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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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2
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Senthilkumar C, Kannan PR, Balashanmugam P, Raghunandhakumar S, Sathiamurthi P, Sivakumar S, A A, Mary SA, Madhan B. Collagen - Annona polysaccharide scaffolds with tetrahydrocurcumin loaded microspheres for antimicrobial wound dressing. CARBOHYDRATE POLYMER TECHNOLOGIES AND APPLICATIONS 2022. [DOI: 10.1016/j.carpta.2022.100204] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
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3
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Wang X, Bie L, Gao J. Structural Insights into the Cofactor Role of Heparin/Heparan Sulfate in Binding between the SARS-CoV-2 Spike Protein and Host Angiotensin-Converting Enzyme II. J Chem Inf Model 2022; 62:656-667. [PMID: 35060381 PMCID: PMC8791032 DOI: 10.1021/acs.jcim.1c01484] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Indexed: 02/07/2023]
Abstract
The viral entry process of the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) requires heparin and heparan sulfates from the cell surface, functioning as a cofactor for human angiotensin-converting enzyme 2 (ACE2) for recognizing the receptor-binding domain (RBD) of the spike (S) protein on the surface of the virion. In the present study, the binding poses of an oligosaccharide with four repeating units of GlcNS6S-IdoA2S (octa) predicted by Vina-Carb in the RBD binding site were employed in molecular dynamics (MD) simulations to provide atomic details for studying the cofactor mechanism. The molecular model in the MD simulations reproduced the length- and sequence-dependent behavior observed from the microarray experiments and revealed an important planar U-turn shape for HP/HS binding to RBD. The model for octa with this shape in the ACE2-RBD complex enhanced the interactions in the binding interface. The comparisons with the ACE2-RBD complex suggested that the presence of octa in the RBD binding site blocked the movements in a loop region at the distal end of the RBD binding interface and promoted the contacts of this loop region with the ACE2 N-terminus helix. This study shed light on the atomic and dynamic details for HP/HS interacting with RBD and provided insights into their cofactor role in the ACE2-RBD interactions.
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Affiliation(s)
- Xiaocong Wang
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics,
Huazhong Agricultural University, Wuhan 430070, Hubei,
China
| | - Lihua Bie
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics,
Huazhong Agricultural University, Wuhan 430070, Hubei,
China
| | - Jun Gao
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics,
Huazhong Agricultural University, Wuhan 430070, Hubei,
China
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4
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Künze G, Huster D, Samsonov SA. Investigation of the structure of regulatory proteins interacting with glycosaminoglycans by combining NMR spectroscopy and molecular modeling - the beginning of a wonderful friendship. Biol Chem 2021; 402:1337-1355. [PMID: 33882203 DOI: 10.1515/hsz-2021-0119] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 04/09/2021] [Indexed: 11/15/2022]
Abstract
The interaction of regulatory proteins with extracellular matrix or cell surface-anchored glycosaminoglycans (GAGs) plays important roles in molecular recognition, wound healing, growth, inflammation and many other processes. In spite of their high biological relevance, protein-GAG complexes are significantly underrepresented in structural databases because standard tools for structure determination experience difficulties in studying these complexes. Co-crystallization with subsequent X-ray analysis is hampered by the high flexibility of GAGs. NMR spectroscopy experiences difficulties related to the periodic nature of the GAGs and the sparse proton network between protein and GAG with distances that typically exceed the detection limit of nuclear Overhauser enhancement spectroscopy. In contrast, computer modeling tools have advanced over the last years delivering specific protein-GAG docking approaches successfully complemented with molecular dynamics (MD)-based analysis. Especially the combination of NMR spectroscopy in solution providing sparse structural constraints with molecular docking and MD simulations represents a useful synergy of forces to describe the structure of protein-GAG complexes. Here we review recent methodological progress in this field and bring up examples where the combination of new NMR methods along with cutting-edge modeling has yielded detailed structural information on complexes of highly relevant cytokines with GAGs.
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Affiliation(s)
- Georg Künze
- Center for Structural Biology, Vanderbilt University, 465 21st Ave S, 5140 MRB3, Nashville, TN37240, USA.,Department of Chemistry, Vanderbilt University, 7330 Stevenson Center, Station B 351822, Nashville, TN37235, USA.,Institute for Drug Discovery, University of Leipzig, Brüderstr. 34, D-04103Leipzig, Germany
| | - Daniel Huster
- Institute for Medical Physics and Biophysics, University of Leipzig, Härtelstr. 16-18, D-04107Leipzig, Germany
| | - Sergey A Samsonov
- Faculty of Chemistry, University of Gdańsk, Ul. Wita Stwosza 63, 80-308Gdańsk, Poland
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5
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Hernandes IS, Da Silva HC, Dos Santos HF, De Almeida WB. Unveiling the Molecular Structure of Antimalarial Drugs Chloroquine and Hydroxychloroquine in Solution through Analysis of 1H NMR Chemical Shifts. J Phys Chem B 2021; 125:3321-3342. [PMID: 33760611 DOI: 10.1021/acs.jpcb.1c00609] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Chloroquine (CQ) and hydroxychloroquine (HCQ) have been standard antimalarial drugs since the early 1950s, and very recently, the possibility of their use for the treatment of COVID-19 patients has been considered. To understand the drug mode of action at the submicroscopic level (atoms and molecules), molecular modeling studies with the aid of computational chemistry methods have been of great help. A fundamental step in such theoretical investigations is the knowledge of the predominant drug molecular structure in solution, which is the real environment for the interaction with biological targets. Our strategy to access this valuable information is to perform density functional theory (DFT) calculations of 1H NMR chemical shifts for several plausible molecular conformers and then find the best match with experimental NMR profile in solution (since it is extremely sensitive to conformational changes). Through this procedure, after optimizing 30 trial distinct molecular structures (ωB97x-D/6-31G(d,p)-PCM level of calculation), which may be considered representative conformations, we concluded that the global minimum (named M24), stabilized by an intramolecular N-H hydrogen bond, is not likely to be observed in water, chloroform, and dimethyl sulfoxide (DMSO) solution. Among fully optimized conformations (named M1 to M30, and MD1 and MD2), we found M12 (having no intramolecular H-bond) as the most probable structure of CQ and HCQ in water solution, which is a good approximate starting geometry in drug-receptor interaction simulations. On the other hand, the preferred CQ and HCQ structure in chloroform (and CQ in DMSO-d6) solution was assigned as M8, showing the solvent effects on conformational preferences. We believe that the analysis of 1H NMR data in solution can establish the connection between the macro level (experimental) and the sub-micro level (theoretical), which is not so apparent to us and appears to be more appropriate than the thermodynamic stability criterion in conformational analysis studies.
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Affiliation(s)
- Isabel S Hernandes
- Laboratório de Química Computacional e Modelagem Molecular (LQC-MM), Departamento de Química Inorgânica, Instituto de Química, Universidade Federal Fluminense (UFF), Outeiro de São João Batista s/n, Campus do Valonguinho, Centro, Niterói 24020-141, Rio de Janeiro, Brazil
| | - Haroldo C Da Silva
- Laboratório de Química Computacional e Modelagem Molecular (LQC-MM), Departamento de Química Inorgânica, Instituto de Química, Universidade Federal Fluminense (UFF), Outeiro de São João Batista s/n, Campus do Valonguinho, Centro, Niterói 24020-141, Rio de Janeiro, Brazil
| | - Hélio F Dos Santos
- Núcleo de Estudos em Química Computacional (NEQC), Departamento de Química, ICE, Universidade Federal de Juiz de Fora (UFJF), Campus Universitário, Martelos, Juiz de Fora 36036-330, Minas Gerais, Brazil
| | - Wagner B De Almeida
- Laboratório de Química Computacional e Modelagem Molecular (LQC-MM), Departamento de Química Inorgânica, Instituto de Química, Universidade Federal Fluminense (UFF), Outeiro de São João Batista s/n, Campus do Valonguinho, Centro, Niterói 24020-141, Rio de Janeiro, Brazil
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6
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Bu C, Jin L. NMR Characterization of the Interactions Between Glycosaminoglycans and Proteins. Front Mol Biosci 2021; 8:646808. [PMID: 33796549 PMCID: PMC8007983 DOI: 10.3389/fmolb.2021.646808] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Accepted: 02/24/2021] [Indexed: 12/16/2022] Open
Abstract
Glycosaminoglycans (GAGs) constitute a considerable fraction of the glycoconjugates found on cellular membranes and in the extracellular matrix of virtually all mammalian tissues. The essential role of GAG-protein interactions in the regulation of physiological processes has been recognized for decades. However, the underlying molecular basis of these interactions has only emerged since 1990s. The binding specificity of GAGs is encoded in their primary structures, but ultimately depends on how their functional groups are presented to a protein in the three-dimensional space. This review focuses on the application of NMR spectroscopy on the characterization of the GAG-protein interactions. Examples of interpretation of the complex mechanism and characterization of structural motifs involved in the GAG-protein interactions are given. Selected families of GAG-binding proteins investigated using NMR are also described.
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Affiliation(s)
- Changkai Bu
- National Glycoengineering Research Center, Shandong Key Laboratory of Carbohydrate Chemistry and Glycobiology, Shandong University, Qingdao, China
| | - Lan Jin
- National Glycoengineering Research Center, Shandong Key Laboratory of Carbohydrate Chemistry and Glycobiology, Shandong University, Qingdao, China
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7
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Yao HYY, Wang JQ, Yin JY, Nie SP, Xie MY. A review of NMR analysis in polysaccharide structure and conformation: Progress, challenge and perspective. Food Res Int 2021; 143:110290. [PMID: 33992390 DOI: 10.1016/j.foodres.2021.110290] [Citation(s) in RCA: 137] [Impact Index Per Article: 45.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Revised: 02/28/2021] [Accepted: 02/28/2021] [Indexed: 12/31/2022]
Abstract
Nuclear magnetic resonance (NMR) has been widely used as an analytical chemistry technique to investigate the molecular structure and conformation of polysaccharides. Combined with 1D spectra, chemical shifts and coupling constants in both homo- and heteronuclear 2D NMR spectra are able to infer the linkage and sequence of sugar residues. Besides, NMR has also been applied in conformation, quantitative analysis, cell wall in situ, degradation, polysaccharide mixture interaction analysis, as well as carbohydrates impurities profiling. This review summarizes the principle and development of NMR in polysaccharides analysis, and provides NMR spectra data collections of some common polysaccharides. It will help to promote the application of NMR in complex polysaccharides of biochemical interest, and provide valuable information on commercial polysaccharide products.
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Affiliation(s)
- Hao-Ying-Ye Yao
- State Key Laboratory of Food Science and Technology, China-Canada Joint Lab of Food Science and Technology (Nanchang), Nanchang University, 235 Nanjing East Road, Nanchang 330047, China.
| | - Jun-Qiao Wang
- State Key Laboratory of Food Science and Technology, China-Canada Joint Lab of Food Science and Technology (Nanchang), Nanchang University, 235 Nanjing East Road, Nanchang 330047, China.
| | - Jun-Yi Yin
- State Key Laboratory of Food Science and Technology, China-Canada Joint Lab of Food Science and Technology (Nanchang), Nanchang University, 235 Nanjing East Road, Nanchang 330047, China.
| | - Shao-Ping Nie
- State Key Laboratory of Food Science and Technology, China-Canada Joint Lab of Food Science and Technology (Nanchang), Nanchang University, 235 Nanjing East Road, Nanchang 330047, China.
| | - Ming-Yong Xie
- State Key Laboratory of Food Science and Technology, China-Canada Joint Lab of Food Science and Technology (Nanchang), Nanchang University, 235 Nanjing East Road, Nanchang 330047, China; National R&D Center for Freshwater Fish Processing, Jiangxi Normal University, Nanchang, Jiangxi 330022, China.
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8
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Ray B, Schütz M, Mukherjee S, Jana S, Ray S, Marschall M. Exploiting the Amazing Diversity of Natural Source-Derived Polysaccharides: Modern Procedures of Isolation, Engineering, and Optimization of Antiviral Activities. Polymers (Basel) 2020; 13:E136. [PMID: 33396933 PMCID: PMC7794815 DOI: 10.3390/polym13010136] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 12/28/2020] [Accepted: 12/28/2020] [Indexed: 12/15/2022] Open
Abstract
Naturally occurring polysaccharide sulfates are highly diverse, owning variations in the backbone structure, linkage pattern and stereochemistry, branching diversity, sulfate content and positions of sulfate group(s). These structural characteristics bring about diverse sulfated polymers with dissimilar negative charge densities and structure-activity relationships. Herein, we start with a short discussion of techniques needed for extraction, purification, chemical sulfation, and structural characterization of polysaccharides. Processes of isolation and sulfation of plant-derived polysaccharides are challenging and usually involve two steps. In this context, we describe an integrated extraction-sulfation procedure that produces polysaccharide sulfates from natural products in one step, thereby generating additional pharmacological activities. Finally, we provide examples of the spectrum of natural source-derived polysaccharides possessing specific features of bioactivity, in particular focusing on current aspects of antiviral drug development and drug-target interaction. Thus, the review presents a detailed view on chemically engineered polysaccharides, especially sulfated derivatives, and underlines their promising biomedical perspectives.
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Affiliation(s)
- Bimalendu Ray
- Department of Chemistry, The University of Burdwan, Burdwan, West Bengal 713104, India; (B.R.); (S.M.); (S.J.)
| | - Martin Schütz
- Institute for Clinical and Molecular Virology, Friedrich-Alexander University (FAU) of Erlangen-Nürnberg, 91054 Erlangen, Germany;
| | - Shuvam Mukherjee
- Department of Chemistry, The University of Burdwan, Burdwan, West Bengal 713104, India; (B.R.); (S.M.); (S.J.)
| | - Subrata Jana
- Department of Chemistry, The University of Burdwan, Burdwan, West Bengal 713104, India; (B.R.); (S.M.); (S.J.)
| | - Sayani Ray
- Department of Chemistry, The University of Burdwan, Burdwan, West Bengal 713104, India; (B.R.); (S.M.); (S.J.)
| | - Manfred Marschall
- Department of Chemistry, The University of Burdwan, Burdwan, West Bengal 713104, India; (B.R.); (S.M.); (S.J.)
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9
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The conformation of the idopyranose ring revisited: How subtle O-substituent induced changes can be deduced from vicinal 1H-NMR coupling constants. Carbohydr Res 2020; 496:108052. [PMID: 32738719 DOI: 10.1016/j.carres.2020.108052] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 05/17/2020] [Accepted: 05/27/2020] [Indexed: 01/18/2023]
Abstract
The idopyranose ring plays a pivotal role in the conformational, dynamical, and intermolecular binding aspects of glycosaminoglycans like heparin and dermatan sulfate and it was early on assigned a role in the Sugar Code governing biological recognition processes. There is consensus that next to the two canonical 1C4 and 4C1 chair conformations, the conformational space accessible to the idopyranose ring entails a 2SO skew-boat conformation, but the equilibrium between these three ring puckers has evaded satisfactory quantification. In this study a meta-analysis of X-ray solid-state data and vicinal NMR coupling constants is presented, based on the Truncated Fourier Puckering (TFP) formalism and the generalized Karplus (CAGPLUS) equation. This approach yields a model-free, granular and consistent reckoning of 159 idopyranose solution puckering equilibria studied by NMR and allows us to reproduce the involved 636 NMR vicinal couplings with an overall residual RMS(Jobs-Jcalc) of 0.184 Hz. Our analyses show that for all ring systems examined, the idopyranosyl chair conformations take up the same ring pucker irrespective of the ring substituent pattern or a vast variety in experimental conditions. Instead, it is the (skew-)boat conformation that adapts to the substitution pattern of the idopyranose ring or a specific sulfation pattern of neighboring saccharides. All idopyranose rings are involved in conformational equilibria that subsume the aforementioned conformers which turn out to differ only a few kJ/mole in conformational energy. Thus, the plasticity and flexibility of idopyranose remains intact under practically all circumstances and, as the glycosidic linkages in heparin are considered to be relatively stiff, the iduronic moiety functions as the linchpin of heparin flexibility thereby being rather a "space(r)" than a "letter" in the alleged Sugar Code alphabet.
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10
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Wei J, Wu J, Tang Y, Ridgeway ME, Park MA, Costello CE, Zaia J, Lin C. Characterization and Quantification of Highly Sulfated Glycosaminoglycan Isomers by Gated-Trapped Ion Mobility Spectrometry Negative Electron Transfer Dissociation MS/MS. Anal Chem 2019; 91:2994-3001. [PMID: 30649866 DOI: 10.1021/acs.analchem.8b05283] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Glycosaminoglycans (GAGs) play vital roles in many biological processes and are naturally present as complex mixtures of polysaccharides with tremendous structural heterogeneity, including many structural isomers. Mass spectrometric analysis of GAG isomers, in particular highly sulfated heparin (Hep) and heparan sulfate (HS), is challenging because of their structural similarity and facile sulfo losses during analysis. Herein, we show that highly sulfated Hep/HS isomers may be resolved by gated-trapped ion mobility spectrometry (gated-TIMS) with negligible sulfo losses. Subsequent negative electron transfer dissociation (NETD) tandem mass spectrometry (MS/MS) analysis of TIMS-separated Hep/HS isomers generated extensive glycosidic and cross-ring fragments for confident isomer differentiation and structure elucidation. The high mobility resolution and preservation of labile sulfo modifications afforded by gated-TIMS MS analysis also allowed relative quantification of highly sulfated heparin isomers. These results show that the gated-TIMS-NETD MS/MS approach is useful for both qualitative and quantitative analysis of highly sulfated Hep/HS compounds in a manner not possible with other techniques.
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Affiliation(s)
- Juan Wei
- Center for Biomedical Mass Spectrometry , Boston University School of Medicine , Boston , Massachusetts 02118 , United States
| | - Jiandong Wu
- Center for Biomedical Mass Spectrometry , Boston University School of Medicine , Boston , Massachusetts 02118 , United States
| | - Yang Tang
- Center for Biomedical Mass Spectrometry , Boston University School of Medicine , Boston , Massachusetts 02118 , United States.,Department of Chemistry , Boston University , Boston , Massachusetts 02215 , United States
| | - Mark E Ridgeway
- Bruker Daltonics , Billerica , Massachusetts 01821 , United States
| | - Melvin A Park
- Bruker Daltonics , Billerica , Massachusetts 01821 , United States
| | - Catherine E Costello
- Center for Biomedical Mass Spectrometry , Boston University School of Medicine , Boston , Massachusetts 02118 , United States.,Department of Chemistry , Boston University , Boston , Massachusetts 02215 , United States
| | - Joseph Zaia
- Center for Biomedical Mass Spectrometry , Boston University School of Medicine , Boston , Massachusetts 02118 , United States
| | - Cheng Lin
- Center for Biomedical Mass Spectrometry , Boston University School of Medicine , Boston , Massachusetts 02118 , United States
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11
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Profant V, Johannessen C, Blanch EW, Bouř P, Baumruk V. Effects of sulfation and the environment on the structure of chondroitin sulfate studied via Raman optical activity. Phys Chem Chem Phys 2019; 21:7367-7377. [DOI: 10.1039/c9cp00472f] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Raman optical activity reflects differences in the secondary structure of chondroitin caused by its sulfation.
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Affiliation(s)
- Václav Profant
- Institute of Physics
- Faculty of Mathematics and Physics
- Charles University
- 121 16 Prague 2
- Czech Republic
| | | | | | - Petr Bouř
- Institute of Organic Chemistry and Biochemistry
- Academy of Sciences
- 166 10 Prague 6
- Czech Republic
| | - Vladimír Baumruk
- Institute of Physics
- Faculty of Mathematics and Physics
- Charles University
- 121 16 Prague 2
- Czech Republic
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12
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Hricovíni M, Hricovíni M. Solution Conformation of Heparin Tetrasaccharide. DFT Analysis of Structure and Spin⁻Spin Coupling Constants. Molecules 2018; 23:molecules23113042. [PMID: 30469334 PMCID: PMC6278409 DOI: 10.3390/molecules23113042] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 11/16/2018] [Accepted: 11/19/2018] [Indexed: 12/28/2022] Open
Abstract
Density functional theory (DFT) has provided detailed information on the molecular structure and spin⁻spin coupling constants of heparin tetrasaccharide (GlcNS,6S-IdoA2S-GlcNS,6S-IdoA2S-OMe) representing the predominant heparin repeating-sequence. The fully optimised molecular structures of two tetrasaccharide conformations (differing from each other in the conformational form of the sulphated iduronic acid residue⁻one ¹C₄ and the other ²S₀) were obtained using the B3LYP/6-311+G(d,p) level of theory and applying explicit water molecules to simulate the presence of a solvent. The theoretical data provided insight into variations of the bond lengths, bond angles and torsion angles, formations of intra- and intermolecular hydrogen bonds and ionic interactions. Optimised molecular structures indicated the formation of a complex hydrogen bond network, including interresidue and intraresidue bonds. The ionic interactions strongly influence the first hydration shell and, together with hydrogen bonds, play an important role in shaping the 3D tetrasaccharide structure. DFT-derived indirect three⁻bond proton⁻proton coupling constants (³JH-C-C-H) showed that the best agreement with experiment was obtained with a weighted average of 67:33 (¹C₄:²S₀) of the IdoA2S forms. Detailed analysis of Fermi-contact contributions to ³JH-C-C-H showed that important contributions arise from the oxygen lone pairs of neighbouring oxygen atoms. The analysis also showed that the magnitude of diamagnetic spin⁻orbit contributions are sufficiently large to determine the magnitude of some proton⁻proton coupling constants. The data highlight the need to use appropriate quantum-chemical calculations for a detailed understanding of the solution properties of heparin oligosaccharides.
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Affiliation(s)
- Miloš Hricovíni
- Institute of Chemistry, Slovak Academy of Sciences, 84538 Bratislava, Slovakia.
| | - Michal Hricovíni
- Institute of Chemistry, Slovak Academy of Sciences, 84538 Bratislava, Slovakia.
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13
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Zheng Z, Geng WC, Gao J, Mu YJ, Guo DS. Differential calixarene receptors create patterns that discriminate glycosaminoglycans. Org Chem Front 2018. [DOI: 10.1039/c8qo00606g] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
A well-designed fluorescence displacement sensing array based on calixarene receptors realizes the discrimination of glycosaminoglycans.
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Affiliation(s)
- Zhe Zheng
- College of Chemistry
- State Key Laboratory of Elemento-Organic Chemistry
- Key Laboratory of Functional Polymer Materials
- Ministry of Education
- Nankai University
| | - Wen-Chao Geng
- College of Chemistry
- State Key Laboratory of Elemento-Organic Chemistry
- Key Laboratory of Functional Polymer Materials
- Ministry of Education
- Nankai University
| | - Jie Gao
- College of Chemistry
- State Key Laboratory of Elemento-Organic Chemistry
- Key Laboratory of Functional Polymer Materials
- Ministry of Education
- Nankai University
| | - Yi-Jiang Mu
- College of Chemistry
- State Key Laboratory of Elemento-Organic Chemistry
- Key Laboratory of Functional Polymer Materials
- Ministry of Education
- Nankai University
| | - Dong-Sheng Guo
- College of Chemistry
- State Key Laboratory of Elemento-Organic Chemistry
- Key Laboratory of Functional Polymer Materials
- Ministry of Education
- Nankai University
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14
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Lacetera A, Berbís MÁ, Nurisso A, Jiménez-Barbero J, Martín-Santamaría S. Computational Chemistry Tools in Glycobiology: Modelling of Carbohydrate–Protein Interactions. COMPUTATIONAL TOOLS FOR CHEMICAL BIOLOGY 2017. [DOI: 10.1039/9781788010139-00145] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Molecular modelling provides a major impact in the field of glycosciences, helping in the characterisation of the molecular basis of the recognition between lectins from pathogens and human glycoconjugates, and in the design of glycocompounds with anti-infectious properties. The conformational properties of oligosaccharides are complex, and therefore, the simulation of these properties is a challenging task. Indeed, the development of suitable force fields is required for the proper simulation of important problems in glycobiology, such as the interatomic interactions responsible for oligosaccharide and glycoprotein dynamics, including O-linkages in oligo- and polysaccharides, and N- and O-linkages in glycoproteins. The computational description of representative examples is discussed, herein, related to biologically active oligosaccharides and their interaction with lectins and other proteins, and the new routes open for the design of glycocompounds with promising biological activities.
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Affiliation(s)
- Alessandra Lacetera
- Center for Biological Research CIB-CSIC. Ramiro de Maeztu, 9 28040-Madrid Spain
| | - M. Álvaro Berbís
- Center for Biological Research CIB-CSIC. Ramiro de Maeztu, 9 28040-Madrid Spain
| | - Alessandra Nurisso
- School of Pharmaceutical Sciences University of Geneva, University of Lausanne, Rue Michel Servet 1 CH-1211 Geneva 4 Switzerland
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15
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Paradigms in the structural biology of the mitogenic ternary complex FGF:FGFR:heparin. Biochimie 2016; 127:214-26. [DOI: 10.1016/j.biochi.2016.05.017] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2016] [Accepted: 05/29/2016] [Indexed: 11/20/2022]
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16
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Abstract
High-resolution NMR and density functional theory (DFT) calculations have been applied to analysis of heparin pentasaccharide 3D structure in aqueous solution. The fully optimized molecular geometry of two pentasaccharide conformations (differing from each other in the form, one (1)C4 and the other (2)S0, of the sulfated iduronic acid residue) were obtained using the B3LYP/6-311+G(d,p) level of theory in the presence of solvent, the latter included as explicit water molecules. The presented approach enabled insight into variations of the bond lengths, bond angles, and torsion angles, formations of intra- and intermolecular hydrogen bonds, and ionic interactions in the two pentasaccharide conformations. A rather complex hydrogen bond network is formed, including inter-residue and intraresidue bonds between the NH group in the GlcN,3,6S with oxygens linked to C-2 at the IdoA2S residue and the glycosidic O-1 and the neighboring OSO3(-) group linked to C-3 in the same residue. On the other hand, because the first hydration shell is strongly influenced by strong ion-ion and ion-dipole interactions between sodium ions, sulfates, carboxylates, and -OH groups, ionic interactions play an important role in the stabilization of the 3D structure. The DFT-computed three-bond proton-proton coupling constants also showed that best agreement with experiment was obtained with a weighted average of 15:85 ((1)C4/(2)S0) of the sulfated iduronic acid forms indicating that the ratio is even more shifted toward the (2)S0 form than previously supposed. The DFT-computed pentasaccharide conformation differs from the previously published data, with the main changes at the glycosidic linkages, namely, the ψ1 torsion angles and the ϕ3 angle. The comparison of the glycosidic linkage torsion angle values in solution with the antithrombin-pentasaccharide complex also indicates that the pentasaccharide conformation changes upon binding to antithrombin III. The data supports the assumption that the protein selects the more populated (2)S0 conformer of heparin pentasaccharide and, consequently, the binding process of heparin pentasaccharide with antithrombin III is energetically more favorable than formerly expected.
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Affiliation(s)
- Miloš Hricovíni
- Institute of Chemistry, Slovak Academy of Sciences , 845 38 Bratislava, Slovakia
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17
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Faller CE, Guvench O. Sulfation and cation effects on the conformational properties of the glycan backbone of chondroitin sulfate disaccharides. J Phys Chem B 2015; 119:6063-73. [PMID: 25906376 DOI: 10.1021/jp511431q] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Chondroitin sulfate (CS) is one of several glycosaminoglycans that are major components of proteoglycans. A linear polymer consisting of repeats of the disaccharide -4GlcAβ1-3GalNAcβ1-, CS undergoes differential sulfation resulting in five unique sulfation patterns. Because of the dimer repeat, the CS glycosidic "backbone" has two distinct sets of conformational degrees of freedom defined by pairs of dihedral angles: (ϕ1, ψ1) about the β1-3 glycosidic linkage and (ϕ2, ψ2) about the β1-4 glycosidic linkage. Differential sulfation and the possibility of cation binding, combined with the conformational flexibility and biological diversity of CS, complicate experimental efforts to understand CS three-dimensional structures at atomic resolution. Therefore, all-atom explicit-solvent molecular dynamics simulations with Adaptive Biasing Force sampling of the CS backbone were applied to obtain high-resolution, high-precision free energies of CS disaccharides as a function of all possible backbone geometries. All 10 disaccharides (β1-3 vs β1-4 linkage × five different sulfation patterns) were studied; additionally, ion effects were investigated by considering each disaccharide in the presence of either neutralizing sodium or calcium cations. GlcAβ1-3GalNAc disaccharides have a single, broad, thermodynamically important free-energy minimum, whereas GalNAcβ1-4GlcA disaccharides have two such minima. Calcium cations but not sodium cations bind to the disaccharides, and binding is primarily to the GlcA -COO(-) moiety as opposed to sulfate groups. This binding alters the glycan backbone thermodynamics in instances where a calcium cation bound to -COO(-) can act to bridge and stabilize an interaction with an adjacent sulfate group, whereas, in the absence of this cation, the proximity of a sulfate group to -COO(-) results in two like charges being both desolvated and placed adjacent to each other and is found to be destabilizing. In addition to providing information on sulfation and cation effects, the present results can be applied to building models of CS polymers and as a point of comparison in studies of CS polymer backbone dynamics and thermodynamics.
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Affiliation(s)
- Christina E Faller
- Department of Pharmaceutical Sciences, University of New England College of Pharmacy, 716 Stevens Avenue, Portland, Maine 04103, United States
| | - Olgun Guvench
- Department of Pharmaceutical Sciences, University of New England College of Pharmacy, 716 Stevens Avenue, Portland, Maine 04103, United States
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18
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Queiroz INL, Wang X, Glushka JN, Santos GRC, Valente AP, Prestegard JH, Woods RJ, Mourão PAS, Pomin VH. Impact of sulfation pattern on the conformation and dynamics of sulfated fucan oligosaccharides as revealed by NMR and MD. Glycobiology 2014; 25:535-47. [PMID: 25527427 DOI: 10.1093/glycob/cwu184] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Sulfated fucans from sea urchin egg jelly express well-defined chemical structures that vary with species. This species specificity regulates the sperm acrosome reaction, a critical step to assure intra-specific fertilization. In addition, these polysaccharides are involved in other biological activities such as anticoagulation. Although sulfation patterns are relevant to the levels of response in both activities, conformation and dynamics of these glycans are also contributing factors. However, data about these features of sulfated fucans are very rare. To address this, we have employed nuclear magnetic resonance experiments combined with molecular dynamics on structurally defined oligosaccharides derived from two sulfated fucans. The results have indicated that the oligosaccharides are flexible in solution. Ring conformation of their composing units displays just the (1)C4 chair configuration. In a particular octasaccharide, composed of two tetrasaccharide sequences, inter-residual hydrogen bonds play a role to decrease dynamics in these repeating units. Conversely, the linking disaccharide [-3)-α-L-Fucp-2(OSO3(-))-(1-3)-α-L-Fucp-4(OCO3(-))-(1-] located right between the two tetrasaccharide units has amplified motions suggested to be promoted by electrostatic repulsion of sulfates on opposite sides of the central glycosidic bond. This conjunction of information about conformation and dynamics of sulfated fucan oligosaccharides provides new insights to explain how these glycans behave free in solution and influenced by sulfation patterns. It may also serve for future studies concerning structure-function relationship of sulfated fucans, especially those involving sea urchin fertilization and anticoagulation.
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Affiliation(s)
- Ismael N L Queiroz
- Programa de Glicobiologia, Instituto de Bioquímica Médica Leopoldo de Meis, and Hospital Universitário Clementino Fraga Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941-913, Brazil
| | - Xiaocong Wang
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA
| | - John N Glushka
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA
| | - Gustavo R C Santos
- Programa de Glicobiologia, Instituto de Bioquímica Médica Leopoldo de Meis, and Hospital Universitário Clementino Fraga Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941-913, Brazil
| | - Ana P Valente
- Centro Nacional de Ressonância Nuclear Magnética de Macromoléculas, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941-902, Brasil
| | - James H Prestegard
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA
| | - Robert J Woods
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA
| | - Paulo A S Mourão
- Programa de Glicobiologia, Instituto de Bioquímica Médica Leopoldo de Meis, and Hospital Universitário Clementino Fraga Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941-913, Brazil
| | - Vitor H Pomin
- Programa de Glicobiologia, Instituto de Bioquímica Médica Leopoldo de Meis, and Hospital Universitário Clementino Fraga Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941-913, Brazil
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19
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Structural and functional analyses of bovine and porcine intestinal heparins confirm they are different drugs. Drug Discov Today 2014; 19:1801-1807. [DOI: 10.1016/j.drudis.2014.07.004] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2014] [Revised: 06/19/2014] [Accepted: 07/07/2014] [Indexed: 11/23/2022]
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20
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Pomin VH. Keratan sulfate: an up-to-date review. Int J Biol Macromol 2014; 72:282-9. [PMID: 25179279 DOI: 10.1016/j.ijbiomac.2014.08.029] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Revised: 08/20/2014] [Accepted: 08/23/2014] [Indexed: 02/01/2023]
Abstract
Keratan sulfate (KS) is a glycosaminoglycan (GAG) type consisted of a sulfated poly-N-acetyl lactosamine chain. Besides acting as a constitutive molecule of the extracellular matrices, this GAG also plays a role as a hydrating and signaling agent in cornea and cartilage tissues. Inasmuch, KS is widely explored in the pharmaceutical industry. This review will cover the major achievements described in the literature of 2010-2014 concerning this GAG. Discussion about KS' roles in physiopathological conditions, as target or therapeutic molecule in diseases, methods of analysis and detection as well as KS-related enzymes, metabolism and developmental biology is properly provided.
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Affiliation(s)
- Vitor H Pomin
- Program of Glycobiology, Institute of Medical Biochemistry Leopoldo de Meis, and University Hospital Clementino Fraga Filho, Federal University of Rio de Janeiro, Rio de Janeiro, RJ 21941-913, Brazil.
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21
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Abstract
Dynamical behaviors of glycosaminoglycans, as here illustrated with a hyaluronan oligosaccharide, are key regulators of biological functions.
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Affiliation(s)
- Vitor H. Pomin
- Program of Glycobiology
- Institute of Medical Biochemistry Leopoldo de Meis, and University Hospital Clementino Fraga Filho
- Federal University of Rio de Janeiro
- Rio de Janeiro, Brazil
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