International Journal of Molecular Sciences

Editorial

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6 pages, 185 KiB

Open AccessEditorial

Complex Carbohydrates and Glycoconjugates: Structure, Functions and Applications

by Alexander O. Chizhov

Int. J. Mol. Sci. 2021, 22(22), 12219; https://doi.org/10.3390/ijms222212219 - 12 Nov 2021

Cited by 1 | Viewed by 2350

Abstract

The study of carbohydrates has a long history: for two centuries, the researches performed the way from “sweet matter” to glycomics [...] Full article

(This article belongs to the Special Issue Complex Carbohydrates and Glycoconjugates: Structure, Functions and Applications)

Research

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21 pages, 3495 KiB

Open AccessArticle

Rational Design of a Glycoconjugate Vaccine against Group A Streptococcus

by Roberta Di Benedetto, Francesca Mancini, Martina Carducci, Gianmarco Gasperini, Danilo Gomes Moriel, Allan Saul, Francesca Necchi, Rino Rappuoli and Francesca Micoli

Int. J. Mol. Sci. 2020, 21(22), 8558; https://doi.org/10.3390/ijms21228558 - 13 Nov 2020

Cited by 25 | Viewed by 3777

Abstract

No commercial vaccine is yet available against Group A Streptococcus (GAS), major cause of pharyngitis and impetigo, with a high frequency of serious sequelae in low- and middle-income countries. Group A Carbohydrate (GAC), conjugated to an appropriate carrier protein, has been proposed as [...] Read more.

No commercial vaccine is yet available against Group A Streptococcus (GAS), major cause of pharyngitis and impetigo, with a high frequency of serious sequelae in low- and middle-income countries. Group A Carbohydrate (GAC), conjugated to an appropriate carrier protein, has been proposed as an attractive vaccine candidate. Here, we explored the possibility to use GAS Streptolysin O (SLO), SpyCEP and SpyAD protein antigens with dual role of antigen and carrier, to enhance the efficacy of the final vaccine and reduce its complexity. All protein antigens resulted good carrier for GAC, inducing similar anti-GAC IgG response to the more traditional CRM₁₉₇ conjugate in mice. However, conjugation to the polysaccharide had a negative impact on the anti-protein responses, especially in terms of functionality as evaluated by an IL-8 cleavage assay for SpyCEP and a hemolysis assay for SLO. After selecting CRM₁₉₇ as carrier, optimal conditions for its conjugation to GAC were identified through a Design of Experiment approach, improving process robustness and yield This work supports the development of a vaccine against GAS and shows how novel statistical tools and recent advancements in the field of conjugation can lead to improved design of glycoconjugate vaccines. Full article

(This article belongs to the Special Issue Complex Carbohydrates and Glycoconjugates: Structure, Functions and Applications)

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22 pages, 4947 KiB

Open AccessArticle

The Post-Translational Modifications, Localization, and Mode of Attachment of Non-Covalently Bound Glucanosyltransglycosylases of Yeast Cell Wall as a Key to Understanding their Functioning

by Valentina V. Rekstina, Tatyana A. Sabirzyanova, Fanis A. Sabirzyanov, Alexei A. Adzhubei, Yaroslav V. Tkachev, Irina B. Kudryashova, Natalia E. Snalina, Anastasia A. Bykova, Alice V. Alessenko, Rustam H. Ziganshin, Sergei A. Kuznetsov and Tatyana S. Kalebina

Int. J. Mol. Sci. 2020, 21(21), 8304; https://doi.org/10.3390/ijms21218304 - 5 Nov 2020

Cited by 6 | Viewed by 2386

Abstract

Glucan linked to proteins is a natural mega-glycoconjugate (mGC) playing the central role as a structural component of a yeast cell wall (CW). Regulation of functioning of non-covalently bound glucanosyltransglycosylases (ncGTGs) that have to remodel mGC to provide CW extension is poorly understood. [...] Read more.

Glucan linked to proteins is a natural mega-glycoconjugate (mGC) playing the central role as a structural component of a yeast cell wall (CW). Regulation of functioning of non-covalently bound glucanosyltransglycosylases (ncGTGs) that have to remodel mGC to provide CW extension is poorly understood. We demonstrate that the main ncGTGs Bgl2 and Scw4 have phosphorylated and glutathionylated residues and are represented in CW as different pools of molecules having various firmness of attachment. Identified pools contain Bgl2 molecules with unmodified peptides, but differ from each other in the presence and combination of modified ones, as well as in the presence or absence of other CW proteins. Correlation of Bgl2 distribution among pools and its N-glycosylation was not found. Glutathione affects Bgl2 conformation, probably resulting in the mode of its attachment and enzymatic activity. Bgl2 from the pool of unmodified and monophosphorylated molecules demonstrates the ability to fibrillate after isolation from CW. Revealing of Bgl2 microcompartments and their mosaic arrangement summarized with the results obtained give the evidence that the functioning of ncGTGs in CW can be controlled by reversible post-translational modifications and facilitated due to their compact localization. The hypothetical scheme of distribution of Bgl2 inside CW is represented. Full article

(This article belongs to the Special Issue Complex Carbohydrates and Glycoconjugates: Structure, Functions and Applications)

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23 pages, 5452 KiB

Open AccessArticle

Tandem Electrospray Mass Spectrometry of Cyclic N-Substituted Oligo-β-(1→6)-D-glucosamines

by Alexander O. Chizhov, Marina L. Gening, Yury E. Tsvetkov and Nikolay E. Nifantiev

Int. J. Mol. Sci. 2020, 21(21), 8284; https://doi.org/10.3390/ijms21218284 - 5 Nov 2020

Cited by 2 | Viewed by 2058

Abstract

High-resolution electrospray mass spectra (MS and MS/MS CID) of positive ions of a series of protonated, ammoniated, and metallated molecules of cyclic N-substituted oligo-β-(1→6)-D-glucosamines differing in cycle size and N-acyl substituents were registered and interpreted. It was shown that the main [...] Read more.

High-resolution electrospray mass spectra (MS and MS/MS CID) of positive ions of a series of protonated, ammoniated, and metallated molecules of cyclic N-substituted oligo-β-(1→6)-D-glucosamines differing in cycle size and N-acyl substituents were registered and interpreted. It was shown that the main type of fragmentation is a cleavage of glycosidic bonds of a cycle, and in some cases fragmentation of amide side chains is possible. If labile fragments in substituents (e.g., carbohydrate chains) are present, a decay of the cycle and an elimination of labile fragments are of comparable possibility. It was found that in some cases rearrangements with loss of an internal carbohydrate residue (IRL), or an internal part of a side chain, are feasible. Full article

(This article belongs to the Special Issue Complex Carbohydrates and Glycoconjugates: Structure, Functions and Applications)

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13 pages, 3459 KiB

Open AccessArticle

Endocytosis and Trafficking of Heparan Sulfate Proteoglycans in Triple-Negative Breast Cancer Cells Unraveled with a Polycationic Peptide

by Elisabetta Mandarini, Eva Tollapi, Marta Zanchi, Lorenzo Depau, Alessandro Pini, Jlenia Brunetti, Luisa Bracci and Chiara Falciani

Int. J. Mol. Sci. 2020, 21(21), 8282; https://doi.org/10.3390/ijms21218282 - 5 Nov 2020

Cited by 8 | Viewed by 3329

Abstract

The process of heparan sulfate proteoglycan (HSPG) internalization has been described as following different pathways. The tumor-specific branched NT4 peptide has been demonstrated to bind HSPGs on the plasma membrane and to be internalized in tumor cell lines. The polycationic peptide has been [...] Read more.

The process of heparan sulfate proteoglycan (HSPG) internalization has been described as following different pathways. The tumor-specific branched NT4 peptide has been demonstrated to bind HSPGs on the plasma membrane and to be internalized in tumor cell lines. The polycationic peptide has been also shown to impair migration of different cancer cell lines in 2D and 3D models. Our hypothesis was that HSPG endocytosis could affect two important phenomena of cancer development: cell migration and nourishment. Using NT4 as an experimental tool mimicking heparin-binding ligands, we studied endocytosis and trafficking of HSPGs in a triple-negative human breast cancer cell line, MDA-MB-231. The peptide entered cells employing caveolin- or clathrin-dependent endocytosis and macropinocytosis, in line with what is already known about HSPGs. NT4 then localized in early and late endosomes in a time-dependent manner. The peptide had a negative effect on CDC42-activation triggered by EGF. The effect can be explained if we consider NT4 a competitive inhibitor of EGF on HS that impairs the co-receptor activity of the proteoglycan, reducing EGFR activation. Reduction of the invasive migratory phenotype of MDA-MB-231 induced by NT4 can be ascribed to this effect. RhoA activation was damped by EGF in MDA-MB-231. Indeed, EGF reduced RhoA-GTP and NT4 did not interfere with this receptor-mediated signaling. On the other hand, the peptide alone determined a small but solid reduction in active RhoA in breast cancer cells. This result supports the observation of few other studies, showing direct activation of the GTPase through HSPG, not mediated by EGF/EGFR. Full article

(This article belongs to the Special Issue Complex Carbohydrates and Glycoconjugates: Structure, Functions and Applications)

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41 pages, 9860 KiB

Open AccessArticle

Constructing 3-Dimensional Atomic-Resolution Models of Nonsulfated Glycosaminoglycans with Arbitrary Lengths Using Conformations from Molecular Dynamics

by Elizabeth K. Whitmore, Devon Martin and Olgun Guvench

Int. J. Mol. Sci. 2020, 21(20), 7699; https://doi.org/10.3390/ijms21207699 - 18 Oct 2020

Cited by 15 | Viewed by 3686

Abstract

Glycosaminoglycans (GAGs) are the linear carbohydrate components of proteoglycans (PGs) and are key mediators in the bioactivity of PGs in animal tissue. GAGs are heterogeneous, conformationally complex, and polydisperse, containing up to 200 monosaccharide units. These complexities make studying GAG conformation a challenge [...] Read more.

Glycosaminoglycans (GAGs) are the linear carbohydrate components of proteoglycans (PGs) and are key mediators in the bioactivity of PGs in animal tissue. GAGs are heterogeneous, conformationally complex, and polydisperse, containing up to 200 monosaccharide units. These complexities make studying GAG conformation a challenge for existing experimental and computational methods. We previously described an algorithm we developed that applies conformational parameters (i.e., all bond lengths, bond angles, and dihedral angles) from molecular dynamics (MD) simulations of nonsulfated chondroitin GAG 20-mers to construct 3-D atomic-resolution models of nonsulfated chondroitin GAGs of arbitrary length. In the current study, we applied our algorithm to other GAGs, including hyaluronan and nonsulfated forms of dermatan, keratan, and heparan and expanded our database of MD-generated GAG conformations. Here, we show that individual glycosidic linkages and monosaccharide rings in 10- and 20-mers of hyaluronan and nonsulfated dermatan, keratan, and heparan behave randomly and independently in MD simulation and, therefore, using a database of MD-generated 20-mer conformations, that our algorithm can construct conformational ensembles of 10- and 20-mers of various GAG types that accurately represent the backbone flexibility seen in MD simulations. Furthermore, our algorithm efficiently constructs conformational ensembles of GAG 200-mers that we would reasonably expect from MD simulations. Full article

(This article belongs to the Special Issue Complex Carbohydrates and Glycoconjugates: Structure, Functions and Applications)

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20 pages, 3698 KiB

Open AccessArticle

Comparison of Methods for Bulk Automated Simulation of Glycosidic Bond Conformations

by Victor Stroylov, Maria Panova and Philip Toukach

Int. J. Mol. Sci. 2020, 21(20), 7626; https://doi.org/10.3390/ijms21207626 - 15 Oct 2020

Cited by 6 | Viewed by 3442

Abstract

Six empirical force fields were tested for applicability to calculations for automated carbohydrate database filling. They were probed on eleven disaccharide molecules containing representative structural features from widespread classes of carbohydrates. The accuracy of each method was queried by predictions of nuclear Overhauser [...] Read more.

Six empirical force fields were tested for applicability to calculations for automated carbohydrate database filling. They were probed on eleven disaccharide molecules containing representative structural features from widespread classes of carbohydrates. The accuracy of each method was queried by predictions of nuclear Overhauser effects (NOEs) from conformational ensembles obtained from 50 to 100 ns molecular dynamics (MD) trajectories and their comparison to the published experimental data. Using various ranking schemes, it was concluded that explicit solvent MM3 MD yielded non-inferior NOE accuracy with newer GLYCAM-06, and ultimately PBE0-D3/def2-TZVP (Triple-Zeta Valence Polarized) Density Functional Theory (DFT) simulations. For seven of eleven molecules, at least one empirical force field with explicit solvent outperformed DFT in NOE prediction. The aggregate of characteristics (accuracy, speed, and compatibility) made MM3 dynamics with explicit solvent at 300 K the most favorable method for bulk generation of disaccharide conformation maps for massive database filling. Full article

(This article belongs to the Special Issue Complex Carbohydrates and Glycoconjugates: Structure, Functions and Applications)

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15 pages, 1145 KiB

Open AccessArticle

Human Natural Antibodies Recognizing Glycan Galβ1-3GlcNAc (Le^C)

by Kira Dobrochaeva, Nailya Khasbiullina, Nadezhda Shilova, Nadezhda Antipova, Polina Obukhova, Oxana Galanina, Mikhail Gorbach, Inna Popova, Sergey Khaidukov, Natalia Grishchenko, Nikolai Tupitsyn, Jacques Le Pendu and Nicolai Bovin

Int. J. Mol. Sci. 2020, 21(18), 6511; https://doi.org/10.3390/ijms21186511 - 5 Sep 2020

Cited by 7 | Viewed by 2577

Abstract

The level of human natural antibodies of immunoglobulin M isotype against Le^C in patients with breast cancer is lower than in healthy women. The epitope specificity of these antibodies has been characterized using a printed glycan array and enzyme-linked immunosorbent assay (ELISA), [...] Read more.

The level of human natural antibodies of immunoglobulin M isotype against Le^C in patients with breast cancer is lower than in healthy women. The epitope specificity of these antibodies has been characterized using a printed glycan array and enzyme-linked immunosorbent assay (ELISA), the antibodies being isolated from donors’ blood using Le^C-Sepharose (Le^C is Galβ1-3GlcNAcβ). The isolated antibodies recognize the disaccharide but do not bind to glycans terminated with Le^C, which implies the impossibility of binding to regular glycoproteins of non-malignant cells. The avidity (as dissociation constant value) of antibodies probed with a multivalent disaccharide is 10⁻⁹ M; the nanomolar level indicates that the concentration is sufficient for physiological binding to the cognate antigen. Testing of several breast cancer cell lines showed the strongest binding to ZR 75-1. Interestingly, only 7% of the cells were positive in a monolayer with a low density, increasing up to 96% at highest density. The enhanced interaction (instead of the expected inhibition) of antibodies with ZR 75-1 cells in the presence of Galβ1-3GlcNAcβ disaccharide, indicates that the target epitope of anti-Le^C antibodies is a molecular pattern with a carbohydrate constituent rather than a glycan. Full article

(This article belongs to the Special Issue Complex Carbohydrates and Glycoconjugates: Structure, Functions and Applications)

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23 pages, 4066 KiB

Open AccessArticle

Rearrangement of the Cellulose-Enriched Cell Wall in Flax Phloem Fibers over the Course of the Gravitropic Reaction

by Nadezda Ibragimova, Natalia Mokshina, Marina Ageeva, Oleg Gurjanov and Polina Mikshina

Int. J. Mol. Sci. 2020, 21(15), 5322; https://doi.org/10.3390/ijms21155322 - 27 Jul 2020

Cited by 14 | Viewed by 2804

Abstract

The plant cell wall is a complex structure consisting of a polysaccharide network. The rearrangements of the cell wall during the various physiological reactions of plants, however, are still not fully characterized. Profound changes in cell wall organization are detected by microscopy in [...] Read more.

The plant cell wall is a complex structure consisting of a polysaccharide network. The rearrangements of the cell wall during the various physiological reactions of plants, however, are still not fully characterized. Profound changes in cell wall organization are detected by microscopy in the phloem fibers of flax (Linum usitatissimum) during the restoration of the vertical position of the inclined stems. To characterize the underlying biochemical and structural changes in the major cell wall polysaccharides, we compared the fiber cell walls of non-inclined and gravistimulated plants by focusing mainly on differences in non-cellulosic polysaccharides and the fine cellulose structure. Biochemical analysis revealed a slight increase in the content of pectins in the fiber cell walls of gravistimulated plants as well as an increase in accessibility for labeling non-cellulosic polysaccharides. The presence of galactosylated xyloglucan in the gelatinous cell wall layer of flax fibers was demonstrated, and its labeling was more pronounced in the gravistimulated plants. Using solid state NMR, an increase in the crystallinity of the cellulose in gravistimulated plants, along with a decrease in cellulose mobility, was demonstrated. Thus, gravistimulation may affect the rearrangement of the cell wall, which can enable restoration in a vertical position of the plant stem. Full article

(This article belongs to the Special Issue Complex Carbohydrates and Glycoconjugates: Structure, Functions and Applications)

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20 pages, 2390 KiB

Open AccessArticle

TETRALEC, Artificial Tetrameric Lectins: A Tool to Screen Ligand and Pathogen Interactions

by Silvia Achilli, João T. Monteiro, Sonia Serna, Sabine Mayer-Lambertz, Michel Thépaut, Aline Le Roy, Christine Ebel, Niels-Christian Reichardt, Bernd Lepenies, Franck Fieschi and Corinne Vivès

Int. J. Mol. Sci. 2020, 21(15), 5290; https://doi.org/10.3390/ijms21155290 - 25 Jul 2020

Cited by 13 | Viewed by 3388

Abstract

C-type lectin receptor (CLR)/carbohydrate recognition occurs through low affinity interactions. Nature compensates that weakness by multivalent display of the lectin carbohydrate recognition domain (CRD) at the cell surface. Mimicking these low affinity interactions in vitro is essential to better understand CLR/glycan interactions. Here, [...] Read more.

C-type lectin receptor (CLR)/carbohydrate recognition occurs through low affinity interactions. Nature compensates that weakness by multivalent display of the lectin carbohydrate recognition domain (CRD) at the cell surface. Mimicking these low affinity interactions in vitro is essential to better understand CLR/glycan interactions. Here, we present a strategy to create a generic construct with a tetrameric presentation of the CRD for any CLR, termed TETRALEC. We applied our strategy to a naturally occurring tetrameric CRD, DC-SIGNR, and compared the TETRALEC ligand binding capacity by synthetic N- and O-glycans microarray using three different DC-SIGNR constructs i) its natural tetrameric counterpart, ii) the monomeric CRD and iii) a dimeric Fc-CRD fusion. DC-SIGNR TETRALEC construct showed a similar binding profile to that of its natural tetrameric counterpart. However, differences observed in recognition of low affinity ligands underlined the importance of the CRD spatial arrangement. Moreover, we further extended the applications of DC-SIGNR TETRALEC to evaluate CLR/pathogens interactions. This construct was able to recognize heat-killed Candida albicans by flow cytometry and confocal microscopy, a so far unreported specificity of DC-SIGNR. In summary, the newly developed DC-SIGNR TETRALEC tool proved to be useful to unravel novel CLR/glycan interactions, an approach which could be applied to other CLRs. Full article

(This article belongs to the Special Issue Complex Carbohydrates and Glycoconjugates: Structure, Functions and Applications)

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15 pages, 11620 KiB

Open AccessArticle

Abberant Immunoglobulin G Glycosylation in Rheumatoid Arthritis by LTQ-ESI-MS

by Zhipeng Su, Qing Xie, Yanping Wang and Yunsen Li

Int. J. Mol. Sci. 2020, 21(6), 2045; https://doi.org/10.3390/ijms21062045 - 17 Mar 2020

Cited by 29 | Viewed by 4296

Abstract

Aberrant glycosylation has been observed in many autoimmune diseases. For example, aberrant glycosylation of immunoglobulin G (IgG) has been implicated in rheumatoid arthritis (RA) pathogenesis. The aim of this study is to investigate IgG glycosylation and whether there is an association with rheumatoid [...] Read more.

Aberrant glycosylation has been observed in many autoimmune diseases. For example, aberrant glycosylation of immunoglobulin G (IgG) has been implicated in rheumatoid arthritis (RA) pathogenesis. The aim of this study is to investigate IgG glycosylation and whether there is an association with rheumatoid factor levels in the serum of RA patients. We detected permethylated N-glycans of the IgG obtained in serum from 44 RA patients and 30 healthy controls using linear ion-trap electrospray ionization mass spectrometry (LTQ-ESI-MS), a highly sensitive and efficient approach in the detection and identification of N-glycans profiles. IgG N-glycosylation and rheumatoid factor levels were compared in healthy controls and RA patients. Our results suggested that total IgG purified from serum of RA patients shows significantly lower galactosylation (p = 0.0012), lower sialylation (p < 0.0001) and higher fucosylation (p = 0.0063) levels compared with healthy controls. We observed a positive correlation between aberrant N-glycosylation and rheumatoid factor level in the RA patients. In conclusion, we identified aberrant glycosylation of IgG in the serum of RA patients and its association with elevated levels of rheumatoid factor. Full article

(This article belongs to the Special Issue Complex Carbohydrates and Glycoconjugates: Structure, Functions and Applications)

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13 pages, 2064 KiB

Open AccessArticle

Burkholderia cenocepacia H111 Produces a Water-Insoluble Exopolysaccharide in Biofilm: Structural Determination and Molecular Modelling

by Barbara Bellich, Ining A. Jou, Marco Caterino, Roberto Rizzo, Neil Ravenscroft, Mustafa Fazli, Tim Tolker-Nielsen, John W. Brady and Paola Cescutti

Int. J. Mol. Sci. 2020, 21(5), 1702; https://doi.org/10.3390/ijms21051702 - 2 Mar 2020

Cited by 13 | Viewed by 3854

Abstract

Biofilms are a multicellular way of life, where bacterial cells are close together and embedded in a hydrated macromolecular matrix which offers a number of advantages to the cells. Extracellular polysaccharides play an important role in matrix setup and maintenance. A water-insoluble polysaccharide [...] Read more.

Biofilms are a multicellular way of life, where bacterial cells are close together and embedded in a hydrated macromolecular matrix which offers a number of advantages to the cells. Extracellular polysaccharides play an important role in matrix setup and maintenance. A water-insoluble polysaccharide was isolated and purified from the biofilm produced by Burkholderia cenocepacia strain H111, a cystic fibrosis pathogen. Its composition and glycosidic linkages were determined using Gas–Liquid Chromatography–Mass Spectrometry (GLC–MS) on appropriate carbohydrate derivatives while its complete structure was unraveled by 1D and 2D NMR spectroscopy in deuterated sodium hydroxide (NaOD) aqueous solutions. All the collected data demonstrated the following repeating unit for the water-insoluble B. cenocepacia biofilm polysaccharide: [3)-α-d-Galp-(1→3)-α-d-Glcp-(1→3)-α-d-Galp-(1→3)-α-d-Manp-(1→]_n Molecular modelling was used, coupled with NMR Nuclear Overhauser Effect (NOE) data, to obtain information about local structural motifs which could give hints about the polysaccharide insolubility. Both modelling and NMR data pointed at restricted dynamics of local conformations which were ascribed to the presence of inter-residue hydrogen bonds and to steric restrictions. In addition, the good correlation between NOE data and calculated interatomic distances by molecular dynamics simulations validated potential energy functions used for calculations. Full article

(This article belongs to the Special Issue Complex Carbohydrates and Glycoconjugates: Structure, Functions and Applications)

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16 pages, 4241 KiB

Open AccessArticle

Protective Effect of l-Hexaguluroic Acid Hexasodium Salt on UVA-Induced Photo-Aging in HaCaT Cells

by Qiong Li, Donghui Bai, Ling Qin, Meng Shao, Xi Liu, Shuai Zhang, Chengxiu Yan, Guangli Yu and Jiejie Hao

Int. J. Mol. Sci. 2020, 21(4), 1201; https://doi.org/10.3390/ijms21041201 - 11 Feb 2020

Cited by 12 | Viewed by 4501

Abstract

This study aimed to show the α-l-Hexaguluroic acid hexasodium salt (G6) protective effect against UVA-induced photoaging of human keratinocyte cells. We found that G6 localized to the mitochondria and improved mitochondrial functions. G6 increased respiratory chain complex activities, which led to [...] Read more.

This study aimed to show the α-l-Hexaguluroic acid hexasodium salt (G6) protective effect against UVA-induced photoaging of human keratinocyte cells. We found that G6 localized to the mitochondria and improved mitochondrial functions. G6 increased respiratory chain complex activities, which led to increased cellular ATP content and NAD⁺/NADH ratio. Thus, G6 alleviated the oxidative stress state in UVA-irradiated cells. Moreover, G6 can regulate the SIRT1/pGC-1α pathway, which enhanced the cells’ viability and mitochondria energy metabolism. Notably, the anti-photoaging potential of G6 was directly associated with the increased level of MMP and SIRT1, which was followed by the upregulation of pGC-1α, D-LOOP, and Mt-TFA, and with the transcriptional activation of NRF1/NRF2. Taking all of the results together, we conclude that G6 could protect HaCaT cells from UVA-induced photo-aging via the regulation of mitochondria energy metabolism and its downstream signaling pathways. Full article

(This article belongs to the Special Issue Complex Carbohydrates and Glycoconjugates: Structure, Functions and Applications)

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15 pages, 2788 KiB

Open AccessArticle

Genome-Wide Analysis of Whole Human Glycoside Hydrolases by Data-Driven Analysis in Silico

by Takahiro Nakamura, Muhamad Fahmi, Jun Tanaka, Kaito Seki, Yukihiro Kubota and Masahiro Ito

Int. J. Mol. Sci. 2019, 20(24), 6290; https://doi.org/10.3390/ijms20246290 - 13 Dec 2019

Cited by 8 | Viewed by 3667

Abstract

Glycans are involved in various metabolic processes via the functions of glycosyltransferases and glycoside hydrolases. Analysing the evolution of these enzymes is essential for improving the understanding of glycan metabolism and function. Based on our previous study of glycosyltransferases, we performed a genome-wide [...] Read more.

Glycans are involved in various metabolic processes via the functions of glycosyltransferases and glycoside hydrolases. Analysing the evolution of these enzymes is essential for improving the understanding of glycan metabolism and function. Based on our previous study of glycosyltransferases, we performed a genome-wide analysis of whole human glycoside hydrolases using the UniProt, BRENDA, CAZy and KEGG databases. Using cluster analysis, 319 human glycoside hydrolases were classified into four clusters based on their similarity to enzymes conserved in chordates or metazoans (Class 1), metazoans (Class 2), metazoans and plants (Class 3) and eukaryotes (Class 4). The eukaryote and metazoan clusters included N- and O-glycoside hydrolases, respectively. The significant abundance of disordered regions within the most conserved cluster indicated a role for disordered regions in the evolution of glycoside hydrolases. These results suggest that the biological diversity of multicellular organisms is related to the acquisition of N- and O-linked glycans. Full article

(This article belongs to the Special Issue Complex Carbohydrates and Glycoconjugates: Structure, Functions and Applications)

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Review

Jump to: Editorial, Research

22 pages, 4618 KiB

Open AccessReview

Preparation of Defined Chitosan Oligosaccharides Using Chitin Deacetylases

by Martin Bonin, Sruthi Sreekumar, Stefan Cord-Landwehr and Bruno M. Moerschbacher

Int. J. Mol. Sci. 2020, 21(21), 7835; https://doi.org/10.3390/ijms21217835 - 22 Oct 2020

Cited by 36 | Viewed by 5306

Abstract

During the past decade, detailed studies using well-defined ‘second generation’ chitosans have amply proved that both their material properties and their biological activities are dependent on their molecular structure, in particular on their degree of polymerisation (DP) and their fraction of acetylation ( [...] Read more.

During the past decade, detailed studies using well-defined ‘second generation’ chitosans have amply proved that both their material properties and their biological activities are dependent on their molecular structure, in particular on their degree of polymerisation (DP) and their fraction of acetylation (F_A). Recent evidence suggests that the pattern of acetylation (PA), i.e., the sequence of acetylated and non-acetylated residues along the linear polymer, is equally important, but chitosan polymers with defined, non-random PA are not yet available. One way in which the PA will influence the bioactivities of chitosan polymers is their enzymatic degradation by sequence-dependent chitosan hydrolases present in the target tissues. The PA of the polymer substrates in conjunction with the subsite preferences of the hydrolases determine the type of oligomeric products and the kinetics of their production and further degradation. Thus, the bioactivities of chitosan polymers will at least in part be carried by the chitosan oligomers produced from them, possibly through their interaction with pattern recognition receptors in target cells. In contrast to polymers, partially acetylated chitosan oligosaccharides (paCOS) can be fully characterised concerning their DP, F_A, and PA, and chitin deacetylases (CDAs) with different and known regio-selectivities are currently emerging as efficient tools to produce fully defined paCOS in quantities sufficient to probe their bioactivities. In this review, we describe the current state of the art on how CDAs can be used in forward and reverse mode to produce all of the possible paCOS dimers, trimers, and tetramers, most of the pentamers and many of the hexamers. In addition, we describe the biotechnological production of the required fully acetylated and fully deacetylated oligomer substrates, as well as the purification and characterisation of the paCOS products. Full article

(This article belongs to the Special Issue Complex Carbohydrates and Glycoconjugates: Structure, Functions and Applications)

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46 pages, 11844 KiB

Open AccessReview

Three-Dimensional Structures of Carbohydrates and Where to Find Them

by Sofya I. Scherbinina and Philip V. Toukach

Int. J. Mol. Sci. 2020, 21(20), 7702; https://doi.org/10.3390/ijms21207702 - 18 Oct 2020

Cited by 25 | Viewed by 13254

Abstract

Analysis and systematization of accumulated data on carbohydrate structural diversity is a subject of great interest for structural glycobiology. Despite being a challenging task, development of computational methods for efficient treatment and management of spatial (3D) structural features of carbohydrates breaks new ground [...] Read more.

Analysis and systematization of accumulated data on carbohydrate structural diversity is a subject of great interest for structural glycobiology. Despite being a challenging task, development of computational methods for efficient treatment and management of spatial (3D) structural features of carbohydrates breaks new ground in modern glycoscience. This review is dedicated to approaches of chemo- and glyco-informatics towards 3D structural data generation, deposition and processing in regard to carbohydrates and their derivatives. Databases, molecular modeling and experimental data validation services, and structure visualization facilities developed for last five years are reviewed. Full article

(This article belongs to the Special Issue Complex Carbohydrates and Glycoconjugates: Structure, Functions and Applications)

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31 pages, 1260 KiB

Open AccessReview

Metabolism of Glycosphingolipids and Their Role in the Pathophysiology of Lysosomal Storage Disorders

by Alex E. Ryckman, Inka Brockhausen and Jagdeep S. Walia

Int. J. Mol. Sci. 2020, 21(18), 6881; https://doi.org/10.3390/ijms21186881 - 19 Sep 2020

Cited by 45 | Viewed by 8037

Abstract

Glycosphingolipids (GSLs) are a specialized class of membrane lipids composed of a ceramide backbone and a carbohydrate-rich head group. GSLs populate lipid rafts of the cell membrane of eukaryotic cells, and serve important cellular functions including control of cell–cell signaling, signal transduction and [...] Read more.

Glycosphingolipids (GSLs) are a specialized class of membrane lipids composed of a ceramide backbone and a carbohydrate-rich head group. GSLs populate lipid rafts of the cell membrane of eukaryotic cells, and serve important cellular functions including control of cell–cell signaling, signal transduction and cell recognition. Of the hundreds of unique GSL structures, anionic gangliosides are the most heavily implicated in the pathogenesis of lysosomal storage diseases (LSDs) such as Tay-Sachs and Sandhoff disease. Each LSD is characterized by the accumulation of GSLs in the lysosomes of neurons, which negatively interact with other intracellular molecules to culminate in cell death. In this review, we summarize the biosynthesis and degradation pathways of GSLs, discuss how aberrant GSL metabolism contributes to key features of LSD pathophysiology, draw parallels between LSDs and neurodegenerative proteinopathies such as Alzheimer’s and Parkinson’s disease and lastly, discuss possible therapies for patients. Full article

(This article belongs to the Special Issue Complex Carbohydrates and Glycoconjugates: Structure, Functions and Applications)

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22 pages, 1840 KiB

Open AccessReview

Biopolymer-Based Microcarriers for Three-Dimensional Cell Culture and Engineered Tissue Formation

by Lixia Huang, Ahmed M.E. Abdalla, Lin Xiao and Guang Yang

Int. J. Mol. Sci. 2020, 21(5), 1895; https://doi.org/10.3390/ijms21051895 - 10 Mar 2020

Cited by 74 | Viewed by 8524

Abstract

The concept of three-dimensional (3D) cell culture has been proposed to maintain cellular morphology and function as in vivo. Among different approaches for 3D cell culture, microcarrier technology provides a promising tool for cell adhesion, proliferation, and cellular interactions in 3D space mimicking [...] Read more.

The concept of three-dimensional (3D) cell culture has been proposed to maintain cellular morphology and function as in vivo. Among different approaches for 3D cell culture, microcarrier technology provides a promising tool for cell adhesion, proliferation, and cellular interactions in 3D space mimicking the in vivo microenvironment. In particular, microcarriers based on biopolymers have been widely investigated because of their superior biocompatibility and biodegradability. Moreover, through bottom-up assembly, microcarriers have opened a bright door for fabricating engineered tissues, which is one of the cutting-edge topics in tissue engineering and regeneration medicine. This review takes an in-depth look into the recent advancements of microcarriers based on biopolymers—especially polysaccharides such as chitosan, chitin, cellulose, hyaluronic acid, alginate, and laminarin—for 3D cell culture and the fabrication of engineered tissues based on them. The current limitations and potential strategies were also discussed to shed some light on future directions. Full article

(This article belongs to the Special Issue Complex Carbohydrates and Glycoconjugates: Structure, Functions and Applications)

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