Seeking Solvation: Exploring the Role of Protein Hydration in Silk Gelation

The mechanism by which arthropods (e.g., spiders and many insects) can produce silk fibres from an aqueous protein (fibroin) solution has remained elusive, despite much scientific investigation. In this work, we used several techniques to explore the role of a hydration shell bound to the fibroin in native silk feedstock (NSF) from Bombyx mori silkworms. Small angle X-ray and dynamic light scattering (SAXS and DLS) revealed a coil size (radius of gyration or hydrodynamic radius) around 12 nm, providing considerable scope for hydration. Aggregation in dilute aqueous solution was observed above 65 °C, matching the gelation temperature of more concentrated solutions and suggesting that the strength of interaction with the solvent (i.e., water) was the dominant factor. Infrared (IR) spectroscopy indicated decreasing hydration as the temperature was raised, with similar changes in hydration following gelation by freezing or heating. It was found that the solubility of fibroin in water or aqueous salt solutions could be described well by a relatively simple thermodynamic model for the stability of the protein hydration shell, which suggests that the affected water is enthalpically favoured but entropically penalised, due to its reduced (vibrational or translational) dynamics. Moreover, while the majority of this investigation used fibroin from B. mori, comparisons with published work on silk proteins from other silkworms and spiders, globular proteins and peptide model systems suggest that our findings may be of much wider significance.

Structural and functional properties of a magnesium transporter of the SLC11/NRAMP family

Members of the ubiquitous SLC11/NRAMP family catalyze the uptake of divalent transition metal ions into cells. They have evolved to efficiently select these trace elements from a large pool of Ca2+ and Mg2+, which are both orders of magnitude more abundant, and to concentrate them in the cytoplasm aided by the cotransport of H+ serving as energy source. In the present study, we have characterized a member of a distant clade of the family found in prokaryotes, termed NRMTs, that were proposed to function as transporters of Mg2+. The protein transports Mg2+ and Mn2+ but not Ca2+ by a mechanism that is not coupled to H+. Structures determined by cryo-EM and X-ray crystallography revealed a generally similar protein architecture compared to classical NRAMPs, with a restructured ion binding site whose increased volume provides suitable interactions with ions that likely have retained much of their hydration shell.

X-ray absorption spectroscopy and actinide electrochemistry: a setup dedicated to radioactive samples applied to neptunium chemistry

A spectroelectrochemical setup has been developed to investigate radioactive elements in small volumes (0.7 to 2 ml) under oxidation–reduction (redox) controlled conditions by X-ray absorption spectroscopy (XAS). The cell design is presented together with in situ XAS measurements performed during neptunium redox reactions. Cycling experiments on the NpO2 2+/NpO2 + redox couple were applied to qualify the cell electrodynamics using XANES measurements and its ability to probe modifications in the neptunyl hydration shell in a 1 mol l−1 HNO3 solution. The XAS results are in agreement with previous structural studies and the NpO2 2+/NpO2 + standard potential, determined using Nernst methods, is consistent with measurements based on other techniques. Subsequently, the NpO2 +, NpO2 2+ and Np4+ ion structures in solution were stabilized and measured using EXAFS. The resulting fit parameters are again compared with other results from the literature and with theoretical models in order to evaluate how this spectroelectrochemistry experiment succeeds or fails to stabilize the oxidation states of actinides. The experiment succeeded in: (i) implementing a robust and safe XAS device to investigate unstable radioactive species, (ii) evaluate in a reproducible manner the NpO2 2+/NpO2 + standard potential under dilute conditions and (iii) clarify mechanistic aspects of the actinyl hydration sphere in solution. In contrast, a detailed comparison of EXAFS fit parameters shows that this method is less appropriate than the majority of the previously reported chemical methods for the stabilization of the Np4+ ion.

Influence of effective polarization on ion and water interactions within a biomimetic nanopore

Interactions between ions and water at hydrophobic interfaces within ion channels and nanopores are suggested to play a key role in the movement of ions across biological membranes. Previous molecular dynamics (MD) simulations have shown that the affinity of polarizable anions to aqueous/hydrophobic interfaces can be markedly influenced by including polarization effects through an electronic continuum correction (ECC). Here, we designed a model biomimetic nanopore to imitate the polar pore openings and hydrophobic gating regions found in pentameric ligand-gated ion channels. MD simulations were then performed using both a non-polarizable force field and the ECC method to investigate the behavior of water, Na+ and Cl- ions confined within the hydrophobic region of the nanopore. Number density distributions revealed preferential Cl- adsorption to the hydrophobic pore walls, with this interfacial layer largely devoid of Na+. Free energy profiles for Na+ and Cl- permeating the pore also display an energy barrier reduction associated with the localization of Cl- to this hydrophobic interface, and the hydration number profiles reflect a corresponding reduction in the first hydration shell of Cl-. Crucially, these ion effects were only observed through inclusion of effective polarization which therefore suggests that polarizability may be essential for an accurate description for the behavior of ions and water within hydrophobic nanoscale pores, especially those that conduct Cl-.

Magnesium Force Fields for OPC Water with Accurate Solvation, Ion-Binding, and Water-Exchange Properties: Successful Transfer from SPC/E

Magnesium plays a vital role in a large variety of biological processes. To model such processes by molecular dynamics simulations, researchers rely on accurate force field parameters for Mg2+ and water. OPC is one of the most promising water models yielding an improved description of biomolecules in water. The aim of this work is to provide force field parameters for Mg2+ that lead to accurate simulation results in combination with OPC water. Using twelve different Mg2+ parameter sets, that were previously optimized with different water models, we systematically assess the transferability to OPC based on a large variety of experimental properties. The results show that the Mg2+ parameters for SPC/E are transferable to OPC and closely reproduce the experimental solvation free energy, radius of the first hydration shell, coordination number, activity derivative, and binding affinity toward the phosphate oxygen on RNA. Two optimal parameter sets are presented: MicroMg yields water exchange in OPC on the microsecond timescale in agreement with experiments. NanoMg yields accelerated exchange on the nanosecond timescale and facilitates the direct observation of ion binding events for enhanced sampling purposes.

Investigation of the process of moisture loss during refrigerated storage of fish

The purpose of current work is to study the effect of carbon dioxide on the shrinkage of smoked fish and to develop a technical solution for the implementation of technology with the use of CO2 in fish trade. We use mackerel, flounder and crucian carp as test samples. The studies were carried out in two versions: storage of fish in a chamber under traditional conditions and with the addition of carbon dioxide (CO2) to the refrigerating chamber. The use of carbon dioxide gas during the storage of smoked fish leads to an increase in the water-holding capacity of the fish in comparison with the traditional storage method. In our proposed method of storage in a cold atmosphere with CO2, fish shrinkage is reduced. The carbonate ions well bind water molecules in the hydration shell due to positive hydration, which slows down the processes of hydrolysis and oxidation of lipids inside the subcutaneous layer and preserves the moisture-retaining capacity of tissues. Thus, the use of carbon dioxide in the storage of smoked fish reduces weight loss and does not affect the appearance of the fish.

Cation Hydration Energy and Surface Hydration Have Crucial Role On Thermodynamics of Clay Swelling

The swelling capacity and stability of clay play a crucial role in various areas ranging from cosmetics to oil extraction; hence change in their swelling behavior after cation exchange with the surrounding medium is important for their efficient utilization. Here we focus on understanding the role of different hydration properties of cation on the thermodynamics of clay swelling by water adsorption. We have used mica as the reference clay, Na+, Li+, and H+ ions as the interstitial cations, and performed grand canonical Monte Carlo simulations of water adsorption in mica pores (of widths d = 4−40 Å). We found that water adsorption in Na-, Li- and H-mica pores is qualitatively similar; however significant quantitative differences are observed, especially at smaller d. Higher water density in H-mica pores (ρH) was expected due to the smaller size of H+ ions having higher hydration energy. However, a counter-intuitive trend of ρLi > ρNa > ρb (bulk density) > ρH was observed due to adsorption energy where the contribution of mica framework atoms was also found to be significant. The disjoining pressure (Π), swelling free energy (∆Ωex), and several structural properties of confined water and ions were calculated to perform thermodynamic analysis of the system. Our detailed calculations have captured the structural evolution of ions and water, especially the transitions from mono- to bi- and multilayer as a function of d. Oscillatory behavior in the Π and ∆Ωex profiles with diminishing to zero for d ≥ 11 Å is observed in all three mica systems. A shift in the location of global minima of ∆Ωex towards the higher d values and ∆Ωex becoming more repulsive is observed in the increasing order of hydration energy of Na+, Li+, and H + ions. The ∆Ωex for Na-mica is characterized by global minima at d = 6 Å corresponding to crystalline swelling, a significant barrier for crystalline swelling from d = 6 to 9 Å and lower for crystalline (d = 9 Å) to osmotic swelling (d > 12 Å). For Li-mica, the energy barrier for crystalline to osmotic swelling is lesser compared to the Na-mica system, whereas for H-mica the ∆Ωex > 0 for all d thus favoring osmotic swelling. We found that the hydration of cations by surface atoms plays a key role in the thermodynamics of clay swelling. The Na+ ions hydrate more number of surface oxygens, act as anchors, and hold the mica pore at d = 6 Å by sharing hydrating water with ions of opposite sides forming an electrostatically connected bridge of mica Na-water-Na-mica. The Li+ ions do hydrate surface oxygen atoms, albeit lesser number and sharing of hydration shell with nearby Li+ ions is also minimum. Both, surface hydration and water sharing, is minimum in the H+ ion case, as they are mostly present in the center of the pore as diffusive ions; thus exerting a consistent osmotic pressure on the mica frameworks, favoring swelling.