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Chen X, Zhang J, Wang Y, Hu Q, Zhao R, Zhong L, Zhan Q, Zhao L. Structure and immunostimulatory activity studies on two novel Flammulina velutipes polysaccharides: revealing potential impacts of →6)-α-D-Glc p(1→ on the TLR-4/MyD88/NF-κB pathway. Food Funct 2024; 15:3507-3521. [PMID: 38465397 DOI: 10.1039/d3fo05468c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Two novel Flammulina velutipes (F. velutipes) polysaccharides, FVPH1 and FVPH2, were isolated and purified after hot water extraction. The structural characterization revealed that the backbone of FVPH1 consisted mainly of →6)-α-D-Glcp(1→, →3,4)-α-D-Galp(1→, →4)-α-L-Fucp(1→, and →4)-β-D-Manp(1→, while the backbone of FVPH2 consisted of →3)-α-D-Galp(1→, →3,4)-α-D-Manp(1→,→6)-α-D-Glcp(1→. The branches of FVPH1 contained →6)-α-D-Glcp(1→ and α-D-Glcp(1→ and the branches of FVPH2 consisted of →3)-α-D-Galp(1→, →6)-α-D-Glcp(1→, and β-L-Fucp(1→. FVPH2 exhibited significantly better immunostimulatory activity than FVPH1 (P < 0.05), as evidenced by the increased expression of NO, IL-1β, IL-6, and TNF-α and pinocytic activity of RAW264.7 cells. As the most abundant structure in the polysaccharides of F. velutipes, the content of →6)-α-D-Glcp(1→ might play a crucial role in influencing the immunostimulatory activity of F. velutipes polysaccharides. The F. velutipes polysaccharide with a lower content of →6)-α-D-Glcp(1→ and a higher branching degree could significantly enhance the immunostimulatory activity of F. velutipes polysaccharides via activating the TLR-4/MyD88/NF-κB pathway more effectively.
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Affiliation(s)
- Xin Chen
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, P. R. China.
| | - Jingsi Zhang
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, P. R. China.
| | - Yifan Wang
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, P. R. China.
| | - Qiuhui Hu
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, P. R. China.
- College of Food Science and Engineering, Nanjing University of Finance and Economics, Nanjing 210023, P. R. China
| | - Ruiqiu Zhao
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, P. R. China.
- College of Animal Science and Food Engineering, Jinling Institute of Technology, Nanjing 210095, P. R. China
| | - Lei Zhong
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, P. R. China.
| | - Qiping Zhan
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, P. R. China.
| | - Liyan Zhao
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, P. R. China.
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Pérez S. Computational modeling of protein-carbohydrate interactions: Current trends and future challenges. Adv Carbohydr Chem Biochem 2023; 83:133-149. [PMID: 37968037 DOI: 10.1016/bs.accb.2023.10.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2023]
Abstract
The article leads the reader through an up-to-date presentation of the concepts, developments, and main applications of computational modeling to study protein-carbohydrate interactions. It follows with the presentation of some current issues and perspectives arising from the expected evolution of generic methodological developments in deep learning, immersive analytics, and virtual reality for molecular visualization and data management. Such methodological developments for macromolecular interactions would greatly benefit a wide range of scientific endeavors in the field of carbohydrate chemistry and biochemistry, including the following interrelated efforts dealing with highly crowded media, with examples concerning glycoside transferases, the extracellular matrix, and the exploration of interactions between complex carbohydrates and intrinsically disordered proteins.
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Affiliation(s)
- Serge Pérez
- Centre de Recherches sur les Macromolécules Végétales, CNRS, Université Grenoble Alpes, Grenoble, France.
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Jaeschke SO, Lindhorst TK, Auer A. Between Two Chairs: Combination of Theory and Experiment for the Determination of the Conformational Dynamics of Xylosides. Chemistry 2022; 28:e202201544. [PMID: 35754398 PMCID: PMC9804333 DOI: 10.1002/chem.202201544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Indexed: 01/05/2023]
Abstract
The conformational properties of monosaccharides constitute fundamental features of oligosaccharides. While the energy landscape of monosaccharides can be altered by a specific biochemical environment or by chemical modifications, the analysis of resulting dynamic conformational equilibria is not feasible by experimental means alone. In this work, a series of β-d-xylopyranosides is used to outline how a combination of experimental NMR parameters and computed molecular properties can be used to determine conformers and quantify the composition of conformational equilibria. We demonstrate that identifying the most stable conformers using energy calculations is challenging and computing of NMR shieldings is typically not sensitive enough. On the other hand, computed spin-spin coupling constants for the xyloside ring can be used to unambiguously assign experimental NMR data of dynamic conformational equilibria and quantify the ratio of different conformers in the mixture. As a proof of principle, this procedure allowed to analyze a hitherto unknown dynamic equilibrium of a diamino-xyloside as a precursor of a molecular switch.
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Affiliation(s)
- Sven Ole Jaeschke
- Otto Diels Institute of Organic ChemistryChristiana Albertina University of KielOtto-Hahn-Platz 3–424118KielGermany
| | - Thisbe K. Lindhorst
- Otto Diels Institute of Organic ChemistryChristiana Albertina University of KielOtto-Hahn-Platz 3–424118KielGermany
| | - Alexander Auer
- Max-Planck-Institut für KohlenforschungKaiser-Wilhelm-Platz 145470Mülheim an der RuhrGermany
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Mukherjee S, Jana S, Khawas S, Kicuntod J, Marschall M, Ray B, Ray S. Synthesis, molecular features and biological activities of modified plant polysaccharides. Carbohydr Polym 2022; 289:119299. [DOI: 10.1016/j.carbpol.2022.119299] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Revised: 02/23/2022] [Accepted: 02/24/2022] [Indexed: 12/17/2022]
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Abstract
Glycoscience assembles all the scientific disciplines involved in studying various molecules and macromolecules containing carbohydrates and complex glycans. Such an ensemble involves one of the most extensive sets of molecules in quantity and occurrence since they occur in all microorganisms and higher organisms. Once the compositions and sequences of these molecules are established, the determination of their three-dimensional structural and dynamical features is a step toward understanding the molecular basis underlying their properties and functions. The range of the relevant computational methods capable of addressing such issues is anchored by the specificity of stereoelectronic effects from quantum chemistry to mesoscale modeling throughout molecular dynamics and mechanics and coarse-grained and docking calculations. The Review leads the reader through the detailed presentations of the applications of computational modeling. The illustrations cover carbohydrate-carbohydrate interactions, glycolipids, and N- and O-linked glycans, emphasizing their role in SARS-CoV-2. The presentation continues with the structure of polysaccharides in solution and solid-state and lipopolysaccharides in membranes. The full range of protein-carbohydrate interactions is presented, as exemplified by carbohydrate-active enzymes, transporters, lectins, antibodies, and glycosaminoglycan binding proteins. A final section features a list of 150 tools and databases to help address the many issues of structural glycobioinformatics.
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Affiliation(s)
- Serge Perez
- Centre de Recherche sur les Macromolecules Vegetales, University of Grenoble-Alpes, Centre National de la Recherche Scientifique, Grenoble F-38041, France
| | - Olga Makshakova
- FRC Kazan Scientific Center of Russian Academy of Sciences, Kazan Institute of Biochemistry and Biophysics, Kazan 420111, Russia
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Toukach PV, Egorova KS. Source files of the Carbohydrate Structure Database: the way to sophisticated analysis of natural glycans. Sci Data 2022; 9:131. [PMID: 35354826 PMCID: PMC8968703 DOI: 10.1038/s41597-022-01186-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 02/03/2022] [Indexed: 11/18/2022] Open
Abstract
The Carbohydrate Structure Database (CSDB, http://csdb.glycoscience.ru/ ) is a free curated repository storing various data on glycans of bacterial, fungal and plant origins. Currently, it maintains a close-to-full coverage on bacterial and fungal carbohydrates up to the year 2020. The CSDB web-interface provides free access to the database content and dedicated tools. Still, the number of these tools and the types of the corresponding analyses is limited, whereas the database itself contains data that can be used in a broader scope of analytical studies. In this paper, we present CSDB source data files and a self-contained SQL dump, and exemplify their possible application in glycan-related studies. By using CSDB in an SQL format, the user can gain access to the chain length distribution or charge distribution (as an example) in a given set of glycans defined according to specific structural, taxonomic, or other parameters, whereas the source text dump files can be imported to any dedicated database with a specific internal architecture differing from that of CSDB.
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Affiliation(s)
- Philip V Toukach
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky prospect 47, Moscow, 119991, Russia.
| | - Ksenia S Egorova
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky prospect 47, Moscow, 119991, Russia.
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Scherbinina SI, Frank M, Toukach PV. Carbohydrate structure database (CSDB) oligosaccharide conformation tool. Glycobiology 2022; 32:460-468. [PMID: 35275211 DOI: 10.1093/glycob/cwac011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Revised: 02/17/2022] [Accepted: 03/04/2022] [Indexed: 11/13/2022] Open
Abstract
Population analysis in terms of glycosidic torsion angles is frequently used to reveal preferred conformers of glycans. However, due to high structural diversity and flexibility of carbohydrates, conformational characterization of complex glycans can be a challenging task. Herein we present a conformation module of oligosaccharide fragments occurring in natural glycan structures developed on the platform of the Carbohydrate Structure Database (CSDB). Currently, this module deposits free energy surface and conformer abundance maps plotted as a function of glycosidic torsions for 194 inter-residue bonds. Data are automatically and continuously derived from explicit-solvent molecular dynamics (MD) simulations. The module was also supplemented with high-temperature MD data of saccharides (2403 maps) provided by GlycoMapsDB (hosted by GLYCOSCIENCES.de project). Conformational data defined by up to four torsional degrees of freedom can be freely explored using a web interface of the module available at http://csdb.glycoscience.ru/database/core/search_conf.html.
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Affiliation(s)
- S I Scherbinina
- Higher Chemical College, D. Mendeleev University of Chemical Technology of Russia, Miusskaya Square 9, 125047 Moscow, Russia
| | - M Frank
- Biognos AB, Box 8963, 40274 Göteborg, Sweden
| | - P V Toukach
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Science, Leninsky prospect 47, 119991 Moscow, Russia
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8
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Guvench O, Martin D, Greene M. Pyranose Ring Puckering Thermodynamics for Glycan Monosaccharides Associated with Vertebrate Proteins. Int J Mol Sci 2021; 23:473. [PMID: 35008898 PMCID: PMC8745717 DOI: 10.3390/ijms23010473] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 12/28/2021] [Accepted: 12/28/2021] [Indexed: 12/22/2022] Open
Abstract
The conformational properties of carbohydrates can contribute to protein structure directly through covalent conjugation in the cases of glycoproteins and proteoglycans and indirectly in the case of transmembrane proteins embedded in glycolipid-containing bilayers. However, there continue to be significant challenges associated with experimental structural biology of such carbohydrate-containing systems. All-atom explicit-solvent molecular dynamics simulations provide a direct atomic resolution view of biomolecular dynamics and thermodynamics, but the accuracy of the results depends on the quality of the force field parametrization used in the simulations. A key determinant of the conformational properties of carbohydrates is ring puckering. Here, we applied extended system adaptive biasing force (eABF) all-atom explicit-solvent molecular dynamics simulations to characterize the ring puckering thermodynamics of the ten common pyranose monosaccharides found in vertebrate biology (as represented by the CHARMM carbohydrate force field). The results, along with those for idose, demonstrate that the CHARMM force field reliably models ring puckering across this diverse set of molecules, including accurately capturing the subtle balance between 4C1 and 1C4 chair conformations in the cases of iduronate and of idose. This suggests the broad applicability of the force field for accurate modeling of carbohydrate-containing vertebrate biomolecules such as glycoproteins, proteoglycans, and glycolipids.
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Affiliation(s)
- Olgun Guvench
- Department of Pharmaceutical Sciences and Administration, School of Pharmacy, University of New England, 716 Stevens Avenue, Portland, ME 04103, USA; (D.M.); (M.G.)
- Graduate School of Biomedical Science and Engineering, University of Maine, 5775 Stodder Hall, Orono, ME 04469, USA
| | - Devon Martin
- Department of Pharmaceutical Sciences and Administration, School of Pharmacy, University of New England, 716 Stevens Avenue, Portland, ME 04103, USA; (D.M.); (M.G.)
- Graduate School of Biomedical Science and Engineering, University of Maine, 5775 Stodder Hall, Orono, ME 04469, USA
| | - Megan Greene
- Department of Pharmaceutical Sciences and Administration, School of Pharmacy, University of New England, 716 Stevens Avenue, Portland, ME 04103, USA; (D.M.); (M.G.)
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Wang YX, Zhang T, Xin Y, Huang XJ, Yin JY, Nie SP. Comprehensive evaluation of alkali-extracted polysaccharides from Agrocybe cylindracea: Comparison on structural characterization. Carbohydr Polym 2021; 255:117502. [DOI: 10.1016/j.carbpol.2020.117502] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Revised: 11/25/2020] [Accepted: 12/08/2020] [Indexed: 12/19/2022]
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10
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Scherbinina SI, Toukach PV. Three-Dimensional Structures of Carbohydrates and Where to Find Them. Int J Mol Sci 2020; 21:E7702. [PMID: 33081008 PMCID: PMC7593929 DOI: 10.3390/ijms21207702] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Revised: 10/15/2020] [Accepted: 10/16/2020] [Indexed: 02/06/2023] Open
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 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.
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Affiliation(s)
- Sofya I. Scherbinina
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Science, Leninsky prospect 47, 119991 Moscow, Russia
- Higher Chemical College, D. Mendeleev University of Chemical Technology of Russia, Miusskaya Square 9, 125047 Moscow, Russia
| | - Philip V. Toukach
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Science, Leninsky prospect 47, 119991 Moscow, Russia
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11
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Comparison of Methods for Bulk Automated Simulation of Glycosidic Bond Conformations. Int J Mol Sci 2020; 21:ijms21207626. [PMID: 33076365 PMCID: PMC7589101 DOI: 10.3390/ijms21207626] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Revised: 10/10/2020] [Accepted: 10/10/2020] [Indexed: 02/08/2023] Open
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 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.
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12
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Metrics of rhamnogalacturonan I with β-(1→4)-linked galactan side chains and structural basis for its self-aggregation. Carbohydr Polym 2017; 158:93-101. [DOI: 10.1016/j.carbpol.2016.11.082] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Revised: 11/28/2016] [Accepted: 11/29/2016] [Indexed: 11/18/2022]
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