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, GalA, chains in the presence of Ca in a ratio of = [Ca]/[GalA] = 0.25 in order to determine to which extent the popular "egg-box model" (EBM) is able to describe the association between Ca cations and polygalacturonate (polyGalA) chains. To this aim, we slightly revised the empirical parameters for the interaction between Ca and the carboxylate oxygen atoms of GalA units so as to reproduce the experimental Ca-GalA association constant.

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.

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

We show here how the structure of polygalacturonate (polyGalA) hydrogels cross-linked by Ca 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. , (7), 2864-2872): they exhibit similar transparencies and gradients of mechanical properties and polyGalA concentrations.

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

The local structure of Fe in Fe-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 Fe both in aqueous solution and in the hydrogel, with similar Fe-O distances (2.09 ± 0.

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 M (Ca, Zn, or Fe) 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 = [M]/[Gal] equal to 0.25, showing that every M cation interacts with four galacturonate (Gal) units all along the gels.

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 Fe ions into aqueous solutions of polygalacturonate (polyGal) chains. The Fe ions act as cross-linkers between the Gal units in such a way that both the molar ratio R ([Fe]/[Gal units] = 0.25) and the mesh size of the polyGal network at the local scale (ξ = 75 ± 5 Å) have constant values within the whole gel, as respectively determined by titration and Small Angle Neutron Scattering.

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, Mg, Ca, Fe, Fe, Al, Cr) have been investigated.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.