Stretching single polysaccharide molecules using AFM: A potential method for the investigation of the intermolecular uronate distribution of alginate?

Diversity of Bioinspired Hydrogels: From Structure to Applications

Hydrogels are three-dimensional networks with a variety of structures and functions that have a remarkable ability to absorb huge amounts of water or biological fluids. They can incorporate active compounds and release them in a controlled manner. Hydrogels can also be designed to be sensitive to external stimuli: temperature, pH, ionic strength, electrical or magnetic stimuli, specific molecules, etc. Alternative methods for the development of various hydrogels have been outlined in the literature over time. Some hydrogels are toxic and therefore are avoided when obtaining biomaterials, pharmaceuticals, or therapeutic products. Nature is a permanent source of inspiration for new structures and new functionalities of more and more competitive materials. Natural compounds present a series of physico-chemical and biological characteristics suitable for biomaterials, such as biocompatibility, antimicrobial properties, biodegradability, and nontoxicity. Thus, they can generate microenvironments comparable to the intracellular or extracellular matrices in the human body. This paper discusses the main advantages of the presence of biomolecules (polysaccharides, proteins, and polypeptides) in hydrogels. Structural aspects induced by natural compounds and their specific properties are emphasized. The most suitable applications will be highlighted, including drug delivery, self-healing materials for regenerative medicine, cell culture, wound dressings, 3D bioprinting, foods, etc.

Structure analysis and antioxidant activity of polysaccharide-iron (III) from Cordyceps militaris mycelia

Iron-enriched Cordyceps militaris was obtained by adding FeSO₄ solution to the mycelia for biotransformation. The polysaccharide-iron (III) was extracted by water extraction and alcohol precipitation. High performance liquid chromatography showed that the crude polysaccharide-iron (III) had three components. The second component was purified by Sephadex G-150 and named as CPS-iron-II. The average molecular weight of CPS-iron-II was 44.136 kDa. The content of iron was 2.73%. The monosaccharide composition analysis indicated that the CPS-iron-II was composed of rhamnose, arabinose, galactose, glucose, mannose, galacturonic acid with percentage ratio of 0.94:3.12:27.01:36.62:30.20:2.12. The results of methylation analysis revealed that the CPS-iron-II was made of →2)-β-D-Glcp-(1→, with →2, 4)-α-D-Glcp-(1→ highly branched. Congo-red test showed that CPS-iron-II can cause flocculation of Congo red solution. The anti-oxidative analysis showed that antioxidant activity of CPS-iron-II was almost equal to that of Vc. The manuscript provided a new way for the preparation of polysaccharide-iron(III) from Cordyceps militaris.

Mechanistic insight into biopolymer induced iron oxide mineralization through quantification of molecular bonding

Microbial production of iron (oxyhydr)oxides on polysaccharide rich biopolymers occurs on such a vast scale that it impacts the global iron cycle and has been responsible for major biogeochemical events. Yet the physiochemical controls these biopolymers exert on iron (oxyhydr)oxide formation are poorly understood. Here we used dynamic force spectroscopy to directly probe binding between complex, model and natural microbial polysaccharides and common iron (oxyhydr)oxides. Applying nucleation theory to our results demonstrates that if there is a strong attractive interaction between biopolymers and iron (oxyhydr)oxides, the biopolymers decrease the nucleation barriers, thus promoting mineral nucleation. These results are also supported by nucleation studies and density functional theory. Spectroscopic and thermogravimetric data provide insight into the subsequent growth dynamics and show that the degree and strength of water association with the polymers can explain the influence on iron (oxyhydr)oxide transformation rates. Combined, our results provide a mechanistic basis for understanding how polymer-mineral-water interactions alter iron (oxyhydr)oxides nucleation and growth dynamics and pave the way for an improved understanding of the consequences of polymer induced mineralization in natural systems.

Unfolding of a comb-like polymer in a poor solvent: translation of macromolecular architecture in the force-deformation spectra

A numerical self-consistent field modeling approach was employed to study the mechanical unfolding of a globule made by comb-like polymers in a poor solvent with the aim of unraveling how the macromolecular architecture affects the shape of the single-molecule force-deformation curves. We demonstrate that the dependence of the restoring force on the imposed extension of the main chain of the comb-like polymer exhibits a characteristic oscillatory shape in the intermediate deformation range. Theoretical arguments are developed that enable us to relate the shape of the patterns on the force-deformation curves to the molecular architecture (grafting density and length of the side chains) and interaction parameters. Thus, the results of our study suggest a new approach for the determination of macromolecular topology from single-molecule mechanical unfolding experiments.

Quantifying the free energy landscape between polymers and minerals

Higher organisms as well as medical and technological materials exploit mineral-polymer interactions, however, mechanistic understanding of these interactions is poorly constrained. Dynamic force spectroscopy can probe the free energy landscape of interacting bonds, but interpretations are challenged by the complex mechanical behavior of polymers. Here we restate the difficulties inherent to applying DFS to polymer-linked adhesion and present an approach to gain quantitative insight into polymer-mineral binding.

Revision of the GROMOS 56A6(CARBO) force field: Improving the description of ring-conformational equilibria in hexopyranose-based carbohydrates chains

This article describes a revised version 56A6(CARBO_R) of the GROMOS 56A6(CARBO) force field for hexopyranose-based carbohydrates. The simulated properties of unfunctionalized hexopyranoses are unaltered with respect to 56A6CARBO . In the context of both O1 -alkylated hexopyranoses and oligosaccharides, the revision stabilizes the regular (4) C1 chair for α-anomers, with the opposite effect for β-anomers. As a result, spurious ring inversions observed in α(1→4)-linked chains when using the original 56A6(CARBO) force field are alleviated. The (4) C1 chair is now the most stable conformation for all d-hexopyranose residues, irrespective of the linkage type and anomery, and of the position of the residue along the chain. The methylation of a d-hexopyranose leads to a systematic shift in the ring-inversion free energy ((4) C1 to (1) C4 ) by 7-8 kJ mol(-1), positive for the α-anomers and negative for the β-anomers, which is qualitatively compatible with the expected enhancement of the anomeric effect upon methylation at O1. The ring-inversion free energies for residues within chains are typically smaller in magnitude compared to those of the monomers, and correlate rather poorly with the latter. This suggests that the crowding of ring substituents upon chain formation alters the ring flexibility in a nonsystematic fashion. In general, the description of carbohydrate chains afforded by 56A6(CARBO_R) suggests a significant extent of ring flexibility, i.e., small but often non-negligible equilibrium populations of inverted chairs, and challenges the "textbook" picture of conformationally locked carbohydrate rings.

Simulation of force spectroscopy experiments on galacturonic acid oligomers

Pectins, forming a matrix for cellulose and hemicellulose, determine the mechanics of plant cell walls. They undergo salient structural changes during their development. In the presence of divalent cations, usually calcium, pectins can form gel-like structures. Because of their importance they have been the subject of many force spectroscopy experiments, which have examined the conformational changes and molecular tensions due to external forces. The most abundant unit present in the pectin backbone is polygalacturonic acid. Unfortunately, experimental force spectroscopy on polygalacturonic acid molecules is still not a trivial task. The mechanism of the single-molecule response to external forces can be inferred by theoretical methods. Therefore, in this work we simulated such force spectroscopy experiments using the Enforced Geometry Optimization (EGO) method. We examined the oligomeric (up to hexamer) structures of α-D-galacturonic acid exposed to external stretching forces. The EGO simulation of the force spectroscopy appropriately reproduced the experimental course of the enforced conformational transition: chair →inverted chair via the twisted boat conformation(s) in the pyranose ring of α-D-galacturonic acid. Additionally, our theoretical approach also allowed to determine the minimum oligomer size adequate for the description of nano-mechanical properties of (poly)-α-D-galacturonic acid.

The dynamics of the conformational changes in the hexopyranose ring: a transition path sampling approach

The transition paths corresponding to the conformational rearrangements in the ring of hexapyranose (α-d- and β-d-glucose) molecules were described by applying the transition path sampling method.

A reoptimized GROMOS force field for hexopyranose-based carbohydrates accounting for the relative free energies of ring conformers, anomers, epimers, hydroxymethyl rotamers, and glycosidic linkage conformers

This article presents a reoptimization of the GROMOS 53A6 force field for hexopyranose-based carbohydrates (nearly equivalent to 45A4 for pure carbohydrate systems) into a new version 56A(CARBO) (nearly equivalent to 53A6 for non-carbohydrate systems). This reoptimization was found necessary to repair a number of shortcomings of the 53A6 (45A4) parameter set and to extend the scope of the force field to properties that had not been included previously into the parameterization procedure. The new 56A(CARBO) force field is characterized by: (i) the formulation of systematic build-up rules for the automatic generation of force-field topologies over a large class of compounds including (but not restricted to) unfunctionalized polyhexopyranoses with arbritrary connectivities; (ii) the systematic use of enhanced sampling methods for inclusion of experimental thermodynamic data concerning slow or unphysical processes into the parameterization procedure; and (iii) an extensive validation against available experimental data in solution and, to a limited extent, theoretical (quantum-mechanical) data in the gas phase. At present, the 56A(CARBO) force field is restricted to compounds of the elements C, O, and H presenting single bonds only, no oxygen functions other than alcohol, ether, hemiacetal, or acetal, and no cyclic segments other than six-membered rings (separated by at least one intermediate atom). After calibration, this force field is shown to reproduce well the relative free energies of ring conformers, anomers, epimers, hydroxymethyl rotamers, and glycosidic linkage conformers. As a result, the 56A(CARBO) force field should be suitable for: (i) the characterization of the dynamics of pyranose ring conformational transitions (in simulations on the microsecond timescale); (ii) the investigation of systems where alternative ring conformations become significantly populated; (iii) the investigation of anomerization or epimerization in terms of free-energy differences; and (iv) the design of simulation approaches accelerating the anomerization process along an unphysical pathway.

Investigation of the effects of fine structure on the nanomechanical properties of pectin

Pectin is an important structural polysaccharide found in the cell walls of all land plants. While in detail its composition and its organization in muro are complex, it is predominantly a copolymer of galacturonic acid and its methylesterified counterpart. Previous single-molecule stretching studies carried out on a sparsely methylesterified pectin sample indicated the importance of force-induced conformational transitions of the pyranose ring during extension, and the possible biological role of such transitions was discussed. More heavily methylesterified samples are better biomimetic models of the polymeric components as found in the plant cell wall, in particular being less restricted by the shackles of the significant intermolecular interactions expected to constrain the behavior of bare galacturonic acid sequences. Density functional theory calculations revealed that upon extending galacturonic acid monomers, whether methylesterified or not, the initial ((4)C1) chair structure is transformed to a ((3)S5) skew boat and that subsequently upon further elongation, via an intermediate inverted skew boat ((5)S3), the inverted chair ((1)C4) is reached. Experimentally, the force-extension curve of highly methylesterified pectin was found to be solvent dependent in the same manner as the un-esterified sample, indicating that minimal changes in the strength of interring hydrogen bonding result from such a substitution, and finally, as only subtle changes in the force-extension behavior of pectin resulted from changes in the degree of methylesterification, previous speculations about the role of force-induced transformations in vivo are supported.