reduction in R _g in the presence of CaCl₂ salt was observed, due to ion bridging of PEA by Ca²⁺ ions, in agreement with results available in literature on other similar polycarboxylates. An increase in salt valency reduces the value of critical C _s for the onset of stabilization of the overall size and shape of the polymer chain. The critical C _s ratio for the divalent to monovalent salt case is in excellent agreement with results of Langevin dynamics studies on model systems available in the literature. PEA-water H-bond half-life increases with C _s for CaCl₂, but no appreciable effect is seen for NaCl. The hydration of PEA becomes stronger in the presence of divalent salt. The strength of H-bond interaction energy is greater for cations as compared to anions of the salt. The salt cation effect in displacing water molecules from the vicinity of PEA, with increase in C _s, is greater for NaCl solution. The decrease in water coordination to PEA carboxylate groups, due to increased C _s, is more pronounced in NaCl solution. The nature of the behavior of the solvation enthalpy of PEA and the type of intermolecular interactions contributing to it, is in agreement with experimental observations from the literature. The hydration enthalpy of PEA in divalent CaCl₂ aqueous salt solution is more exothermic compared to monovalent NaCl salt solution, in agreement with experimental data. The solvation of PEA is thermodynamically more favorable in the case of CaCl₂ solution. The exothermic solvation enthalpy, H-bond lifetime, number of H-bonds and H-bond interaction energy are greater in magnitude in CaCl₂ aqueous solution.

Effects of thermodynamic inhibitors on the dissociation of methane hydrate: a molecular dynamics study

We investigate the effects of methanol and NaCl, which are known as thermodynamic hydrate inhibitors, on the dissociation kinetics of methane hydrate in aqueous solutions by using molecular dynamics simulations. It is shown that the dissociation rate is not constant but changes with time. The dissociation rate in the initial stage is increased by methanol whereas it is decreased by NaCl. This difference arises from the opposite effects of the two thermodynamic inhibitors on the hydration free energy of methane. The dissociation rate of methane hydrate is increased by the formation of methane bubbles in the aqueous phase because the bubbles absorb surrounding methane molecules. It is found that both methanol and NaCl facilitate the bubble formation. However, their mechanisms are completely different from each other. The presence of ions enhances the hydrophobic interactions between methane molecules. In addition, the ions in the solution cause a highly non-uniform distribution of dissolved methane molecules. These two effects result in the easy formation of bubbles in the NaCl solution. In contrast, methanol assists the bubble formation because of its amphiphilic character.

Free energetics of carbon nanotube association in aqueous inorganic NaI salt solutions: Temperature effects using all-atom molecular dynamics simulations

In this study, we examine the temperature dependence of free energetics of nanotube association using graphical processing unit-enabled all-atom molecular dynamics simulations (FEN ZI) with two (10,10) single-walled carbon nanotubes in 3 m NaI aqueous salt solution. Results suggest that the free energy, enthalpy and entropy changes for the association process are all reduced at the high temperature, in agreement with previous investigations using other hydrophobes. Via the decomposition of free energy into individual components, we found that solvent contribution (including water, anion, and cation contributions) is correlated with the spatial distribution of the corresponding species and is influenced distinctly by the temperature. We studied the spatial distribution and the structure of the solvent in different regions: intertube, intratube and the bulk solvent. By calculating the fluctuation of coarse-grained tube-solvent surfaces, we found that tube-water interfacial fluctuation exhibits the strongest temperature dependence. By taking ions to be a solvent-like medium in the absence of water, tube-anion interfacial fluctuation shows similar but weaker dependence on temperature, while tube-cation interfacial fluctuation shows no dependence in general. These characteristics are discussed via the malleability of their corresponding solvation shells relative to the nanotube surface. Hydrogen bonding profiles and tetrahedrality of water arrangement are also computed to compare the structure of solvent in the solvent bulk and intertube region. The hydrophobic confinement induces a relatively lower concentration environment in the intertube region, therefore causing different intertube solvent structures which depend on the tube separation. This study is relevant in the continuing discourse on hydrophobic interactions (as they impact generally a broad class of phenomena in biology, biochemistry, and materials science and soft condensed matter research), and interpretations of hydrophobicity in terms of alternative but parallel signatures such as interfacial fluctuations, dewetting transitions, and enhanced fluctuation probabilities at interfaces.

Ionic strength-modulated catalytic efficiency of a multienzyme cascade nanoconfined on charged hierarchical scaffolds

Understanding the effect of ionic strength on the efficiency of this enzyme cascade within charged hierarchical nanospace is not only fundamentally interesting, but also important for translating biochemical pathways to noncellular environments.

Structural conservation of the short α-helix in modified higher and lower polarity water solutions

Which conformation is preferred when the polarity of water molecules is scaled byE_P=E_LJ+S²E_C?

The structure of a PII signaling protein from a halophilic archaeon reveals novel traits and high-salt adaptations

To obtain insights into archaeal nitrogen signaling and haloadaptation of the nitrogen/carbon/energy-signaling protein PII, we determined crystal structures of recombinantly produced GlnK2 from the extreme halophilic archaeon Haloferax mediterranei, complexed with AMP or with the PII effectors ADP or ATP, at respective resolutions of 1.49 Å, 1.45 Å, and 2.60 Å. A unique trait of these structures was a three-tongued crown protruding from the trimer body convex side, formed by an 11-residue, N-terminal, highly acidic extension that is absent from structurally studied PII proteins. This extension substantially contributed to the very low pI value, which is a haloadaptive trait of H. mediterranei GlnK2, and participated in hexamer-forming contacts in one crystal. Similar acidic N-extensions are shown here to be common among PII proteins from halophilic organisms. Additional haloadaptive traits prominently represented in H. mediterranei GlnK2 are a very high ratio of small residues to large hydrophobic aliphatic residues, and the highest ratio of polar to nonpolar exposed surface for any structurally characterized PII protein. The presence of a dense hydration layer in the region between the three T-loops might also be a haloadaptation. Other unique findings revealed by the GlnK2 structure that might have functional relevance are: the adoption by its T-loop of a three-turn α-helical conformation, perhaps related to the ability of GlnK2 to directly interact with glutamine synthetase; and the firm binding of AMP, confirmed by biochemical binding studies with ATP, ADP, and AMP, raising the possibility that AMP could be an important PII effector, at least in archaea.

DATABASE

The atomic coordinates and structure factors have been deposited in the Protein Data Bank under the accession numbers 4OZL (hmGlnK2-AMP), 4OZJ (hmGlnK2-ADP), and 4OZN (hmGlnK2-ATP).

STRUCTURED DIGITAL ABSTRACT

hmGlnK2 and hmGlnK2 bind by x-ray crystallography (View interaction).

Electric field effects on alanine tripeptide in sodium halide solutions

The electric field effects on conformational properties of trialanine in different halide solutions were explored with long-scale molecular dynamics simulations. NaF, NaCl, NaBr and NaI solutions of low (0.2 M) and high (2 M) concentrations were exposed to a constant electric field of 1000 V/m. Generally, the electric field does not disturb trialanine's structure. Large structural changes appear only in the case of the supersaturated 2.0 M NaF solution containing NaF crystals. Although the electric field affects in a complex way, all the ions-water-peptide interactions, it predominantly affects the electroselectivity effect, which describes specific interactions such as the ion-pair formation.

An Investigation of Ion-Pairing of Alkali Metal Halides in Aqueous Solutions Using the Electrical Conductivity and the Monte Carlo Computer Simulation Methods

The ion pairing is, in very dilute aqueous solutions, of rather small importance for solutions' properties, which renders its precise quantification quite a laborious task. Here we studied the ion pairing of alkali halides in water by using the precise electric conductivity measurements in dilute solutions, and in a wide temperature range. The low-concentration chemical model was used to analyze the results, and to estimate the association constant of different alkali halide salts. It has been shown that the association constant is related to the solubility of salts in water and produces a 'volcano relationship', when plotted against the difference between the free energy of hydration of the corresponding individual ions. The computer simulation, using the simple MB+dipole water model, were used to interprete the results, to find a microscopic basis for Collins' law of matching water affinities.

Mixed-salt effects on the conformation of a short salt-bridge-forming α helix: a simulation study

The structure of a single alanine-based ACE-AEAAAKEAAAKA-NH2 peptide in explicit aqueous solutions with mixed inorganic salts (NaCl and KCl) is investigated by using molecular simulations. The concentration of Na(+), c(Na(+)), varies from 0.0M to 1.0M, whereas the concentration of K(+) is 1-c(Na(+)). The simulated peptide is very sensitive to the change of concentration ratio between Na(+) and K(+). When the concentration ratio between Na^{+} and K^{+} is changed from 0.5/0.5, the structure of the peptide becomes loose or disordered. This specific phenomenon is confirmed via checking the changes of helix parameters and mapping the free energy along different coordinates. The higher normalized probability of forming direct and indirect salt bridges between residues Glu7(+) and Lys11(+) and the smallest probability of forming ringlike structures should be responsible for the stabilized helix structure in the 0.5 Na(+)/0.5 K(+) solution. Furthermore, a noticeable conformational transition from an extended helix to an α helix is found in the 0.5 Na(+)/0.5 K(+) solution, where a local ion cloud shows that some Na(+) ions in the inner shells are still directly binding with the peptide, while K(+) in the outer shells are moving into the inner shells, keeping the peptide in the collapsed state.

Solvation free energies of alanine peptides: the effect of flexibility

The electrostatic (ΔGel), van der Waals cavity-formation (ΔGvdw), and total (ΔG) solvation free energies for 10 alanine peptides ranging in length (n) from 1 to 10 monomers were calculated. The free energies were computed both with fixed, extended conformations of the peptides and again for some of the peptides without constraints. The solvation free energies, ΔGel, and components ΔGvdw, and ΔG, were found to be linear in n, with the slopes of the best-fit lines being γel, γvdw, and γ, respectively. Both γel and γ were negative for fixed and flexible peptides, and γvdw was negative for fixed peptides. That γvdw was negative was surprising, as experimental data on alkanes, theoretical models, and MD computations on small molecules and model systems generally suggest that γvdw should be positive. A negative γvdw seemingly contradicts the notion that ΔGvdw drives the initial collapse of the protein when it folds by favoring conformations with small surface areas. When we computed ΔGvdw for the flexible peptides, thereby allowing the peptides to assume natural ensembles of more compact conformations, γvdw was positive. Because most proteins do not assume extended conformations, a ΔGvdw that increases with increasing surface area may be typical for globular proteins. An alternative hypothesis is that the collapse is driven by intramolecular interactions. We find few intramolecular H-bonds but show that the intramolecular van der Waals interaction energy is more favorable for the flexible than for the extended peptides, seemingly favoring this hypothesis. The large fluctuations in the vdw energy may make attributing the collapse of the peptide to this intramolecular energy difficult.

Diversity in the mechanisms of cosolute action on biomolecular processes

Numerous cellular cosolutes significantly impact the way that proteins and other biomacromolecules act and interact. We have followed the thermodynamic effect of several cosolute classes, including polymers, cellular osmolytes, and inorganic salts, on the stability of biomolecular folding and complexation. By comparing changes in free energy, enthalpy, and entropy upon cosolutes addition for these processes, we identify several thermodynamically distinct mechanisms. Surprisingly, even while many cosolutes display similar scaling of the change in stabilizing free energy with their concentration, a breakdown of this free energy into enthalpic and entropic contributions distinguishes different families of cosolutes. We discuss how these "thermodynamic fingerprints" can direct towards possible underlying mechanisms that govern the cosolute effect.

Free energetics of carbon nanotube association in pure and aqueous ionic solutions

Carbon nanotubes are a promising platform across a broad spectrum of applications ranging from separations technology, drug delivery, to bio(electronic) sensors. Proper dispersion of carbon nanotube materials is important to retaining the electronic properties of nanotubes. Experimentally it has been shown that salts can regulate the dispersing properties of CNTs in aqueous system with surfactants (Niyogi, S.; Densmore, C. G.; Doorn, S. K. J. Am. Chem. Soc.2009, 131, 1144-1153); details of the physicochemical mechanisms underlying such effects continue to be explored. We address the effects of inorganic monovalent salts (NaCl and NaI) on dispersion stability of carbon nanotubes.We perform all-atom molecular dynamics simulations using nonpolarizable interaction models to compute the potential of mean force between two (10,10) single-walled carbon nanotubes (SWNTs) in the presence of NaCl/NaI and compare to the potential of mean force between SWNTs in pure water. Addition of salts enhances stability of the contact state between two SWNT's on the order of 4 kcal/mol. The ion-specific spatial distribution of different halide anions gives rise to starkly different contributions to the free energy stability of nanotubes in the contact state. Iodide anion directly stabilizes the contact state to a much greater extent than chloride anion. The enhanced stability arises from the locally repulsive forces imposed on nanotubes by the surface-segregated iodide anion. Within the time scale of our simulations, both NaI and NaCl solutions stabilize the contact state by equivalent amounts. The marginally higher stability for contact state in salt solutions recapitulates results for small hydrophobic solutes in NaCl solutions (Athawale, M. V.; Sarupria, S.; Garde, S. J. Phys. Chem. B2008, 112, 5661-5670) as well as single-walled carbon nanotubes in NaCl and CaCl2 aqueous solutions.

Reversible electrochemical switching of polymer brushes grafted onto conducting polymer films

We demonstrate the electrochemical switching of conformation of surface-bound polymer brushes, by grafting environmentally sensitive polymer brushes from an electrochemically active conducting polymer (ECP). Using atom transfer radical polymerization (ATRP), we grafted zwitterionic betaine homopolymer and block copolymer brushes of poly(3-(methacryloylamido)propyl)-N,N'-dimethyl(3-sulfopropyl)ammonium hydroxide) (PMPDSAH) and poly(methyl methacrylate)-b-PMPDSAH, from an initiator, surface-coupled to a poly(pyrrole-co-pyrrolyl butyric acid) film. The changes in ionic solution composition in the surface layer, resulting from oxidation and reduction of the ECP, trigger a switch in conformation of the surface-bound polymer brushes, demonstrated here by electrochemical impedance spectroscopy (EIS) and in a change of wettability. The switch is dependent upon temperature in a way that is analogous to the temperature-dependent solubility and aggregation of similar betaine polymers in aqueous solution but has a quite different dependence on salt concentration in solution. The switch is fully reversible and reproducible. We interpret the switching behavior in terms of a transition to a "supercollapsed" state on the surface that is controlled by ions that balance the charge state of the ECP and are adsorbed to the opposite charges of the zwitterionic graft, close to the graft-ECP interface. The behavior is significantly modified by hydrophobic interactions of the block copolymer graft. We speculate that the synergistic combination of properties embodied in these "smart" materials may find applications in electrochemical control of surface wetting and in the interaction with biomolecules and living cells.

Hydrophobicity of proteins and interfaces: insights from density fluctuations

Macroscopic characterizations of hydrophobicity (e.g., contact angle measurements) do not extend to the surfaces of proteins and nanoparticles. Molecular measures of hydrophobicity of such surfaces need to account for the behavior of hydration water. Theory and state-of-the-art simulations suggest that water density fluctuations provide such a measure; fluctuations are enhanced near hydrophobic surfaces and quenched with increasing surface hydrophilicity. Fluctuations affect conformational equilibria and dynamics of molecules at interfaces. Enhanced fluctuations are reflected in enhanced cavity formation, more favorable binding of hydrophobic solutes, increased compressibility of hydration water, and enhanced water-water correlations at hydrophobic surfaces. These density fluctuation-based measures can be used to develop practical methods to map the hydrophobicity/philicity of heterogeneous surfaces including those of proteins. They highlight that the hydrophobicity of a group is context dependent and is significantly affected by its environment (e.g., chemistry and topography) and especially by confinement. The ability to include information about hydration water in mapping hydrophobicity is expected to significantly impact our understanding of protein-protein interactions as well as improve drug design and discovery methods and bioseparation processes.

Effects of Hofmeister ions on the α-helical structure of proteins

The molecular conformation of proteins is sensitive to the nature of the aqueous environment. In particular, the presence of ions can stabilize or destabilize (denature) protein secondary structure. The underlying mechanisms of these actions are still not fully understood. Here, we combine circular dichroism (CD), single-molecule Förster resonance energy transfer, and atomistic computer simulations to elucidate salt-specific effects on the structure of three peptides with large α-helical propensity. CD indicates a complex ion-specific destabilization of the α-helix that can be rationalized by using a single salt-free computer simulation in combination with the recently introduced scheme of ion-partitioning between nonpolar and polar peptide surfaces. Simulations including salt provide a molecular underpinning of this partitioning concept. Furthermore, our single-molecule Förster resonance energy transfer measurements reveal highly compressed peptide conformations in molar concentrations of NaClO(4) in contrast to strong swelling in the presence of GdmCl. The compacted states observed in the presence of NaClO(4) originate from a tight ion-backbone network that leads to a highly heterogeneous secondary structure distribution and an overall lower α-helical content that would be estimated from CD. Thus, NaClO(4) denatures by inducing a molten globule-like structure that seems completely off-pathway between a fully folded helix and a coil state.

Role of spatial ionic distribution on the energetics of hydrophobic assembly and properties of the water/hydrophobe interface

We present results from all-atom molecular dynamics simulations of large-scale hydrophobic plates solvated in NaCl and NaI salt solutions. As observed in studies of ions at the air-water interface, the density of iodide near the water-plate interface is significantly enhanced relative to chloride and in the bulk. This allows for the partial hydration of iodide while chloride remains more fully hydrated. In 1 M solutions, iodide directly pushes the hydrophobes together (contributing -2.51 kcal mol(-1)) to the PMF. Chloride, however, strengthens the water-induced contribution to the PMF by ~-2.84 kcal mol(-1). These observations are enhanced in 3 M solutions, consistent with the increased ion density in the vicinity of the hydrophobes. The different salt solutions influence changes in the critical hydrophobe separation distance and characteristic wetting/dewetting transitions. These differences are largely influenced by the ion-specific expulsion of iodide from bulk water. Results of this study are of general interest to the study of ions at interfaces and may lend insight to the mechanisms underlying the Hofmeister series.