Carbohydrate Polymers at the Center of Life’s Origins: The Importance of Molecular Processivity

Chemically Recyclable Pseudo-Polysaccharides from Living Ring-Opening Polymerization of Glucurono-1,6-lactones

Recent advances in synthetic methods and monomer design have given access to precision carbohydrate polymers that extend beyond native polysaccharides. In this article, we present the synthesis of a class of chemically recyclable ester-linked pseudo-polysaccharides via the living anionic ring-opening polymerization of glucurono-1,6-lactones. Notably, the pseudo-polysaccharides exhibited defined chain-end groups, well-controlled molecular weights, and narrow molecular weight distributions, all hallmarks of living polymerization. Furthermore, we demonstrate that our approach is modular, as evidenced by tunable glass transition temperatures (Tg) and the ability to produce both amorphous and semicrystalline polymers by adjusting the monomer side chain structure. Lastly, we showcased the complete catalytic chemical recycling of these pseudo-polysaccharides back to the monomers. The flexibility of the polymerization and the recyclability of these pseudo-polysaccharides promote a sustainable circular economy while offering the potential to access polysaccharide-like materials with tunable thermal and mechanical properties.

Fluorescence 'Turn-on' Probe for Chromium Reduction, Adsorption and Detection Based on Cellulosic Nitrogen-Doped Carbon Quantum Dots Hydrogels

This paper proposes a new, highly effective fluorescence test for Cr(VI) detection. This method utilizes a hydrogel composed of hydroxyethyl cellulose (HEC), nitrogen-doped carbon quantum dots (N-CQDs), and poly(co-acrylamido-2-methyl-1-propane sulfonic acid) (AMPS). The N-CQDs were successfully synthesized using a simple microwave method, and then conjugated with HEC and AMPS. The higher adsorption (99.41%) and higher reduction rate in H1 likely stems from both the presence of N-CQDs (absent in HB) and their increased free functional groups (compared to H2/H3, where N-CQDs block them). This facilitates the release (desorption) of Cr(VI) from the hydrogels, making it more available for reduction to the less toxic Cr(III). The fluorescent brightness of the HEC-N-CQDs-g-poly(AMPS) hydrogel increases gradually when Cr(VI) is added in amounts ranging from 15 to 120 mg/L. The fluorescent enhancement of the HEC-N-CQDs-g-poly(AMPS) hydrogel appeared to exhibit a good linear relationship with the 15-120 mg of the Cr(VI) concentration, with a detection limit of 0.0053 mg/L, which is lower than the standard value published by WHO. Our study found that the HEC-N-CQDs-g-poly(AMPS) hydrogel served effectively as a fluorescent probe for Cr(VI) detection in aqueous solutions, demonstrating high sensitivity.

Architecture, Function, Regulation, and Evolution of α-Glucans Metabolic Enzymes in Prokaryotes

Bacteria have acquired sophisticated mechanisms for assembling and disassembling polysaccharides of different chemistry. α-d-Glucose homopolysaccharides, so-called α-glucans, are the most widespread polymers in nature being key components of microorganisms. Glycogen functions as an intracellular energy storage while some bacteria also produce extracellular assorted α-glucans. The classical bacterial glycogen metabolic pathway comprises the action of ADP-glucose pyrophosphorylase and glycogen synthase, whereas extracellular α-glucans are mostly related to peripheral enzymes dependent on sucrose. An alternative pathway of glycogen biosynthesis, operating via a maltose 1-phosphate polymerizing enzyme, displays an essential wiring with the trehalose metabolism to interconvert disaccharides into polysaccharides. Furthermore, some bacteria show a connection of intracellular glycogen metabolism with the genesis of extracellular capsular α-glucans, revealing a relationship between the storage and structural function of these compounds. Altogether, the current picture shows that bacteria have evolved an intricate α-glucan metabolism that ultimately relies on the evolution of a specific enzymatic machinery. The structural landscape of these enzymes exposes a limited number of core catalytic folds handling many different chemical reactions. In this Review, we present a rationale to explain how the chemical diversity of α-glucans emerged from these systems, highlighting the underlying structural evolution of the enzymes driving α-glucan bacterial metabolism.

Conformational preferences of guanine-containing threose nucleic acid building blocks in B3LYP studies

In this paper, detailed and systematic gas-phase B3LYP conformational studies of four monomers of threose nucleic acid (TNA) with guanine attached at the C1' atom and bearing different substituents (OH, OP(=O)OH2 and OCH3) in the C2' and C3' positions of the α-l-threofuranose moiety are presented. All exocyclic single-bond (χ, ε and γ) rotations, as well as the ν0-ν4 endocyclic torsion angles, were taken into consideration. Three (threoguanosines TG1-TG3) or two (TG4) energy minima were found for the rotation about the χ torsion angle. The syn orientation (the A rotamer family) is strongly privileged in geometries TG1 and TG2, whereas the anti orientation (the C rotamer family) and the syn orientation are observed to be in equilibrium (with populations of 56% and 44%, respectively) for TG3. In the case of TG4, the high-anti orientation (the B rotamer family) turned out to be by far the most favourable, with the contribution exceeding 90% in equilibrium. Such a preference can be attributed to the inability of H-bonding between sugar and nucleobase and possibly because of the steric strains. The low-energy conformers of TG1-TG4 occupy the northeastern (P ∼ 40°) and/or southern (P ∼ 210°) parts of the pseudorotational wheel, which fits the A- and B-type DNA helices quite well. Additionally, in the case of TG4, some relatively stable geometries have the furanoid ring in conformation lying on the northwestern part of the pseudorotational wheel (P ∼ 288°).

Acetyl group for proper protection of β-sugar-amino acids used in SPPS

The synthesis of D-glucosamine-1-carboxylic acid based β-sugar amino acids (β-SAAs) is typically performed in nine consecutive steps via an inefficient OAc → Br → CN conversion protocol with low overall yield. Here, we present the improved and more efficient synthesis of both Fmoc-GlcAPC-OH and Fmoc-GlcAPC(Ac)-OH, β-SAAs consisting of only 4-5 synthetic steps. Their active ester and amide bond formation with glycine methyl ester (H-Gly-OMe) was completed and monitored by 1H NMR. The stability of the pyranoid OHs protecting the acetyl groups was investigated under three different Fmoc cleavage conditions and was found to be satisfactory even at high piperidine concentration (e.g. 40%). We designed a SPPS protocol using Fmoc-GlcAPC(Ac)-OH to produce model peptides Gly-β-SAA-Gly as well as Gly-β-SAA-β-SAA-Gly with high coupling efficiency. The products were deacetylated using the Zemplén method, which allows the hydrophilicity of a building block and/or chimera to be fine-tuned, even after the polypeptide chain has already been synthesized.

Catalytic Approaches to Chemo- and Site-Selective Transformation of Carbohydrates

Carbohydrates are a fundamental unit playing pivotal roles in all the biological processes. It is thus essential to develop methods for synthesizing, functionalizing, and manipulating carbohydrates for further understanding of their functions and the creation of sugar-based functional materials. It is, however, not trivial to develop such methods, since carbohydrates are densely decorated with polar and similarly reactive hydroxy groups in a stereodefined manner. New approaches to chemo- and site-selective transformations of carbohydrates are, therefore, of great significance for revolutionizing sugar chemistry to enable easier access to sugars of interest. This review begins with a brief overview of the innate reactivity of hydroxy groups of carbohydrates. It is followed by discussions about catalytic approaches to enhance, override, or be orthogonal to the innate reactivity for the transformation of carbohydrates. This review avoids making a list of chemo- and site-selective reactions, but rather focuses on summarizing the concept behind each reported transformation. The literature references were sorted into sections based on the underlying ideas of the catalytic approaches, which we hope will help readers have a better sense of the current state of chemistry and develop innovative ideas for the field.

On the Origin of Sugar Handedness: Facts, Hypotheses and Missing Links-A Review

By paraphrasing one of Kipling's most amazing short stories (How the Leopard Got His Spots), this article could be entitled "How Sugars Became Homochiral". Obviously, we have no answer to this still unsolved mystery, and this perspective simply brings recent models, experiments and hypotheses into the homochiral homogeneity of sugars on earth. We shall revisit the past and current understanding of sugar chirality in the context of prebiotic chemistry, with attention to recent developments and insights. Different scenarios and pathways will be discussed, from the widely known formose-type processes to less familiar ones, often viewed as unorthodox chemical routes. In particular, problems associated with the spontaneous generation of enantiomeric imbalances and the transfer of chirality will be tackled. As carbohydrates are essential components of all cellular systems, astrochemical and terrestrial observations suggest that saccharides originated from environmentally available feedstocks. Such substances would have been capable of sustaining autotrophic and heterotrophic mechanisms integrating nutrients, metabolism and the genome after compartmentalization. Recent findings likewise indicate that sugars' enantiomeric bias may have emerged by a transfer of chirality mechanisms, rather than by deracemization of sugar backbones, yet providing an evolutionary advantage that fueled the cellular machinery.

Recyclable Fluorous-Tag Assisted Two-Directional Oligosaccharide Synthesis Enabled by Interrupted Pummerer Reaction Mediated Glycosylation

Herein, we report a novel fluorous-tag assisted two-directional oligosaccharide assembly strategy, which combines the advantages of solution-phase synthesis and solid-phase synthesis. A well-designed fluorous-tag was decorated on the latent anomeric...

Chance and Necessity in the Evolution of Matter to Life: A Comprehensive Hypothesis

Specialists in several branches of life sciences are trying to solve, piece by piece, the immensely complex puzzle of the origin of life. Some parts of the puzzle seem to appear with a rather high degree of clarity, while others remain totally obscure. We cannot be sure that life emerged only on our Earth, but we believe that the presence of large amounts of water in its liquid state is absolutely essential for the emergence and evolution of living matter. We can also assume that the latter exploits everywhere the same light elements, mainly C, H, O, N, S, and P, and somehow manipulates the same simple monomeric and polymeric organic compounds, such as alpha-amino acids, carbohydrates, nucleic bases, and surface-active carboxylic acids. The author contributes to the field by stating that all fundamental particles of our matter are “homochiral” and predominantly produce in an absolute asymmetric synthesis amino acids of L-configuration and carbohydrates of D-series. Another important point is that free atmospheric oxygen mainly stems from the photolysis of water molecules by cosmic irradiation and is not necessarily bound to living organisms on the planet.

Recent progress and advanced technology in carbohydrate-based drug development

Carbohydrates, one of the most abundant and widespread biomolecules in nature, play indispensable roles in diverse biological functions, and represent a treasure trove of untapped potential for pharmaceutical applications. Here, we provide a brief overview of carbohydrate-based drug development (CBDD) over the past two decades. More importantly, advanced techniques and methodologies related to CBDD are emerging, including enzymatic synthesis, metabolic engineering, site-specific glycoconjugation, carbohydrate libraries and microarrays as well as carbohydrate-gut microbiome evaluation. These technologies have dramatically accelerated the speed of CBDD. The recently approved drugs and emerging techniques summarized herein will inspire new sights into potential opportunities to discover novel carbohydrate drugs.

Sustainable synthesis of CO2-derived polycarbonates from d-xylose

Synthetic transformation of d-xylose into a four-membered cyclic ether allows for reactions with CO2 leading to linear polycarbonates by either ring-opening copolymerisation directly or by isolation of a six-membered cyclic carbonate followed by ring-opening polymerisation.

GDP-altrose as novel product of GDP-mannose 3,5-epimerase: Revisiting its reaction mechanism

GDP-mannose 3,5-epimerase (GM35E) catalyzes the double epimerization of GDP-mannose to yield GDP-l-galactose. GDP-l-gulose (C5-epimer) has previously been detected as a byproduct of this reaction, indicating that C3,5-epimerization occurs through an initial epimerization at C5. Given these products, GM35E constitutes a valuable bridge between d- and l-hexoses. In order to fully exploit this potential, the enzyme might be subjected to specificity engineering for which profound mechanistic insights are beneficial. Accordingly, this study further elucidated GM35E's reaction mechanism. For the first time, the production of the C3-epimer GDP-altrose was demonstrated, resulting in an adjustment of the acknowledged reaction mechanism. As GM35E converts GDP-mannose to GDP-l-gulose, GDP-altrose and GDP-l-galactose in a 72:4:4:20 ratio, this indicates that the enzyme does not discriminate between the C3 and C5 position as initial epimerization site. This was also confirmed by a structural investigation. Based on a mutational analysis of the active site, residues S115 and R281 were attributed a stabilizing function, which is believed to support the reactivation process of the catalytic residues. This paper eventually reflected on some engineering strategies that aim to change the enzyme towards a single specificity.

Phosphorylation and acylation transfer reactions: Clues to a dual origin of metabolism

Many theories of the origin of life focus on only one primitive polymer as an archetype of a world paradigm. However, life would have emerged within more complex scenarios where a variety of molecules and diverse polymers interconnected by a few similar chemical reactions. Previous work suggested that the ancestors of all major biopolymers would have arisen from abiotic template independent replication processes. They would have been organized in two closed sets of polymerization cycles: polysaccharides, polyribonucleotides and polyphosphates on one site; and peptides, fatty acids and polyhydroxyalkanoates on the other site. Then, these polymerization reaction cycles integrated into a minimal organization closure. Here, the purpose was to explore which kind of reactions could have supported the chemical networks that led to the early (bio)polymers. As a result, the proposed overview suggests that phosphorylation and acylation transfer reactions would have arisen independently and forged two distinct chemical systems that provided the phosphorylated and carboxylated intermediates used for the synthesis of the corresponding polymers. In this sense, modern metabolism may still reflect its dual nature, probably relying on these two reaction networks from the beginnings.

Chemoenzymatic synthesis of carboxylate-terminated maltooligosaccharides and their use for cross-linking of chitin

In this paper, we report chemoenzymatic synthesis of maltooligosaccharides having carboxylate groups at both ends (carboxylate-terminated maltooligosaccharides, GlcA-Glc_n-GlcCOONa). The products were further used as cross-linker for water-soluble chitin (WSCh) to obtain network chitins. The synthesis of GlcA-Glc_n-GlcCOONa was achieved by thermostable phosphorylase-catalyzed enzymatic α-glucuronylation using α-d-glucuronic acid 1-phosphate with a carboxylated maltooligosaccharide, which was prepared by chemical oxidation at the reducing end of maltoheptaose with sodium hypoiodite. The structures of GlcA-Glc_n-GlcCOONa were evaluated by ¹H NMR and MALDI-TOF mass spectra. The obtained GlcA-Glc_n-GlcCOONa were used as cross-linker for WSCh by condensation in the presence of condensing agent. The reaction mixtures totally turned into hydrogel form in most cases. Morphologies of lyophilized samples (cryogels) from the hydrogels were evaluated by SEM measurement. The hydrogels could be converted into films by pressing. Furthermore, mechanical properties of the hydrogels and films were investigated by compression and tensile tests, respectively.

Tools for generating and analyzing glycan microarray data

Glycans are one of the major biological polymers found in the mammalian body. They play a vital role in a number of physiologic and pathologic conditions. Glycan microarrays allow a plethora of information to be obtained on protein–glycan binding interactions. In this review, we describe the intricacies of the generation of glycan microarray data and the experimental methods for studying binding. We highlight the importance of this knowledge before moving on to the data analysis. We then highlight a number of tools for the analysis of glycan microarray data such as data repositories, data visualization and manual analysis tools, automated analysis tools and structural informatics tools.

Biological molecules in dental applications: hyaluronic acid as a companion biomaterial for diverse dental applications

Objectives

The application of hyaluronic acid (HA) in dental treatments is relatively new, and modified-HA products can be vastly different from each other. This study aims to provide a basis for bridging specific characteristics of HA with its potential applications in dental treatments, evaluating and comparing different types of HA products and for future research on HA applications in dentistry.

Data sources

Information from the existing literature on HA applications has been cited.

Study selection

Furthermore, this study is specifically oriented to provide oral health care providers with a scientific basis for HA use along with the clinical aspects of HA.

Conclusions

Outcomes from existing and future studies cannot be generalised for HA use in dental applications. Therefore, we have proposed a scheme to bridge HA specific characteristics to its applications in dental treatments and compare different HA products used for the same clinical application to identify the most suitable one.

Clinical significance

Highlighting the use of HA in dental treatments and providing a basis for developing new methods, protocols, and products specifically oriented for dentistry.

Prebiotic Peptides: Molecular Hubs in the Origin of Life

The fundamental roles that peptides and proteins play in today's biology makes it almost indisputable that peptides were key players in the origin of life. Insofar as it is appropriate to extrapolate back from extant biology to the prebiotic world, one must acknowledge the critical importance that interconnected molecular networks, likely with peptides as key components, would have played in life's origin. In this review, we summarize chemical processes involving peptides that could have contributed to early chemical evolution, with an emphasis on molecular interactions between peptides and other classes of organic molecules. We first summarize mechanisms by which amino acids and similar building blocks could have been produced and elaborated into proto-peptides. Next, non-covalent interactions of peptides with other peptides as well as with nucleic acids, lipids, carbohydrates, metal ions, and aromatic molecules are discussed in relation to the possible roles of such interactions in chemical evolution of structure and function. Finally, we describe research involving structural alternatives to peptides and covalent adducts between amino acids/peptides and other classes of molecules. We propose that ample future breakthroughs in origin-of-life chemistry will stem from investigations of interconnected chemical systems in which synergistic interactions between different classes of molecules emerge.

A Novel Polyester Hydrolase From the Marine Bacterium Pseudomonas aestusnigri - Structural and Functional Insights

Biodegradation of synthetic polymers, in particular polyethylene terephthalate (PET), is of great importance, since environmental pollution with PET and other plastics has become a severe global problem. Here, we report on the polyester degrading ability of a novel carboxylic ester hydrolase identified in the genome of the marine hydrocarbonoclastic bacterium Pseudomonas aestusnigri VGXO14^T. The enzyme, designated PE-H, belongs to the type IIa family of PET hydrolytic enzymes as indicated by amino acid sequence homology. It was produced in Escherichia coli, purified and its crystal structure was solved at 1.09 Å resolution representing the first structure of a type IIa PET hydrolytic enzyme. The structure shows a typical α/β-hydrolase fold and high structural homology to known polyester hydrolases. PET hydrolysis was detected at 30°C with amorphous PET film (PETa), but not with PET film from a commercial PET bottle (PETb). A rational mutagenesis study to improve the PET degrading potential of PE-H yielded variant PE-H (Y250S) which showed improved activity, ultimately also allowing the hydrolysis of PETb. The crystal structure of this variant solved at 1.35 Å resolution allowed to rationalize the improvement of enzymatic activity. A PET oligomer binding model was proposed by molecular docking computations. Our results indicate a significant potential of the marine bacterium P. aestusnigri for PET degradation.

Organic acid shift reagents for the discrimination of carbohydrate isobars by ion mobility-mass spectrometry

Traveling wave and drift tube ion mobility were utilized to separate isomeric disaccharides. Organic acid shift reagents were necessary to increase the resolution of these separations for mixture analysis.

The Oligomerization of Glucose Under Plausible Prebiotic Conditions

The prebiotic origin of polysaccharides, the largest class of biopolymers by mass in extant biology, has seldom been investigated experimentally. Herein, we report on the acid-catalyzed condensation of aqueous solutions of glucose, a model monosaccharide, under plausible prebiotic conditions employing a wet-dry (night-day) protocol with 0.01 M HCl at 50 °C. This protocol leads to the formation of oligosaccharides containing up to eight monomeric units identified by high resolution mass spectrometry. The regio- and stereochemistry of the oligomeric acetal linkages, as well as the quantitative analysis of glucose conversion, are elucidated by combining 1H, 13C and 2D NMR spectroscopy. Ten out of eleven possible acetal linkages, including α- and β- anomers, have been identified with the α- and β- 1,6-acetals being the dominant linkages observed. In addition, the acid-catalyzed oligomerization of several glucose disaccharides such as cellobiose, maltose, and gentiobiose are presented along with an accompanying comparison with the corresponding oligomerization of glucose.

Chemical Basis of Biological Homochirality during the Abiotic Evolution Stages on Earth

Spontaneous mirror symmetry breaking (SMSB), a phenomenon leading to non-equilibrium stationary states (NESS) that exhibits biases away from the racemic composition is discussed here in the framework of dissipative reaction networks. Such networks may lead to a metastable racemic non-equilibrium stationary state that transforms into one of two degenerate but stable enantiomeric NESSs. In such a bifurcation scenario, the type of the reaction network, as well the boundary conditions, are similar to those characterizing the currently accepted stages of emergence of replicators and autocatalytic systems. Simple asymmetric inductions by physical chiral forces during previous stages of chemical evolution, for example in astrophysical scenarios, must involve unavoidable racemization processes during the time scales associated with the different stages of chemical evolution. However, residual enantiomeric excesses of such asymmetric inductions suffice to drive the SMSB stochastic distribution of chiral signs into a deterministic distribution. According to these features, we propose that a basic model of the chiral machinery of proto-life would emerge during the formation of proto-cell systems by the convergence of the former enantioselective scenarios.

Carbohydrate isomer resolutionviamulti-site derivatization cyclic ion mobility-mass spectrometry

Cyclic ion mobility-tandem mass spectrometry enhances the separation and identification of small carbohydrate isomers.

Structure characterization, physicochemical property and immunomodulatory activity on RAW264.7 cells of a novel triple-helix polysaccharide from Craterellus cornucopioides

In the study, a new triple-helix polysaccharide with favorable stability was purified from C. cornucopioides. Its structural characterization, stability and solution behavior were investigated by the GC-MS, periodate oxidation-smith degradation, FT-IR, 1D and 2D NMR spectroscopy, methylation analysis, Scanning electron microscope, Congo-red, CD, TGA and DSC analysis. The results showed that Craterellus cornucopioide polysaccharide (CCP) possessed the molecular weight of 1.97 × 10³ kDa, is mainly composed of mannose (48.73%), galactose (17.37%), glucose (15.97%) and xylose (17.93%), respectively. It was a heteroglycan with (1 → 3)‑linked‑β‑d‑Manp‑(1 → 6)‑linked α‑d‑Galp backbone distributed by (1 → 4)‑linked‑α‑d‑Xylp‑t‑α‑d‑Manp and t‑β‑d‑Glup units at O-6. The result of TGA and DSC assay indicated that CCP has a favorable thermal stability. MTT and Scanning electro microscopy (SEM) assay showed that CCP could significantly improve the proliferation activity and induce cells activation of RAW264.7 in a certain range of concentrations and period.

Deoxyribose and deoxysugar derivatives from photoprocessed astrophysical ice analogues and comparison to meteorites

Sugars and their derivatives are essential to all terrestrial life. Their presence in meteorites, together with amino acids, nucleobases, amphiphiles, and other compounds of biological importance, may have contributed to the inventory of organics that played a role in the emergence of life on Earth. Sugars, including ribose (the sugar of RNA), and other sugar derivatives have been identified in laboratory experiments simulating photoprocessing of ices under astrophysical conditions. In this work, we report the detection of 2-deoxyribose (the sugar of DNA) and several deoxysugar derivatives in residues produced from the ultraviolet irradiation of ice mixtures consisting of H2O and CH3OH. The detection of deoxysugar derivatives adds to the inventory of compounds of biological interest that can form under astrophysical conditions and puts constraints on their abiotic formation pathway. Finally, we report that some of the deoxysugar derivatives found in our residues are also newly identified in carbonaceous meteorites.

Effect of temperature modulations on TEMPO-mediated regioselective oxidation of unprotected carbohydrates and nucleosides

Regioselective oxidation of unprotected and partially protected oligosaccharides is a much sought-after goal. Herein, we report a notable improvement in the efficiency of TEMPO-catalyzed oxidation by modulating the temperature of the reaction. Mono-, di-, and tri-saccharides are oxidized regioselectively in yields of 75 to 92%. The present method is simple to implement and is also applicable for selective oxidations of other mono- and poly-hydroxy compounds including unprotected and partially protected nucleosides.

Rapid resolution of carbohydrate isomers via multi-site derivatization ion mobility-mass spectrometry

Identifying small sugar isomers can be challenging by ion mobility-mass spectrometry (IM-MS) alone due to their small collision cross section differences.

Who's on base? Revealing the catalytic mechanism of inverting family 6 glycoside hydrolases

In several important classes of inverting carbohydrate-active enzymes, the identity of the catalytic base remains elusive, including in family 6 Glycoside Hydrolase (GH6) enzymes, which are key components of cellulase cocktails for cellulose depolymerization. Despite many structural and kinetic studies with both wild-type and mutant enzymes, especially on the Trichoderma reesei (Hypocrea jecorina) GH6 cellulase (TrCel6A), the catalytic base in the single displacement inverting mechanism has not been definitively identified in the GH6 family. Here, we employ transition path sampling to gain insight into the catalytic mechanism, which provides unbiased atomic-level understanding of key order parameters involved in cleaving the strong glycosidic bond. Our hybrid quantum mechanics and molecular mechanics (QM/MM) simulations reveal a network of hydrogen bonding that aligns two active site water molecules that play key roles in hydrolysis: one water molecule drives the reaction by nucleophilic attack on the substrate and a second shuttles a proton to the putative base (D175) via a short water wire. We also investigated the case where the putative base is mutated to an alanine, an enzyme that is experimentally still partially active. The simulations predict that proton hopping along a water wire via a Grotthuss mechanism provides a mechanism of catalytic rescue. Further simulations reveal that substrate processive motion is 'driven' by strong electrostatic interactions with the protein at the product sites and that the -1 sugar adopts a 2SO ring configuration as it reaches its binding site. This work thus elucidates previously elusive steps in the processive catalytic mechanism of this important class of enzymes.

Synthetic Biomaterials from Metabolically Derived Synthons

The utility of metabolic synthons as the building blocks for new biomaterials is based on the early application and success of hydroxy acid based polyesters as degradable sutures and controlled drug delivery matrices. The sheer number of potential monomers derived from the metabolome (e.g., lactic acid, dihydroxyacetone, glycerol, fumarate) gives rise to almost limitless biomaterial structural possibilities, functionality, and performance characteristics, as well as opportunities for the synthesis of new polymers. This review describes recent advances in new chemistries, as well as the inventive use of traditional chemistries, toward the design and synthesis of new polymers. Specific polymeric biomaterials can be prepared for use in varied medical applications (e.g., drug delivery, tissue engineering, wound repair, etc.) through judicious selection of the monomer and backbone linkage.

Aromatic-Mediated Carbohydrate Recognition in Processive Serratia marcescens Chitinases

Microorganisms use a host of enzymes, including processive glycoside hydrolases, to deconstruct recalcitrant polysaccharides to sugars. Processive glycoside hydrolases closely associate with polymer chains and repeatedly cleave glycosidic linkages without dissociating from the crystalline surface after each hydrolytic step; they are typically the most abundant enzymes in both natural secretomes and industrial cocktails by virtue of their significant hydrolytic potential. The ubiquity of aromatic residues lining the enzyme catalytic tunnels and clefts is a notable feature of processive glycoside hydrolases. We hypothesized that these aromatic residues have uniquely defined roles, such as substrate chain acquisition and binding in the catalytic tunnel, that are defined by their local environment and position relative to the substrate and the catalytic center. Here, we investigated this hypothesis with variants of Serratia marcescens family 18 processive chitinases ChiA and ChiB. We applied molecular simulation and free energy calculations to assess active site dynamics and ligand binding free energies. Isothermal titration calorimetry provided further insight into enthalpic and entropic contributions to ligand binding free energy. Thus, the roles of six aromatic residues, Trp-167, Trp-275, and Phe-396 in ChiA, and Trp-97, Trp-220, and Phe-190 in ChiB, have been examined. We observed that point mutation of the tryptophan residues to alanine results in unfavorable changes in the free energy of binding relative to wild-type. The most drastic effects were observed for residues positioned at the "entrances" of the deep substrate-binding clefts and known to be important for processivity. Interestingly, phenylalanine mutations in ChiA and ChiB had little to no effect on chito-oligomer binding, in accordance with the limited effects of their removal on chitinase functionality.

Functional role of R462 in the degradation of hyaluronan catalyzed by hyaluronate lyase from Streptococcus pneumoniae

Hyaluronan lyase from Streptococcus pneumoniae can degrade hyaluronic acid, which is one of the major components in the extracellular matrix. Hyaluronan can regulate water balance, osmotic pressure, and act as an ion exchange resin. Followed by our recent work on the catalytic reaction mechanism and substrate binding mode, we in this work further investigate the functional role of active site arginine residue, R462, in the degradation of hyaluronan. The site directed mutagenesis simulation of R462A and R462Q were modeled using a combined quantum mechanical and molecular mechanical method. The overall substrate binding features upon mutations do not have significant changes. The energetic profiles for the reaction processes are essentially the same as that in wild type enzyme, but significant activation barrier height changes can be observed. Both mutants were shown to accelerate the overall enzymatic activity, e.g., R462A can reduce the barrier height by about 2.8 kcal mol(-1), while R462Q reduces the activation energy by about 2.9 kcal mol(-1). Consistent with the active site model calculated using density functional theory, our results can support that the positive charge on R462 guanidino side chain group plays a negative role in the catalysis. Finally, the functional role of R462 was proposed to facilitate the formation of initial enzyme-substrate complex, but not in the subsequent catalytic degradation reaction. Graphical Abstract Degradation of hyaluronan catalyzed by hyaluronate lyase from Streptococcus pneumoniae.

Glyco Star Polymers as Helical Multivalent Host and Biofunctional Nano-Platform

A series of amylose-based star polymers (1, 2, 4, and 8 arms) as a new glyco biomaterial was synthesized by a click reaction and enzymatic polymerization of specific primers with phosphorylase. The molecular weights were controlled by the enzymatic reaction. Further polymerization resulted in a viscous solution and, especially, for the 8-arm primer, a hydrogel was obtained due to effective cross-linking between the multiarmed structures. The star polymers with a degree of polymerization of about 60 per arm acted as an allosteric multivalent host for hydrophobic molecules by helical formation. A cationic 8-arm star polymer catalyzed DNA strand exchange as a nucleic acid chaperone. Amylose-based star polymers are promising building blocks for producing advanced hybrid glyco biomaterials.

Stratification of chondroitin sulfate binding sites in 3D-model of bovine testicular hyaluronidase and effective size of glycosaminoglycan coat of the modified protein

A 3D-model of bovine testicular hyaluronidase (BTH) was constructed based on established tertiary structure of human hyaluronidase Hyal1 using a molecular homological modeling method in silico. The analysis of the BTH 3D-model demonstrated lysine residue stratification during enzyme modification. The 3D-model of chondroitin sulfate (CHS)-modified hyaluronidase (BTH-CHS) was obtained by modeling covalent binding of lysine residues with benzoquinone-activated CHS. The degree of enzyme modification and the length of CHS chains were varied during 3D modeling. The importance of deep BTH modification degree for the formation of active and stable enzyme derivatives was shown, as determined earlier experimentally. The effective size of the CHS coat for productive BTH modification was confirmed. It is theoretically achieved at the increase in molecular mass of BTH-CHS derivative to approximately 140-180 kDa and can be practically obtained, according to experimental data, using CHS of different molecular mass (30-50 as well as 120-140 kDa).

Formation of spherical and core-shell polymeric microparticles from glycopolymers

6-O-methacryloyl-α-d-glucoside 2 and 4-bromophenyl-6-O-methacryloyl-d-glucothioside 7, obtained by enzyme-catalyzed synthesis, have been homo-polymerized and copolymerized with styrene by a free radical process, yielding polymer materials with sugar moieties, attached to the polymer backbone via ester linkages. The results demonstrated that modifying the structural features of the monomers greatly affected the thermal and rheological properties of the polymers. The polymer materials obtained have been characterized by NMR, MALDI-MS, DSC, AFM, and EWC (equilibrium water content). The AFM images indicated the formation of spherical and core-shell polymeric microparticles.

Modified biopolymer-dextrin based crosslinked hydrogels: application in controlled drug delivery

This review describes hydrogels and their classifications along with the synthesis and properties of biopolymer-dextrin based crosslinked hydrogels towards potential application in controlled drug delivery.