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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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Molecular dynamics simulations to understand glycosaminoglycan interactions in the free- and protein-bound states. Curr Opin Struct Biol 2022; 74:102356. [DOI: 10.1016/j.sbi.2022.102356] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 02/08/2022] [Accepted: 02/13/2022] [Indexed: 11/18/2022]
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3
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Roy R, Jonniya NA, Kar P. Effect of Sulfation on the Conformational Dynamics of Dermatan Sulfate Glycosaminoglycan: A Gaussian Accelerated Molecular Dynamics Study. J Phys Chem B 2022; 126:3852-3866. [PMID: 35594147 DOI: 10.1021/acs.jpcb.2c01807] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Glycosaminoglycans (GAGs) are anionic biopolymers present on cell surfaces as a part of proteoglycans. The biological activities of GAGs depend on the sulfation pattern. In our study, we have considered three octadecasaccharide dermatan sulfate (DS) chains with increasing order of sulfation (dp6s, dp7s, and dp12s) to illuminate the role of sulfation on the GAG units and its chain conformation through 10 μs-long Gaussian accelerated molecular dynamics simulations. DS is composed of repeating disaccharide units of iduronic acid (IdoA) and N-acetylgalactosamine (N-GalNAc). Here, N-GalNAc is linked to IdoA via β(1-4), while IdoA is linked to N-GalNAc through α(1-3). With the increase in sulfation, the DS structure becomes more rigid and linear, as is evident from the distribution of root-mean-square deviations (RMSDs) and end-to-end distances. The tetrasaccharide linker region of the main chain shows a rigid conformation in terms of the glycosidic linkage. We have observed that upon sulfation (i.e., dp12s), the ring flip between two chair forms vanished for IdoA. The dynamic cross-correlation analysis reveals that the anticorrelation motions in dp12s are reduced significantly compared to dp6s or dp7s. An increase in sulfation generates relatively more stable hydrogen-bond networks, including water bridging with the neighboring monosaccharides. Despite the favorable linear structures of the GAG chains, our study also predicts few significant bendings related to the different puckering states, which may play a notable role in the function of the DS. The relation between the global conformation with the micro-level parameters such as puckering and water-mediated hydrogen bonds shapes the overall conformational space of GAGs. Overall, atomistic details of the DS chain provided in this study will help understand their functional and mechanical roles, besides developing new biomaterials.
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Affiliation(s)
- Rajarshi Roy
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Khandwa Road, Indore 453552, Madhya Pradesh, India
| | - Nisha Amarnath Jonniya
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Khandwa Road, Indore 453552, Madhya Pradesh, India
| | - Parimal Kar
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Khandwa Road, Indore 453552, Madhya Pradesh, India
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The Influences of Sulphation, Salt Type, and Salt Concentration on the Structural Heterogeneity of Glycosaminoglycans. Int J Mol Sci 2021; 22:ijms222111529. [PMID: 34768961 PMCID: PMC8583755 DOI: 10.3390/ijms222111529] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 10/12/2021] [Accepted: 10/14/2021] [Indexed: 12/15/2022] Open
Abstract
The increasing recognition of the biochemical importance of glycosaminoglycans (GAGs) has in recent times made them the center of attention of recent research investigations. It became evident that subtle conformational factors play an important role in determining the relationship between the chemical composition of GAGs and their activity. Therefore, a thorough understanding of their structural flexibility is needed, which is addressed in this work by means of all-atom molecular dynamics (MD) simulations. Four major GAGs with different substitution patterns, namely hyaluronic acid as unsulphated GAG, heparan-6-sulphate, chondroitin-4-sulphate, and chondroitin-6-sulphate, were investigated to elucidate the influence of sulphation on the dynamical features of GAGs. Moreover, the effects of increasing NaCl and KCl concentrations were studied as well. Different structural parameters were determined from the MD simulations, in combination with a presentation of the free energy landscape of the GAG conformations, which allowed us to unravel the conformational fingerprints unique to each GAG. The largest effects on the GAG structures were found for sulphation at position 6, as well as binding of the metal ions in the absence of chloride ions to the carboxylate and sulphate groups, which both increase the GAG conformational flexibility.
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5
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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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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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Abstract
The conformation of a molecule strongly affects its function, as demonstrated for peptides and nucleic acids. This correlation is much less established for carbohydrates, the most abundant organic materials in nature. Recent advances in synthetic and analytical techniques have enabled the study of carbohydrates at the molecular level. Recurrent structural features were identified as responsible for particular biological activities or material properties. In this Minireview, recent achievements in the structural characterization of carbohydrates, enabled by systematic studies of chemically defined oligosaccharides, are discussed. These findings can guide the development of more potent glycomimetics. Synthetic carbohydrate materials by design can be envisioned.
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Affiliation(s)
- Yang Yu
- Department of Biomolecular SystemsMax-Planck-Institute of Colloids and InterfacesAm Mühlenberg 114476PotsdamGermany
- Department of Chemistry and BiochemistryFreie Universität BerlinArnimallee 2214195BerlinGermany
| | - Martina Delbianco
- Department of Biomolecular SystemsMax-Planck-Institute of Colloids and InterfacesAm Mühlenberg 114476PotsdamGermany
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Smith P, Ziolek RM, Gazzarrini E, Owen DM, Lorenz CD. On the interaction of hyaluronic acid with synovial fluid lipid membranes. Phys Chem Chem Phys 2019; 21:9845-9857. [PMID: 31032510 DOI: 10.1039/c9cp01532a] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
All-atom molecular dynamics simulations have been used to investigate the adsorption of low molecular weight hyaluronic acid to lipid membranes. We have determined the interactions that govern the adsorption of three different molecular weight hyaluronic acid molecules (0.4, 3.8 & 15.2 kDa) to lipid bilayers that are representative of the surface-active phospholipid bilayers found in synovial joints. We have found that both direct hydrogen bonds and water-mediated interactions with the lipid headgroups play a key role in the binding of hyaluronic acid to the lipid bilayer. The water-mediated interactions become increasingly important in stabilising the adsorbed hyaluronic acid molecules as the molecular weight of hyaluronic acid increases. We also observe a redistribution of ions around bound hyaluronic acid molecules and the associated lipid headgroups, and that the degree of redistribution increases with the molecular weight of hyaluronic acid. By comparing this behaviour to that observed in simulations of the charge-neutral polysaccharide dextran (MW ∼ 15 kDa), we show that this charge redistribution leads to an increased alignment of the lipid headgroups with the membrane normal, and therefore to more direct and water-mediated interactions between hyaluronic acid and the lipid membrane. These findings provide a detailed understanding of the general structure of hyaluronic acid-lipid complexes that have recently been presented experimentally, as well as a potential mechanism for their enhanced tribological properties.
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Affiliation(s)
- Paul Smith
- Biological Physics & Soft Matter Group, Department of Physics, King's College London, London, UK.
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9
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Nagarajan B, Sankaranarayanan NV, Desai UR. Perspective on computational simulations of glycosaminoglycans. WILEY INTERDISCIPLINARY REVIEWS. COMPUTATIONAL MOLECULAR SCIENCE 2019; 9:e1388. [PMID: 31080520 PMCID: PMC6504973 DOI: 10.1002/wcms.1388] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 07/07/2018] [Indexed: 01/06/2023]
Abstract
Glycosaminoglycans (GAGs) represent a formidable frontier for chemists, biochemists, biologists, medicinal chemists and drug delivery specialists because of massive structural complexity. GAGs are arguably the most complex, natural linear biopolymers with theoretical diversity orders of magnitude higher than proteins and nucleic acids. Yet, this diversity remains generally untapped. Computational approaches offer major routes to understand GAG structure and dynamics so as to enable novel applications of these biopolymers. In fact, computational algorithms, softwares, online tools and techniques have reached a level of sophistication that help understand atomistic details of conformational variation and protein recognition of individual GAG sequences. This review describes current approaches and challenges in computational study of GAGs. It presents a history of major findings since the earliest mention of GAGs (the 1960s), the development of parameters and force fields specific for GAGs, and the application of these tools in understanding GAG structure-function relationship. This review also presents a section on how to perform simulation of GAGs, which is directed toward researchers interested in entering this promising field with potential to impact therapy.
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Affiliation(s)
- Balaji Nagarajan
- Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond,
VA 23298, USA
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Nehru Viji Sankaranarayanan
- Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond,
VA 23298, USA
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Umesh R. Desai
- Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond,
VA 23298, USA
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA 23298, USA
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10
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Cai Z, Zhang F, Wei Y, Zhang H. Freeze–Thaw-Induced Gelation of Hyaluronan: Physical Cryostructuration Correlated with Intermolecular Associations and Molecular Conformation. Macromolecules 2017. [DOI: 10.1021/acs.macromol.7b01264] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Zhixiang Cai
- Advanced Rheology Institute, Department
of Polymer Science and Engineering, School of Chemistry and Chemical
Technology, Shanghai Jiao Tong University, Shanghai 200240, People’s Republic of China
| | - Fei Zhang
- Advanced Rheology Institute, Department
of Polymer Science and Engineering, School of Chemistry and Chemical
Technology, Shanghai Jiao Tong University, Shanghai 200240, People’s Republic of China
| | - Yue Wei
- Advanced Rheology Institute, Department
of Polymer Science and Engineering, School of Chemistry and Chemical
Technology, Shanghai Jiao Tong University, Shanghai 200240, People’s Republic of China
| | - Hongbin Zhang
- Advanced Rheology Institute, Department
of Polymer Science and Engineering, School of Chemistry and Chemical
Technology, Shanghai Jiao Tong University, Shanghai 200240, People’s Republic of China
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11
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Nestor G, Sandström C. NMR study of hydroxy and amide protons in hyaluronan polymers. Carbohydr Polym 2017; 157:920-928. [DOI: 10.1016/j.carbpol.2016.10.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Revised: 10/03/2016] [Accepted: 10/04/2016] [Indexed: 11/26/2022]
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12
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Teixeira R, Reis RL, Pashkuleva I. Influence of the sulfation degree of glycosaminoglycans on their multilayer assembly with poly-l-lysine. Colloids Surf B Biointerfaces 2016; 145:567-575. [DOI: 10.1016/j.colsurfb.2016.05.069] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Revised: 05/03/2016] [Accepted: 05/25/2016] [Indexed: 10/21/2022]
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13
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Pokki J, Ergeneman O, Sevim S, Enzmann V, Torun H, Nelson BJ. Measuring localized viscoelasticity of the vitreous body using intraocular microprobes. Biomed Microdevices 2015; 17:85. [DOI: 10.1007/s10544-015-9988-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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14
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Glycosaminoglycan monosaccharide blocks analysis by quantum mechanics, molecular dynamics, and nuclear magnetic resonance. BIOMED RESEARCH INTERNATIONAL 2014; 2014:808071. [PMID: 24804247 PMCID: PMC3997902 DOI: 10.1155/2014/808071] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Accepted: 01/22/2014] [Indexed: 01/25/2023]
Abstract
Glycosaminoglycans (GAGs) play an important role in many biological processes in the extracellular matrix. In a theoretical approach, structures of monosaccharide building blocks of natural GAGs and their sulfated derivatives were optimized by a B3LYP6311ppdd//B3LYP/6-31+G(d) method. The dependence of the observed conformational properties on the applied methodology is described. NMR chemical shifts and proton-proton spin-spin coupling constants were calculated using the GIAO approach and analyzed in terms of the method's accuracy and sensitivity towards the influence of sulfation, O1-methylation, conformations of sugar ring, and ω dihedral angle. The net sulfation of the monosaccharides was found to be correlated with the 1H chemical shifts in the methyl group of the N-acetylated saccharides both theoretically and experimentally. The ω dihedral angle conformation populations of free monosaccharides and monosaccharide blocks within polymeric GAG molecules were calculated by a molecular dynamics approach using the GLYCAM06 force field and compared with the available NMR and quantum mechanical data. Qualitative trends for the impact of sulfation and ring conformation on the chemical shifts and proton-proton spin-spin coupling constants were obtained and discussed in terms of the potential and limitations of the computational methodology used to be complementary to NMR experiments and to assist in experimental data assignment.
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15
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Higman VA, Briggs DC, Mahoney DJ, Blundell CD, Sattelle BM, Dyer DP, Green DE, DeAngelis PL, Almond A, Milner CM, Day AJ. A refined model for the TSG-6 link module in complex with hyaluronan: use of defined oligosaccharides to probe structure and function. J Biol Chem 2014; 289:5619-34. [PMID: 24403066 PMCID: PMC3937638 DOI: 10.1074/jbc.m113.542357] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Indexed: 11/25/2022] Open
Abstract
Tumor necrosis factor-stimulated gene-6 (TSG-6) is an inflammation-associated hyaluronan (HA)-binding protein that contributes to remodeling of HA-rich extracellular matrices during inflammatory processes and ovulation. The HA-binding domain of TSG-6 consists solely of a Link module, making it a prototypical member of the superfamily of proteins that interacts with this high molecular weight polysaccharide composed of repeating disaccharides of D-glucuronic acid and N-acetyl-D-glucosamine (GlcNAc). Previously we modeled a complex of the TSG-6 Link module in association with an HA octasaccharide based on the structure of the domain in its HA-bound conformation. Here we have generated a refined model for a HA/Link module complex using novel restraints identified from NMR spectroscopy of the protein in the presence of 10 distinct HA oligosaccharides (from 4- to 8-mers); the model was then tested using unique sugar reagents, i.e. chondroitin/HA hybrid oligomers and an octasaccharide in which a single sugar ring was (13)C-labeled. The HA chain was found to make more extensive contacts with the TSG-6 surface than thought previously, such that a D-glucuronic acid ring makes stacking and ionic interactions with a histidine and lysine, respectively. Importantly, this causes the HA to bend around two faces of the Link module (resembling the way that HA binds to CD44), potentially providing a mechanism for how TSG-6 can reorganize HA during inflammation. However, the HA-binding site defined here may not play a role in TSG-6-mediated transfer of heavy chains from inter-α-inhibitor onto HA, a process known to be essential for ovulation.
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Affiliation(s)
- Victoria A. Higman
- From the Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
| | - David C. Briggs
- Wellcome Trust Centre for Cell Matrix Research
- Faculty of Life Sciences, University of Manchester, Oxford Road, Manchester M13 9PT United Kingdom, and
| | - David J. Mahoney
- From the Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
| | - Charles D. Blundell
- Faculty of Life Sciences, University of Manchester, Oxford Road, Manchester M13 9PT United Kingdom, and
| | - Benedict M. Sattelle
- Faculty of Life Sciences, University of Manchester, Oxford Road, Manchester M13 9PT United Kingdom, and
| | - Douglas P. Dyer
- Wellcome Trust Centre for Cell Matrix Research
- Faculty of Life Sciences, University of Manchester, Oxford Road, Manchester M13 9PT United Kingdom, and
| | - Dixy E. Green
- the Department of Biochemistry and Molecular Biology, Oklahoma Center for Medical Glycobiology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma 73104
| | - Paul L. DeAngelis
- the Department of Biochemistry and Molecular Biology, Oklahoma Center for Medical Glycobiology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma 73104
| | - Andrew Almond
- Faculty of Life Sciences, University of Manchester, Oxford Road, Manchester M13 9PT United Kingdom, and
| | - Caroline M. Milner
- Faculty of Life Sciences, University of Manchester, Oxford Road, Manchester M13 9PT United Kingdom, and
| | - Anthony J. Day
- Wellcome Trust Centre for Cell Matrix Research
- Faculty of Life Sciences, University of Manchester, Oxford Road, Manchester M13 9PT United Kingdom, and
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16
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Minaberry Y, Chiappetta DA, Sosnik A, Jobbágy M. Micro/Nanostructured Hyaluronic Acid Matrices with Tuned Swelling and Drug Release Properties. Biomacromolecules 2012; 14:1-9. [DOI: 10.1021/bm300814h] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
| | | | | | - Matías Jobbágy
- National Science Research Council (CONICET)
- Centro Interdisciplinario de Nanociencia y Nanotecnología
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17
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Rheology of the vitreous gel: Effects of macromolecule organization on the viscoelastic properties. J Biomech 2011; 44:419-23. [DOI: 10.1016/j.jbiomech.2010.10.002] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2010] [Revised: 10/02/2010] [Accepted: 10/06/2010] [Indexed: 11/23/2022]
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18
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19
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Hu X, Carmichael I, Serianni AS. N-Acetyl Side-Chains in Saccharides: NMR J-Coupling Equations Sensitive to CH−NH and NH−CO Bond Conformations in 2-Acetamido-2-deoxy-aldohexopyranosyl Rings. J Org Chem 2010; 75:4899-910. [DOI: 10.1021/jo100521g] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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20
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Nestor G, Kenne L, Sandström C. Experimental evidence of chemical exchange over the β(1→3) glycosidic linkage and hydrogen bonding involving hydroxy protons in hyaluronan oligosaccharides by NMR spectroscopy. Org Biomol Chem 2010; 8:2795-802. [DOI: 10.1039/b927159g] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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21
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Matteini P, Dei L, Carretti E, Volpi N, Goti A, Pini R. Structural behavior of highly concentrated hyaluronan. Biomacromolecules 2009; 10:1516-22. [PMID: 19358524 DOI: 10.1021/bm900108z] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
When investigated under high concentration conditions, hyaluronan (HA) solutions in physiological saline are shown to generate stable superstructures. An abrupt change in the rheological properties observed on increasing the temperature suggests the breaking of certain cooperative bonds. The thermal disruption of the HA superstructure is accompanied by a sharp transition from a long- to a restricted-connectivity water structuring, which is interpreted as a concurrent transition from a stable to a temporary polymer network. The intermolecular associations are considered to be originated by hydrophobic interactions between the nonpolar groups of the polymer backbones.
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Affiliation(s)
- Paolo Matteini
- Institute of Applied Physics Nello Carrara, National Research Council, Florence, Italy
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22
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Conformational properties of the disaccharide building units of hyaluronan. Carbohydr Res 2009; 344:1745-52. [DOI: 10.1016/j.carres.2009.05.030] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2009] [Revised: 05/22/2009] [Accepted: 05/31/2009] [Indexed: 11/24/2022]
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23
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Coxon B. Developments in the Karplus equation as they relate to the NMR coupling constants of carbohydrates. Adv Carbohydr Chem Biochem 2009; 62:17-82. [PMID: 19501704 DOI: 10.1016/s0065-2318(09)00003-1] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- Bruce Coxon
- National Institutes of Health, Bethesda, MD 20892, USA
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The influence of Hofmeister series ions on hyaluronan swelling and viscosity. Molecules 2008; 13:1025-34. [PMID: 18560327 PMCID: PMC6245326 DOI: 10.3390/molecules13051025] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2008] [Revised: 04/17/2008] [Accepted: 04/30/2008] [Indexed: 11/17/2022] Open
Abstract
The dissolution of hyaluronan in water leads to its degradation, and as a result its molecular weight decreases. The degradation of hyaluronan is mainly influenced by temperature, solution composition, and also its pH. This study describes the influence of Hofmeister series ions on hyaluronan behaviour and hyaluronan film swelling by solutions of these ions. It was found that Hofmeister ions show lyotropic effects influencing the entanglement of hyaluronan coils and their expansion from solid polymer films into swollen gel state. The hydrophobic and hydrophilic interactions in the structure of hyaluronan macromolecules are represented by the mutual diffusion coefficient D(c), the mean mutual diffusion coefficient Ds, the expansion work of coil swelling RAδ,s, the activation enthalpy of diffusion connected with swelling HD,s and kinematic viscosity of hyaluronan-ions solutions ν.
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Mrácek A, Benesová K, Minarík A, Urban P, Lapcík L. The diffusion process of sodium hyaluronate (Na-Ha) and Na-Ha-n-alkyl derivatives films swelling. J Biomed Mater Res A 2007; 83:184-90. [PMID: 17397039 DOI: 10.1002/jbm.a.31188] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The process of diffusion of sodium hyaluronate and its hydrophobically modified alkyl derivatives in water was studied by measuring the kinetics of solid polymer film swelling. The following fundamental thermodynamic parameters of the swelling process were calculated: the apparent diffusion coefficient of swelling by water D(s) determined at three temperatures (25, 37, and 45 degrees C), the activation enthalpy of diffusion connected with the swelling DeltaH(D,s) and the activation enthalpy of the swelling process DeltaH(s). The thermodynamic activity of the solvent for the given sodium hyaluronate and its four alkyl derivatives has been expressed through the internal quantity RA(delta,s), that is expansion work of polymer coil accomplished by the action of the internal pressure.
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Affiliation(s)
- Ales Mrácek
- Department of Physics and Material Engineering, Faculty of Technology, Tomas Bata University in Zlín, Nad Stránemi 4511, 760 05, Zlín, Czech Republic.
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MINAMISAWA T, SUZUKI K, MAEDA H, SHIMOKATA S, SUGIURA N, KIMATA K, HIRABAYASHI J. Characterization of Isomeric Unsulfated Glycosaminoglycan Oligosaccharides by Mass Spectrometry/Mass Spectrometry. ACTA ACUST UNITED AC 2007. [DOI: 10.5702/massspec.55.1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Blundell C, Deangelis P, Almond A. Hyaluronan: the absence of amide-carboxylate hydrogen bonds and the chain conformation in aqueous solution are incompatible with stable secondary and tertiary structure models. Biochem J 2006; 396:487-98. [PMID: 16506956 PMCID: PMC1482818 DOI: 10.1042/bj20060085] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2006] [Revised: 02/22/2006] [Accepted: 03/01/2006] [Indexed: 11/17/2022]
Abstract
Contradictory descriptions for the aqueous solution conformation of the glycosaminoglycan hyaluronan (HA) exist in the literature. According to hydrodynamic and simulation data, HA molecules are stiffened by a rapidly interchanging network of transient hydrogen bonds at the local level and do not significantly associate at the global level. In marked contrast, models derived from NMR data suggest that the secondary structure involves persistent hydrogen bonds and that strong associations between chains can occur to form vast stable tertiary structures. These models require an extended 2-fold helical conformation of the HA chain and specific hydrogen bonds between amide and carboxylate groups. To test these descriptions, we have used 15N-labelled oligosaccharides and high-field NMR to measure pertinent properties of the acetamido group. The amide proton chemical shift perturbation and carboxylate group pK(a) value are inconsistent with a highly populated hydrogen bond between the amide and carboxylate groups. Amide proton temperature coefficients and chemical exchange rates confirm this conclusion. Comparison of oligomer properties with polymeric HA indicates that there is no discernible difference in amide proton environment between the centre of octasaccharides and the polymer, inconsistent with the formation of tertiary structures. A [1H-1H-15N] NOESY-HSQC (heteronuclear single-quantum correlation) spectrum recorded on an HA octasaccharide revealed that amide groups in the centre are in a trans orientation and that the average solution conformation is not an extended 2-fold helix. Therefore the two key aspects of the secondary and tertiary structure models are unlikely to be correct. Rather, these new NMR data agree with descriptions from hydrodynamic and simulations data.
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Key Words
- carboxylate pka
- hyaluronan
- hydrogen bond
- 15n-labelled carbohydrate
- structure model
- temperature coefficient
- dyn, dynamic model for secondary structure
- glca, d-glucuronic acid
- glcnac, n-acetyl-d-glucosamine
- ha, hyaluronan
- hsqc, heteronuclear single-quantum correlation
- noe, nuclear overhauser effect
- p.p.b., parts per billion
- tf-inter-s, tertiary structure model involving an extended 2-fold helical conformation, intermolecular hydrogen bonds and hydrophobic stacking interactions
- tf-intra, secondary structure model involving an extended 2-fold helical conformation and intramolecular hydrogen bonds
- tf-wb, secondary structure model involving an extended 2-fold helical conformation and stably bound bridging water molecules
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Affiliation(s)
- Charles D. Blundell
- *Faculty of Life Sciences, Manchester Interdisciplinary Biocentre, University of Manchester, 131 Princess Street, Manchester M1 7ND, U.K
| | - Paul L. Deangelis
- †Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, OK 73104, U.S.A
| | - Andrew Almond
- *Faculty of Life Sciences, Manchester Interdisciplinary Biocentre, University of Manchester, 131 Princess Street, Manchester M1 7ND, U.K
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Almond A, Deangelis PL, Blundell CD. Hyaluronan: The Local Solution Conformation Determined by NMR and Computer Modeling is Close to a Contracted Left-handed 4-Fold Helix. J Mol Biol 2006; 358:1256-69. [PMID: 16584748 DOI: 10.1016/j.jmb.2006.02.077] [Citation(s) in RCA: 85] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2005] [Revised: 01/27/2006] [Accepted: 02/28/2006] [Indexed: 11/27/2022]
Abstract
The polysaccharide hyaluronan (HA) is a ubiquitous component of the vertebrate extracellular matrix with diverse physiological roles from space-filling to acting as a scaffold for other macromolecules. The molecular interactions responsible for these solution properties have been the subject of much debate and, primarily due to the lack of residue-specific experimental data, no consensus model for the three-dimensional conformation nor dynamics of HA in solution has emerged. Here, the solution conformation of HA is investigated using molecular dynamics (MD) simulations and high-field nuclear magnetic resonance (NMR). In contrast to previous studies, MD simulations incorporated explicit water molecules and sodium ions, while NMR experiments utilized (15)N-enriched oligosaccharides to allow residue-specific information to be obtained. The resultant average conformation is predicted to be almost a contracted left-handed 4-fold helix; i.e. similar to that observed for sodium hyaluronate fibers by X-ray diffraction, but with the acetamido side-chain trans to H(2). The glycosidic linkages and acetamido side-chains are predicted to have standard deviation rotations of 13 degrees and 18 degrees around their mean conformations in free solution, respectively, and are not observed to be stabilized by strong intramolecular hydrogen bonds as X-ray fiber diffraction refinements describe for the solid-state. Rather, weak and transient hydrogen bonds that are in rapid interchange with solvent molecules are predicted. These predictions are quantitatively consistent with demanding residue-specific NMR data and correspond to an HA molecule that is rod-like as an oligosaccharide and behaves as a stiffened random coil at large molecular mass, in close agreement with previous hydrodynamic observations. This new description of the solution conformation of HA is consistent with all available experimental data and accounts for its viscoelastic space-filling properties. This representation can be used as a basis for modeling the association between HA and proteins, which will elucidate important aspects of extracellular matrix assembly.
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Affiliation(s)
- Andrew Almond
- Faculty of Life Sciences, University of Manchester, Manchester Interdisciplinary Biocentre, Princess Street, Manchester, M1 7ND, UK.
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30
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Affiliation(s)
- Robert Stern
- Department of Pathology and Comprehensive Cancer Center, School of Medicine, University of California, San Francisco, CA 94143-0511, USA
| | - Mark J. Jedrzejas
- Children’s Hospital Oakland Research Institute, Oakland, CA 94609, USA
- To whom correspondence should be addressed: Children’s Hospital Oakland Research Institute, 5700 Martin Luther King, Jr. Way, Oakland, California 94609, USA, Phone: +1 510-450-7932, Fax +1 510-450-7914, e-mail: , Web: www.chori.org/investigators/jedrzejas.html
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31
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Dais P, Tylianakis E, Kanetakis J, Taravel FR. 13C Nuclear magnetic relaxation study of segmental dynamics of hyaluronan in aqueous solutions. Biomacromolecules 2006; 6:1397-404. [PMID: 15877358 DOI: 10.1021/bm040076d] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
(13)C spin-lattice relaxation times (T(1)) and nuclear Overhauser enhancements (NOE) were measured as a function of temperature and magnetic field strength for the hetero-polysaccharide hyaluronan in water solutions. The relaxation data of the endocyclic ring carbons were successfully interpreted in terms of chain segmental motions by using the bimodal time-correlation function of Dejean de la Batie, Laupretre and Monnerie. On the basis of the calculated correlation times for segmental motion and amplitudes of librational motions of the C-H vectors at the various carbon sites of the HA repeating unit, we concluded that intramolecular hydrogen bonding of the secondary structure of HA plays a major role in the conformational flexibility of this carbohydrate molecule. The internal rotation of the free hydroxymethyl groups about the exocyclic C-5-C-6 bonds superimposed on segmental motion has been described as a diffusion process of restricted amplitude. The rate and amplitude of the internal rotation indicate that the hydroxymethyl groups are not involved in intramolecular hydrogen bonding. Finally, the motional parameters describing the local dynamics of the HA chain were correlated with the secondary structure of HA in aqueous solutions.
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Affiliation(s)
- Photis Dais
- NMR Laboratory, Department of Chemistry, University of Crete, 71409 Heraklion, Crete, Greece
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32
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Colebrooke SA, Blundell CD, DeAngelis PL, Campbell ID, Almond A. Exploiting the carboxylate chemical shift to resolve degenerate resonances in spectra of 13C-labelled glycosaminoglycans. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2005; 43:805-15. [PMID: 15996005 DOI: 10.1002/mrc.1620] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Glycosaminoglycans (GAG) are important vertebrate extracellular matrix polysaccharides that comprise repeated units of an acidic and an N-acetylated sugar. The constituent acidic sugars are central to their biological functions, but have been largely inaccessible to NMR because the (1)H resonances overlap with those from other residues. Here, pulse sequences that address this failure are developed using (13)C-enriched oligosaccharides of the glycosaminoglycan, hyaluronan, as model systems. Two pulse sequences are presented that exploit the unique chemical shifts and scalar couplings present at the carboxylate moiety to filter out coherences from the N-acetylated sugars and produce simple spectra containing only resonances from the acidic sugars. The first sequence uses one-bond couplings to correlate the carboxylate carbon with the adjacent carbon and its directly attached proton, while the second sequence exploits a long-range coupling to correlate the carboxylate carbon with the anomeric proton and carbon of the same residue. In addition, inclusion of an isotropic mixing block into these sequences allows resonances from the otherwise degenerate ring protons to be resolved. Spectra from the hyaluronan tetra- and hexasaccharides show that all glucuronic acid (GlcA) residues can be resolved from one another, allowing nuclei to be assigned in a sequence-specific manner. However, in some spectra, resonances are observed at positions not predicted by spin-operator analysis, and simulations reveal that these additional magnetisation transfers result from strong-coupling. These experiments represent a foundation from which new structural and biochemical information can be obtained in a sequence-specific manner for the acidic sugar residues in hyaluronan and other glycosaminoglycans.
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Affiliation(s)
- Simon A Colebrooke
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
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33
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Abstract
In this paper, we have examined the behavior of hyaluronan solutions at different pH values. A slight degradation is observed in acidic conditions (pH = 1.6) and basic medium (pH = 12.6) from molecular weight distribution analysis, but the rheological behavior is relatively not influenced much by the pH at the exclusion of two domains: around pH = 2.5, a gel-like behavior is shown and is attributed to cooperative interchain interactions due to the reduction of the polymer net charge and may be the protonation of the acetamido groups; for pH > 12, the decrease of viscosity is mainly attributed to a reduction of the stiffness of the polymeric backbone in alkaline conditions due to the partial breakage of the H-bond network.
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Affiliation(s)
- Iuliana Gatej
- Centre de Recherches sur les Macromolécules Végétales, CNRS, affiliated to Joseph Fourier University, BP 53, 38041 Grenoble Cedex 9, France
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34
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Blundell CD, Almond A, Mahoney DJ, DeAngelis PL, Campbell ID, Day AJ. Towards a Structure for a TSG-6·Hyaluronan Complex by Modeling and NMR Spectroscopy. J Biol Chem 2005; 280:18189-201. [PMID: 15718240 DOI: 10.1074/jbc.m414343200] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The Link module from human TSG-6, a hyaladherin with roles in ovulation and inflammation, has a hyaluronan (HA)-binding groove containing two adjacent tyrosine residues that are likely to form CH-pi stacking interactions with sequential rings in the sugar. We have used this observation to construct a model of a protein.HA complex, which was then tested against existing experimental information and by acquisition of new NMR data sets of [(13)C, (15)N]HA (8-mer) complexed with unlabeled protein. A major finding of this analysis was that acetamido side chains of two GlcNAc rings fit into hydrophobic pockets on either side of the adjacent tyrosines, providing a selectivity mechanism of HA over other polysaccharides. Furthermore, two basic residues have a separation that matches that of glucuronic acids in the sugar, consistent with the formation of salt bridges; NMR experiments at a range of pH values identified protein groups that titrate due to their proximity to a free carboxylate in HA. Sequence alignment and construction of homology models for all human Link modules in their HA-bound states revealed that many of these features are conserved across the superfamily, thus allowing the prediction of functionally important residues. In the case of cartilage link protein, its two Link modules were docked together (using bound HA as a guide), identifying hydrophobic residues likely to form an intra-Link module interface as well as amino acids that could be involved in supporting intermolecular interactions between link proteins and chondroitin sulfate proteoglycans. Here, we propose a mechanism for ternary complex formation that generates higher order helical structures, as may exist in cartilage aggregates.
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Affiliation(s)
- Charles D Blundell
- Medical Research Council Immunochemistry Unit, University of Oxford, Oxford OX1 3QU, United Kingdom
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35
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Abstract
This review addresses the area of study that defines the field of surface modification of biomedical materials and devices by hyaluronan (HA), as related to the exploitation of HA biological properties. To provide a comprehensive view of the subject matter, initial sections give a quick introduction to basic information on HA-protein and HA-cell interactions, together with some discussion on the bioactive role of HA in wound healing and related phenomena. This is followed by a description of current theories that correlate HA properties to its molecular structure in aqueous media, underlying how HA molecular details are crucial for its biological interaction and role. Finally, existing approaches to surface modification by HA are reviewed, stressing the need for HA-surface engineering founded on the knowledge and control of the surface-linked HA molecular conformation at the solid/aqueous interface.
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Affiliation(s)
- Marco Morra
- Nobil Bio Ricerche s.r.l., Str. S. Rocco 36, 14018 Villafranca d'Asti, Italy
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36
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Bosco M, Segre A, Miertus S, Cesàro A, Paoletti S. The disordered conformation of κ-carrageenan in solution as determined by NMR experiments and molecular modeling. Carbohydr Res 2005; 340:943-58. [PMID: 15780259 DOI: 10.1016/j.carres.2005.01.035] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2004] [Accepted: 01/23/2005] [Indexed: 10/25/2022]
Abstract
The conformation of kappa-carrageenan in solution was studied combining 1H and 13C NMR with molecular mechanics. The experimental conditions were chosen to characterize the disordered conformation of the polymer. Particular attention has been given to explore a wide range of experimental conditions as to the dependence on solvent (water and Me2SO), polymer concentration, temperature, pH, presence of a denaturing agent (guanidinium chloride), and of ions otherwise able to induce conformational order of the carrageenan chains, either in solution (I-) or in the gel state (Rb+). Two-dimensional NOE experiments were analyzed to obtain information on internuclear distances, and molecular mechanics provided the range of energetically accessible conformations. Two inter-residue topological constraints were clearly identified: their combination is rather restricting for the chain and suggests that the disordered conformation of kappa-carrageenan is characterized by an intrinsic stiffness with high values of persistent length and characteristic ratio. They also rule out any postulated interchain hydrogen bonds. In contrast, experiments on the temperature dependence of the chemical shift in Me2SO reveal the existence of two inter-residue intramolecular H-bonds which might contribute positively to the rigidity of the polymer chain. The overall picture emerging from the present results is that of a locally elongated 'loose single helix'.
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Affiliation(s)
- Marco Bosco
- POLY-biós Research Center, AREA Science Park, Padriciano 99, I-34012 Trieste, Italy
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37
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Furlan S, La Penna G, Perico A, Cesàro A. Hyaluronan chain conformation and dynamics. Carbohydr Res 2005; 340:959-70. [PMID: 15780260 DOI: 10.1016/j.carres.2005.01.030] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2004] [Accepted: 01/25/2005] [Indexed: 11/20/2022]
Abstract
An overview of the present state of research in the field of hyaluronan chain conformational aspects is presented. The relationship between structure and dynamics are illustrated for a series of hyaluronan oligomers. Conformational characteristics of hyaluronan chains are discussed, together with the dynamic chain patterns, evaluated by using a theoretical approach to diffusive polymer dynamics. The dependence of correlation times and NMR relaxation parameters from the chain dimension are investigated. Topological features and dimensional properties are related to the structural determinants by using classical computational methods of molecular mechanics and Monte Carlo simulation.
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Affiliation(s)
- Sara Furlan
- Department of Biochemistry, Biophysics and Macromolecular Chemistry, UdR INSTM, University of Trieste, I-34127 Trieste, Italy
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38
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Bathe M, Rutledge GC, Grodzinsky AJ, Tidor B. A coarse-grained molecular model for glycosaminoglycans: application to chondroitin, chondroitin sulfate, and hyaluronic acid. Biophys J 2005; 88:3870-87. [PMID: 15805173 PMCID: PMC1305620 DOI: 10.1529/biophysj.104.058800] [Citation(s) in RCA: 87] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A coarse-grained molecular model is presented for the study of the equilibrium conformation and titration behavior of chondroitin (CH), chondroitin sulfate (CS), and hyaluronic acid (HA)-glycosaminoglycans (GAGs) that play a central role in determining the structure and biomechanical properties of the extracellular matrix of articular cartilage. Systematic coarse-graining from an all-atom description of the disaccharide building blocks retains the polyelectrolytes' specific chemical properties while enabling the simulation of high molecular weight chains that are inaccessible to all-atom representations. Results are presented for the characteristic ratio, the ionic strength-dependent persistence length, the pH-dependent expansion factor for the end-to-end distance, and the titration behavior of the GAGs. Although 4-sulfation of the N-acetyl-D-galactosamine residue is found to increase significantly the intrinsic stiffness of CH with respect to 6-sulfation, only small differences in the titration behavior of the two sulfated forms of CH are found. Persistence length expressions are presented for each type of GAG using a macroscopic (wormlike chain-based) and a microscopic (bond vector correlation-based) definition. Model predictions agree quantitatively with experimental conformation and titration measurements, which support use of the model in the investigation of equilibrium solution properties of GAGs.
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Affiliation(s)
- Mark Bathe
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, 02139, USA
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39
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Bayraktar H, Akal E, Sarper O, Varnali T. Modeling glycosaminoglycans—hyaluronan, chondroitin, chondroitin sulfate A, chondroitin sulfate C and keratan sulfate. ACTA ACUST UNITED AC 2004. [DOI: 10.1016/j.theochem.2004.07.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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40
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Furlan S, La Penna G, Perico A, Cesàro A. Conformational Dynamics of Hyaluronan Oligomers in Solution. 3. Molecular Dynamics from Monte Carlo Replica-Exchange Simulations and Mode-Coupling Diffusion Theory. Macromolecules 2004. [DOI: 10.1021/ma049641v] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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41
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Blundell CD, DeAngelis PL, Day AJ, Almond A. Use of 15N-NMR to resolve molecular details in isotopically-enriched carbohydrates: sequence-specific observations in hyaluronan oligomers up to decasaccharides. Glycobiology 2004; 14:999-1009. [PMID: 15215231 DOI: 10.1093/glycob/cwh117] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The glycosaminoglycan hyaluronan is a vital structural component of extracellular matrices with diverse biological functions, a molecular understanding of which requires a detailed description of secondary and tertiary solution structures. Various models of these structures have been proposed on the basis of 1H and 13C natural-abundance nuclear magnetic resonance (NMR) experiments, but resonance overlap limits further progress with these techniques. We have therefore produced 15N- and 13C- isotopically-labeled hyaluronan oligosaccharides and applied triple-resonance and 3D experiments to overcome this restriction. Spectra recorded on oligosaccharides (of lengths 4, 6, 8, 10, and 12 sugar rings), reveal that the 15N nucleus allows resolution of the amide groups in a decamer at high magnetic field, whereas 13C natural-abundance NMR can only resolve internal groups up to hexamers. Complete 13N sequence- specific assignments of these oligosaccharides indicate that the chemical shift dispersion can be explained by end-effects, which are seen even in the middle of octamers. Triple- resonance and 15N-edited 3D experiments, among the first of their kind in oligosaccharides, have been used to achieve resolution of ring 1H and 13C nuclei where not possible previously. The subtle chemical shift perturbations resolved suggest that different conformations and dynamics occur at the ends, which may contribute to the range of biological activities displayed by varying lengths of hyaluronan. 15N-NMR in carbohydrates has not received much attention before, however, this study demonstrates it has clear advantages for achieving resolution and assessing dynamic motion. These conclusions are likely to be applicable to the study of the structure and dynamics of other nitrogen-containing carbohydrates.
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Affiliation(s)
- Charles D Blundell
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1, 3QU, UK
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42
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Rigden DJ, Jedrzejas MJ. Structures of Streptococcus pneumoniae Hyaluronate Lyase in Complex with Chondroitin and Chondroitin Sulfate Disaccharides. J Biol Chem 2003; 278:50596-606. [PMID: 14523022 DOI: 10.1074/jbc.m307596200] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Streptococcus pneumoniae hyaluronate lyase is a surface enzyme of this Gram-positive bacterium. The enzyme degrades hyaluronan and chondroitin/chondroitin sulfates by cleaving the beta1,4-glycosidic linkage between the glycan units of these polymeric substrates. This degradation helps spreading of this bacterial organism throughout the host tissues and facilitates the disease process caused by pneumococci. The mechanism of this degradative process is based on beta-elimination, is termed proton acceptance and donation, and involves selected residues of a well defined catalytic site of the enzyme. The degradation of hyaluronan alone is thought to proceed through a processive mode of action. The structures of complexes between the enzyme and chondroitin as well as chondroitin sulfate disaccharides allowed for the first detailed insights into these interactions and the mechanism of action on chondroitins. This degradation of chondroitin/chondroitin sulfates is nonprocessive and is selective for the chondroitin sulfates only with certain sulfation patterns. Chondroitin sulfation at the 4-position on the nonreducing site of the linkage to be cleaved or 2-sulfation prevent degradation due to steric clashes with the enzyme. Evolutionary studies suggest that hyaluronate lyases evolved from chondroitin lyases and still retained chondroitin/chondroitin sulfate degradation abilities while being specialized in the degradation of hyaluronan. The more efficient processive degradation mechanism has come to be preferred for the unsulfated substrate hyaluronan.
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Affiliation(s)
- Daniel J Rigden
- Children's Hospital Oakland Research Institute, Oakland, California 94609, USA
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43
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Krause WE, Bellomo EG, Colby RH. Rheology of sodium hyaluronate under physiological conditions. Biomacromolecules 2002; 2:65-9. [PMID: 11749156 DOI: 10.1021/bm0055798] [Citation(s) in RCA: 158] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Sodium hyaluronate NaHA in phosphate-buffered saline behaves as a typical polyelectrolyte in the high-salt limit, as Newtonian viscosities are observed over a wide range of shear rates. There is no evidence of intermolecule hydrogen bonding causing gel formation in NaHA solutions without protein present. The concentration dependences of viscosity, relaxation time, and terminal modulus are consistent with observations on flexible, neutral polymers in good solvents, which are known to be in the same universality class as flexible polyelectrolytes in the presence of excess salt.
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Affiliation(s)
- W E Krause
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
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44
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Letardi S, La Penna G, Chiessi E, Perico A, Cesàro A. Conformational Dynamics of Hyaluronan in Solution. 2. Mode-Coupling Diffusion Approach to Oligomers. Macromolecules 2002. [DOI: 10.1021/ma0112220] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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45
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Abstract
Molecular dynamics simulations of hyaluronan have revealed the inherent flexibility of this glycosaminoglycan in solution. Crystal structures of hyaluronan-digesting enzymes have provided the first direct insights into the molecular basis of hyaluronan-protein interactions. Various studies on hyaluronan-binding proteins suggest there is considerable diversity in their mode of interaction with hyaluronan, which might result in many different bound conformations of the polysaccharide.
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Affiliation(s)
- A J Day
- Department of Biochemistry, University of Oxford, UK.
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46
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Cavalieri F, Chiessi E, Paci M, Paradossi G, Flaibani A, Cesàro A. Conformational Dynamics of Hyaluronan in Solution. 1. A 13C NMR Study of Oligomers. Macromolecules 2000. [DOI: 10.1021/ma001076i] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- F. Cavalieri
- Department of Chemistry Science and Technology, University of Rome “Tor Vergata”, 00133 Rome, Italy; Section B of I.N.F.M. Roma-II, 00133 Rome, Italy; Section B of I.N.F.M. Roma-I, 00185 Rome, Italy; POLY-tech, Area Science Park, Padriciano 99, 34012 Trieste, Italy; and Department of Biochemistry, Biophysics, and Macromolecular Chemistry, University of Trieste, 34127 Trieste, Italy
| | - E. Chiessi
- Department of Chemistry Science and Technology, University of Rome “Tor Vergata”, 00133 Rome, Italy; Section B of I.N.F.M. Roma-II, 00133 Rome, Italy; Section B of I.N.F.M. Roma-I, 00185 Rome, Italy; POLY-tech, Area Science Park, Padriciano 99, 34012 Trieste, Italy; and Department of Biochemistry, Biophysics, and Macromolecular Chemistry, University of Trieste, 34127 Trieste, Italy
| | - M. Paci
- Department of Chemistry Science and Technology, University of Rome “Tor Vergata”, 00133 Rome, Italy; Section B of I.N.F.M. Roma-II, 00133 Rome, Italy; Section B of I.N.F.M. Roma-I, 00185 Rome, Italy; POLY-tech, Area Science Park, Padriciano 99, 34012 Trieste, Italy; and Department of Biochemistry, Biophysics, and Macromolecular Chemistry, University of Trieste, 34127 Trieste, Italy
| | - G. Paradossi
- Department of Chemistry Science and Technology, University of Rome “Tor Vergata”, 00133 Rome, Italy; Section B of I.N.F.M. Roma-II, 00133 Rome, Italy; Section B of I.N.F.M. Roma-I, 00185 Rome, Italy; POLY-tech, Area Science Park, Padriciano 99, 34012 Trieste, Italy; and Department of Biochemistry, Biophysics, and Macromolecular Chemistry, University of Trieste, 34127 Trieste, Italy
| | - A. Flaibani
- Department of Chemistry Science and Technology, University of Rome “Tor Vergata”, 00133 Rome, Italy; Section B of I.N.F.M. Roma-II, 00133 Rome, Italy; Section B of I.N.F.M. Roma-I, 00185 Rome, Italy; POLY-tech, Area Science Park, Padriciano 99, 34012 Trieste, Italy; and Department of Biochemistry, Biophysics, and Macromolecular Chemistry, University of Trieste, 34127 Trieste, Italy
| | - A. Cesàro
- Department of Chemistry Science and Technology, University of Rome “Tor Vergata”, 00133 Rome, Italy; Section B of I.N.F.M. Roma-II, 00133 Rome, Italy; Section B of I.N.F.M. Roma-I, 00185 Rome, Italy; POLY-tech, Area Science Park, Padriciano 99, 34012 Trieste, Italy; and Department of Biochemistry, Biophysics, and Macromolecular Chemistry, University of Trieste, 34127 Trieste, Italy
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47
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Cowman MK, Feder-Davis J, Hittner DM. 13C NMR Studies of Hyaluronan. 2. Dependence of Conformational Dynamics on Chain Length and Solvent. Macromolecules 2000. [DOI: 10.1021/ma001082e] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Mary K. Cowman
- Department of Chemistry and Herman F. Mark Polymer Research Institute, Polytechnic University, Six Metrotech Center, Brooklyn, New York 11201
| | - Joan Feder-Davis
- Department of Chemistry and Herman F. Mark Polymer Research Institute, Polytechnic University, Six Metrotech Center, Brooklyn, New York 11201
| | - Daniel M. Hittner
- Department of Chemistry and Herman F. Mark Polymer Research Institute, Polytechnic University, Six Metrotech Center, Brooklyn, New York 11201
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48
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Almond A, Brass A, Sheehan JK. Oligosaccharides as Model Systems for Understanding Water−Biopolymer Interaction: Hydrated Dynamics of a Hyaluronan Decamer. J Phys Chem B 2000. [DOI: 10.1021/jp000402t] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- A. Almond
- Division of Biochemistry, School of Biological Sciences, University of Manchester, Oxford Road, Manchester, M13 9PT, United Kingdom
| | - A. Brass
- Division of Biochemistry, School of Biological Sciences, University of Manchester, Oxford Road, Manchester, M13 9PT, United Kingdom
| | - J. K. Sheehan
- Division of Biochemistry, School of Biological Sciences, University of Manchester, Oxford Road, Manchester, M13 9PT, United Kingdom
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49
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Almond A, Sheehan JK. Glycosaminoglycan conformation: do aqueous molecular dynamics simulations agree with x-ray fiber diffraction? Glycobiology 2000; 10:329-38. [PMID: 10704532 DOI: 10.1093/glycob/10.3.329] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Glycosaminoglycan-protein interactions are biologically important and require an appreciation of glycan molecular shape in solution, which is presently unavailable. In previous studies we found strong similarity between aqueous molecular dynamics (MD) simulations and published x-ray diffraction refinements of hyaluronan. We have applied a similar approach here to chondroitin and dermatan, attempting to clarify some of the issues raised by the x-ray diffraction literature relating to chondroitin and dermatan sulfate. We predict that chondroitin has the same beta(1-->4) linkage conformation as hyaluronan, and that their average beta(1-->3) conformations differ. This is explained by changes in hydrogen-bonding across this linkage, resulting from its axial hydroxyl, causing a different sampling of left-handed helices in chondroitin (2.5- to 3.5-fold) as compared with hyaluronan (3.0- to 4.0-fold). Few right-handed helices, which lack intramolecular hydrogen-bonds, were sampled during our MD simulations. Thus, we propose that the 8-fold helix observed in chondroitin-6-sulfate, represented in the literature as an 8(3) helix (right-handed), though it has never been refined, is more likely to be 8(5) (left-handed) helix. Molecular dynamics simulations implied that (4)C(1) and (2)S(O), but not (1)C(4), forms of iduronate could be used in refinements of dermatan x-ray fiber diffraction patterns. Current models of 8-fold dermatan sulfate chains containing (4)C(1) iduronate refine to right-handed helices, which possess no intramolecular hydrogen-bonds. However, MD simulations predict that models containing (2)S(O) iduronate could provide better (8(5) helix) starting structures for refinement. Thus, the 8-fold dermatan sulfate refinement (8(3) helix) could be in error.
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Affiliation(s)
- A Almond
- School of Biological Sciences, University of Manchester, 2.205 Stopford Building, Oxford Road, Manchester M13 9PT, UK
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50
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Gribbon P, Heng BC, Hardingham TE. The molecular basis of the solution properties of hyaluronan investigated by confocal fluorescence recovery after photobleaching. Biophys J 1999; 77:2210-6. [PMID: 10512840 PMCID: PMC1300501 DOI: 10.1016/s0006-3495(99)77061-x] [Citation(s) in RCA: 93] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
Hyaluronan (HA) is a highly hydrated polyanion, which is a network-forming and space-filling component in the extracellular matrix of animal tissues. Confocal fluorescence recovery after photobleaching (confocal-FRAP) was used to investigate intramolecular hydrogen bonding and electrostatic interactions in hyaluronan solutions. Self and tracer lateral diffusion coefficients within hyaluronan solutions were measured over a wide range of concentrations (c), with varying electrolyte and at neutral and alkaline pH. The free diffusion coefficient of fluoresceinamine-labeled HA of 500 kDa in PBS was 7.9 x 10(-8) cm(2) s(-1) and of 830 kDa HA was 5.6 x 10(-8) cm(2) s(-1). Reductions in self- and tracer-diffusion with c followed a stretched exponential model. Electrolyte-induced polyanion coil contraction and destiffening resulted in a 2.8-fold increase in self-diffusion between 0 and 100 mM NaCl. Disruption of hydrogen bonds by strong alkali (0.5 M NaOH) resulted in further larger increases in self- and tracer-diffusion coefficients, consistent with a more dynamic and permeable network. Concentrated hyaluronan solution properties were attributed to hydrodynamic and entanglement interactions between domains. There was no evidence of chain-chain associations. At physiological electrolyte concentration and pH, the greatest contribution to the intrinsic stiffness of hyaluronan appeared to be due to hydrogen bonds between adjacent saccharides.
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Affiliation(s)
- P Gribbon
- Wellcome Trust Centre for Cell-Matrix Research, School of Biological Sciences, University of Manchester, Manchester M13 9PT, United Kingdom
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