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Guvench O. Atomic-Resolution Experimental Structural Biology and Molecular Dynamics Simulations of Hyaluronan and Its Complexes. Molecules 2022; 27:7276. [PMID: 36364098 PMCID: PMC9658939 DOI: 10.3390/molecules27217276] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 10/20/2022] [Accepted: 10/21/2022] [Indexed: 11/28/2023] Open
Abstract
This review summarizes the atomic-resolution structural biology of hyaluronan and its complexes available in the Protein Data Bank, as well as published studies of atomic-resolution explicit-solvent molecular dynamics simulations on these and other hyaluronan and hyaluronan-containing systems. Advances in accurate molecular mechanics force fields, simulation methods and software, and computer hardware have supported a recent flourish in such simulations, such that the simulation publications now outnumber the structural biology publications by an order of magnitude. In addition to supplementing the experimental structural biology with computed dynamic and thermodynamic information, the molecular dynamics studies provide a wealth of atomic-resolution information on hyaluronan-containing systems for which there is no atomic-resolution structural biology either available or possible. Examples of these summarized in this review include hyaluronan pairing with other hyaluronan molecules and glycosaminoglycans, with ions, with proteins and peptides, with lipids, and with drugs and drug-like molecules. Despite limitations imposed by present-day computing resources on system size and simulation timescale, atomic-resolution explicit-solvent molecular dynamics simulations have been able to contribute significant insight into hyaluronan's flexibility and capacity for intra- and intermolecular non-covalent interactions.
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Affiliation(s)
- Olgun Guvench
- Department of Pharmaceutical Sciences and Administration, School of Pharmacy, Westbrook College of Health Professions, University of New England, 716 Stevens Avenue, Portland, ME 04103, USA
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2
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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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3
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Boni FI, Cury BSF, Ferreira NN, Teixeira DA, Gremião MPD. Computational and experimental approaches for chitosan-based nano PECs design: Insights on a deeper comprehension of nanostructure formation. Carbohydr Polym 2021; 254:117444. [PMID: 33357914 DOI: 10.1016/j.carbpol.2020.117444] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 11/17/2020] [Accepted: 11/23/2020] [Indexed: 01/09/2023]
Abstract
Nanostructured polyelectrolyte complexes (nano PECs) based on biopolymers are an important technological strategy to target drugs to the action and/or absorption site in a more effective way. In this work, computational studies were performed to predict the ionization, spatial arrangement and interaction energies of chitosan (CS), hyaluronic acid (HA), and hypromellose phthalate (HP), for the design of nano PEC carriers for methotrexate (MTX). The optimal pH range (5.0-5.5) for preparing nano PECs was selected by experimental and computational methodologies, favoring the polymers interactions. CS, HA, HP and MTX addition order was also rationalized, maximizing their interactions and MTX entrapment. Spherical nano-sized particles (256-575 nm, by dynamic light scattering measurement) with positive surface charge (+25.5 to +29.2 mV) were successfully prepared. The MTX association efficiency ranged from 20 to 32 %. XRD analyses evidenced the formation of a new material with an organized structure, in relation to raw polymers.
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Affiliation(s)
- Fernanda Isadora Boni
- School of Pharmaceutical Sciences, São Paulo State University (UNESP), Araraquara, Road Araraquara-Jaú, Km 01, 14801-902, Araraquara, São Paulo, Brazil.
| | - Beatriz Stringhetti Ferreira Cury
- School of Pharmaceutical Sciences, São Paulo State University (UNESP), Araraquara, Road Araraquara-Jaú, Km 01, 14801-902, Araraquara, São Paulo, Brazil.
| | - Natália Noronha Ferreira
- School of Pharmaceutical Sciences, São Paulo State University (UNESP), Araraquara, Road Araraquara-Jaú, Km 01, 14801-902, Araraquara, São Paulo, Brazil.
| | - Deiver Alessandro Teixeira
- Federal Institute of Mato Grosso (IFMT), Cuiabá Campus, Bela Vista, Juliano Costa Marques Avenue, 78050-560, Cuiabá, Mato Grosso, Brazil.
| | - Maria Palmira Daflon Gremião
- School of Pharmaceutical Sciences, São Paulo State University (UNESP), Araraquara, Road Araraquara-Jaú, Km 01, 14801-902, Araraquara, São Paulo, Brazil.
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4
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Whitmore EK, Martin D, Guvench O. Constructing 3-Dimensional Atomic-Resolution Models of Nonsulfated Glycosaminoglycans with Arbitrary Lengths Using Conformations from Molecular Dynamics. Int J Mol Sci 2020; 21:ijms21207699. [PMID: 33080973 PMCID: PMC7589010 DOI: 10.3390/ijms21207699] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 10/15/2020] [Accepted: 10/15/2020] [Indexed: 12/24/2022] Open
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 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.
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Affiliation(s)
- Elizabeth K. Whitmore
- Department of Pharmaceutical Sciences and Administration, University of New England School of Pharmacy, 716 Stevens Avenue, Portland, ME 04103, USA; (E.K.W.); (D.M.)
- 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, University of New England School of Pharmacy, 716 Stevens Avenue, Portland, ME 04103, USA; (E.K.W.); (D.M.)
- Graduate School of Biomedical Science and Engineering, University of Maine, 5775 Stodder Hall, Orono, ME 04469, USA
| | - Olgun Guvench
- Department of Pharmaceutical Sciences and Administration, University of New England School of Pharmacy, 716 Stevens Avenue, Portland, ME 04103, USA; (E.K.W.); (D.M.)
- Graduate School of Biomedical Science and Engineering, University of Maine, 5775 Stodder Hall, Orono, ME 04469, USA
- Correspondence: ; Tel.: +1-207-221-4171
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5
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Effect of aggrecan degradation on the nanomechanics of hyaluronan in extra-fibrillar matrix of annulus fibrosus: A molecular dynamics investigation. J Mech Behav Biomed Mater 2020; 107:103752. [PMID: 32278311 DOI: 10.1016/j.jmbbm.2020.103752] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 03/18/2020] [Accepted: 03/20/2020] [Indexed: 12/19/2022]
Abstract
Intervertebral Disc (IVD) Degeneration is one of the primary causes of low back pain among the adult population - the most significant cause being the degradation of aggrecan present in the extra-fibrillar matrix (EFM). Aggrecan degradation is closely associated with loss of water content leading to an alteration in the mechanical behaviour of the IVD. The loss in water content has a significant impact on the chemo-mechanical interplay of IVD biochemical constituents at the fundamental level. This work presents a mechanistic understanding of the effect of hydration, closely associated with aggrecan degradation, on the nanoscale mechanical behaviour of the hyaluronan present in the EFM of the Annulus Fibrosus. For this purpose, explicit three-dimensional molecular dynamics analyses of tensile and compressive tests are performed on a representative atomistic model of the hyaluronan present in the EFM. To account for the degradation of aggrecan, hydration levels are varied from 0 to 75% by weight of water. Analyses show that an increase in the hydration levels decreases the elastic modulus of hyaluronan in tension from ~4.6 GPa to ~2.1 GPa. On the other hand, the increase in hydration level increases the elastic moduli in axial compression from ~1.6 GPa in un-hydrated condition to ~6 GPa in 50% hydrated condition. But as the hydration levels increase to 75%, the elastic modulus reduces to ~3.5 GPa signifying a shift in load-bearing characteristic, from the solid hyaluronan component to the fluid component. Furthermore, analyses show a reduction in the intermolecular energy between hyaluronan and water, under axial tensile loading, indicating a nanoscale intermolecular debonding between hyaluronan and water molecules. This is attributed to the ability of hyaluronan to form stabilizing intra-molecular hydrogen bonds between adjacent residues. Compressive loading, on the other hand, causes intensive coiling of hyaluronan molecule, which traps more water through hydrogen bonding and aids in bearing compressive loads. Overall, study shows that hydration level has a strong influence on the atomistic level interactions between hyaluronan molecules and hyaluronan and water molecules in the EFM which influences the nanoscale mechanics of the Annulus Fibrosus.
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Payne WM, Svechkarev D, Kyrychenko A, Mohs AM. The role of hydrophobic modification on hyaluronic acid dynamics and self-assembly. Carbohydr Polym 2018; 182:132-141. [PMID: 29279107 PMCID: PMC5748244 DOI: 10.1016/j.carbpol.2017.10.054] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Revised: 09/28/2017] [Accepted: 10/13/2017] [Indexed: 01/02/2023]
Abstract
The advent of nanomedicine has rejuvenated the need for increased understanding of the fundamental physicochemical properties of polymeric amphiphiles. Hyaluronic acid (HA) is a hydrophilic polysaccharide that is frequently conjugated to hydrophobic moieties and then used to entrap dyes and therapeutics. Here, we develop computational models to examine the effects of the hydrophobic modification on supramolecular behavior among three systematically designed HA derivatives substituted with alkyl chains of increasing length. Our simulations coalesce with experimentally obtained results to demonstrate the dependence of supramolecular behavior on intramolecular forces. We show that the formation of clearly defined hydrophobic domains in samples of octadecylamine-modified HA compared to HA conjugates with shorter alkyl chains is a result of more favorable hydrophobic interactions. Trends in hydrodynamic radius and polydispersity are observed in experimental results that coalesce with theoretical calculations, suggesting that supramolecular properties are dependent on the physicochemical characteristics of individual polymer strands.
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Affiliation(s)
- William M Payne
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, 986858 Nebraska Medical Center, Omaha, NE 68198-6858, United States.
| | - Denis Svechkarev
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, 986858 Nebraska Medical Center, Omaha, NE 68198-6858, United States.
| | - Alexander Kyrychenko
- Institute for Chemistry, V. N. Karazin Kharkiv National University, 4 Svobody Square, 61022 Kharkiv, Ukraine.
| | - Aaron M Mohs
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, 986858 Nebraska Medical Center, Omaha, NE 68198-6858, United States; Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, 986858 Nebraska Medical Center, Omaha, NE 68198-6858, United States; Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, 986858 Nebraska Medical Center, Omaha, NE 68198-6858, United States.
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7
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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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8
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Reller M, Wesp S, Koos MRM, Reggelin M, Luy B. Biphasic Liquid Crystal and the Simultaneous Measurement of Isotropic and Anisotropic Parameters by Spatially Resolved NMR Spectroscopy. Chemistry 2017. [DOI: 10.1002/chem.201702126] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Malin Reller
- Institut für Organische Chemie and Institut für Biologische Grenzflächen 4 - Magnetische Resonanz; Karlsruher Institut für Technologie (KIT); Fritz-Haber-Weg 6 76131 Karlsruhe Germany
| | - Svenja Wesp
- Organische Chemie; Technische Universität Darmstadt; Alarich-Weiss Str. 4 64287 Darmstadt Germany
| | - Martin R. M. Koos
- Institut für Organische Chemie and Institut für Biologische Grenzflächen 4 - Magnetische Resonanz; Karlsruher Institut für Technologie (KIT); Fritz-Haber-Weg 6 76131 Karlsruhe Germany
| | - Michael Reggelin
- Organische Chemie; Technische Universität Darmstadt; Alarich-Weiss Str. 4 64287 Darmstadt Germany
| | - Burkhard Luy
- Institut für Organische Chemie and Institut für Biologische Grenzflächen 4 - Magnetische Resonanz; Karlsruher Institut für Technologie (KIT); Fritz-Haber-Weg 6 76131 Karlsruhe Germany
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9
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Tzvetkova P, Luy B. Q.E.COSY: determining sign and size of small deuterium residual quadrupolar couplings using an extended E.COSY principle. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2016; 54:351-357. [PMID: 26763050 DOI: 10.1002/mrc.4386] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Revised: 09/30/2015] [Accepted: 10/23/2015] [Indexed: 06/05/2023]
Abstract
Residual quadrupolar couplings contain important structural information comparable with residual dipolar couplings. However, the measurement of sign and size of especially small residual quadrupolar couplings is difficult. Here, we present an extension of the E.COSY principle to spin systems consisting of a Spin 1 coupled to a spin ½ nucleus, which allows the determination of the sign of the quadrupolar coupling of the Spin 1 nucleus relative to the heteronuclear coupling between the spins. The so-called Q.E.COSY approach is demonstrated with its sign-sensitivity using variable angle NMR, stretched gels and liquid crystalline phases applied to various CD and CD3 groups. Especially the sign-sensitive measurement of residual quadrupolar couplings that remain unresolved in conventional deuterium 1D spectra is shown.
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Affiliation(s)
- Pavleta Tzvetkova
- Institute of Organic Chemistry and Institute for Biological Interfaces 4 - Magnetic Resonance, Fritz-Haber-Weg 6, 76131, Karlsruhe, Germany
| | - Burkhard Luy
- Institute of Organic Chemistry and Institute for Biological Interfaces 4 - Magnetic Resonance, Fritz-Haber-Weg 6, 76131, Karlsruhe, Germany
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10
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Tobata H, Sagawa T. Specific excitonic interactions in the aggregates of hyaluronic acid and cyanine dyes with different lengths of methine group. Photochem Photobiol Sci 2016; 15:329-33. [PMID: 26815728 DOI: 10.1039/c5pp00343a] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The absorption and circular dichroism (CD) spectra of three types of cyanine dyes with different lengths of methine group (3,3'-diethylthiadicarbocyanine iodide, DTDC; 3,3'-diethylthiacarbocyanine iodide, DTC; and 3,3'-diethylthiacyanine iodide, DTTHC) in an aqueous solution were compared with and without hyaluronic acid (HA), which has a helical structure. DTDC forms chiral H- and J-aggregates, whereas DTC and DTTHC are unable to form any aggregates. DTDC also forms H- and J-aggregates in the presence of sodium polyacrylate (PA) with a random-coil structure; however, the PA-DTDC aggregates exhibit no chirality. These results suggest that the chirality of HA-DTDC aggregates is induced by the helical structure of HA. In 2.4 vol% and 10 vol% methanol, HA-DTDC aggregates displayed different patterns of temperature dependence, whereas no aggregation was observed in 30 vol% methanol. The solubility of DTDC in a mixed solvent of water and methanol is generally improved by the addition of methanol, which prevents the aggregation of DTDC.
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Affiliation(s)
- H Tobata
- Graduate School of Energy Science, Kyoto University, Yoshida-Honmachi, Sakyo-Ku, Kyoto 606-8501, Japan.
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11
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Cilurzo F, Vistoli G, Gennari CGM, Selmin F, Gardoni F, Franzè S, Campisi M, Minghetti P. The Role of the Conformational Profile of Polysaccharides on Skin Penetration: The Case of Hyaluronan and Its Sulfates. Chem Biodivers 2014; 11:551-61. [DOI: 10.1002/cbdv.201300130] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2013] [Indexed: 11/09/2022]
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12
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Solution NMR conformation of glycosaminoglycans. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2014; 114:61-8. [DOI: 10.1016/j.pbiomolbio.2014.01.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2013] [Revised: 01/10/2014] [Accepted: 01/17/2014] [Indexed: 11/18/2022]
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13
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Sletmoen M, Stokke BT. Structure-Function Relationships in Glycopolymers: Effects of Residue Sequences, Duplex, and Triplex Organization. Biopolymers 2013; 99:757-71. [DOI: 10.1002/bip.22320] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2013] [Accepted: 06/07/2013] [Indexed: 12/18/2022]
Affiliation(s)
- Marit Sletmoen
- Biophysics and Medical Technology, Department of Physics, The Norwegian University of Science and Technology; Trondheim; Norway
| | - Bjørn Torger Stokke
- Biophysics and Medical Technology, Department of Physics, The Norwegian University of Science and Technology; Trondheim; Norway
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14
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Development and characterization of novel alginate-based hydrogels as vehicles for bone substitutes. Carbohydr Polym 2013; 95:134-42. [DOI: 10.1016/j.carbpol.2013.02.067] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2012] [Revised: 02/17/2013] [Accepted: 02/27/2013] [Indexed: 02/06/2023]
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15
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Canales A, Jiménez-Barbero J, Martín-Pastor M. Review: Use of residual dipolar couplings to determine the structure of carbohydrates. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2012; 50 Suppl 1:S80-S85. [PMID: 23280664 DOI: 10.1002/mrc.3888] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2012] [Revised: 09/08/2012] [Accepted: 09/20/2012] [Indexed: 05/28/2023]
Abstract
Solution nuclear magnetic resonance spectroscopy is especially useful in the carbohydrate field. The measurement of residual dipolar couplings provides long-range structural information, a valuable complement for the structural study of carbohydrates either in its free form or in the bound state to proteins. They permit to deduce the geometry and the flexibility of the glycosidic linkages, which have a major influence on the conformation of carbohydrates and their overall shape. This article reviews the current application of the residual dipolar couplings methodology to carbohydrates.
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Affiliation(s)
- A Canales
- Department Organic Chemistry, Universidad Complutense de Madrid, Madrid, Spain
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16
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Przybylski C, Gonnet F, Buchmann W, Daniel R. Critical parameters for the analysis of anionic oligosaccharides by desorption electrospray ionization mass spectrometry. JOURNAL OF MASS SPECTROMETRY : JMS 2012; 47:1047-1058. [PMID: 22899514 DOI: 10.1002/jms.3052] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Sulfated oligosaccharides derived from glycosaminoglycans (GAGs) are fragile compounds, highly polar and anionic. We report here on the rare but successful application of desorption electrospray ionization (DESI) - LTQ-Orbitrap mass spectrometry (MS) to the high-resolution analysis of anionic and sulfated oligosaccharides derived from the GAGs hyaluronic acid and heparin. For that purpose, key parameters affecting DESI performance, comprising the geometric parameters of the DESI source, the probed surface and the spraying conditions, applied spray voltage, flow rates and solvent composition were investigated. Under suitable conditions, the DESI technique allows the preservation of the structural integrity of such fragile compounds. DESI enabled the sensitive detection of anionic hyaluronic acid and heparin oligosaccharides with a limit of detection (LOD) down to 5 fmol (≈10 pg) for the hyaluronic acid decasaccharide. Detection of hyaluronic acid oligosaccharides in urine sample was also successfully achieved with LOD values inferior to the ng range. Multistage tandem mass spectrometry (MS(n) ) through the combination of the DESI source with a hybrid linear ion trap-orbitrap mass spectrometer allowed the discrimination of isomeric sulfated oligosaccharides and the sequence determination of a hyaluronic acid decasaccharide. These results open promising ways in glycomic and glycobiology fields where structure-activity relationships of bioactive carbohydrates are currently questioned.
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Affiliation(s)
- Cédric Przybylski
- CNRS UMR 8587, Laboratoire Analyse et Modélisation pour la Biologie et l'Environnement, F-91025, Evry, France
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17
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Attili S, Borisov OV, Richter RP. Films of End-Grafted Hyaluronan Are a Prototype of a Brush of a Strongly Charged, Semiflexible Polyelectrolyte with Intrinsic Excluded Volume. Biomacromolecules 2012; 13:1466-77. [DOI: 10.1021/bm3001759] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Seetharamaiah Attili
- Biosurfaces Unit, CIC biomaGUNE, Paseo Miramon 182, 20009
Donostia - San Sebastian, Spain
- Max-Planck-Institute for Intelligent Systems, Heisenbergstrasse 3, 70569
Stuttgart, Germany
| | - Oleg V. Borisov
- Institut Pluridisciplinaire de Recherche sur l’Environnement et les Matériaux, UMR 5254 CNRS UPPA, 2 Avenue Pierre Angot, 64053 Pau, France
| | - Ralf P. Richter
- Biosurfaces Unit, CIC biomaGUNE, Paseo Miramon 182, 20009
Donostia - San Sebastian, Spain
- Max-Planck-Institute for Intelligent Systems, Heisenbergstrasse 3, 70569
Stuttgart, Germany
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18
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Schmidt M, Sun H, Rogne P, Scriba GKE, Griesinger C, Kuhn LT, Reinscheid UM. Determining the Absolute Configuration of (+)-Mefloquine HCl, the Side-Effect-Reducing Enantiomer of the Antimalaria Drug Lariam. J Am Chem Soc 2012; 134:3080-3. [DOI: 10.1021/ja209050k] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Manuel Schmidt
- Department of NMR-Based Structural
Biology, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Han Sun
- Department of NMR-Based Structural
Biology, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Per Rogne
- European Neuroscience Institute Göttingen (ENI-G), Grisebachstraße
5, 37077 Göttingen, Germany
- DFG Research Center Molecular Physiology of the Brain (CMPB) and Cluster
of Excellence 171 “Microscopy at the Nanometer
Range”, Göttingen, Germany
| | - Gerhard K. E. Scriba
- Department of Pharmaceutical
Chemistry, University of Jena, Philosophenweg
14, 07743 Jena, Germany
| | - Christian Griesinger
- Department of NMR-Based Structural
Biology, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Lars T. Kuhn
- European Neuroscience Institute Göttingen (ENI-G), Grisebachstraße
5, 37077 Göttingen, Germany
- DFG Research Center Molecular Physiology of the Brain (CMPB) and Cluster
of Excellence 171 “Microscopy at the Nanometer
Range”, Göttingen, Germany
| | - Uwe M. Reinscheid
- Department of NMR-Based Structural
Biology, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
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Plazinski W, Knys-Dzieciuch A. Interactions between CD44 protein and hyaluronan: insights from the computational study. ACTA ACUST UNITED AC 2012; 8:543-7. [DOI: 10.1039/c2mb05399c] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Säwén E, Stevensson B, Ostervall J, Maliniak A, Widmalm G. Molecular conformations in the pentasaccharide LNF-1 derived from NMR spectroscopy and molecular dynamics simulations. J Phys Chem B 2011; 115:7109-21. [PMID: 21545157 DOI: 10.1021/jp2017105] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The conformational dynamics of the human milk oligosaccharide lacto-N-fucopentaose (LNF-1), α-L-Fucp-(1 → 2)-β-D-Galp-(1 → 3)-β-D-GlcpNAc-(1 → 3)-β-D-Galp-(1 → 4)-D-Glcp, has been analyzed using NMR spectroscopy and molecular dynamics (MD) computer simulations. Employing the Hadamard (13)C-excitation technique and the J-HMBC experiment, (1)H,(13)C trans-glycosidic J coupling constants were obtained, and from one- and two-dimensional (1)H,(1)H T-ROESY experiments, proton-proton cross-relaxation rates were determined in isotropic D(2)O solution. In the lyotropic liquid-crystalline medium consisting of ditetradecylphosphatidylcholine, dihexylphosphatidylcholine, N-cetyl-N,N,N-trimethylammonium bromide, and D(2)O, (1)H, (1)H and one-bond (1)H, (13)C residual dipolar couplings (RDCs), as well as relative sign information on homonuclear RDCs, were determined for the pentasaccharide. Molecular dynamics simulations with explicit water were carried out from which the internal isomerization relaxation time constant, τ(N), was calculated for transitions at the ψ torsion angle of the β-(1 → 3) linkage to the lactosyl group in LNF-1. Compared to the global reorientation time, τ(M), of ∼0.6 ns determined experimentally in D(2)O solution, the time constant for the isomerization relaxation process, τ(N(scaled)), is about one-third as large. The NMR parameters derived from the isotropic solution show very good agreement with those calculated from the MD simulations. The only notable difference occurs at the reducing end, which should be more flexible than observed by the molecular simulation, a conclusion in complete agreement with previous (13)C NMR relaxation data. A hydrogen-bond analysis of the MD simulation revealed that inter-residue hydrogen bonds on the order of ∼30% were present across the glycosidic linkages to sugar ring oxygens. This finding highlights that intramolecular hydrogen bonds might be important in preserving well-defined structures in otherwise flexible molecules. An analysis including generalized order parameters obtained from nuclear spin relaxation experiments was performed and successfully shown to limit the conformational space accessible to the molecule when the number of experimental data are too scarce for a complete conformational analysis.
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Affiliation(s)
- Elin Säwén
- Department of Organic Chemistry, Stockholm University, Stockholm, Sweden
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Roldós V, Cañada FJ, Jiménez-Barbero J. Carbohydrate-Protein Interactions: A 3D View by NMR. Chembiochem 2011; 12:990-1005. [DOI: 10.1002/cbic.201000705] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2010] [Indexed: 12/29/2022]
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