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Meneghetti M, Naughton L, O’Shea C, Koffi Teki DSE, Chagnault V, Nader HB, Rudd TR, Yates EA, Kovensky J, Miller GJ, Lima MA. Using NMR to Dissect the Chemical Space and O-Sulfation Effects within the O- and S-Glycoside Analogues of Heparan Sulfate. ACS OMEGA 2022; 7:24461-24467. [PMID: 35874203 PMCID: PMC9301708 DOI: 10.1021/acsomega.2c02070] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Heparan sulfate (HS), a sulfated linear carbohydrate that decorates the cell surface and extracellular matrix, is ubiquitously distributed throughout the animal kingdom and represents a key regulator of biological processes and a largely untapped reservoir of potential therapeutic targets. The temporal and spatial variations in the HS structure underpin the concept of "heparanome" and a complex network of HS binding proteins. However, despite its widespread biological roles, the determination of direct structure-to-function correlations is impaired by HS chemical heterogeneity. Attempts to correlate substitution patterns (mostly at the level of sulfation) with a given biological activity have been made. Nonetheless, these do not generally consider higher-level conformational effects at the carbohydrate level. Here, the use of NMR chemical shift analysis, NOEs, and spin-spin coupling constants sheds new light on how different sulfation patterns affect the polysaccharide backbone geometry. Furthermore, the substitution of native O-glycosidic linkages to hydrolytically more stable S-glycosidic forms leads to observable conformational changes in model saccharides, suggesting that alternative chemical spaces can be accessed and explored using such mimetics. Employing a series of systematically modified heparin oligosaccharides (as a proxy for HS) and chemically synthesized O- and S-glycoside analogues, the chemical space occupied by such compounds is explored and described.
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Affiliation(s)
- Maria
C.Z. Meneghetti
- Departamento
de Bioquímica, Instituto de Farmacologia e Biologia Molecular,
Escola Paulista de Medicina, Universidade
Federal de São Paulo, Rua Três de Maio, 100, São Paulo 04044-020, São Paulo, Brazil
| | - Lucy Naughton
- School
of Life Sciences, Keele University, Keele ST55BG, Staffordshire, U.K.
- Centre
for Glycosciences, Keele University, Keele ST55BG, Staffordshire, U.K.
| | - Conor O’Shea
- Centre
for Glycosciences, Keele University, Keele ST55BG, Staffordshire, U.K.
- Lennard-Jones
Laboratories, School of Chemical and Physical Sciences, Keele University, Keele ST55BG, Staffordshire, U.K.
| | - Dindet S.-E. Koffi Teki
- Laboratoire
de Glycochimie, des Antimicrobiens et des Agroressources (LG2A), UMR
7378 CNRS, Université de Picardie
Jules Verne, 33 rue Saint Leu, Amiens Cedex F-80039, France
| | - Vincent Chagnault
- Laboratoire
de Glycochimie, des Antimicrobiens et des Agroressources (LG2A), UMR
7378 CNRS, Université de Picardie
Jules Verne, 33 rue Saint Leu, Amiens Cedex F-80039, France
| | - Helena B. Nader
- Departamento
de Bioquímica, Instituto de Farmacologia e Biologia Molecular,
Escola Paulista de Medicina, Universidade
Federal de São Paulo, Rua Três de Maio, 100, São Paulo 04044-020, São Paulo, Brazil
| | - Timothy R. Rudd
- National
Institute for Biological Standards and Control (NIBSC), Blanche Lane, South Mimms, Potters Bar EN6 3QG, Hertfordshire, U.K.
- Department
of Biochemistry and Systems Biology, Institute of Systems, Molecular
and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, U.K.
| | - Edwin A. Yates
- Department
of Biochemistry and Systems Biology, Institute of Systems, Molecular
and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, U.K.
| | - José Kovensky
- Laboratoire
de Glycochimie, des Antimicrobiens et des Agroressources (LG2A), UMR
7378 CNRS, Université de Picardie
Jules Verne, 33 rue Saint Leu, Amiens Cedex F-80039, France
| | - Gavin J. Miller
- Centre
for Glycosciences, Keele University, Keele ST55BG, Staffordshire, U.K.
- Lennard-Jones
Laboratories, School of Chemical and Physical Sciences, Keele University, Keele ST55BG, Staffordshire, U.K.
| | - Marcelo A. Lima
- School
of Life Sciences, Keele University, Keele ST55BG, Staffordshire, U.K.
- Centre
for Glycosciences, Keele University, Keele ST55BG, Staffordshire, U.K.
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2
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Bodoor K, El-Barghouthi MI, Alhamed DF, Assaf KI, Alrawashdeh L. Cucurbit[7]uril recognition of glucosamine anomers in water. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.119178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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3
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Ryan EO, Jiang Z, Nguyen H, Wang X. Interactions of Pleiotrophin with a Structurally Defined Heparin Hexasaccharide. Biomolecules 2021; 12:biom12010050. [PMID: 35053198 PMCID: PMC8773689 DOI: 10.3390/biom12010050] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 12/21/2021] [Accepted: 12/27/2021] [Indexed: 11/21/2022] Open
Abstract
Pleiotrophin (PTN) is a potent cytokine that plays an important role in neural generation, angiogenesis, inflammation, and cancers. Its interactions with the polysaccharide glycosaminoglycan (GAG) are crucial to PTN’s biological activities. In this study, we investigated the interaction of selectively protonated PTN with the heparin hexasaccharide ΔUA2S-(GlcNS6S-IdoA2S)2-GlcNS6S using solution NMR. The use of a structurally defined oligosaccharide and selectively protonated PTN enabled us to obtain intermolecular contacts using unfiltered NOESY experiments, significantly increasing the amount of high-resolution structural information obtainable. Our data showed that PTN’s arginines, lysines, and tryptophans in the two structured domains have strong interactions with the 2-O-sulfated uronate protons in the heparin hexasaccharide. Consistent with the NMR data is the observation that 2-O-desulfation and N-desulfation/N-acetylation significantly decreased heparin hexasaccharides’ affinity for PTN, while 6-O-desulfation only modestly affected the interactions with PTN. These results allowed us to hypothesize that PTN has a preference for sulfate clusters centered on the GlcNS6S-IdoA2S disaccharide. Using these data and the fact that PTN domains mostly bind heparin hexasaccharides independently, models of the PTN-heparin complex were constructed.
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Affiliation(s)
| | | | | | - Xu Wang
- Correspondence: ; Tel.: +1-480-7278256
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4
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Ma ST, Lee CW, Liu WM. Synthesis of 4-thiol-furanosidic uronate via hydrothiolation reaction. RSC Adv 2021; 11:18409-18416. [PMID: 35480947 PMCID: PMC9033442 DOI: 10.1039/d1ra02110a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 05/05/2021] [Indexed: 11/25/2022] Open
Abstract
Uronic acids are not only important building blocks of polysaccharides and oligosaccharides but also are widely used in the food and pharmaceutical industries. Inspired by the structure of natural products, here, we disclosed base-mediated and radical-mediated hydrothiolation reactions for the preparation of thiol-contained uronates. In comparison with base-mediated reaction, radical-mediated hydrothiolation is inefficient due to the electron-withdrawing group on the ethylene group; nevertheless, the adduct had excellent stereoselectivity at both C-4 and C-5 positions. For the alkaline approach, thiols as nucleophiles can regioselectively and stereoselectively attach to the C-4 position of Δ-4,5-unsaturated uronate with moderate to good yields. However, poor stereoselectivity at the C-5 position was observed due to retro thiol-Michael addition. After removing the protecting group of the thiol, the thiol adduct was isomerized to the furanosidic form and the 4-thiol-furanosidic uronate derivative was synthesized for the first time. Uronic acids are not only important building blocks of bioactive molecules but also are widely used in the food and pharmaceutical industries. Its derivative, 4-thiol-furanosidic uronate was successfully synthesized and firstly reported here.![]()
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Affiliation(s)
- Shih-Ting Ma
- Department of Chemistry
- Fu Jen Catholic University
- New Taipei City 24205
- Republic of China
| | - Chia-Wei Lee
- Department of Chemistry
- Fu Jen Catholic University
- New Taipei City 24205
- Republic of China
| | - Wei-Min Liu
- Department of Chemistry
- Fu Jen Catholic University
- New Taipei City 24205
- Republic of China
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5
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Nagarajan B, Sankaranarayanan NV, Desai UR. Rigorous analysis of free solution glycosaminoglycan dynamics using simple, new tools. Glycobiology 2020; 30:516-527. [PMID: 32080710 PMCID: PMC8179626 DOI: 10.1093/glycob/cwaa015] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 02/03/2020] [Accepted: 02/09/2020] [Indexed: 11/15/2022] Open
Abstract
Heparin/heparan sulfates (H/HS) are ubiquitous biopolymers that interact with many proteins to induce a range of biological functions. Unfortunately, how these biopolymers recognize their preferred protein targets remain poorly understood. It is suggested that computational simulations offer attractive avenues but a number of challenges, e.g., difficulty of selecting a comprehensive force field, few simple tools to interpret data, among others, remain. This work addresses several such challenges so as to help ease the implementation and analysis of computational experiments. First, this work presents a rigorous comparison of two different recent force fields, CHARMM36 and GLYCAM06, for H/HS studies. Second, it introduces two new straightforward parameters, i.e., end-to-end distance and minimum volume enclosing ellipsoid, to understand the myriad conformational forms of oligosaccharides that evolve over time in water. Third, it presents an application to elucidate the number and nature of inter and intramolecular, nondirect bridging water molecules, which help stabilize unique forms of H/HS. The results show that nonspecialists can use either CHARMM36 or GLYCAM06 force fields because both gave comparable results, albeit with small differences. The comparative study shows that the HS hexasaccharide samples a range of conformations with nearly equivalent energies, which could be the reason for its recognition by different proteins. Finally, analysis of the nondirect water bridges across the dynamics trajectory shows their importance in stabilization of certain conformational forms, which may become important for protein recognition. Overall, the work aids nonspecialists employ computational studies for understanding the solution behavior of H/HS.
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Affiliation(s)
- Balaji Nagarajan
- Institute for Structural Biology, Drug Discovery and Development, 800 E. Leigh Street, Suite 212, Richmond, VA 23219, USA
- Department of Medicinal Chemistry, 800 E. Leigh Street, Suite 205, Richmond, VA 23298, USA
| | - Nehru Viji Sankaranarayanan
- Institute for Structural Biology, Drug Discovery and Development, 800 E. Leigh Street, Suite 212, Richmond, VA 23219, USA
- Department of Medicinal Chemistry, 800 E. Leigh Street, Suite 205, Richmond, VA 23298, USA
| | - Umesh R Desai
- Institute for Structural Biology, Drug Discovery and Development, 800 E. Leigh Street, Suite 212, Richmond, VA 23219, USA
- Department of Medicinal Chemistry, 800 E. Leigh Street, Suite 205, Richmond, VA 23298, USA
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6
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García-Jiménez MJ, Gil-Caballero S, Canales Á, Jiménez-Barbero J, de Paz JL, Nieto PM. Interactions between a Heparin Trisaccharide Library and FGF-1 Analyzed by NMR Methods. Int J Mol Sci 2017. [PMID: 28629128 PMCID: PMC5486114 DOI: 10.3390/ijms18061293] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
FGF-1 is a potent mitogen that, by interacting simultaneously with Heparan Sulfate Glycosaminoglycan HSGAG and the extracellular domains of its membrane receptor (FGFR), generates an intracellular signal that finally leads to cell division. The overall structure of the ternary complex Heparin:FGF-1:FGFR has been finally elucidated after some controversy and the interactions within the ternary complex have been deeply described. However, since the structure of the ternary complex was described, not much attention has been given to the molecular basis of the interaction between FGF-1 and the HSGAG. It is known that within the complex, the carbohydrate maintains the same helical structure of free heparin that leads to sulfate groups directed towards opposite directions along the molecular axis. The precise role of single individual interactions remains unclear, as sliding and/or rotating of the saccharide along the binding pocket are possibilities difficult to discard. The HSGAG binding pocket can be subdivided into two regions, the main one can accommodate a trisaccharide, while the other binds a disaccharide. We have studied and analyzed the interaction between FGF-1 and a library of trisaccharides by STD-NMR and selective longitudinal relaxation rates. The library of trisaccharides corresponds to the heparin backbone and it has been designed to interact with the main subsite of the protein.
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Affiliation(s)
- María José García-Jiménez
- Glycosystems Laboratory, Instituto de Investigaciones Químicas (IIQ), Centro de Investigaciones Científicas Isla de La Cartuja, CSIC and Universidad de Sevilla, Américo Vespucio, 49, 41092 Sevilla, Spain.
| | - Sergio Gil-Caballero
- Glycosystems Laboratory, Instituto de Investigaciones Químicas (IIQ), Centro de Investigaciones Científicas Isla de La Cartuja, CSIC and Universidad de Sevilla, Américo Vespucio, 49, 41092 Sevilla, Spain.
| | - Ángeles Canales
- Complutense University of Madrid, Fac CC Quim, Department Quim Organ 1, Avd Complutense S/N, E-28040 Madrid, Spain.
| | - Jesús Jiménez-Barbero
- CIC bioGUNE, Bizkaia Technology Park, Building 801A, 48170 Derio, Spain.
- Basque Foundation for Science, Maria Diaz de Haro 13, 48009 Bilbao, Spain.
- Department of Organic Chemistry II, Faculty of Science and Technology, University of the Basque Country, 48940 Leioa, Bizkaia, Spain.
| | - José L de Paz
- Glycosystems Laboratory, Instituto de Investigaciones Químicas (IIQ), Centro de Investigaciones Científicas Isla de La Cartuja, CSIC and Universidad de Sevilla, Américo Vespucio, 49, 41092 Sevilla, Spain.
| | - Pedro M Nieto
- Glycosystems Laboratory, Instituto de Investigaciones Químicas (IIQ), Centro de Investigaciones Científicas Isla de La Cartuja, CSIC and Universidad de Sevilla, Américo Vespucio, 49, 41092 Sevilla, Spain.
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7
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Singh A, Tessier MB, Pederson K, Wang X, Venot AP, Boons GJ, Prestegard JH, Woods RJ. Extension and validation of the GLYCAM force field parameters for modeling glycosaminoglycans. CAN J CHEM 2016; 94:927-935. [PMID: 28603292 PMCID: PMC5464424 DOI: 10.1139/cjc-2015-0606] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Glycosaminoglycans (GAGs) are an important class of carbohydrates that serve critical roles in blood clotting, tissue repair, cell migration and adhesion, and lubrication. The variable sulfation pattern and iduronate ring conformations in GAGs influence their polymeric structure and nature of interaction. This study characterizes several heparin-like GAG disaccharides and tetrasaccharides using NMR and molecular dynamics simulations to assist in the development of parameters for GAGs within the GLYCAM06 force field. The force field additions include parameters and charges for a transferable sulfate group for O- and N-sulfation, neutral (COOH) forms of iduronic and glucuronic acid, and Δ4,5-unsaturated uronate (ΔUA) residues. ΔUA residues frequently arise from the enzymatic digestion of heparin and heparin sulfate. Simulations of disaccharides containing ΔUA reveal that the presence of sulfation on this residue alters the relative populations of 1H2 and 2H1 ring conformations. Simulations of heparin tetrasaccharides containing N-sulfation in place of N-acetylation on glucosamine residues influence the ring conformations of adjacent iduronate residues.
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Affiliation(s)
- Arunima Singh
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, GA 30602, USA
| | - Matthew B Tessier
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, GA 30602, USA
| | - Kari Pederson
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, GA 30602, USA
| | - Xiaocong Wang
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, GA 30602, USA
| | - Andre P Venot
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, GA 30602, USA
| | - Geert-Jan Boons
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, GA 30602, USA
| | - James H Prestegard
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, GA 30602, USA
| | - Robert J Woods
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, GA 30602, USA
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8
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Wu L, Viola CM, Brzozowski AM, Davies GJ. Structural characterization of human heparanase reveals insights into substrate recognition. Nat Struct Mol Biol 2015; 22:1016-22. [PMID: 26575439 PMCID: PMC5008439 DOI: 10.1038/nsmb.3136] [Citation(s) in RCA: 121] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Accepted: 11/09/2015] [Indexed: 12/13/2022]
Abstract
Heparan sulfate (HS) is a glycosaminoglycan that forms a key component of the extracellular matrix (ECM). Breakdown of HS is carried out by heparanase (HPSE), an endo-β-glucuronidase of the glycoside hydrolase 79 (GH79) family. Overexpression of HPSE results in breakdown of extracellular HS and release of stored growth factors and hence is strongly linked to cancer metastasis. Here we present crystal structures of human HPSE at 1.6-Å to 1.9-Å resolution that reveal how an endo-acting binding cleft is exposed by proteolytic activation of latent proHPSE. We used oligosaccharide complexes to map the substrate-binding and sulfate-recognition motifs. These data shed light on the structure and interactions of a key enzyme involved in ECM maintenance and provide a starting point for the design of HPSE inhibitors for use as biochemical tools and anticancer therapeutics.
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Affiliation(s)
- Liang Wu
- Department of Chemistry, University of York, York, UK
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9
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Remko M, Broer R, Remková A, Van Duijnen PT. How strong are Ca2+–heparin and Zn2+–heparin interactions? Chem Phys Lett 2015. [DOI: 10.1016/j.cplett.2014.12.018] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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10
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Sankaranarayanan NV, Sarkar A, Desai UR, Mosier PD. Designing "high-affinity, high-specificity" glycosaminoglycan sequences through computerized modeling. Methods Mol Biol 2015; 1229:289-314. [PMID: 25325961 DOI: 10.1007/978-1-4939-1714-3_24] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The prediction of high-affinity and/or high-specificity protein-glycosaminoglycan (GAG) interactions is an inherently difficult task, due to several factors including the shallow nature of the typical GAG-binding site and the inherent size, flexibility, diversity, and polydisperse nature of the GAG molecules. Here, we present a generally applicable methodology termed Combinatorial Library Virtual Screening (CVLS) that can identify potential high-affinity, high-specificity protein-GAG interactions from very large GAG combinatorial libraries and a suitable GAG-binding protein. We describe the CVLS approach along with the rationale behind it and provide validation for the method using the well-known antithrombin-thrombin-heparin system.
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Affiliation(s)
- Nehru Viji Sankaranarayanan
- Department of Medicinal Chemistry, Institute for Structural Biology and Drug Discovery, Virginia Commonwealth University, 800 E. Leigh Street, Suite 212, Richmond, VA, 23298, USA
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11
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Hricovíni M, Driguez PA, Malkina OL. NMR and DFT analysis of trisaccharide from heparin repeating sequence. J Phys Chem B 2014; 118:11931-42. [PMID: 25254635 DOI: 10.1021/jp508045n] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
NMR and density functional theory (DFT) have afforded detailed information on the molecular geometry and spin-spin coupling constants of a trisaccharide from the heparin repeating-sequence. The fully optimized molecular structures of two trisaccharide conformations (differing from each other in the form of the central iduronic acid residue) were obtained using the B3LYP/6-311+G(d,p) level of theory in the presence of solvent, the latter included as either explicit water molecules or via a continuum solvent model. NMR spin-spin coupling constants were also computed using various basis sets and functionals and then compared with measured experimental values. Optimized structures for both conformers showed differences in geometry at the glycosidic linkages and in the formation of intramolecular hydrogen bonds. Three-bond proton-proton coupling constants ((3)JH-C-C-H), based on fully optimized geometry computed using the B3LYP/6-311+G(d,p)/UFF level of theory and hydrated with 57 water molecules, showed that the best agreement with experiment was obtained with the 6-311+G(d,p) basis set and a weighted average of 55:45 ((1)C4:(2)S0) of the IdoA2S forms. Other basis sets, DGDZVP and TZVP, also gave acceptable data for most coupling constants, with DGDZVP outperforming the TZVP. Detailed analysis of Fermi-contact contributions to (3)JH-C-C-H showed that important contributions arise from oxygen at both glycosidic linkages, as well as from oxygen atoms on the neighboring monosaccharide units. Their contribution to the Fermi term cannot be neglected and must be taken into account for a correct description of coupling constants. The analysis also showed that the magnitude of paramagnetic (PSO) and diamagnetic (DSO) spin-orbit contributions is comparable to the magnitude of the Fermi-contact contribution in some coupling constants in the IdoA2S residue. Calculations of the localized molecular orbital contributions to the DSO terms from separate conformational residues showed that the contribution from adjacent residues is not negligible and can be important for the spin-spin coupling constants between protons located close to the geometrical center of the molecule. These contributions should be taken into account when interpreting DSO terms in spin-spin coupling constants especially in large molecules.
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Affiliation(s)
- Miloš Hricovíni
- Institute of Chemistry, Slovak Academy of Sciences , 845 38 Bratislava, Slovakia
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12
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Casu B, Naggi A, Torri G. Re-visiting the structure of heparin. Carbohydr Res 2014; 403:60-8. [PMID: 25088334 DOI: 10.1016/j.carres.2014.06.023] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Accepted: 06/22/2014] [Indexed: 01/12/2023]
Abstract
The sulfated polysaccharide heparin has been used as a life-saving anticoagulant in clinics well before its detailed structure was known. This mini-review is a survey of the evolution in the discovery of the primary and secondary structure of heparin. Highlights in this history include elucidation and synthesis of the specific sequence that binds to antithrombin, the development of low-molecular-weight heparins currently used as antithrombotic drugs, and the most promising start of chemo-enzymatic synthesis. Special emphasis is given to peculiar conformational properties contributing to interaction with proteins that modulate different biological properties.
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Affiliation(s)
- Benito Casu
- G. Ronzoni Institute for Chemical and Biochemical Research, via G. Colombo, 81 20133 Milan, Italy.
| | - Annamaria Naggi
- G. Ronzoni Institute for Chemical and Biochemical Research, via G. Colombo, 81 20133 Milan, Italy
| | - Giangiacomo Torri
- G. Ronzoni Institute for Chemical and Biochemical Research, via G. Colombo, 81 20133 Milan, Italy
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13
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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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14
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15
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García-Mayoral MF, Canales Á, Díaz D, López-Prados J, Moussaoui M, de Paz JL, Angulo J, Nieto PM, Jiménez-Barbero J, Boix E, Bruix M. Insights into the glycosaminoglycan-mediated cytotoxic mechanism of eosinophil cationic protein revealed by NMR. ACS Chem Biol 2013; 8:144-51. [PMID: 23025322 DOI: 10.1021/cb300386v] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Protein-glycosaminoglycan interactions are essential in many biological processes and human diseases, yet how their recognition occurs is poorly understood. Eosinophil cationic protein (ECP) is a cytotoxic ribonuclease that interacts with glycosaminoglycans at the cell surface; this promotes the destabilization of the cellular membrane and triggers ECP's toxic activity. To understand this membrane destabilization event and the differences in the toxicity of ECP and its homologues, the high resolution solution structure of the complex between full length folded ECP and a heparin-derived trisaccharide (O-iPr-α-D-GlcNS6S-α(1-4)-L-IdoA2S-α(1-4)-D-GlcNS6S) has been solved by NMR methods and molecular dynamics simulations. The bound protein retains the tertiary structure of the free protein. The (2)S(0) conformation of the IdoA ring is preferably recognized by the protein. We have identified the precise location of the heparin binding site, dissected the specific interactions responsible for molecular recognition, and defined the structural requirements for this interaction. The structure reveals the contribution of Arg7, Gln14, and His15 in helix α1, Gln40 in strand β1, His64 in loop 4, and His128 in strand β6 in the recognition event and corroborates the previously reported participation of residues Arg34-Asn39. The participation of the catalytic triad (His15, Lys38, His128) in recognizing the heparin mimetic reveals, at atomic resolution, the mechanism of heparin's inhibition of ECP's ribonucleolytic activity. We have integrated all the available data to propose a molecular model for the membrane interaction process. The solved NMR complex provides the structural model necessary to design inhibitors to block ECP's toxicity implicated in eosinophil pathologies.
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Affiliation(s)
- M. Flor García-Mayoral
- Departamento
de Química
Física Biológica, Instituto de Química Física Rocasolano, CSIC, Madrid, Spain
| | - Ángeles Canales
- Departamento de Química
Orgánica I, Facultad de Ciencias Químicas, Universidad Complutense, Madrid, Spain
| | - Dolores Díaz
- Departamento de Biología
Físico Química, Centro de Investigaciones Biológicas, CSIC, Madrid, Spain
| | - Javier López-Prados
- Departamento de Química
Orgánica y Biológica, Instituto de Investigaciones Químicas, CSIC-Universidad de Sevilla, Sevilla,
Spain
| | - Mohammed Moussaoui
- Departamento de Bioquímica
y Biología Molecular, Facultad de Biociencias, Universidad Autónoma de Barcelona, Barcelona,
Spain
| | - José L. de Paz
- Departamento de Química
Orgánica y Biológica, Instituto de Investigaciones Químicas, CSIC-Universidad de Sevilla, Sevilla,
Spain
| | - Jesús Angulo
- Departamento de Química
Orgánica y Biológica, Instituto de Investigaciones Químicas, CSIC-Universidad de Sevilla, Sevilla,
Spain
| | - Pedro M. Nieto
- Departamento de Química
Orgánica y Biológica, Instituto de Investigaciones Químicas, CSIC-Universidad de Sevilla, Sevilla,
Spain
| | - Jesús Jiménez-Barbero
- Departamento de Biología
Físico Química, Centro de Investigaciones Biológicas, CSIC, Madrid, Spain
| | - Ester Boix
- Departamento de Bioquímica
y Biología Molecular, Facultad de Biociencias, Universidad Autónoma de Barcelona, Barcelona,
Spain
| | - Marta Bruix
- Departamento
de Química
Física Biológica, Instituto de Química Física Rocasolano, CSIC, Madrid, Spain
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16
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Chabrol E, Nurisso A, Daina A, Vassal-Stermann E, Thepaut M, Girard E, Vivès RR, Fieschi F. Glycosaminoglycans are interactants of Langerin: comparison with gp120 highlights an unexpected calcium-independent binding mode. PLoS One 2012; 7:e50722. [PMID: 23226363 PMCID: PMC3511376 DOI: 10.1371/journal.pone.0050722] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2012] [Accepted: 10/24/2012] [Indexed: 12/29/2022] Open
Abstract
Langerin is a C-type lectin specifically expressed in Langerhans cells. As recently shown for HIV, Langerin is thought to capture pathogens and mediate their internalisation into Birbeck Granules for elimination. However, the precise functions of Langerin remain elusive, mostly because of the lack of information on its binding properties and physiological ligands. Based on recent reports that Langerin binds to sulfated sugars, we conducted here a comparative analysis of Langerin interaction with mannose-rich HIV glycoprotein gp120 and glycosaminoglycan (GAGs), a family of sulfated polysaccharides expressed at the surface of most mammalian cells. Our results first revealed that Langerin bound to these different glycans through very distinct mechanisms and led to the identification of a novel, GAG-specific binding mode within Langerin. In contrast to the canonical lectin domain, this new binding site showed no Ca(2+)-dependency, and could only be detected in entire, trimeric extracellular domains of Langerin. Interestingly binding to GAGs, did not simply rely on a net charge effect, but rather on more discrete saccharide features, such as 6-O-sulfation, or iduronic acid content. Using molecular modelling simulations, we proposed a model of Langerin/heparin complex, which located the GAG binding site at the interface of two of the three Carbohydrate-recognition domains of the protein, at the edge of the a-helix coiled-coil. To our knowledge, the binding properties that we have highlighted here for Langerin, have never been reported for C-type lectins before. These findings provide new insights towards the understanding of Langerin biological functions.
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Affiliation(s)
- Eric Chabrol
- Groupe Membrane & Pathogens, Institut de Biologie Structurale, Université Joseph Fourier, Grenoble, France
- UMR 5075, CNRS, Grenoble, France
- Departement des sciences du vivant, CEA, Grenoble, France
| | - Alessandra Nurisso
- Département de Pharmacochimie, Université de Genève, Genève, Switzerland
| | - Antoine Daina
- Département de Pharmacochimie, Université de Genève, Genève, Switzerland
- Molecular Modeling Group, Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Emilie Vassal-Stermann
- UMR 5075, CNRS, Grenoble, France
- Departement des sciences du vivant, CEA, Grenoble, France
- Groupe SAGAG, Institut de Biologie Structurale, Université Joseph Fourier, Grenoble, France
| | - Michel Thepaut
- Groupe Membrane & Pathogens, Institut de Biologie Structurale, Université Joseph Fourier, Grenoble, France
- UMR 5075, CNRS, Grenoble, France
- Departement des sciences du vivant, CEA, Grenoble, France
| | - Eric Girard
- UMR 5075, CNRS, Grenoble, France
- Departement des sciences du vivant, CEA, Grenoble, France
- Groupe ELMA, Institut de Biologie Structurale, Université Joseph Fourier, Grenoble, France
| | - Romain R. Vivès
- UMR 5075, CNRS, Grenoble, France
- Departement des sciences du vivant, CEA, Grenoble, France
- Molecular Modeling Group, Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Franck Fieschi
- Groupe Membrane & Pathogens, Institut de Biologie Structurale, Université Joseph Fourier, Grenoble, France
- UMR 5075, CNRS, Grenoble, France
- Departement des sciences du vivant, CEA, Grenoble, France
- Institut Universitaire de France, Paris, France
- * E-mail:
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17
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The efficient structure elucidation of minor components in heparin digests using microcoil NMR. Carbohydr Res 2011; 346:2244-54. [DOI: 10.1016/j.carres.2011.07.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2011] [Accepted: 07/09/2011] [Indexed: 11/23/2022]
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18
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Hricovíni M. Effect of Solvent and Counterions upon Structure and NMR Spin−Spin Coupling Constants in Heparin Disaccharide. J Phys Chem B 2011; 115:1503-11. [DOI: 10.1021/jp1098552] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Miloš Hricovíni
- Institute of Chemistry, Slovak Academy of Sciences, 845 38 Bratislava, Slovakia
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19
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Ponedel’kina IY, Lukina ES, Odinokov VN. Acid glycosaminoglycans and their chemical modification. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2011. [DOI: 10.1134/s1068162008010019] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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20
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Jones CJ, Beni S, Limtiaco JFK, Langeslay DJ, Larive CK. Heparin characterization: challenges and solutions. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2011; 4:439-465. [PMID: 21469955 DOI: 10.1146/annurev-anchem-061010-113911] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Although heparin is an important and widely prescribed pharmaceutical anticoagulant, its high degree of sequence microheterogeneity and size polydispersity make molecular-level characterization challenging. Unlike nucleic acids and proteins that are biosynthesized through template-driven assembly processes, heparin and the related glycosaminoglycan heparan sulfate are actively remodeled during biosynthesis through a series of enzymatic reactions that lead to variable levels of O- and N-sulfonation and uronic acid epimers. As summarized in this review, heparin sequence information is determined through a bottom-up approach that relies on depolymerization reactions, size- and charge-based separations, and sensitive mass spectrometric and nuclear magnetic resonance experiments to determine the structural identity of component oligosaccharides. The structure-elucidation process, along with its challenges and opportunities for future analytical improvements, is reviewed and illustrated for a heparin-derived hexasaccharide.
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Affiliation(s)
- Christopher J Jones
- Department of Chemistry, University of California, Riverside, California 92521, USA.
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21
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Limtiaco JFK, Beni S, Jones CJ, Langeslay DJ, Larive CK. NMR methods to monitor the enzymatic depolymerization of heparin. Anal Bioanal Chem 2010; 399:593-603. [PMID: 20814667 PMCID: PMC3015211 DOI: 10.1007/s00216-010-4132-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2010] [Revised: 08/09/2010] [Accepted: 08/15/2010] [Indexed: 11/30/2022]
Abstract
Heparin and the related glycosaminoglycan, heparan sulfate, are polydisperse linear polysaccharides that mediate numerous biological processes due to their interaction with proteins. Because of the structural complexity and heterogeneity of heparin and heparan sulfate, digestion to produce smaller oligosaccharides is commonly performed prior to separation and analysis. Current techniques used to monitor the extent of heparin depolymerization include UV absorption to follow product formation and size exclusion or strong anion exchange chromatography to monitor the size distribution of the components in the digest solution. In this study, we used 1H nuclear magnetic resonance (NMR) survey spectra and NMR diffusion experiments in conjunction with UV absorption measurements to monitor heparin depolymerization using the enzyme heparinase I. Diffusion NMR does not require the physical separation of the components in the reaction mixture and instead can be used to monitor the reaction solution directly in the NMR tube. Using diffusion NMR, the enzymatic reaction can be stopped at the desired time point, maximizing the abundance of larger oligosaccharides for protein-binding studies or completion of the reaction if the goal of the study is exhaustive digestion for characterization of the disaccharide composition. In this study, porcine intestinal mucosa heparin was depolymerized using the enzyme heparinase I. The unsaturated bond formed by enzymatic cleavage serves as a UV chromophore that can be used to monitor the progress of the depolymerization and for the detection and quantification of oligosaccharides in subsequent separations. The double bond also introduces a unique multiplet with peaks at 5.973, 5.981, 5.990, and 5.998 ppm in the 1H-NMR spectrum downfield of the anomeric region. This multiplet is produced by the proton of the C-4 double bond of the non-reducing end uronic acid at the cleavage site. Changes in this resonance were used to monitor the progression of the enzymatic digestion and compared to the profile obtained from UV absorbance measurements. In addition, in situ NMR diffusion measurements were explored for their ability to profile the different-sized components generated over the course of the digestion. DOSY spectra of intact (blue) and digested (red) heparin illustrating the differences in their diffusion coefficients. ![]()
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22
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Molecular structure of basic oligomeric building units of heparan-sulfate glycosaminoglycans. Struct Chem 2010. [DOI: 10.1007/s11224-010-9633-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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23
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Synthesis and conformational analysis of carbasugar bioisosteres of α-l-iduronic acid and its methyl glycoside. Carbohydr Res 2010; 345:984-93. [DOI: 10.1016/j.carres.2010.03.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2009] [Revised: 02/15/2010] [Accepted: 03/01/2010] [Indexed: 11/18/2022]
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24
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Gandhi NS, Mancera RL. Can current force fields reproduce ring puckering in 2-O-sulfo-α-l-iduronic acid? A molecular dynamics simulation study. Carbohydr Res 2010; 345:689-95. [DOI: 10.1016/j.carres.2009.12.020] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2009] [Revised: 11/30/2009] [Accepted: 12/20/2009] [Indexed: 10/20/2022]
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25
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Kövér KE, Szilágyi L, Batta G, Uhrín D, Jiménez-Barbero J. Biomolecular Recognition by Oligosaccharides and Glycopeptides: The NMR Point of View. COMPREHENSIVE NATURAL PRODUCTS II 2010:197-246. [DOI: 10.1016/b978-008045382-8.00193-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/27/2023]
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26
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Xia J, Margulis CJ. Computational Study of the Conformational Structures of Saccharides in Solution Based on J Couplings and the “Fast Sugar Structure Prediction Software”. Biomacromolecules 2009; 10:3081-8. [DOI: 10.1021/bm900756q] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Junchao Xia
- Department of Chemistry, University of Iowa, Iowa City, Iowa 52242
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27
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Jin L, Hricovíni M, Deakin JA, Lyon M, Uhrín D. Residual dipolar coupling investigation of a heparin tetrasaccharide confirms the limited effect of flexibility of the iduronic acid on the molecular shape of heparin. Glycobiology 2009; 19:1185-96. [PMID: 19648354 PMCID: PMC2757574 DOI: 10.1093/glycob/cwp105] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The solution conformation of a fully sulfated heparin-derived tetrasaccharide, I, was studied in the presence of a 4-fold excess of Ca2+. Proton–proton and proton–carbon residual dipolar couplings (RDCs) were measured in a neutral aligning medium. The order parameters of two rigid hexosamine rings of I were determined separately using singular value decomposition and ab initio structures of disaccharide fragments of I. The order parameters were very similar implying that a common order tensor can be used to analyze the structure of I. Using one order tensor, RDCs of both hexosamine rings were used as restraints in molecular dynamics simulations. RDCs of the inner iduronic acid were calculated for every point of the molecular dynamics trajectory. The fitting of the calculated RDCs of the two forms of the iduronic acid to the experimental values yielded a population of 1C4 and 2So conformers of iduronic acid that agreed well with the analysis based on proton–proton scalar coupling constants. The glycosidic linkage torsion angles in RDC-restrained molecular dynamics (MD) structures of I are consistent with the interglycosidic three-bond proton–carbon coupling constants. These structures also show that the shape of heparin is not affected dramatically by the conformational flexibility of the iduronic acid ring. This is in line with conclusions of previous studies based on MD simulations and the analysis of 1H-1H NOEs. Our work therefore demonstrates the effectiveness of RDCs in the conformational analysis of glycosaminoglycans.
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Affiliation(s)
- Lan Jin
- School of Chemistry, University of Edinburgh, Edinburgh, Scotland
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28
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Gandhi NS, Mancera RL. Free energy calculations of glycosaminoglycan-protein interactions. Glycobiology 2009; 19:1103-15. [PMID: 19643843 DOI: 10.1093/glycob/cwp101] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Glycosaminoglycans (GAGs) are complex highly charged linear polysaccharides that have a variety of roles in biological processes. We report the first use of molecular dynamics (MD) free energy calculations using the MM/PBSA method to investigate the binding of GAGs to protein molecules, namely the platelet endothelial cell adhesion molecule 1 (PECAM-1) and annexin A2. Calculations of the free energy of the binding of heparin fragments of different sizes reveal the existence of a region of low GAG-binding affinity in domains 5-6 of PECAM-1 and a region of high affinity in domains 2-3, consistent with experimental data and ligand-protein docking studies. A conformational hinge movement between domains 2 and 3 was observed, which allows the binding of heparin fragments of increasing size (pentasaccharides to octasaccharides) with an increasingly higher binding affinity. Similar simulations of the binding of a heparin fragment to annexin A2 reveal the optimization of electrostatic and hydrogen bonding interactions with the protein and protein-bound calcium ions. In general, these free energy calculations reveal that the binding of heparin to protein surfaces is dominated by strong electrostatic interactions for longer fragments, with equally important contributions from van der Waals interactions and vibrational entropy changes, against a large unfavorable desolvation penalty due to the high charge density of these molecules.
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Affiliation(s)
- Neha S Gandhi
- Curtin Health Innovation Research Institute, Curtin University of Technology, Perth WA 6945, Australia
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29
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Doneanu CE, Chen W, Gebler JC. Analysis of oligosaccharides derived from heparin by ion-pair reversed-phase chromatography/mass spectrometry. Anal Chem 2009; 81:3485-99. [PMID: 19344114 DOI: 10.1021/ac802770r] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Current chromatographic and mass spectrometric techniques have limitations for analyzing heparin and heparin oligomers due to their high polarity, structural diversity, and sulfate lability. A rapid method for the analysis of heparin oligosaccharides was developed using ion-pair reversed-phase ultraperformance liquid chromatography coupled with electrospray quadruple time-of-flight mass spectrometry (IPRP-UPLC ESI Q-TOF MS). The method utilizes an optimized buffer system containing a linear pentylamine and a unique additive, 1,1,1,3,3,3-hexafluoro-2-propanol (HFIP), to achieve highly efficient separation together with enhanced mass response of heparin oligosaccharides. Analyses of a heparin oligosaccharide test mixture, dp6 through dp22, reveal that the chromatographic conditions enable baseline resolution of isomeric heparin oligosaccharides (dp6) and produce intact molecular ions with no sulfate losses during mass spectrometric analysis. In addition, the described conditions are amenable to the detection of heparin oligosaccharides in positive ion mode, yield stronger positive ion signals for corresponding oligosaccharides compared to the negative ion mode, and allow identification of structural isomers by an MS/MS approach. Because sensitive detection of oligosaccharides is also achieved with ultraviolet (UV) detection, the method utilizes a dual detection scheme (UV and MS in series) along with IPRP UPLC to simultaneously obtain quantification (UV) and characterization (MS) data for heparin oligosaccharides. The broad potential of this new method is further demonstrated for the analysis of a low-molecular-weight heparin (LMWH) preparation from porcine heparin. This approach will be of particular utility for profiling the molecular entities of heparin materials, as well as for structural variability comparison for samples from various sources.
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Affiliation(s)
- Catalin E Doneanu
- Biopharmaceutical Sciences, Waters Corporation, 34 Maple Street, Milford, Massachusetts 01757, USA
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30
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Guglieri S, Hricovíni M, Raman R, Polito L, Torri G, Casu B, Sasisekharan R, Guerrini M. Minimum FGF2 Binding Structural Requirements of Heparin and Heparan Sulfate Oligosaccharides As Determined by NMR Spectroscopy. Biochemistry 2008; 47:13862-9. [DOI: 10.1021/bi801007p] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Sara Guglieri
- G. Ronzoni Institute for Chemical and Biochemical Research, Milan, Italy, Institute of Chemistry, Slovak Academy of Sciences, Bratislava, Slovakia, Department of Biological Engineering, Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, and Department of Organic and Industrial Chemistry, University of Milan, Milan, Italy
| | - Miloš Hricovíni
- G. Ronzoni Institute for Chemical and Biochemical Research, Milan, Italy, Institute of Chemistry, Slovak Academy of Sciences, Bratislava, Slovakia, Department of Biological Engineering, Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, and Department of Organic and Industrial Chemistry, University of Milan, Milan, Italy
| | - Rahul Raman
- G. Ronzoni Institute for Chemical and Biochemical Research, Milan, Italy, Institute of Chemistry, Slovak Academy of Sciences, Bratislava, Slovakia, Department of Biological Engineering, Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, and Department of Organic and Industrial Chemistry, University of Milan, Milan, Italy
| | - Laura Polito
- G. Ronzoni Institute for Chemical and Biochemical Research, Milan, Italy, Institute of Chemistry, Slovak Academy of Sciences, Bratislava, Slovakia, Department of Biological Engineering, Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, and Department of Organic and Industrial Chemistry, University of Milan, Milan, Italy
| | - Giangiacomo Torri
- G. Ronzoni Institute for Chemical and Biochemical Research, Milan, Italy, Institute of Chemistry, Slovak Academy of Sciences, Bratislava, Slovakia, Department of Biological Engineering, Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, and Department of Organic and Industrial Chemistry, University of Milan, Milan, Italy
| | - Benito Casu
- G. Ronzoni Institute for Chemical and Biochemical Research, Milan, Italy, Institute of Chemistry, Slovak Academy of Sciences, Bratislava, Slovakia, Department of Biological Engineering, Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, and Department of Organic and Industrial Chemistry, University of Milan, Milan, Italy
| | - Ram Sasisekharan
- G. Ronzoni Institute for Chemical and Biochemical Research, Milan, Italy, Institute of Chemistry, Slovak Academy of Sciences, Bratislava, Slovakia, Department of Biological Engineering, Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, and Department of Organic and Industrial Chemistry, University of Milan, Milan, Italy
| | - Marco Guerrini
- G. Ronzoni Institute for Chemical and Biochemical Research, Milan, Italy, Institute of Chemistry, Slovak Academy of Sciences, Bratislava, Slovakia, Department of Biological Engineering, Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, and Department of Organic and Industrial Chemistry, University of Milan, Milan, Italy
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31
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Zhang Z, McCallum SA, Xie J, Nieto L, Corzana F, Jiménez-Barbero J, Chen M, Liu J, Linhardt RJ. Solution structures of chemoenzymatically synthesized heparin and its precursors. J Am Chem Soc 2008; 130:12998-3007. [PMID: 18767845 DOI: 10.1021/ja8026345] [Citation(s) in RCA: 141] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We report the first chemoenzymatic synthesis of the stable isotope-enriched heparin from a uniformly labeled [(13)C,(15)N]N-acetylheparosan (-GlcA(1,4)GlcNAc-) prepared from E. coli K5. Glycosaminoglycan (GAG) precursors and heparin were formed from N-acetylheparosan by the following steps: chemical N-deacetylation and N-sulfonation leading to N-sulfoheparosan (-GlcA(1,4)GlcNS-); enzyme-catalyzed C5-epimerization and 2-O-sulfonation leading to undersulfated heparin (-IdoA2S(1,4)GlcNS-); enzymatic 6-O-sulfonation leading to the heparin backbone (-IdoA2S(1,4)GlcNS6S-); and selective enzymatic 3-O-sulfonation leading to the anticoagulant heparin, containing the GlcNS6S3S residue. Heteronuclear, multidimensional nuclear magnetic resonance spectroscopy was employed to analyze the chemical composition and solution structure of [(13)C,(15)N]N-acetylheparosan, precursors, and heparin. Isotopic enrichment was found to provide well-resolved (13)C spectra with the high sensitivity required for conformational studies of these biomolecules. Stable isotope-labeled heparin was indistinguishable from heparin derived from animal tissues and is a novel reagent for studying the interaction of heparin with proteins.
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Affiliation(s)
- Zhenqing Zhang
- Department of Chemistry, Rensselaer Polytechnic Institute, Troy, New York 12180, USA
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32
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Affiliation(s)
- Mark Nitz
- Department of Chemistry, University of Toronto, 80 St. George Street Toronto, ON, Canada.
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33
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Silipo A, Zhang Z, Cañada FJ, Molinaro A, Linhardt RJ, Jiménez-Barbero J. Conformational analysis of a dermatan sulfate-derived tetrasaccharide by NMR, molecular modeling, and residual dipolar couplings. Chembiochem 2008; 9:240-52. [PMID: 18072186 PMCID: PMC4135520 DOI: 10.1002/cbic.200700400] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2007] [Indexed: 11/08/2022]
Abstract
The solution conformation behavior of a dermatan-derived tetrasaccharide--Delta HexA-(1-->3)-GalNAc4S-beta-(1-->4)-IdoA-alpha-(1-->3)-red-GalNAc4S (S is a sulfate group)--has been explored by means of NMR spectroscopy, especially by NOE-based conformational analysis. The tetrasaccharide was present as four species, two of which are chemically different in the anomeric orientation of the reducing 2-deoxy-2-acetamido-galactose (red-GalNAc) residue, while the other two are the result of different conformations of the iduronic acid (IdoA) unit. The two alpha-beta-interconverting anomers were present in a 0.6:1 ratio. Ring conformations have been defined by analysis of (3)J(H,H) coupling constants and interresidual NOE contacts. Both 2-deoxy-2-acetamido-galactose (GalNAc) residues were found in the (4)C(1) chair conformation, the unsaturated uronic acid (Delta-Hex A) adopts a strongly predominant half-chair (1)H(2) conformation, while the IdoA residue exists either in the (1)C(4) chair or in the (2)S(0) skewed boat geometries, in a 4:1 ratio. There is a moderate flexibility of Phi and Psi torsions as suggested by nuclear Overhauser effects (NOEs), molecular modeling (MM), and molecular dynamics (MD) studies. This was further investigated by residual dipolar couplings (RDCs). One-bond C--H RDCs ((1)D(C,H)) and long-range H-H ((3)D(H,H)) RDCs were measured for the tetrasaccharide in a phage solution and interpreted in combination with restrained MD simulation. The RDC-derived data substantially confirmed the validity of the conformer distribution resulting from the NOE-derived simulations, but allowed an improved definition of the conformational behavior of the oligosaccharides in solution. In summary, the data show a moderate flexibility of the four tetrasaccharide species at the central glycosidic linkage. Differences in the shapes of species with the IdoA in skew and in chair conformations and in the distribution of the sulfate groups have also been highlighted.
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Affiliation(s)
- Alba Silipo
- Centro de Investigaciones Biològicas, CSIC, Ramiro de Maeztu 9,28040 Madrid (Spain)
- Dipartimento di Chimica Organica e Biochimica Università di Napoli “Federico II” Complesso Universitario Monte S. Angelo, Via Cintia 4, 80126 Napoli (Italy)
| | - Zhenqing Zhang
- Departments of Chemistry and Chemical Biology, Biology, and Chemical and Biological Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 12180 (USA)
| | - F. Javier Cañada
- Centro de Investigaciones Biològicas, CSIC, Ramiro de Maeztu 9,28040 Madrid (Spain)
| | - Antonio Molinaro
- Dipartimento di Chimica Organica e Biochimica Università di Napoli “Federico II” Complesso Universitario Monte S. Angelo, Via Cintia 4, 80126 Napoli (Italy)
| | - Robert J. Linhardt
- Departments of Chemistry and Chemical Biology, Biology, and Chemical and Biological Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 12180 (USA)
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34
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Remko M, von der Lieth CW. Conformational structure of some trimeric and pentameric structural units of heparin. J Phys Chem A 2007; 111:13484-91. [PMID: 18052350 DOI: 10.1021/jp075330l] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The molecular structure of trimeric units (D-E-F and F-G-H) and the pentamer D-E-F-G-H of heparin (sodium salts and their anionic forms) was studied using the B3LYP/6-31G(d) method. The equilibrium structure of the sodium salts of the trimers and pentamer investigated in the isolated state was determined by multidentate coordination of the sodium cations with oxygen atoms of the sulfate, carboxyl, and hydroxyl (hydroxymethyl) groups, respectively. The displacement of Na+ ions from the binding sites in the sodium salt of oligosaccharides studied resulted in the appreciable change of the overall conformation of the corresponding anion. Upon dissociation, a large change in both the position of the sulfate groups and the conformation across the glycosidic bonds was observed. The stable energy conformations around the glysosidic bonds found for the pentamer investigated are compared and discussed with the available experimental X-ray structural data for the structurally related heparin-derived pentasaccharides in cocrystals with proteins.
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Affiliation(s)
- Milan Remko
- Department of Pharmaceutical Chemistry, Comenius University, Odbojarov 10, SK-832 32 Bratislava, Slovakia.
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35
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Yu F, Wolff JJ, Amster IJ, Prestegard JH. Conformational Preferences of Chondroitin Sulfate Oligomers Using Partially Oriented NMR Spectroscopy of 13C-Labeled Acetyl Groups. J Am Chem Soc 2007; 129:13288-97. [DOI: 10.1021/ja075272h] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Fei Yu
- Contribution from the Complex Carbohydrate Research Center and Department of Chemistry, University of Georgia, Athens, Georgia 30602-4712
| | - Jeremy J. Wolff
- Contribution from the Complex Carbohydrate Research Center and Department of Chemistry, University of Georgia, Athens, Georgia 30602-4712
| | - I. Jonathan Amster
- Contribution from the Complex Carbohydrate Research Center and Department of Chemistry, University of Georgia, Athens, Georgia 30602-4712
| | - James H. Prestegard
- Contribution from the Complex Carbohydrate Research Center and Department of Chemistry, University of Georgia, Athens, Georgia 30602-4712
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36
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Gemma E, Hulme AN, Jahnke A, Jin L, Lyon M, Müller RM, Uhrín D. DMT-MM mediated functionalisation of the non-reducing end of glycosaminoglycans. Chem Commun (Camb) 2007:2686-8. [PMID: 17594020 DOI: 10.1039/b617038b] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Efficient functionalisation of the non-reducing end of uronic acid derivatives and glycosaminoglycan-derived disaccharides using peptide coupling has been achieved, mediated by the water-soluble agent DMT-MM.
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Affiliation(s)
- Emiliano Gemma
- School of Chemistry, University of Edinburgh, West Mains Road, Edinburgh, UK EH9 3JJ
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37
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B3LYP/6-311++G* * study of structure and spin-spin coupling constant in heparin disaccharide. Carbohydr Res 2007; 342:1350-6. [PMID: 17445784 DOI: 10.1016/j.carres.2007.03.020] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2006] [Revised: 03/16/2007] [Accepted: 03/19/2007] [Indexed: 10/23/2022]
Abstract
Structures of heparin disaccharide have been analyzed by DFT using the B3LYP/6-311++G( * *) method. The optimized geometries of two forms of this disaccharide, differing in the conformation ((1)C(4) and (2)S(0)) of the IdoA2S residue, confirmed considerable influences of the sulfate and the carboxylate groups upon the pyranose ring geometries. The computed energies showed that disaccharide having the (1)C(4) form of the IdoA2S residue is more stable than that with the (2)S(0) form. Interatomic distances, bond and torsion angles showed that interconversion of the IdoA2S residue results in geometry changes in the GlcN,6S residue as well. Three-bond proton-proton and proton-carbon spin-spin coupling constants computed for both forms agree with the experimental data and indicate that only two chair forms contribute to the conformational equilibrium in disaccharide. Influences of the charged groups upon the magnitudes of spin-spin coupling constants are also discussed.
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38
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Remko M, Swart M, Bickelhaupt FM. Conformational Behavior of Basic Monomeric Building Units of Glycosaminoglycans: Isolated Systems and Solvent Effect. J Phys Chem B 2007; 111:2313-21. [PMID: 17295532 DOI: 10.1021/jp0646271] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Our work reports in detail the results of systematic large-scale theoretical investigations of the glycosaminoglycan building units 1-OMe DeltaIdoA-2SNa2 (1; 2H1 and 1H2 forms), 1-OMe GlcN-S6SNa2 (2), 1,4-DiOMe GlcNa (3), 1,4-DiOMe GlcN-S3S6SNa3 (4), 1,4-DiOMe IdoA-2SNa2 (5; 4C1, 1C4, and 2So conformations), and 1,4-DiOMe GlcN-S6SNa2 (6) at the BP86/TZ2P level of the density functional theory. The optimized geometries indicate that the most stable structure of these monomeric units in the neutral state is stabilized via "multifurcated" sodium bonds. The equilibrium structure of the biologically active anionic forms of the glycosaminoglycans studied changed considerably in a water solution. The computed interaction energies, DeltaE, of sodium coordinated systems 1-6 are negative and span a rather broad energy interval (from -130 to -590 kcal mol-1). Computations that include the effect of solvation indicated that in water the relative stability of Na+...ligand ionic bonds is considerably diminished. The computed interaction energy in water is small (from -20 to -53 kcal mol-1) and negative, that is, stabilizing.
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Affiliation(s)
- Milan Remko
- Department of Pharmaceutical Chemistry, Comenius University, Odbojarov 10, SK-83232 Bratislava, Slovakia.
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39
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Becker CF, Guimarães JA, Mourão PAS, Verli H. Conformation of sulfated galactan and sulfated fucan in aqueous solutions: implications to their anticoagulant activities. J Mol Graph Model 2007; 26:391-9. [PMID: 17307002 DOI: 10.1016/j.jmgm.2007.01.008] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2006] [Revised: 01/13/2007] [Accepted: 01/15/2007] [Indexed: 11/18/2022]
Abstract
The discovery of sulfated galactans and sulfated fucans in marine invertebrates with simple and ordered structures opened new perspectives to investigate the biological activity of these molecules and to determine whether different structures confer high affinity for a particular protein. We undertook a conformational analysis of a 2-sulfated, 3-linked alpha-L-galactan and of a alpha-L-fucan with similar structure. Through comparison between theoretical and NMR derived coupling constants, we observed that the pyranose rings are predominantly in the (1)C(4) conformation in these polysaccharides. Additionally, the geometry of the glycosidic linkages was determined based on force field calculations, indicating that the two polysaccharides have similar conformations in solution. Since the sulfated alpha-L-galactan, but not the alpha-L-fucan potentiates antithrombin (AT) inhibition of thrombin, the solution conformations of the compounds were docked into AT and the complexes obtained were refined through molecular dynamics calculations. The obtained results indicates extremely different orientations for the two polysaccharides, which well correlates and explain their distinct anticoagulant activities. Finally, the molecular mechanism of a selective 2-desulfation reaction, observed among sulfated fucans, was explained as a consequence of an intramolecular hydrogen bond capable of assisting in the removal of the charged group.
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Affiliation(s)
- Camila F Becker
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Av Bento Gonçalves 9500, CP 15005, Porto Alegre 91500-970, Brazil
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40
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Kurihara Y, Ueda K. An investigation of the pyranose ring interconversion path of α-l-idose calculated using density functional theory. Carbohydr Res 2006; 341:2565-74. [PMID: 16920091 DOI: 10.1016/j.carres.2006.07.015] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2006] [Revised: 07/04/2006] [Accepted: 07/18/2006] [Indexed: 11/22/2022]
Abstract
The interconversion pathways of the pyranose ring conformation of alpha-L-idose from a (4)C1 chair to other conformations were investigated using density functional calculations. From these calculations, four different ring interconversion paths and their transition state structures from the (4)C1 chair to other conformations, such as B(3,O), and (1)S3, were obtained. These four transition-state conformations cover four possible combinations of the network patterns of the hydroxyl group hydrogen bonds (clockwise and counterclockwise) and the conformations of the primary alcohol group (tg and gg). The optimized conformations, transition states, and their intrinsic reaction coordinates (IRC) were all calculated at the B3LYP/6-31G** level. The energy differences among the structures obtained were evaluated at the B3LYP/6-311++G** level. The optimized conformations indicate that the conformers of (4)C1, (2)S(O), and B(3,O) have similar energies, while (1)S3 has a higher energy than the others. The comparison of the four transition states and their ring interconversion paths, which were confirmed using the IRC calculation, suggests that the most plausible ring interconversion of the alpha-L-idopyranose ring occurs between (4)C1 and B(3,O) through the E3 envelope, which involves a 5.21 kcal/mol energy barrier.
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Affiliation(s)
- Youji Kurihara
- Department of Advanced Materials Chemistry, Graduate School of Engineering, Yokohama National University, 79-5 Tokiwadai, Hodogaya-Ku, Yokohama 240-8501, Japan
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41
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The Fibroblast Growth Factor (FGF) – FGF Receptor Complex: Progress Towards the Physiological State. Top Curr Chem (Cham) 2006. [DOI: 10.1007/128_068] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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42
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Raghuraman A, Mosier PD, Desai UR. Finding a needle in a haystack: development of a combinatorial virtual screening approach for identifying high specificity heparin/heparan sulfate sequence(s). J Med Chem 2006; 49:3553-62. [PMID: 16759098 PMCID: PMC2516555 DOI: 10.1021/jm060092o] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We describe a combinatorial virtual screening approach for predicting high specificity heparin/heparan sulfate sequences using the well-studied antithrombin-heparin interaction as a test case. Heparan sulfate hexasaccharides were simulated in the 'average backbone' conformation, wherein the inter-glycosidic bond angles were held constant at the mean of the known solution values, irrespective of their sequence. Molecular docking utilized GOLD with restrained inter-glycosidic torsions and intra-ring conformations, but flexible substituents at the 2-, 3-, and 6-positions and explicit incorporation of conformational variability of the iduronate residues. The approach reproduces the binding geometry of the sequence-specific heparin pentasaccharide to within 2.5 A. Screening of a combinatorial virtual library of 6,859 heparin hexasaccharides using a dual filter strategy, in which predicted antithrombin affinity was the first filter and self-consistency of docking was the second, resulted in only 10 sequences. Of these, nine were found to bind antithrombin in a manner identical to the natural pentasaccharide, while a novel hexasaccharide bound the inhibitor in a unique but dramatically different geometry and orientation. This work presents the first approach on combinatorial library screening for heparin/heparan sulfate GAGs to determine high specificity sequences and opens up huge opportunities to investigate numerous other physiologically relevant GAG-protein interactions.
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Affiliation(s)
- Arjun Raghuraman
- Department of Medicinal Chemistry, Institute for Structural Biology and Drug Discovery, Virginia Commonwealth University, Richmond, 23298, USA
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43
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Remko M, von der Lieth CW. Gas-Phase and Solution Conformations of Selected Dimeric Structural Units of Heparin. J Chem Inf Model 2006; 46:1687-94. [PMID: 16859300 DOI: 10.1021/ci060060+] [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] [Indexed: 11/28/2022]
Abstract
The molecular structure of four dimeric units (D-E, E-F, F-G, and G-H) of the DEFGH structural unit of heparin, their anionic forms, and their sodium salts have been studied using the B3LYP/6-31+G(d) method. The optimized geometries indicate that the most stable structure of these dimeric units in neutral state is stabilized via "bifurcated" sodium bonds. The equilibrium structure of the biologically active anionic forms of the glycosaminoglycans studied changed considerably in a water solution. The stable-energy conformations around glysosidic bonds found for the individual dimeric species investigated are in agreement with the available experimental structural data for the structurally related heparin-derived oligosaccharides.
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Affiliation(s)
- Milan Remko
- Department of Pharmaceutical Chemistry, Comenius University, Odbojarov 10, SK-832 32 Bratislava, Slovakia, and German Cancer Research Center, Im Neuenheimer Feld 280, D-69120 Heidelberg, Germany.
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44
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Remko M, von der Lieth CW. Gas-Phase and Solution Conformations of the α-L-Iduronic Acid Structural Unit of Heparin. J Chem Inf Model 2006; 46:1194-200. [PMID: 16711739 DOI: 10.1021/ci0504667] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The IdoA2S structural unit of heparin (subunit G) may oscillate among the three conformations (4C1, 1C4, and 2So). Only the twisted boat conformation allowed the biologically active pentasaccharide unit of heparin (DEFGH) to bind to antithrombin. Our work reports, in detail, the results of systematic large-scale theoretical investigations of the three basic conformations (4C1, 1C4, and 2So) of the IdoA2S structural unit of heparin, its anionic forms, and its sodium salt using the B3LYP/6-311++G(d, p) and B3LYP/6-31+G(d) model chemistries. According to our calculations, the most stable structure of these molecules corresponds to the 2So skew-boat conformation. This form is also the most stable in a water solution. The 2So conformation of neutral molecules is not maintained in the anionic species. With anions, both 1C4 and 4C1 conformations are present. The relative stability of individual species of the substituted iduronic acid affects extra stabilization by means of intramolecular hydrogen bonds. The calculated macroscopic pKa of 1,4-DiOMe IdoA2S are as follows: pKa = 0.25 for the terminal C(2)-OSO3H group, pKa = 3.67 for the terminal C(5)-CO2H group, and pKa = 14.00 for the C(3)-OH hydroxyl group. The computed Gibbs interaction energies, DeltaGdegrees , for the reaction 1,4-DiOMe IdoA2S(2-) + 2Na+ <==> 1,4-DiOMe IdoA2SNa2 (4C1, 1C4, and 2So conformations) are negative and span a rather small energy interval (from -1244 to -1290 kJ mol(-1)).
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Affiliation(s)
- Milan Remko
- Department of Pharmaceutical Chemistry, Comenius University, Odbojarov 10, SK-832 32 Bratislava, Slovakia.
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45
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Becker CF, Guimarães JA, Verli H. Molecular dynamics and atomic charge calculations in the study of heparin conformation in aqueous solution. Carbohydr Res 2005; 340:1499-507. [PMID: 15882850 DOI: 10.1016/j.carres.2005.03.018] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2005] [Accepted: 03/27/2005] [Indexed: 11/18/2022]
Abstract
HF/6-31G** and molecular dynamics (MD) simulations were used to evaluate the performance of different atomic charge basis sets (i.e., Mulliken, Lowdin, and Electrostatic Potential Derived Charges--ESP) in heparin simulations. HF/3-21 G calculations were also used to study the NMR conformation of the IdoA residue. The results thus obtained indicated that ESP and Lowdin charges gave the better results in heparin simulations, followed by Mulliken charges, and that the minimum-energy conformation of IdoA can be different from that observed by NMR spectroscopy by less than 1 Angstrom. However, it was found that this small conformational modification is capable of inducing a change of almost 200 kJ/mol in the interactions of heparin with the surrounding environment, which is a meaningful amount of energy in the context of ligand-receptor interactions. This information can be potentially of great relevance in the design of heparin-derived antithrombotic compounds.
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Affiliation(s)
- Camila F Becker
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
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46
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Vivès RR, Imberty A, Sattentau QJ, Lortat-Jacob H. Heparan sulfate targets the HIV-1 envelope glycoprotein gp120 coreceptor binding site. J Biol Chem 2005; 280:21353-7. [PMID: 15797855 DOI: 10.1074/jbc.m500911200] [Citation(s) in RCA: 99] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Human immunodeficiency virus (HIV) attachment to host cells is a multi-step process that involves interaction of the viral envelope gp120 with the primary receptor CD4 and coreceptors. HIV gp120 also binds to other cell surface components, including heparan sulfate (HS), a sulfated polysaccharide whose wide interactive properties are exploited by many pathogens for attachment and concentration at the cell surface. To analyze the structural features of gp120 binding to HS, we used soluble CD4 to constrain gp120 in a specific conformation. We first found that CD4 induced conformational change of gp120, dramatically increasing binding to HS. We then showed that HS binding interface on gp120 comprised, in addition to the well characterized V3 loop, a CD4-induced epitope. This epitope is efficiently targeted by nanomolar concentrations of size-defined heparin/HS-derived oligosaccharides. Because this domain of the protein also constitutes the binding site for the viral coreceptors, these results support an implication of HS at late stages of the virus-cell attachment process and suggest potential therapeutic applications.
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Affiliation(s)
- Romain R Vivès
- Institut de Biologie Structurale, CNRS-Commissariat à l'Energie Atomique-Université Joseph Fourier, UMR 5075, 41 Rue Horowitz, 38027 Grenoble, France
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47
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Lee SC, Guan HH, Wang CH, Huang WN, Tjong SC, Chen CJ, Wu WG. Structural Basis of Citrate-dependent and Heparan Sulfate-mediated Cell Surface Retention of Cobra Cardiotoxin A3. J Biol Chem 2005; 280:9567-77. [PMID: 15590643 DOI: 10.1074/jbc.m412398200] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Anionic citrate is a major component of venom, but the role of venom citrate in toxicity other than its inhibitory effect on the cation-dependent action of venom toxins is poorly understood. By immobilizing Chinese hamster ovary cells in microcapillary tubes and heparin on sensor chips, we demonstrated that heparan sulfate-mediated cell retention of the major cardiotoxin (CTX) from the Taiwan cobra, CTX A3, near membrane surfaces is citrate-dependent. X-ray determination of a CTX A3-heparin hexasaccharide complex structure at 2.4 A resolution revealed a molecular mechanism for toxin retention in which heparin-induced conformational changes of CTX A3 lead to citrate-mediated dimerization. A citrate ion bound to Lys-23 and Lys-31 near the tip of loop II stabilizes hydrophobic contact of the CTX A3 homodimer at the functionally important loop I and II regions. Additionally, the heparin hexasaccharide interacts with five CTX A3 molecules in the crystal structure, providing another mechanism whereby the toxin establishes a complex network of interactions that result in a strong interaction with cell surfaces presenting heparan sulfate. Our results suggest a novel role for venom citrate in biological activity and reveal a structural model that explains cell retention of cobra CTX A3 through heparan sulfate-CTX interactions.
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Affiliation(s)
- Shao-Chen Lee
- Institute of Bioinformatics and Structural Biology, National TsingHua University, Hsinchu 30043, Taiwan
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48
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Tejo BA, Salleh AB, Pleiss J. Structure and dynamics of Candida rugosa lipase: the role of organic solvent. J Mol Model 2004; 10:358-66. [PMID: 15597204 DOI: 10.1007/s00894-004-0203-z] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2004] [Accepted: 07/13/2004] [Indexed: 11/27/2022]
Abstract
The effect of organic solvent on the structure and dynamics of proteins was investigated by multiple molecular dynamics simulations (1 ns each) of Candida rugosa lipase in water and in carbon tetrachloride. The choice of solvent had only a minor structural effect. For both solvents the open and the closed conformation of the lipase were near to their experimental X-ray structures (C(alpha) rms deviation 1-1.3 A). However, the solvents had a highly specific effect on the flexibility of solvent-exposed side chains: polar side chains were more flexible in water, but less flexible in organic solvent. In contrast, hydrophobic residues were more flexible in organic solvent, but less flexible in water. As a major effect solvent changed the dynamics of the lid, a mobile element involved in activation of the lipase, which fluctuated as a rigid body about its average position. While in water the deviations were about 1.6 A, organic solvent reduced flexibility to 0.9 A. This increase rigidity was caused by two salt bridges (Lys85-Asp284, Lys75-Asp79) and a stable hydrogen bond (Lys75-Asn 292) in organic solvent. Thus, organic solvents stabilize the lid but render the side chains in the hydrophobic substrate-binding site more mobile. [figure: see text]. Superimposition of open (black, PDB entry 1CRL) and closed (gray, PDB entry 1TRH) conformers of C. rugosa lipase. The mobile lid is indicated.
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Affiliation(s)
- Bimo Ario Tejo
- Department of Biochemistry and Microbiology, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
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49
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Verli H, Guimarães JA. Molecular dynamics simulation of a decasaccharide fragment of heparin in aqueous solution. Carbohydr Res 2004; 339:281-90. [PMID: 14698886 DOI: 10.1016/j.carres.2003.09.026] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Molecular dynamics (MD) simulations on heparin-water-sodium systems were carried out in order to establish a simulation protocol able to represent heparin solution conformation under physiological conditions. Atomic charges suitable for heparin oligosaccharides were obtained from ab initio quantum-mechanical computations, at the 6-31G(**) level. The GROMACS forcefield, the SPC, and SPC/E water models were employed. Also heparin was simulated with IdoA residues in 1C(4) or 2S(0) conformational states. The results of the performed MD simulations are in agreement with the available experimental data, suggesting that this approach can be applied for the study of heparin interactions with its target proteins and thus play a role in the development of new antithrombotic agents.
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Affiliation(s)
- Hugo Verli
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Av. Bento Gonçalves, 9500, CP 15005, 91500-970, RS, Porto Alegre, Brazil
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50
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Thanawiroon C, Rice KG, Toida T, Linhardt RJ. Liquid Chromatography/Mass Spectrometry Sequencing Approach for Highly Sulfated Heparin-derived Oligosaccharides. J Biol Chem 2004; 279:2608-15. [PMID: 14610083 DOI: 10.1074/jbc.m304772200] [Citation(s) in RCA: 129] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Liquid chromatography/mass spectrometry (LC/MS) is applied to the analysis of complex mixtures of oligosaccharides obtained through the controlled, heparinase-catalyzed depolymerization of heparin. Reversed-phase ion-pairing chromatography, utilizing a volatile mobile phase, results in the high resolution separation of highly sulfated, heparin-derived oligosaccharides. Simultaneous detection by UV absorbance and electrospray ionization-mass spectrometry (ESI-MS) provides important structural information on the oligosaccharide components of this mixture. Highly sensitive and easily interpretable spectra were obtained through post-column addition of tributylamine in acetonitrile. High resolution mass spectrometry afforded elemental composition of many known and previously unknown heparin-derived oligosaccharides. UV in combination with MS detection led to the identification of oligosaccharides arising from the original non-reducing end (NRE) of the heparin chain. The structural identification of these oligosaccharides provided sequence from a reading frame that begins at the non-reducing terminus of the heparin chain. Interestingly, 16 NRE oligosaccharides are observed, having both an even and an odd number of saccharide residues, most of which are not predicted based on biosynthesis or known pathways of heparin catabolism. Quantification of these NRE oligosaccharides afforded a number-averaged molecular weight consistent with that expected for the pharmaceutical heparin used in this analysis. Molecular ions could be assigned for oligosaccharides as large as a tetradecasaccharide, having a mass of 4625 Da and a net charge of -32. Furthermore, MS detection was demonstrated for oligosaccharides with up to 30 saccharide units having a mass of >10000 Da and a net charge of -60.
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Affiliation(s)
- Charuwan Thanawiroon
- Division of Medicinal and Natural Products Chemistry, University of Iowa, Iowa City, Iowa 52242, USA
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