How Accurate Is the Egg-Box Model in Describing the Binding of Calcium to Polygalacturonate? A Molecular Dynamics Simulation Study.

We performed molecular dynamics (MD) simulations of octameric galacturonate, GalA8, chains in the presence of Ca2+ in a ratio of R = [Ca2+]/[GalA] = 0.25 in order to determine to which extent the popular "egg-box model" (EBM) is able to describe the association between Ca2+ cations and polygalacturonate (polyGalA) chains. To this aim, we slightly revised the empirical parameters for the interaction between Ca2+ and the carboxylate oxygen atoms of GalA units so as to reproduce the experimental Ca2+-GalA association constant. We also defined an ad hoc order parameter, referred to as the egg-box score (EBS), that quantifies any deviation of the local coordination geometry of calcium cations with respect to an "ideal" EBM coordination geometry. The results reveal that the local coordination geometry of Ca2+ cations bound to polyGalA chains differs from that of the EBM. Moreover, polyGalA chains exhibit significant conformational disorder, and the cross-link angles formed between polyGalA chain axes are broadly distributed. Overall, the present study suggests that the EBM fails to describe accurately the association modes between calcium and polyGalA chains at a molar ratio R of 0.25.

Slow water dynamics in polygalacturonate hydrogels revealed by NMR relaxometry and molecular dynamics simulation.

Diffusions in gels are of prime importance, but their measurements are mainly focused on the diffusion in the pores or through the mesh of the gels. In this study, we performed a deeper dynamic analysis of the water in close interaction with the fibers structuring two heterogeneous polygalacturonate (polyGalA) hydrogels formed by Ca and Zn ions (crosslinking agents). Nuclear magnetic resonance dispersion (NMRD) profiles recorded in-situ by fast-field cycling relaxometry allow to observe the very slow dynamics of water within the gels. Two distinct interpretations of the NMRD profiles are discussed, the first in regard of rotational and translational dynamics in the fibers and the second with respect to a Levy-walk on the fibers' surface. These discussions are confronted with molecular dynamics simulations on a model Ca-polyGalA fiber.

Controlled Loading and Release of Beta-Lactoglobulin in Calcium-Polygalacturonate Hydrogels.

We show here how the structure of polygalacturonate (polyGalA) hydrogels cross-linked by Ca2+ cations via external gelation controls the loading and release rate of beta-lactoglobulin (BLG), a globular protein. Hydrogels prepared from a polyGalA/BLG solution are found to be similar to those obtained from a polyGalA solution in our previous study (Maire du Poset et al. Biomacromolecules 2019, 20 (7), 2864-2872): they exhibit similar transparencies and gradients of mechanical properties and polyGalA concentrations. The nominal BLG/polyGalA ratio of the mixtures is almost recovered within the whole mixed hydrogel despite such strong concentration gradients, except in the part of the hydrogels with the largest mesh size, where more BLG proteins are present. This gradient enables one to tune the amount of protein loaded within the hydrogel. At a local scale, the proteins are distributed evenly within the hydrogel network, as shown by small-angle neutron scattering (SANS). The release of proteins from hydrogels is driven by Fickian diffusion, and the release rate increases with the mesh size of the network, with a characteristic time of a few hours. The specific structure of these polysaccharide-based hydrogels allows for control of both the dosage and the release rate of the loaded protein and makes them good candidates for use as oral controlled-delivery systems.

Evidence for an egg-box-like structure in iron(ii)-polygalacturonate hydrogels: a combined EXAFS and molecular dynamics simulation study.

The local structure of Fe2+ in Fe2+-polygalacturonic acid (polyGalA) hydrogels has been studied by coupling Extended X-ray Absorption Fine Structure (EXAFS) spectroscopy and molecular dynamics (MD) simulation. The EXAFS fitting results reveal an octahedral coordination geometry of Fe2+ both in aqueous solution and in the hydrogel, with similar Fe-O distances (2.09 ± 0.01 Å in the hydrogel and 2.11 ± 0.01 Å in aqueous solution). The MD simulations evidence that standard empirical force fields are unable to accurately reproduce the EXAFS spectra of Fe2+ in both aqueous solution and hydrogel. Based on the EXAFS distance determinations, we then performed restrained MD simulations of hypothetical octahedral coordination modes of Fe2+ with polyGalA chains. The best agreement between experimental and simulated EXAFS spectra was found when Fe2+ is monodentately coordinated to two carboxylate and two hydroxyl oxygens from a pair of polyGalA chains as well as to two water oxygens in an octahedral coordination geometry compatible with the "egg-box model".

Tuning the Structure of Galacturonate Hydrogels: External Gelation by Ca, Zn, or Fe Cationic Cross-Linkers.

We show here how the nature of various divalent cations M2+ (Ca2+, Zn2+, or Fe2+) influences the structure and mechanical properties of ionotropic polygalacturonate (polyGal) hydrogels designed by the diffusion of cations along one direction (external gelation). All hydrogels exhibit strong gradients of polyGal and cation concentrations, which are similar for all studied cations with a constant ratio R = [M2+]/[Gal] equal to 0.25, showing that every M2+ cation interacts with four galacturonate (Gal) units all along the gels. The regions of the hydrogels formed in the early stages of the gelation process are also similar for all cations and are homogeneous, with the same characteristic mesh size (75 ± 5 Å, as measured by small angle neutron scattering (SANS)) and the same storage modulus G' (∼5 × 104 Pa). Conversely, in the regions of the gels formed in later stages of the process there exist differences in mechanical properties, turbidity, and local structure from one cation to another. Zn(II)-polyGal and Fe(II)-polyGal hydrogels display mesoscopic heterogeneities, more marked in case of Fe than for Zn, that are not present in Ca(II)-polyGal hydrogels. This comes from the mode and the strength of association between the cation and the Gal unit (bidentate for Ca2+ and monodentate "egg-box" for Zn2+ and Fe2+). Cross-links formed by Zn2+ and Fe2+ have a higher stability (lower ability to untie and reform) that induces the formation of local heterogeneities in the early stages of the gelation process whose size progressively increases during the gel growth, a mechanism that does not occur for cross-links made by Ca2+ that are less stable and enable possible reorganizations between polyGal chains.

Design of polygalacturonate hydrogels using iron(II) as cross-linkers: A promising route to protect bioavailable iron against oxidation.

We designed stable and highly reproducible hydrogels by external unidirectional diffusion of Fe2+ ions into aqueous solutions of polygalacturonate (polyGal) chains. The Fe2+ ions act as cross-linkers between the Gal units in such a way that both the molar ratio R ([Fe2+]/[Gal units] = 0.25) and the mesh size of the polyGal network at the local scale (ξ = 75 ±â€¯5 Å) have constant values within the whole gel, as respectively determined by titration and Small Angle Neutron Scattering. From macroscopic point of view, there is a progressive decrease of polyGal concentration from the part of the gel formed in the early stages of the gelation process, which is homogeneous, transparent and whose Young modulus has a high value of ∼105 Pa, up to the part of the gel formed in the late stages, which is heterogeneous, highly turbid and has a much lower Young modulus of ∼103 Pa. Since the local organization of the polyGal chains remains identical all along the hydrogels, this macroscopic concentration gradient originates from the formation of heterogeneities at a mesoscopic length scale during the gelation process. In addition, X-ray Absorption Spectroscopy measurements remarkably reveal that Fe2+ ions keep their +II oxidation state in the whole gels once they have cross-linked the Gal units. These polyGal hydrogels thus protect iron against oxidation and could be used for iron fortification.

Specific binding of trivalent metal ions to λ-carrageenan.

Carrageenans are a family of sulphated cell wall polysaccharides extracted from seaweeds and are widely used in different industrial sectors. Relative to κ-carrageenan (κ-car) and ι-carrageenan (ι-car), the ionic binding behavior of λ-carrageenan (λ-car) is far less studied. In this work, the interaction and binding behavior between λ-car and metal ions of different valency (Na+, K+, Mg2+, Ca2+, Fe2+, Fe3+, Al3+, Cr3+) have been investigated. In contrast to the non-specific interaction of the monovalent and divalent cations, specific binding has been identified between λ-car and Fe3+/Al3+. The specific binding could lead to either precipitation or gelation of λ-car, depending on the way of introducing Fe3+/Al3+ ions. Fe3+ and Al3+ exhibit the same binding stoichiometry of [M3+]/[repeating unit] = 1.0, with the former having a relatively larger binding constant. Cr3+, though having very similar physical properties with Fe3+/Al3+, is incapable of binding specifically to Cr3+. The phenomena could not be interpreted in terms of counterion condensation, and are rather attributable to a mechanism in which hexa-coordination of Fe3+/Al3+ and entropy-driven cation dehydration play crucial roles in driving the binding of the trivalent metal ions to λ-car.

Molecular Packing, Hydrogen Bonding, and Fast Dynamics in Lysozyme/Trehalose/Glycerol and Trehalose/Glycerol Glasses at Low Hydration.

Water and glycerol are well-known to facilitate the structural relaxation of amorphous protein matrices. However, several studies evidenced that they may also limit fast (∼picosecond-nanosecond, ps-ns) and small-amplitude (∼Å) motions of proteins, which govern their stability in freeze-dried sugar mixtures. To determine how they interact with proteins and sugars in glassy matrices and, thereby, modulate their fast dynamics, we performed molecular dynamics (MD) simulations of lysozyme/trehalose/glycerol (LTG) and trehalose/glycerol (TG) mixtures at low glycerol and water concentrations. Upon addition of glycerol and/or water, the glass transition temperature, Tg, of LTG and TG mixtures decreases, the molecular packing of glasses is improved, and the mean-square displacements (MSDs) of lysozyme and trehalose either decrease or increase, depending on the time scale and on the temperature considered. A detailed analysis of the hydrogen bonds (HBs) formed between species reveals that water and glycerol may antiplasticize the fast dynamics of lysozyme and trehalose by increasing the total number and/or the strength of the HBs they form in glassy matrices.

Binding of Divalent Cations to Polygalacturonate: A Mechanism Driven by the Hydration Water.

We have investigated the interactions between polygalacturonate (polyGal) and four divalent cations (M(2+) = Ba(2+), Ca(2+), Mg(2+), Zn(2+)) that differ in size and affinity for water. Our results evidence that M(2+)-polyGal interactions are intimately linked to the affinity of M(2+) for water. Mg(2+) interacts so strongly with water that it remains weakly bound to polyGal (polycondensation) by sharing water molecules from its first coordination shell with the carboxylate groups of polyGal. In contrast, the other cations form transient ionic pairs with polyGal by releasing preferentially one water molecule (for Zn(2+)) or two (for Ca(2+) and Ba(2+)), which corresponds to monodentate and bidentate binding modes with carboxylates, respectively. The mechanism for the binding of these three divalent cations to polyGal can be described by two steps: (i) monocomplexation and formation of point-like cross-links between polyGal chains (at low M(2+)/Gal molar ratios, R) and (ii) dimerization (at higher R). The threshold molar ratio, R*, between these two steps depends on the nature of divalent cations and is lower for calcium ions (R* < 0.1) than for zinc and barium ions (R* > 0.3). This difference may be explained by the intermediate affinity of Ca(2+) for water with respect to those of Zn(2+) and Ba(2+), which may induce the formation of cross-links of intermediate flexibility. By comparison, the lower and higher flexibilities of the cross-links formed by Zn(2+) and Ba(2+), respectively, may shift the formation of dimers to higher molar ratios (R*).

Binding characteristics of molecularly imprinted polymers based on fungicides in hydroalcoholic media.

An iprodione-imprinted polymer was prepared by copolymerization of methacrylamide and ethylene glycol dimethacrylate using a noncovalent imprinting approach. Methacrylamide was chosen using molecular dynamics simulations. To concentrate iprodione from hydro-alcoholic solutions, batch sorption of iprodione on the imprinted polymer were conducted. The equilibrium time for iprodione sorption is 20 min, and the corresponding kinetic mechanism follows the pseudo-second order indicating a strong interaction between iprodione and the imprinted polymer. Langmuir, Freundlich, and Dubinin-Radushkevich models were used to fit the isotherm of iprodione sorption. The imprinted polymer was found to be more efficient than the nonimprinted polymer for the uptake of iprodione, as revealed by its higher adsorption energy, affinity, and capacity. Finally, a selectivity study was conducted on the imprinted and the nonimprinted polymers to sorb three fungicides. It shows that the imprinted polymer could be used as a preconcentration phase in a multiresidue analysis of fungicides in hydroalcoholic medium.

Structural behaviour differences in low methoxy pectin solutions in the presence of divalent cations (Ca(2+) and Zn(2+)): a process driven by the binding mechanism of the cation with the galacturonate unit.

In this paper, we compare the interactions between low methoxy pectin (LMP) and either Ca(2+) or Zn(2+) in semi-dilute solutions. Intrinsic viscosity and turbidity measurements reveal that pectin-calcium solutions are more viscous, but yet less turbid, than pectin-zinc ones. To get a molecular understanding of the origin of this rather unexpected behavior, we further performed isothermal titration calorimetry, small angle neutron scattering experiments, as well as molecular dynamics simulations. Our results suggest that calcium cations induce the formation of a more homogeneous network of pectin than zinc cations do. The molecular dynamics simulations indicate that this difference could originate from the way the two cations bind to the galacturonate unit (Gal), the main component of LMP: zinc interacts with both carboxylate and hydroxyl groups of Gal, in a similar way to that described in the so-called egg-box model, whereas calcium only interacts with carboxylate groups. This different binding behavior seems to arise from the stronger interaction of water molecules with zinc than with calcium. Accordingly, galacturonate chains are more loosely associated with each other in the presence of Ca(2+) than with Zn(2+). This may improve their ability to form a gel, not only by dimerization, but also by the formation of point-like cross-links. Overall, our results show that zinc binds less easily to pectin than calcium does.

Influence of pressure on the low-frequency vibrational modes of lysozyme and water: a complementary inelastic neutron scattering and molecular dynamics simulation study.

We performed complementary inelastic neutron scattering (INS) experiments and molecular dynamics (MD) simulations to study the influence of pressure on the low-frequency vibrational modes of lysozyme in aqueous solution in the 1 atm-6 kbar range. Increasing pressure induces a high-frequency shift of the low-frequency part (<10 meV = 80 cm(-1)) of the vibrational density of states (VDOS), g(ω), of both lysozyme and water that reveals a stiffening of the interactions ascribed to the reduction of the protein and water volumes. Accordingly, high pressures increase the curvature of the free energy profiles of the protein quasiharmonic vibrational modes. Furthermore, the nonlinear influence of pressure on the g(ω) of lysozyme indicates a change of protein dynamics that reflects the nonlinear pressure dependence of the protein compressibility. An analogous dynamical change is observed for water and stems from the distortion of its tetrahedral structure under pressure. Moreover, our study reveals that the structural, dynamical, and vibrational properties of the hydration water of lysozyme are less sensitive to pressure than those of bulk water, thereby evidencing the strong influence of the protein surface on hydration water.

How strongly does trehalose interact with lysozyme in the solid state? Insights from molecular dynamics simulation and inelastic neutron scattering.

Therapeutic proteins are usually conserved in glassy matrixes composed of stabilizing excipients and a small amount of water, which both control their long-term stability, and thus their potential use in medical treatments. To shed some light on the protein-matrix interactions in such systems, we performed molecular dynamics (MD) simulations on matrixes of (i) the model globular protein lysozyme (L), (ii) the well-known bioprotectant trehalose (T), and (iii) the 1:1 (in weight) lysozyme/trehalose mixture (LT), at hydration levels h of 0.0, 0.075, and 0.15 (in g of water/g of protein or sugar). We also supplemented these simulations with complementary inelastic neutron scattering (INS) experiments on the L, T, and LT lyophilized (freeze-dried) samples. The densities and free volume distributions indicate that trehalose improves the molecular packing of the LT glass with respect to the L one. Accordingly, the low-frequency vibrational densities of states (VDOS) and the mean square displacements (MSDs) of lysozyme reveal that it is less flexible-and thus less likely to unfold-in the presence of trehalose. Furthermore, at low contents (h = 0.075), water systematically stiffens the vibrational motions of lysozyme and trehalose, whereas it increases their MSDs on the nanosecond (ns) time scale. This stems from the hydrogen bonds (HBs) that lysozyme and trehalose form with water, which, interestingly, are stronger than the ones they form with each other but which, nonetheless, relax faster on the ns time scale, given the larger mobility of water. Moreover, lysozyme interacts preferentially with water in the hydrated LT mixtures, and trehalose appears to slow down significantly the relaxation of lysozyme-water HBs. Overall, our results suggest that the stabilizing efficiency of trehalose arises from its ability to (i) increase the number of HBs formed by proteins in the dry state and (ii) make the HBs formed by water with proteins stable on long (>ns) time scales.

Glucose interactions with a model peptide.

Molecular dynamics simulations have been conducted of the helical polypeptide melittin, in concentrated aqueous solutions of the alpha and beta anomers of D-glucopyranose. Glucose is an osmolyte, and it is expected to be preferentially excluded from the surfaces of proteins. This was indeed found to be the case in the simulations. The results indicate that the observed exclusion may have a contribution from an under-representation of hydrogen bonding interactions between glucose groups and exposed side chains, compared to water. However, glucose was found to bind quite specifically to melittin by stacking its hydrophobic face, consisting of aliphatic protons, against the flat hydrophobic face of the indole group of the tryptophan-19 side chain. Although the binding site for this interaction is localized, the binding is weak for both anomers, with a binding free energy estimated as only ∼0.5 kcal/mol (i.e. near k(B)T). The face of the sugar stacked against the Trp indole ring is different for the two anomers of glucose, due to the disruption of the H1-H3-H5 hydrophobic triad of the beta anomer by the axial C1 hydroxyl group in the alpha anomer. The measurable affinity of the sugar for the Trp side chain is consistent with the very frequent occurrence of this group in the binding sites of proteins that complex with sugars.

Molecular dynamics and neutron scattering study of glucose solutions confined in MCM-41.

Glucose aqueous solutions confined in MCM-41 cylindrical pores of diameter 3.2 nm have been studied by molecular dynamics (MD) simulations and quasielastic neutron scattering (QENS). MD simulations reveal a strong preferential interaction of glucose molecules with the silica walls, which induces significant concentration gradients within the pore. The influence of glucose on the structural and dynamical properties of water strongly depends on the region of the pore considered. The distortion of the hydrogen bond network (HBN) and of the tetrahedral organization of interfacial water molecules induced by silica is much stronger than that induced by glucose molecules. The interfacial glucose molecules diffuse about 1 order of magnitude slower than those in the core region. Differences in affinities for silica of the different species in confined hydrogen-bonded mixtures induce significant structural and dynamical heterogeneities not present in bulk solutions.

Water Confined in Cylindrical Pores: A Molecular Dynamics Study.

Molecular dynamics simulations of water confined in two hydrophilic cylindrical pores-PH and PL-that differ in their silanol surface concentration (7.6 and 3.0 nm(-2), respectively) have been performed at 300 K. A strong interaction of interfacial water molecules with the pore was systematically found and gives rise to a layering effect, a significant distortion of both the hydrogen bond network (HBN) and the tetrahedral structure of these water molecules, and a corresponding subdiffusive mean square displacement along the main axis of the pores. By contrast, water molecules in the inner part of both pores were found to behave similarly to bulk water. The HBN and the tetrahedral configuration of water were more gradually distorted in the PL pore given the larger heterogeneity and rugosity of the surface, and the number of water-pore hydrogen bonds did not scale linearly with the silanol surface concentration of the pores, in part because of the close proximity between silanols in the PH pore. With the PL pore, the dynamic slowing down of water was found consistent with the experiment, suggesting that it provides a better model for the cylindrical MCM-41 mesopores. The structural and dynamical properties of water vary little with the silica force field.

Thermal denaturation of beta-lactoglobulin and stabilization mechanism by trehalose analyzed from Raman spectroscopy investigations.

The thermal denaturation process of beta-lactoglobulin has been analyzed in the 20-100 degrees C temperature range by Raman spectroscopy experiments simultaneously performed in the region of amide modes (800-1800 cm(-1)) and in the low-frequency range (10-350 cm(-1)). The analysis of amide modes reveals a two-step thermal denaturation process in the investigated temperature range. The first step corresponds to the dissociation of dimers associated with an increase of flexibility of the tertiary structure. In the second step, large conformational changes are detected in the secondary structure and described as a loss of alpha-helix structures and a concomitant formation of beta-sheets. Raman investigations in the low-frequency range provide important information on the origin of the denaturation process through the analysis of the solvent dynamics and its coupling with that of the protein. The softening of the tetrahedral structure of water induces the dissociation of dimers and makes the tertiary structure softer, leading to the water penetration in the protein interior. The methodology based on Raman investigations of amide modes and in the low-frequency region was used to analyze the mechanism of beta-lactoglobulin thermostabilization by trehalose. The main effect of trehalose is determined to be related to its capabilities to distort the tetrahedral organization of water molecules.

Thermostabilization mechanism of bovine serum albumin by trehalose.

Thermal denaturation of bovine serum albumin (BSA) is analyzed from differential scanning calorimetry (DSC) and Raman spectroscopy investigations. DSC curves exhibit a marked dependence on protein concentration. BSA thermal denaturation becomes broader and bimodal, and the temperature of denaturation increases with increasing protein concentration. Raman scattering investigations simultaneously carried out in the low-frequency range (10-350 cm(-1)) and in the amide I band region (1500-1800 cm(-1)) indicate that the denaturation process is described as a biphasic process independent of protein concentration. The dependence of the protein stability upon the protein concentration can be interpreted from the coupling of protein and solvent dynamics. The confrontation of previous results obtained from Raman investigations on lysozyme (LYS) and the present study of BSA brings out significant information on protein dynamics and the coupling of protein and hydration-water dynamics in relation with the solvent accessible surface area. Contrary to LYS, the modification of the dynamics of hydration water by the protein is clearly observed on BSA. The influence of trehalose on the protein dynamics was analyzed. We found that trehalose reduces the dynamic fluctuations of polar side chains at the protein-solvent interface. The mechanism of thermostabilization by trehalose is related to the reduction of the exposure of hydrophobic groups of BSA to the water molecules, and to a strengthening of intermolecular O-H interactions in the hydrogen-bond network of water, leading to the stabilization of the tertiary structure.

Influence of homologous disaccharides on the hydrogen-bond network of water: complementary Raman scattering experiments and molecular dynamics simulations.

A comparative investigation of trehalose, sucrose, and maltose in water solution has been performed using Raman scattering experiments and Molecular Dynamics simulations. From the analysis of the O-H stretching region in the [2500,4000] cm(-1) Raman spectral range, which includes for the first time the contribution of 'free' water, and the statistical distribution of water HB probabilities from MD simulations, this study confirms the privileged interaction of trehalose with water above a peculiar threshold weight concentration of about 30%. The role of the hydration number of sugars--found higher for trehalose--on the destructuring effect of the water hydrogen bond network is also addressed. The analysis of the water O-H-O bending spectral range [1500,1800] cm(-1) reveals a change of the homogeneity of water molecules influenced by sugars, but the three investigated sugars are found to behave similarly.