Sugar Ring Research Articles

Collision-Induced Dissociation of Fucose and Identification of Anomericity.

Structural determination of carbohydrates using mass spectrometry remains challenging, particularly, the differentiation of anomeric configurations. In this work, we studied the collision-induced dissociation (CID) mechanisms of sodiated α- and β-l-fucose using an experimental method and quantum chemistry calculations. The calculations show that α-l-fucose is more likely to undergo dehydration due to the fact that O1 and O2 are on the same side of the sugar ring. In contrast, β-l-fucose is more prone to the ring-opening reaction because more OH groups are on the same side of the sugar ring as O1. These differences suggest a higher preference for the dehydration reaction in sodiated α-l-fucose but a lower preference for ring-opening compared to that of β-l-fucose. The calculation results, which are used to assign the CID mass spectra of α- and β-l-fucose separated by high-performance liquid chromatography, are supported by the fucose produced from the CID of disaccharides Fuc-β-(1 → 3)-GlcNAc and Fuc-α-(1 → 4)-GlcNAc. This study demonstrates that the correlation of cis- and trans-configurations of O1 and O2 to the relative branching ratios of dehydration and cross-ring dissociation in CID, observed in aldohexose and ketohexose in the pyranose form, can be extended to deoxyhexoses for anomericity determination.

Theoretical Study on The Effect of Metal Ions on The Structural Properties of Base

Metal ions play an important role in living organisms, for example Mg2+ is a cofactor for many biological enzymes (including DNA and RNA synthesis), Ca2+ is an important component of bone composition, and metal ions such as Fe, Co, Zn, Ni and Cu also play an important role in the normal functioning of living organisms. One of the main targets of metal ions in living organisms is deoxyribonucleic acid (DNA), which is an important carrier of information stored and transmitted by organisms. The direct interaction between DNA base pairs and metal ions have a significant impact on the structure and function of DNA base pairs, which is demonstrated as following: the binding of metals to bases usually breaks the hydrogen bonds of the base pairs. The N7 atom of a purine residue or the N3 atom of a pyrimidine residue, as well as the outer ring O atom and the phosphate oxygen atom, are the preferred sites for metal binding. The binding of metals to DNA and RNA also indirectly affects the conformation of the sugar ring. REDOX active metal ions have the ability to bind to DNA and can mediate oxidative DNA damage by reacting with endogenous oxidants. According to studies of antioxidants in the field of metal-mediated oxidative DNA damage, metal ion coordination also plays a key role in the mechanism of some antioxidants. Also, metal-DNA interactions are the basis for many anti-cancer drugs, anti-viral drugs and anti-bacterial agents. Metal-mediated oxidative DNA damage is associated with a variety of diseases and conditions, and understanding the binding interactions and subsequent reactivity can facilitate the management or prevention of oxidative damage. It can be seen that the study of the effect of metal ions on the structural properties of DNA bases has far-reaching implications, providing a theoretical basis for the development of novel anticancer drugs, DNA-based metal nanodevice technologies and the fabrication of spectroscopic and reactive probes.

Essential Structural Profile of Novel Adenosine Derivatives as Antiplatelet Aggregation Inhibitors based on 3D-QSAR Analysis

Aims: In this research, 3D-QSAR evaluation on a set of fresh purinoid compounds that we produced was conducted. This analysis aims to illustrate the correlation between the structure of purine and its ability to prevent platelet aggregation. Our findings could pave the way to discovering novel antithrombotic medications. background: Cardiovascular disease caused by platelet aggregation is a serious threat to human health. Purine derivatives are important molecules with antiplatelet aggregation activity. Background: The incidence of cardiovascular disease triggered by the clumping of platelets poses a significant danger to human health. Purine derivatives are important molecules with antiplatelet aggregation activity. Objective: The objectives of this research are to establish the correlation between the structure of purine and its ability to prevent platelet aggregation. Such a correlation could aid in the development of innovative antithrombotic medications. method: In this study, 3D-QSAR analysis was performed on a series of novel purine derivatives synthesized by us based on comparative molecular field analysis (CoMFA) and comparative molecular similarity index analysis (CoMSIA). Methods: In this study, 3D-QSAR investigation on a collection of 75 new purine derivatives, which we synthesized, was conducted, utilizing Comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA). result: Significant correlation coefficients (CoMFA, q2=0.843, r2=0.930, F value=266.755, SEE=0.165; CoMSIA, q2=0.869, r2=0.918, F value=222.571, SEE=0.179) were obtained, and the model prediction ability was validated using the test set. Results: Significant correlation coefficients (CoMFA, q2= 0.843, r2= 0.930, F value= 266.755, SEE= 0.165; CoMSIA, q2= 0.869, r2= 0.918, F value= 222.571, SEE= 0.179) were obtained, and assessed the model's predictive capabilities by validating it with the test set. conclusion: The results suggest that it is beneficial to introduce a group of appropriate size at position C-2 of the purine ring, and that an excessively large group is disadvantageous; a bulky substituent group cannot be directly attached at the C-6 position of the purine ring, and the attachment of a group with low electron cloud density increases the activity, and the attachment of a bulky group at the C-5' of the sugar ring is beneficial, and the presence of hydrogen bond receptors in this region also increases the activity. Conclusion: Our findings indicate that the introduction of an appropriately sized structure at position 2 of the compound yields significant benefits. Conversely, the attachment of an excessively large group is detrimental. Direct attachment of a bulky substituent at C-6 of the compound is not feasible, and its activity increases when the structure with low electron cloud density is added. Moreover, the presence of a voluminous functional group at the 5' position of the compound is advantageous, and its activity will be further increased by the presence of hydrogen bond receptors in this region. These discoveries furnish significant comprehension for the formation of innovative structures with heightened efficacy.

Screening and Characteristics Analysis of Polysaccharides from Orah Mandarin (Citrus reticulata cv. Orah).

This study aimed to screen out polysaccharides with the ability to activate NK cells. Ten polysaccharides (OP) were isolated from orah mandarin (Citrus reticulata cv. Orah) peel using hot-water extraction combined with the alcohol precipitation method and the ultrafiltration-membrane separation method. After measuring the effects of 10 OPs on NK-92MI cell proliferation and cytotoxicity, it was found that the polysaccharide OP5 had the highest activity in vitro. OP5 can significantly promote the proliferation of and increase the gene expression of perforin, granzyme B and IFN-γ in NK-92MI cells. Its molecular weight was between 50 and 70 kDa. The identification results of monosaccharide composition indicated that OP5 was composed of arabinose (31.52%), galacturonic acid (22.35%), galactose (16.72%), glucose (15.95%), mannose (7.67%), rhamnose (2.39%), fucose (1.41%), xylose (1.30%), glucuronic acid (0.42%) and ribose (0.27%). The sugar ring of the β-configuration was the main, and that of the α-configuration was the auxiliary. These results would provide a foundation for the functional product development of OPs.

Synthesis and applications of cyclonucleosides: an update (2010-2023).

Cyclonucleosides are a group of nucleoside derivatives which, in addition to the classical N-glycosidic bond, have an additional covalent bond (linker, bridge) in their structure, which connects the heterocyclic base and sugar ring. The majority of them have been discovered in the laboratory; however, few such compounds have also been found in natural sources, including metabolites of sponges or radical damage occurring in nucleic acids. Due to their structural properties-rigid, fixed conformation-they have found wide applications in medicinal chemistry and biochemistry as biocides as well as enzyme inhibitors and molecular probes. They have also found use as convenient synthetic tools for the preparation of new nucleoside analogues, enabling structural modifications of both the sugar ring and heterocyclic base. This review summarizes the recent progress in the synthesis of various purine and pyrimidine cyclonucleosides using diverse chemical approaches based on radical, "click", metal-mediated, and other types of reactions. It also presents recent reports concerning possible applications in medicinal chemistry, as well as their applications as valuable key intermediates in the synthesis of sugar- and base-modified nucleoside analogues and heterocyclic compounds.

Structural Characterization of the Metalized Radical Cations of Adenosine ([Ade+Li-H]•+ and [Ade+Na-H]•+) by Infrared Multiphoton Dissociation Spectroscopy and Theoretical Studies.

Nucleoside radicals are key intermediates in the process of DNA damage, and alkali metal ions are a common group of ions in living organisms. However, so far, there has been a significant lack of research on the structural effects of alkali metal ions on nucleoside free radicals. In this study, we report a new method for generating metalized nucleoside radical cations in the gas phase. The radical cations [Ade+M-H]•+ (M = Li, Na) are generated by the 280 nm ultraviolet photodissociation (UVPD) of the precursor ions of lithiated and sodiated ions of 2-iodoadenine in a Fourier transform ion cyclotron resonance (FT ICR) cell. Further infrared multiphoton dissociation (IRMPD) spectra of both radical cations were recorded in the region of 2750-3750 cm-1. By combining these results with theoretical calculations, the most stable isomers of both radicals can be identified, which share the common characteristics of triple coordination patterns of the metal ions. For both radical species, the lowest-energy isomers undergo hydrogen transfer. Although the sugar ring in the most stable isomer of [Ade+Li-H]•+ is in a (South, syn) conformation similar to that of [Ado+Na]+, [Ade+Na-H]•+ is distinguished by the unexpected opening of the sugar ring. Their theoretical spectra are in good agreement with experimental spectra. However, due to the flexibility of the structures and the complexity of their potential energy surfaces, the hydrogen transfer pathways still need to be further studied. Considering that the free radicals formed directly after C-I cleavage have some similar spectral characteristics, the existence of these corresponding isomers cannot be ruled out. The findings imply that the structures of nucleoside radicals may be significantly influenced by the attached alkali metal ions. More detailed experiments and theoretical calculations are still crucial.

Catalytic Reaction Mechanism of Bacterial GH92 α-1,2-Mannosidase: A QM/MM Metadynamics Study.

The catalytic mechanism of a -dependent family 92 -mannosidase, which is abundantly present in human gut flora and malfunctions leading to the lysosomal storage disease α-mannosidosis, has been investigated using quantum mechanics/molecular mechanics and metadynamics methods. Computational efforts show that the enzyme follows a conformational itinerary of and the ion serves a dual purpose, as it not only distorts the sugar ring but also plays a crucial role in orchestrating the arrangement of catalytic residues. This orchestration, in turn, contributes to the facilitation of conformers for the ensuing reaction. This mechanistic insight is well-aligned with the experimental predictions of the catalytic pathway, and the computed energies are of the same order of magnitude as the experimental estimations. Hence, our results extend the mechanistic understanding of glycosidases.

Synthesis and interaction with growth factors of sulfated oligosaccharides containing an anomeric fluorinated tail

Compounds that mimic the biological properties of glycosaminoglycans (GAGs) and can be more easily prepared than the native GAG oligosaccharides are highly demanded. Here, we present the synthesis of sulfated oligosaccharides displaying a perfluorinated aliphatic tag at the reducing end as GAG mimetics. The preparation of these molecules was greatly facilitated by the presence of the fluorinated tail since the reaction intermediates were isolated by simple fluorous solid-phase extraction. Fluorescence polarization competition assays indicated that the synthesized oligosaccharides interacted with two heparin-binding growth factors, midkine (MK) and FGF-2, showing higher binding affinities than the natural oligosaccharides, and can be therefore considered as useful GAG mimetics. Moreover, NMR experiments showed that the 3D structure of these compounds is similar to that of the native sequences, in terms of sugar ring and glycosidic linkage conformations. Finally, we also demonstrated that these derivatives are able to block the MK-stimulating effect on NIH3T3 cells growth.

Preorganized Internal Electric Field Promotes a Double-Displacement Mechanism for the Adenine Excision Reaction by Adenine DNA Glycosylase.

Adenine DNA glycosylase (MutY) is a monofunctional glycosylase, removing adenines (A) misinserted opposite 8-oxo-7,8-dihydroguanine (OG), a common product of oxidative damage to DNA. Through multiscale calculations, we decipher a detailed adenine excision mechanism of MutY that is consistent with all available experimental data, involving an initial protonation step and two nucleophilic displacement steps. During the first displacement step, N-glycosidic bond cleavage is accompanied by the attack of the carboxylate group of residue Asp144 at the anomeric carbon (C1'), forming a covalent glycosyl-enzyme intermediate to stabilize the fleeting oxocarbenium ion. After departure of the excised base, water nucleophiles can be recruited to displace Asp144, completing the catalytic cycle with retention of stereochemistry at the C1' position. The two displacement reactions are found to mostly involve the movement of the oxocarbenium ion, occurring with large charge reorganization and thus sensitive to the internal electric field (IEF) exerted by the polar protein environment. Intriguingly, we find that the negatively charged carboxylate group is a good nucleophile for the oxocarbenium ion, yet an unactivated water molecule is not, and that the electric field catalysis strategy is used by the enzyme to enable its unique double-displacement reaction mechanism. A strong IEF, pointing toward 5' direction of the substrate sugar ring, greatly facilitates the second displacement reaction at the expense of elevating the barrier of the first one, thereby allowing both reactions to occur. These findings not only increase our understanding of the strategies used by DNA glycosylases to repair DNA lesions, but also have important implications for how internal/external electric field can be applied to modulate chemical reactions.

Recent Advances Related to Anomeric and Exo-anomeric Effects in Carbohydrate Chemistry

The anomeric effect in carbohydrate chemistry is known as the interaction between the OHd substituent at the anomeric position to favor an axial orientation rather than an equatorial one, despite the increased 1,3-diaxial interactions. In the anomeric effect, a sugar ring is stabilized by an electronegative substituent at the C1 carbon, also known as the anomeric carbon. The stabilization is thought to result from interactions between lone electron pairs on oxygen and a C1 antibonding orbital. On the other hand, the anomeric effect can be of two types: endo-anomeric and exo-anomeric. The effect is called endo-anomeric when the lone pair comes from the oxygen atom in the sugar ring and exo-anomeric when the lone pair comes from oxygen in a substituent on C1. Several factors influence the anomeric effect. In this way, this review aims to describe the recent advances in main theories, observations, and advances achieved in the last decades related to the anomeric effect.
 GRAPHICAL ABSTRACT

Pyrolytic conversion of waste hemp: Kinetics, product characterization, and boosted regression tree modeling

This study investigated the pyrolysis of hemp residue using kinetic analysis. The thermal degradation of hemp residue occurred in three temperature ranges, and the activation energy (Ea) varied between 147.5 kJ/mol and 299.2 kJ/mol depending on the model-free method used. Combined kinetics, statistical approach, was used to calculate the kinetic triplets including the reaction mechanism and pre-exponential factor besides Ea. Boosted regression trees (BRT), machine learning approach, was used to predict the Ea during the course of conversion at different heating rates. Bio-oil extracted from hemp residues at different temperatures was examined. The oil contained valuable compounds, including phenols, esters, ethers, aromatics, hydrocarbons, organic acids, furans, alkanes, and ketones. The production of hydrocarbons was found to increase at elevated temperatures, indicating their bioenergy potential. However, acids and esters formation decreased at higher temperatures, while aldehydes were produced by the breakdown of a sugar ring. The study provides insights into the potential of hemp residue to be used in the production of value-added products.

Molecular characterization of interactions between lectin - a protein from common edible mushroom (Agaricus bisporus) - and dietary carbohydrates

This work investigates the molecular interactions between Agaricus bisporus lectin (ABL) and the dietary carbohydrates, glucose and galactose, in comparison to their N-acetylated amino sugar counterparts. Intrinsic fluorescence quenching suggests the presence of binding between ABL and each of the investigated ligands (glucose, galactose, N-acetyl-d-glucosamine and N-acetyl-d-galactosamine), with the former exhibiting the strongest interaction. Molecular docking highlights the likely binding positions, showing the presence of stable interactions between protein and ligands. The conformational difference of a single epimeric hydroxyl group at carbon four of the sugar ring appears to be the main factor in determining binding location, with galactose containing molecules favouring the T-antigen binding site whereas glucose containing molecules favouring another binding location. Fourier transform infrared (FTIR) and circular dichroism (CD) record spectral changes, suggesting that the heterologous interactions affect the secondary structure of the protein molecule. The magnitude of structural alteration in the complex is related to the binding strength. Findings provide a theoretical basis for the potential application of ABL in functional foods and hypoglycaemic nutraceuticals, as well as contributing to the fundamental understanding of the molecular mechanism behind ABL and dietary carbohydrate complexation.

Synthesis of L‐Hexopyranosyl Fluorides Enabled by Radical Decarboxylative Fluorination: Assembly of a Pentasaccharide Repeating Unit Corresponding to Extracellular Polysaccharide S‐88

Comprehensive SummaryL‐Hexoses are key components of many biologically relevant natural products and pharmaceuticals. As rare sugars, L‐hexoses are not readily obtained from natural sources. Access to L‐hexose building blocks from commercially available and inexpensive D‐sugars is highly desirable from the viewpoints of organic synthesis and drug discovery. As demonstrated by the convenient preparation of L‐glucosyl, L‐galactosyl, and L‐mannosyl fluorides from readily available β‐D‐C‐glucosyl, β‐D‐C‐mannosyl, and β‐D‐C‐galactosyl derivatives, we describe a novel and efficient approach to the demanding L‐glycosyl fluorides. The transformation features the installation of anomeric hydroxymethyl group under mild conditions and C1‐to‐C5 switch of sugar rings through radical decarboxylative fluorination of uronic acids. The power of this protocol is highlighted by the first assembly of a pentasaccharide repeating unit of Pseudomonas ATCC 31554 extracellular polysaccharide (S‐88). This synthesis relies on the efficient extension of sugar chain at the sterically hindered hydroxy group and the facile introduction of L‐mannosyl unit using L‐mannosyl fluoride as glycosylating agent. The methods developed in this work would provide new tools to the arsenal of synthesis of L‐sugar building blocks and of assembly of glycans containing L‐sugar moieties.

Radical Pathway Glycosylation Empowered by Bench-Stable Glycosyl Donors.

ConspectusThe study of carbohydrates has emerged as a crucial research area in various disciplines due to their pivotal roles in cellular processes. To facilitate in-depth exploration of their biological functions, chemical glycosylation reactions that allow facile access of glycoconjugates to a broad research community are highly needed. In classical glycosylation reactions, a glycosyl donor is activated by an acid to generate a reactive electrophilic intermediate, which subsequently forms a glycosidic bond upon reaction with a nucleophilic acceptor. Such an ionic pathway glycosylation has been the mainstay technique for glycoconjugate synthesis and allowed the synthesis of numerous intricate structures. Nevertheless, limitations still exist. For instance, when labile glycosyl donors or harsh activating conditions are required, these methods show limited tolerance to hydroxyl groups that are abundant on sugar rings. In addition, achieving good stereocontrol represents another longstanding obstacle. In recent years, new modes of donor activation have been sought to tackle the above challenges.We noted that glycosylation methods passing through the intermediacy of glycosyl radicals via a cascade of single-electron transfer steps possess significant but underexplored potential. Progress in this area has been slow due in large part to a dearth of handy methods to generate and maneuver glycosyl radicals. Most existing methods call for either forcing conditions or unstable/inconvenient starting materials. In order to better exploit the power of the radical pathway glycosylation, we have developed a range of glycosyl donors─namely, glycosyl sulfoxides, glycosyl sulfones, and glycosyl sulfinates─that are bench stable and can be readily prepared from simple starting materials. These donors can be activated to form glycosyl radicals under mild conditions. Enabled by the use of these donors, we have developed a series of glycosylation methods that could be used for making O-, S-, or C-glycosides, some of which were previously difficult to access. In many cases, no protecting group on glycosyl donors is required. As an illustration of their potential utility, our methods have been adopted in the preparation of sugar-drug conjugates, sugar-DNA conjugates, glycopeptides, and even glycoproteins. While in most cases the intrinsic reactivity of glycosyl radical intermediates can be explored to access axially configured products, some of the methods also allow the utilization of external, delicate reagents, or catalysts to override such innate preference and achieve catalyst-controlled stereoselectivity.We believe that radical pathway glycosylation has enormous potential and can inspire the development of novel methods for glycoside synthesis. In this Account, we highlight the design principles for the development of our glycosyl donors, summarize our recent advancements in radical pathway glycosylation enabled by their use, and provide an outlook on the future directions of this field.

Effective Treatment of Knee Osteoarthritis Using a Nano-Enabled Drug Acupuncture Technology in Mice.

A nano-enabled drug delivery acupuncture technology (nd-Acu) is developed that is based on traditional acupuncture needles where the stainless-steel surface is designed to deliver various payload molecules. To create the nd-Acu platform, an electrochemistry procedure is used to attach methyl salicylate-modified cyclodextrin in which the sugar rings allow the encapsulation of structurally defined single or multiple payload molecules via an inclusion complexation process. Drug loading and release profile are first studied using fluorescent dyes abiotically and at intact animal level. nd-Acu allows more efficient dye loading and time-dependent release compared to pristine needles without cyclodextrin modification. Subsequently, a proof-of-principle efficacy study is conducted using the platform to load a local anesthetic, lidocaine, for the treatment of knee osteoarthritis (KOA) in mice. It is demonstrated that lidocaine-laden nd-Acu can effectively alleviate pain, reduce inflammation, and slow down KOA development biochemically and histologically. Hypothesis-driven and proteomic approaches are utilized to investigate the working mechanisms of lidocaine nd-Acu, indicating that the therapeutic outcome is attributed to the in vivo modulation of the HMGB1/TLR4 signaling pathway. The study also obtained preliminary evidence suggesting the involvement of mitochondria as well as small GTPase such as cdc42 during the treatment by lidocaine nd-Acu.

Review of fragmentation of synthetic single-stranded oligonucleotides by tandem mass spectrometry from 2014 to 2022.

The fragmentation of oligonucleotides by mass spectrometry allows for the determination of their sequences. It is necessary to understand how oligonucleotides dissociate in the gas phase, which allows interpretation of data to obtain sequence information. Since 2014, a range of fragmentation mechanisms, including a novel internal rearrangement, have been proposed using different ion dissociation techniques. The recent publications have focused on the fragmentation of modified oligonucleotides such as locked nucleic acids, modified nucleobases (methylated, spacer, nebularine and aminopurine) and modification to the carbon 2'-position on the sugar ring; these modified oligonucleotides are of great interest as therapeutics. Comparisons of different dissociation techniques have been reported, including novel approaches such as plasma electron detachment dissociation and radical transfer dissociation. This review covers the period 2014-2022 and details the new knowledge gained with respect to oligonucleotide dissociation using tandem mass spectrometry (without priori sample digestion) during that time, with a specific focus on synthetic single-stranded oligonucleotides.

Simultaneous refinement of molecular dynamics ensembles and forward models using experimental data.

A novel method combining the maximum entropy principle, the Bayesian-inference of ensembles approach, and the optimization of empirical forward models is presented. Here, we focus on the Karplus parameters for RNA systems, which relate the dihedral angles of γ, β, and the dihedrals in the sugar ring to the corresponding 3J-coupling signal between coupling protons. Extensive molecular simulations are performed on a set of RNA tetramers and hexamers and combined with available nucleic-magnetic-resonance data. Within the new framework, the sampled structural dynamics can be reweighted to match experimental data while the error arising from inaccuracies in the forward models can be corrected simultaneously and consequently does not leak into the reweighted ensemble. Carefully crafted cross-validation procedure and regularization terms enable obtaining transferable Karplus parameters. Our approach identifies the optimal regularization strength and new sets of Karplus parameters balancing good agreement between simulations and experiments with minimal changes to the original ensemble.

Ultrasonic extraction, structural modification and gastric mucosal cells protective activity of a polysaccharide from Dendrobium denneanum

Optimize the ultrasonic extraction process of polysaccharides from Dendrobium denneanum by Response surface design (RSM). The main polysaccharide (DP40) from was separated by anion exchange chromatography, and its structure was modified by low-temperature plasma. The results showed that the polysaccharide extraction rate of ultrasonic was 22.98 ± 0.97%, which was significantly higher than water extraction method(P < 0.05). FT-IR showed that low-temperature plasma modification could improve the water solubility and OH content. NMR showed that the 1 → 6 glycosidic bonds of DP40 are transformed into 1 → 4 glycosidic bonds and 1 → 3 glycosidic bonds, and the α-configuration sugar ring is transformed into β-configuration after plasma treatment. SEM and TEM analysis showed that the morphology of modified DP40 changed from layered porous network structure to smooth morphology, and bulged into semicircular particles, and the degree of cross-linking of surface molecules increased. The results of biological activity experiments indicated that the modified polysaccharide (500–1000 μg·mL−1) can significantly improve the survival rate of GES-1 cells (p < 0.01). Compared with the untreated group, the high concentration of 1000 μg·mL−1 DP40-plasma could not only reduce ROS by 14.5% (p < 0.05) and MDA by 27.45% (p < 0.05), increase SOD activity by 28.27%, but also reduce cytokines (IL-8, TNF-α, IL-1β) by 31.82% (p < 0.05), 33.23% (p < 0.05) and 21.97% (p < 0.05), respectively. At the same time, low-temperature plasma modification can effectively reduce the caspase 3 activity, prevent cell apoptosis, and protect gastric mucosal cells from ethanol damage. Therefore, low-temperature plasma modification can improve the biological activity of DP40 polysaccharide by altering its structural characteristics. The results provide a new idea for the application of low-temperature plasma modification in biomacromolecules.

Effects of the Degree of Deacetylation on the Single-Molecule Mechanics of Chitosans.

Chitosan is one of the most prevalent biomass materials, and its physicochemical and biological characteristics, such as solubility, crystallinity, flocculation ability, biodegradability, and amino-related chemical processes, are directly connected to the degree of deacetylation (DD). However, the specifics about the effects of the DD on the characteristics of chitosan are still unclear up to now. In this work, atomic force microscopy-based single-molecule force spectroscopy was used to study the role of the DD in the single-molecule mechanics of chitosan. Even though the DD varies largely (17% ≤ DD ≤ 95%), the experimental results demonstrate that the chitosans exhibit the same natural (in nonane) and backbone (in dimethyl sulfoxide (DMSO)) single-chain elasticity. This suggests that chitosans have the same intra-chain hydrogen bond (H-bond) state in nonane and to which these H-bonds can be eliminated in DMSO. However, when the experiments are carried out in ethylene glycol (EG) and water, the single-chain mechanics are increased with the increases of the DD. The energy consumed to stretch chitosans in water is larger than that in EG, indicating that amino can form a strong interaction with water and induce the formation of the binding water around the sugar rings. The strong interaction between water and amino may be the key factor for the well solubility and chemical activity of chitosan. The results of this work are anticipated to provide fresh light on the significant role played by the DD and water in the structures and functions of chitosan at the single molecular level.

Reaction Mechanism of Glycoside Hydrolase Family 116 Utilizes Perpendicular Protonation.

Retaining glycoside hydrolases use acid/base catalysis with an enzymatic acid/base protonating the glycosidic bond oxygen to facilitate leaving-group departure alongside attack by a catalytic nucleophile to form a covalent intermediate. Generally, this acid/base protonates the oxygen laterally with respect to the sugar ring, which places the catalytic acid/base and nucleophile carboxylates within about 4.5-6.5 Å of each other. However, in glycoside hydrolase (GH) family 116, including disease-related human acid β-glucosidase 2 (GBA2), the distance between the catalytic acid/base and the nucleophile is around 8 Å (PDB: 5BVU) and the catalytic acid/base appears to be above the plane of the pyranose ring, rather than being lateral to that plane, which could have catalytic consequences. However, no structure of an enzyme-substrate complex is available for this GH family. Here, we report the structures of Thermoanaerobacterium xylanolyticum β-glucosidase (TxGH116) D593N acid/base mutant in complexes with cellobiose and laminaribiose and its catalytic mechanism. We confirm that the amide hydrogen bonding to the glycosidic oxygen is in a perpendicular rather than lateral orientation. Quantum mechanics/molecular mechanics (QM/MM) simulations of the glycosylation half-reaction in wild-type TxGH116 indicate that the substrate binds with the nonreducing glucose residue in an unusual relaxed 4C1 chair at the -1 subsite. Nevertheless, the reaction can still proceed through a 4H3 half-chair transition state, as in classical retaining β-glucosidases, as the catalytic acid D593 protonates the perpendicular electron pair. The glucose C6OH is locked in a gauche, trans orientation with respect to the C5-O5 and C4-C5 bonds to facilitate perpendicular protonation. These data imply a unique protonation trajectory in Clan-O glycoside hydrolases, which has strong implications for the design of inhibitors specific to either lateral protonators, such as human GBA1, or perpendicular protonators, such as human GBA2.